2024-03-29T13:50:46Zhttps://escholarship.org/oaioai:escholarship.org:ark:/13030/qt1ds5m35c2024-01-11T17:24:25Zqt1ds5m35cFAIRsharing.orgSmith, Elliott2022-12-01The benefits of data sharing have been powerfully demonstrated during the COVID-19 pandemic: shared data made possible the rapid development of public health policies, treatment guidelines, therapies, and vaccines. And with the issuance of the NIH Data Management and Sharing Policy and the OSTP memo on public access to research, funders are mandating that research data should be well-described and, whenever possible, readily discoverable to enable re-use.FAIRsharing.org is a curated, searchable registry of metadata standards; databases and repositories; and funder and journal policies that are relevant to specific domains or types of data.data scienceopen accessreproducibilityCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1ds5m35cpublicationoai:escholarship.org:ark:/13030/qt9dn751z62024-01-11T17:23:31Zqt9dn751z6Ana Hatherly Micro-collection @ UC BerkeleyPotts, Claude, H2022-06-23Throughout her long life, Portuguese visual artist/poet/scholar/filmmaker Ana Hatherly (1929-2015) reflected creatively and profoundly across diverse media. While her drawings and paintings have been deposited in museums such as the Gulbenkian Museum and the National Museum of Contemporary Art in Lisbon, UC Berkeley is where she earned her PhD and where her published works have been archived. This precious collection, now mostly housed at The Bancroft Library is not large and does not include her personal papers nor very much manuscript material, but it is the most complete of its kind on this side of the Atlantic. The collection of mostly short-run books published by independent presses serves as a textual archive to one of the most prolific visual poets of the latter 20th century.This lightning talk raises questions about the evolving importance of micro-collections and necessity for custodial acquisitions during an unprecedented age of austerity resulting from the COVID-19 pandemic. Where would our archives and special collections be if we didn’t have the foresight to begin collecting and preserving potentially valuable materials outside of our institution’s collecting parameters when we did? The discussion also affirms the importance of intentional redundancy between circulating and non-circulating collections, and critically interrogates privileged notions of “special” and “rare” which have historically kept outsiders like Ana Hatherly out, and others in. For more information about Ana Hather's publications at UC Berkeley, please see: See also: https://guides.lib.berkeley.edu/ana-hatherlyThis presentation was given at RBMS 2022. The Rare Books and Manuscripts Section (RBMS) is a section of the Association of College and Research Libraries (ACRL).concrete poetryexperimental poetryPortugalLusophone poetrypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9dn751z6publicationoai:escholarship.org:ark:/13030/qt9j02r41p2023-12-14T15:52:01Zqt9j02r41pSeismica: Open science and community building in a new diamond open access journalTeplitzky, SamanthaConvers, JaimeFunning, GarethHicks, StephenKarasozen, EzgiRowe, ChristieRychert, Catherine2023-12-11Seismica, a new Diamond Open Access journal in Seismology and Earthquake Science, launched in July 2022. One year into production, we have received 90 submissions, published 25 articles and have over 50 works in the pipeline. Seismica is an independent journal, designed and built by a global community of researchers with the aim of making scientific research freely available, with no publication or subscription fees.Beyond traditional research articles, Seismica publishes an innovative set of peer-reviewed reports including fast reports, null results/failed experiments, software reports, and instrument deployment/field campaign reports. Seismica accepts papers within the very broad scope of fault slip and earthquake source phenomena, earthquake records, imaging the Earth, theoretical and computational seismology, beyond Earth-tectonic applications, techniques and instrumentation, earthquake engineering and engineering seismology, and earthquake education, community engagement, and other social science methods.The new journal's philosophy was developed through continuous communication among broader community members and strives to be accessible, transparent, respectful, credible, and progressive. In the past year, Seismica has evolved both as a journal and a community dedicated to transparency in science, and supporting not not only open access articles, but also a fully open research process. Seismica addresses community needs by publishing public reviews along with the paper, promoting a fair and unbiased reviewing process while providing an insider look into reviewing that benefits early-career researchers; valuing time and expertise by crediting all contributors to a publication; encouraging preprint sharing; allowing authors to keep the copyright to their work; and helping authors share and promote their research once published.The need for a Diamond Open Access journal and the necessity to share seismology research for broader community benefits is evident. The successful launch and growth of Seismica in the past year demonstrates that this model is responsive, inclusive and sustainable.application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/9j02r41ppublicationoai:escholarship.org:ark:/13030/qt0w52s77f2023-12-02T01:08:42Zqt0w52s77fPulling the Plug: Equitable Guidelines for Machine Learning NeuroprognosticationIyer, MedhaLarkin, Michael2023-04-01Lower Division Honorable Mention 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0w52s77fpublicationoai:escholarship.org:ark:/13030/qt45d0b98w2023-12-02T01:04:11Zqt45d0b98wPavement, Placement, and Displacement:A Spatial History of Freeways in the Bay Area, 1893-2005Kirsch, SilasLunine, Seth2023-04-01Upper Division Honorable Mention 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/45d0b98wpublicationoai:escholarship.org:ark:/13030/qt2rw8f0c02023-12-02T00:54:57Zqt2rw8f0c0Negotiating Boundaries, Space, and Power: The Top-Down Institutional Assertion of Boundaries and Claims and the Taos Pueblo People’s Bottom-Up Defense of Their Cultural LandscapePatel, MansiCovey, Catherine2023-04-01Upper Division Honorable Mention 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2rw8f0c0publicationoai:escholarship.org:ark:/13030/qt8ns2f4772023-12-02T00:28:26Zqt8ns2f477“Don't worry, it's a game! It's a game just like usual.” — Metal Gear Solid 2, the Military-Entertainment Complex, and Memetics in the Digital AgeMacey, InigoAcevedo-Butcher, Carmen2023-04-01Lower Division Winner 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8ns2f477publicationoai:escholarship.org:ark:/13030/qt6ps3b0b32023-10-16T20:45:04Zqt6ps3b0b3Male Impersonation in the Late 19th Century as a Reflection of Social ChangeKozuka, HanaJohnson, Tulasi2023-04-01Lower Division Winner 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6ps3b0b3publicationoai:escholarship.org:ark:/13030/qt1db5350t2023-10-03T22:05:15Zqt1db5350tBuilding Legal Literacies for Text Data Mining: Institute White PaperSamberg, RachaelVollmer, Timothy2021-07-26UC Berkeley Library secured a grant from the National Endowment for the Humanities to support an Institute for Advanced Topics in the Digital Humanities to help key stakeholders to learn to better navigate legal issues in text data mining. UC Berkeley Library’s Office of Scholarly Communication Services led a national team from more than a dozen institutions and organizations to teach humanities researchers, librarians, and research staff how to confidently navigate the major legal issues that arise in text data mining research. Our institute was called Building Legal Literacies for Text Data Mining (Building LLTDM), and ran from June 23-26, 2020.This white paper describes the institute’s origins and goals, project overview and activities, and reflections and possible follow-on actions.legal literacies for text data miningTDMlawpolicyethicscopyrightcontractsprivacydigital humanitiesapplication/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/1db5350tpublicationoai:escholarship.org:ark:/13030/qt1w03f9r22023-10-02T17:47:11Zqt1w03f9r2Legal Literacies for Text Data Mining – Cross-Border (“LLTDM-X”): Case StudySamberg, RachaelVollmer, TimothyPadilla, Thomas2023-10-02Legal Literacies for Text Data Mining - Cross-Border (“LLTDM-X”) is a National Endowment for the Humanities Level 1 Advancement Grant project addressing legal and ethical issues faced by U.S. digital humanities (DH) practitioners whose text data mining (TDM) research and practice intersects with foreign-held or - licensed content, or involves international cooperations.LLTDM-X is a collaboration between the University of California Berkeley Library and Internet Archive, and builds upon the previous NEH-sponsored institute, Building Legal Literacies for Text Data Mining (Building LLTDM). That institute provided guidance and strategies to DH TDM researchers on navigating legal literacies for text data mining (including copyright, contracts, privacy, and ethics) within a U.S. context.A common challenge highlighted during Building LLTDM was the fact that TDM practitioners encounter numerous and complex legal problems in cross-border TDM research. These occur when: (i) the materials practitioners want to mine are housed in a foreign jurisdiction, or are otherwise subject to foreign database licensing or laws; (ii) the human subjects they are studying or who created the underlying content reside in another country; or, (iii) the colleagues with whom they are collaborating reside abroad, yielding uncertainty about which country’s laws, agreements, and policies apply.We designed LLTDM-X to identify and better understand the cross-border issues that DH TDM practitioners face, with the aim of using these issues to inform prospective research and education. We also hoped that LLTDM-X would yield preliminary guidance to benefit researchers in the meantime, as instructional materials are being developed. In early 2023, we hosted a series of three online round tables with U.S.-based cross-border TDM practitioners (“Practitioners”), and law and ethics experts (“Experts”) practicing in six countries. The round table conversations were structured to illustrate the empirical issues that researchers face, and also for the Practitioners to benefit from guidance on legal and ethical challenges. Upon the completion of the round tables, the LLTDM-X project team created a robust and hypothetical case study that (i) reflects the observed cross-border LLTDM issues and (ii) contains analysis to facilitate the development of future instructional materials.text and data mininglegal literacies for text data miningcase studyTDMcomputational analysisdigital humanitieslawpolicycopyrightethicsapplication/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/1w03f9r2publicationoai:escholarship.org:ark:/13030/qt5k91r1s12023-10-02T17:40:28Zqt5k91r1s1Legal Literacies for Text Data Mining – Cross-Border (“LLTDM-X”): White PaperSamberg, RachaelVollmer, TimothyPadilla, Thomas2023-10-02Legal Literacies for Text Data Mining - Cross-Border (“LLTDM-X”) is a National Endowment for the Humanities Level 1 Advancement Grant project addressing legal and ethical issues faced by U.S. digital humanities (DH) practitioners whose text data mining (TDM) research and practice intersects with foreign-held or - licensed content, or involves international cooperations.LLTDM-X is a collaboration between the University of California Berkeley Library and Internet Archive, and builds upon the previous NEH-sponsored institute, Building Legal Literacies for Text Data Mining (Building LLTDM). That institute provided guidance and strategies to DH TDM researchers on navigating legal literacies for text data mining (including copyright, contracts, privacy, and ethics) within a U.S. context.A common challenge highlighted during Building LLTDM was the fact that TDM practitioners encounter numerous and complex legal problems in cross-border TDM research. These occur when: (i) the materials practitioners want to mine are housed in a foreign jurisdiction, or are otherwise subject to foreign database licensing or laws; (ii) the human subjects they are studying or who created the underlying content reside in another country; or, (iii) the colleagues with whom they are collaborating reside abroad, yielding uncertainty about which country’s laws, agreements, and policies apply.We designed LLTDM-X to identify and better understand the cross-border issues that DH TDM practitioners face, with the aim of using these issues to inform prospective research and education. We also hoped that LLTDM-X would yield preliminary guidance to benefit researchers in the meantime, as instructional materials are being developed. In early 2023, we hosted a series of three online round tables with U.S.-based cross-border TDM practitioners (“Practitioners”), and law and ethics experts (“Experts”) practicing in six countries. The round table conversations were structured to illustrate the empirical issues that researchers face, and also for the Practitioners to benefit from guidance on legal and ethical challenges. Upon the completion of the round tables, the LLTDM-X project team created a robust and hypothetical case study that (i) reflects the observed cross-border LLTDM issues and (ii) contains analysis to facilitate the development of future instructional materials.text and data miningcross-borderdigital humanitieslegal literacies for text data miningcomputational researchcopyrightethicspolicyapplication/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/5k91r1s1publicationoai:escholarship.org:ark:/13030/qt6cc6f8bx2023-09-26T21:09:00Zqt6cc6f8bxSeismica: Open science and community building in a new diamond open access journalTeplitzky, Samantha2023-09-19Seismica, a pioneering diamond open access journal in Seismology and Earthquake Science, launched in July 2022. Seismica is an independent journal supported by McGill University, designed and built by a global community of researchers with the aim of making scientific research freely available. Our international team of over 40 people includes disciplinary experts as well as specialists in open science and data; equity, diversity and inclusion; outreach and communication; and digital media and branding. Volunteers cover traditional editorial roles as well as the journal’s full-time management and operation (including technical support, copy editing, branding and communications). Now in its second year of publication, Seismica has evolved as both a journal and a community dedicated to transparency in science, and supporting not only open access articles, but also a fully open publication process. Beyond traditional research articles, Seismica publishes an innovative set of peer-reviewed reports including fast reports, null results/failed experiments, software reports, and instrument deployment/field campaign reports; we also require the sharing of related data and code. This initial year of growth has included the development of of our own reproducible workflows on the backend, the publication of a special issue in response to the Turkiye earthquakes of February 2023, and much work behind the scenes fostering community, mentoring new editors, opening peer review, investigating future funding and planning for sustainable succession. This presentation will demonstrate how Seismica contributors have responded to community needs and changing expectations in the field while gaining invaluable professional experience along the way.publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6cc6f8bxpublicationoai:escholarship.org:ark:/13030/qt00p3t7w72023-09-21T16:55:05Zqt00p3t7w7Redlining the Sky: Air pollution and the Legacy of Redlining in West OaklandEdwards, VioletFreeman, Kimberly2023-04-01Lower Division Honorable Mention 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/00p3t7w7publicationoai:escholarship.org:ark:/13030/qt8z20g3tq2023-09-13T01:14:00Zqt8z20g3tq‘Ghostly’ Histories: Alternative Frameworks for Understanding the Memories,Experiences, and Representations of South Korean ‘Comfort Women’Lee, JennyKaicker, Abhishek2023-04-01Upper Division Winner 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8z20g3tqpublicationoai:escholarship.org:ark:/13030/qt5jh2b6cd2023-09-13T01:02:19Zqt5jh2b6cdKey Development Moment: Story of the Xiaogang VillageHu, GraceLin, Edwin2023-04-01Lower Division Honorable Mention 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5jh2b6cdpublicationoai:escholarship.org:ark:/13030/qt9779n7nq2023-09-13T00:54:58Zqt9779n7nqErased: An Exploration of Queer Japanese Americans’ Experience During the Internment PeriodGottschalk, RyanSteenland, Pat2023-04-01Lower Division Winner 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9779n7nqpublicationoai:escholarship.org:ark:/13030/qt80f960462023-09-13T00:51:12Zqt80f96046Educational Quotas and the Politics of the Native-Migrant Divide in Late Imperial China, 1720-1810Li, YongkangTackett, Nicholas2023-04-01Upper Division Winner 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/80f96046publicationoai:escholarship.org:ark:/13030/qt56s7n45k2023-09-13T00:42:40Zqt56s7n45kMother of Maladies: An Ethnographic and Netnographic Analysis of Pandemic Goddesses in South Asian CultureMuthukumar, AarthiGe, Jing2023-04-01Upper Division Winner 2023application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/56s7n45kpublicationoai:escholarship.org:ark:/13030/qt56m584cc2023-04-13T19:49:32Zqt56m584ccResearch Organization RegistrySmith, Elliott2023-04-01The Research Organization Registry (ROR), a recent initiative by California Digital Library (CDL), Crossref, and DataCite, attempts to address the issue of institutional disambiguation through the development of a non-commercial, open, and interoperable system of unique persistent identifiers for research organizations.publiceScholarship, University of Californiahttps://escholarship.org/uc/item/56m584ccpublicationoai:escholarship.org:ark:/13030/qt3dp7312t2023-01-09T21:00:10Zqt3dp7312tReady 4 Research: A Pilot WorkshopGlusker, Ann2021-08-05Ready 4 Research is a 3-hour workshop to support students in learning about and getting ready to participate in research as research assistants and researchers themselves. It is aimed at UC Berkeley social sciences students, at the sophomore level and above, but there is content that can be used by students in other majors, other universities, and other educational levels.Researchdatasocial sciences researchstudent research jobsresearch data managementresearch toolslibrary resourcesapplication/pdfCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/3dp7312tpublicationoai:escholarship.org:ark:/13030/qt0tj6t0tr2022-12-12T18:48:18Zqt0tj6t0trOpinion: CASE Act will Harm Researchers and Freedom of InquiryBenson, SaraVollmer, Timothy2021-03-18The Copyright Alternative in Small-Claims Enforcement Act of 2020 (CASE Act) was swept into law during the final days of 2020 as a part of the 5,500 page federal spending bill. In theory, the CASE Act aims to provide a venue for individual creators (such as photographers, graphic artists, musicians) to address smaller copyright infringement claims without spending the time and money required to pursue a copyright infringement lawsuit in Federal court. In reality, however, this additional bureaucratic structure created outside of the traditional court system is fraught with problems that will mostly incentivize large, well-resourced rightsholders or overly litigious copyright owners to take advantage of the system. At the same time, it will confuse and harm innocuous users of content, who may not understand the complexities of copyright law, and who do not know whether or how to respond to a notice of infringement via this small claims process. From our perspective, it will chill users who rely on crucial statutory exceptions to copyright, such as fair use, in their research and teaching activities.copyrightCASE Actadvocacylegislationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0tj6t0trarticleJournal of Copyright in Education & Librarianshipvol 5, iss 12473-8336oai:escholarship.org:ark:/13030/qt3n01230w2022-08-24T17:19:36Zqt3n01230wLost Lands and Targeted Policy: Reaction to Mapuche Activism in Twenty-First Century ChileBuchanan, BoyceBallenger, Stephanie2022-04-01Upper Division Winner 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3n01230wpublicationoai:escholarship.org:ark:/13030/qt40f9g9vf2022-07-15T16:14:42Zqt40f9g9vfMiners Undermining Geology: The Gold-fueled Chokehold on the California Geological Survey of 1860Chavez, LiamAlaniz, Rodolfo John2016-11-012017 WinnerLower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/40f9g9vfpublicationoai:escholarship.org:ark:/13030/qt3gx448gj2022-06-13T23:52:33Zqt3gx448gjArchiving e-phemera of Belarus Political Crisis 2020-2021Pendse, Liladhar Ramchandra2021-10-01It will be almost a year since the Presidential elections in Belarus; they took place last year on August 9, 2020. And the outcome of these elections did not surprise anyone when the Central Elections Commission of Belarus declared that the incumbent President Lukashenko was yet again elected with approximately 80% of votes cast. However, one can see that 20% of the votes cast and counted or counterfeited or undercounted meant there was an underlying level of dissent in the country. The ensuing persistent popular demonstrations that continued although the police actions of OMON (Атрад міліцыі асобага прызначэння) and the use of social media by multiple individuals represented an opportunity to harvest robust and granular archival data related to social protest moment in Belarus. Thus the idea of the web-archiving project took hold at UC Berkeley. At the same time, one can contest the ephemeral nature of digitally born content or even argue the need for documenting and preserving multiple views as expressed in the popular media of Belarus, the importance of preservation and representing the diverse voice in Belarus.BelarusSlavic StudiesEast European StudiesWeb ArchivingArchive-itCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/3gx448gjpublicationoai:escholarship.org:ark:/13030/qt2p3293k82022-06-01T20:44:21Zqt2p3293k8Beyond the Chinese Façade: A Preliminary Study of Three Sino-Vietnamese Legends from Lĩnh Nam Chích
Quái 嶺南摭怪 (Wonders Selected from South of the Passes)Leung, JenkinEdwards, Penny2022-04-01Upper division winner 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2p3293k8publicationoai:escholarship.org:ark:/13030/qt7qq295gk2022-06-01T20:32:01Zqt7qq295gkMissing White Woman Syndrome: A Historical and Sociological Look Into the Case of Gabby PetitoChang-Yeh, LarkSloan, Ryan2022-04-01Lower division winner 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7qq295gkpublicationoai:escholarship.org:ark:/13030/qt4kw6v4qf2022-06-01T20:30:46Zqt4kw6v4qfSugarcoating the Truth: The Sugar Association's Impact on ObesitySood, RiaSloan, Ryan2022-04-01Lower division winner 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4kw6v4qfpublicationoai:escholarship.org:ark:/13030/qt7127g85r2022-06-01T20:17:42Zqt7127g85rFlowers Plucked From Berkeley: A Japanese American Nursery During the 1940sRen, AnnieLovell, Margaretta2022-04-01Upper division honorable mention 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7127g85rpublicationoai:escholarship.org:ark:/13030/qt1j63q9n22022-06-01T20:13:43Zqt1j63q9n2A Biography of Marguerite Dice: Daughter of Republicanism and Mother of ConservatismLong, AnnabelleKelly, Daniel2022-04-01Upper division winner 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1j63q9n2publicationoai:escholarship.org:ark:/13030/qt3009g0js2022-06-01T20:06:12Zqt3009g0jsSociophonetic Differences in Queer Speech of Spanish SpeakersDuarte, JesusDavidson, Justin2022-04-01Upper division winner 2022application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3009g0jspublicationoai:escholarship.org:ark:/13030/qt15s4z7x62022-06-01T19:40:07Zqt15s4z7x6Research Resource Identification (RRID)Smith, Elliott2021-08-17One barrier to reproducibility is the lack of specificity in the materials and tools used in research. The Research Resource Identification (RRID) Initiative is a community-based solution addressing the issue of experimental resource identification, primarily in the biomedical and life sciences. Citing the RRID for research materials and tools in scientific publications eliminates ambiguity and enhances reproducibility.data managementopen scienceresearch materialsRRIDscientific publicationCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/15s4z7x6publicationoai:escholarship.org:ark:/13030/qt3qv5z4r82022-05-27T19:48:12Zqt3qv5z4r8Durability of effects from short-term economic incentives for clinic attendance among HIV positive adults in Tanzania: long-term follow-up of a randomised controlled trialFahey, Carolyn ANjau, Prosper FKelly, Nicole KMfaume, Rashid SBradshaw, Patrick TDow, William HMcCoy, Sandra I2021-12-24Introduction Conditional economic incentives are shown to promote medication adherence across a range of health conditions and settings; however, any long-term harms or benefits from these time-limited interventions remainlargely unevaluated. We assessed 2–3 years outcomes from a 6-month incentive programme in Tanzania that originally improved short-term retention in HIV care and medication possession.Methods We traced former participants in a 2013–2016 trial, which randomised 800 food-insecure adults starting HIV treatment at three clinics to receive eitherusual care (control) or up to 6 months of cash or food transfers (~US$11/month) contingent on timely attendance at monthly clinic appointments. The primaryintention-to-treat analysis estimated 24-month and 36-month marginal risk differences (RD) between incentive and control groups for retention in care and all-cause mortality, using multiple imputation for a minority of missing outcomes. We also estimated mortality HRs from time-stratified Cox regression.Results From 3 March 2018 to 19 September 2019, we determined 36-month retention and mortality statusesfor 737 (92%) and 700 (88%) participants, respectively. Overall, approximately 660 (83%) participants were in care at 36 months while 43 (5%) had died. Therewere no differences between groups in retention at 24 months (86.5% intervention vs 84.4% control, RD 2.1,95% CI −5.2 to 9.3) or 36 months (83.3% vs 77.8%, RD 5.6, –2.7 to 13.8), nor in mortality at either time point. The intervention group had a lower rate of death during the first 18 months (HR 0.27, 95% CI 0.10 to 0.74); mortality was similar thereafter (HR 1.13, 95% CI 0.33to 3.79).Conclusion These findings confirm that incentives are a safe and effective tool to promote short-term adherence and potentially avert early deaths at thecritical time of HIV treatment initiation. Complementary strategies are recommended to sustain lifelongretention in HIV care.Trial registration number NCT01957917BRII recipient: FaheypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3qv5z4r8articleBMJ Global Healthvol 6, iss 12, e0072482059-7908oai:escholarship.org:ark:/13030/qt1zx139472022-05-25T21:08:42Zqt1zx13947Research Data Management Needs Assessment: Survey ResultsGlusker, AnnMadhavan, Ann2017-10-01The National Network of Libraries of Medicine’s Pacific Northwest Region (PNR) conducted a needs assessment in April/May 2017, focusing on respondents’ responses to questions about which types of assistance and programs related to data would be the most useful. The survey focused specifically on respondents in settings offering research data services. They mentioned collaboration as a highly-regarded method for keeping up with the data librarianship field, so it may be that the PNR’s support for collaborative efforts, whether through funding or another mechanism, may make an important contribution. These respondents also noted that besides subject-specific liaison work, they were very likely to work with their university’s sponsored research and/or IRB offices. If the PNR can offer suggestions for developing and sustaining these relationships, that may also be helpful.research data managementneeds assessmenthealth scienceshealth sciences librariesmedical librariansapplication/pdfCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/1zx13947publicationoai:escholarship.org:ark:/13030/qt7w12k3g32022-05-04T15:30:57Zqt7w12k3g3PrefaceLee, Corliss S.2022-02-01Academic library workers often make use of systemic, bureaucratic, political, collegial, and symbolic dimensions of organizational behavior to achieve their diversity, equity, and inclusion goals, but many are also doing the crucial work of pushing back at the structures surrounding them in ways small and large. Implementing Excellence in Diversity, Equity, and Inclusion captures emerging practices that academic libraries and librarians can use to create more equitable and representative institutions. 19 chapters are divided into 6 sections:Recruitment, Retention and PromotionProfessional DevelopmentLeveraging Collegial NetworksReinforcing the MessageOrganizational ChangeAssessmentChapters cover topics including active diversity recruitment strategies; inclusive hiring; gendered ageism; librarians with disabilities; diversity and inclusion with student workers; residencies and retention; creating and implementing a diversity strategic plan; cultural competency training; libraries’ responses to Canadian Truth and Reconciliation Commission Calls to Action; and accountability and assessment. Authors provide practical guiding principles, effective practices, and sample programs and training. Implementing Excellence in Diversity, Equity, and Inclusion explores how academic libraries have leveraged and deployed their institutions’ resources to effect DEI improvements while working toward implementing systemic solutions. It provides means and inspiration for continuing to try to hire, retain, and promote the change we want to see in the world regardless of existing structures and systems, and ways to improve those structures and systems for the future.diversityequityinclusionacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7w12k3g3publicationoai:escholarship.org:ark:/13030/qt72q6p5z72022-05-04T15:30:40Zqt72q6p5z7IntroductionLee, Corliss S.Lym, Brian2022-02-01Academic library workers often make use of systemic, bureaucratic, political, collegial, and symbolic dimensions of organizational behavior to achieve their diversity, equity, and inclusion goals, but many are also doing the crucial work of pushing back at the structures surrounding them in ways small and large. Implementing Excellence in Diversity, Equity, and Inclusion captures emerging practices that academic libraries and librarians can use to create more equitable and representative institutions. 19 chapters are divided into 6 sections:Recruitment, Retention and PromotionProfessional DevelopmentLeveraging Collegial NetworksReinforcing the MessageOrganizational ChangeAssessmentChapters cover topics including active diversity recruitment strategies; inclusive hiring; gendered ageism; librarians with disabilities; diversity and inclusion with student workers; residencies and retention; creating and implementing a diversity strategic plan; cultural competency training; libraries’ responses to Canadian Truth and Reconciliation Commission Calls to Action; and accountability and assessment. Authors provide practical guiding principles, effective practices, and sample programs and training. Implementing Excellence in Diversity, Equity, and Inclusion explores how academic libraries have leveraged and deployed their institutions’ resources to effect DEI improvements while working toward implementing systemic solutions. It provides means and inspiration for continuing to try to hire, retain, and promote the change we want to see in the world regardless of existing structures and systems, and ways to improve those structures and systems for the future.diversityequityinclusionacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/72q6p5z7publicationoai:escholarship.org:ark:/13030/qt6cj5455j2022-05-04T15:30:06Zqt6cj5455jAfterwordLee, Corliss S.Lym, Brian2022-02-01Academic library workers often make use of systemic, bureaucratic, political, collegial, and symbolic dimensions of organizational behavior to achieve their diversity, equity, and inclusion goals, but many are also doing the crucial work of pushing back at the structures surrounding them in ways small and large. Implementing Excellence in Diversity, Equity, and Inclusion captures emerging practices that academic libraries and librarians can use to create more equitable and representative institutions. 19 chapters are divided into 6 sections:Recruitment, Retention and PromotionProfessional DevelopmentLeveraging Collegial NetworksReinforcing the MessageOrganizational ChangeAssessmentChapters cover topics including active diversity recruitment strategies; inclusive hiring; gendered ageism; librarians with disabilities; diversity and inclusion with student workers; residencies and retention; creating and implementing a diversity strategic plan; cultural competency training; libraries’ responses to Canadian Truth and Reconciliation Commission Calls to Action; and accountability and assessment. Authors provide practical guiding principles, effective practices, and sample programs and training. Implementing Excellence in Diversity, Equity, and Inclusion explores how academic libraries have leveraged and deployed their institutions’ resources to effect DEI improvements while working toward implementing systemic solutions. It provides means and inspiration for continuing to try to hire, retain, and promote the change we want to see in the world regardless of existing structures and systems, and ways to improve those structures and systems for the future.diversityequityinclusionacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6cj5455jpublicationoai:escholarship.org:ark:/13030/qt9qm721jd2022-04-29T22:40:56Zqt9qm721jdThe Languages of Berkeley: An Online ExhibitionPotts, Claude H.Alter, RobertAstourian, StephanBergmann, EmilieButler, JudithChang, JaeyongChaver, YaelClemons, AdamCole, EmilyDjalius, YusmarniDouzjian, MyrnaEstrada, NataliaFerko, FrankFollett, TaylorGali, NeilHaber, RuthHamed, MohamedHayes, John L.He, JianyeJiamrattanyo, ArthitJohnson, Ida MoenKern, RickLukasik, CandaceMacías Prieto, CarlosMalik, AdnanMarcus, Alexander W.Marra, ToshieMagarik, RaphaelMeerkhan, NasserMendoza, SteveNaiman, EricNelson, JenniferOtt, JeremyPascua, GabriellePendse, LiladharReardon, StacyRedondo-Campillos, Ana-BelénRitchey, ElyseRosado, BrendaRudolph, DeborahShih, VirginiaShirvani, ShahrzadSmith, FrankSmith, TroyTran, HanhXue, SusanWeckström, LottaWong, KennethZwicker, JonathanBocus, AchilleGertzman, FedoraMendoza, SteveRosado, Brenda2021-06-13The Languages of Berkeley: An Online Exhibition celebrates the magnificent diversity of languages that advance research, teaching, and learning at the University of California, Berkeley. It is the point of embarkation for an exciting sequential exhibit that built on one post per week, showcasing an array of digitized works in the original language chosen by those who work with these languages on a daily basis. Many of these early-published works are now in the public domain and are open to the world to read and share without restriction. Preparations for the online exhibition began in early 2018 with the final installment published online in October 2020. Using the Library’s instance of WordPress, the library exhibit comprises short essays of nearly all of the 59 modern and ancient languages that are currently taught across 14 departments on campus plus a dozen more languages that contributors wished to include. From September 2019 to August 2020, exhibit designer Aisha Hamilton and curator Claude Potts also installed a physical companion exhibition in Moffitt Library’s Free Speech Movement Café (FSM) centering on endangered languages which was cut short by the campus closure due to the COVID-19 Pandemic. Photos from that installation are archived in this catalog with the open book publishing platform Pressbooks, along with the complete entries from the online exhibition. Aside from core support from the Library and the Berkeley Language Center, this multi-year project would not have been possible without the contributions and hard work of more than 45 librarians, professors, lecturers, staff, and students. linguistic diversitymulticulturalisminternational & area studieslanguagesonline exhibitsresearch librariesnon-English languageslanguage acquisitionlanguage learningendangered languagesminority languageshigher educationDEIdiversityequityinclusionapplication/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/9qm721jdmonographoai:escholarship.org:ark:/13030/qt6nz7x6742022-04-12T18:15:48Zqt6nz7x674Accessing Gender Affirming Care from the Margins: Comparing the Strategies of Transgender People Pre-1980 and Non-Binary People TodayChung, LindseySterzing, Paul2021-04-01Upper DivisionWinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6nz7x674publicationoai:escholarship.org:ark:/13030/qt7cd6j4zz2022-04-12T18:13:07Zqt7cd6j4zzRun Like a Girl: Renewing the Western Gender Binary through Testosterone Regulations in an Age of NeocolonialismChung, LindseyCole, Chisako2019-04-01Lower Division winnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7cd6j4zzpublicationoai:escholarship.org:ark:/13030/qt7vh439t12022-03-04T17:01:21Zqt7vh439t1Narrative Medicine as an Outlet of Expression for Healthcare Workers Experiencing Moral InjurySumra, SaffanatMargi, Wald2020-10-01Lower DivisionWinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7vh439t1publicationoai:escholarship.org:ark:/13030/qt2wd960hr2022-02-01T23:17:15Zqt2wd960hrArchiving e-phemera of Belarus Political Crisis 2020-2021Pendse, Liladhar Ramchandra2021-10-01Dr. Liladhar Pendse presented this paper at the 10th ICCEES World Congress 3–8 August 2021, Concordia University – Montreal. In the aftermath of the Presidential elections, the UC Berkeley Library's curator for Slavic, East European, and Eurasian Studies created a web archive of Belarus Protests (2020-2021) to document contemporary dissent and protest movements against the autocratic rule of President Lukashenko. This paper provides information about the process management, selection criteria for the websites, and the project outcomes.BelarusBelarus Political CrisisWeb-archiving.CC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/2wd960hrpublicationoai:escholarship.org:ark:/13030/qt3d80f62q2021-12-08T21:26:46Zqt3d80f62qData Sharing, Storage, and the Social Sciences Working GroupWittenberg, JamieChurch, JamesDekker, HarrisonEmmelhainz, CeliaStiles, Jon2021-12-08application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3d80f62qpublicationoai:escholarship.org:ark:/13030/qt9v34x3rr2021-12-08T18:51:24Zqt9v34x3rrData Engagement for the Data-Hesitant Librarian (Presentation at ICPSR Data Fair)Glusker, Ann2020-10-02In our data-driven world, what are the best ways to engage librarians who are hesitant to work with data-related content and questions? Can we? Must we? Should we? Critical data literacy will be the starting place for the presentation, followed by suggestions for how to engage “non-data” librarians with data training and activities in the library setting. We’ll discuss the issue of how feasible it is to expect universal data-savvy, and how to empower librarians to choose their own approaches to the issue, both in the workplace and in their career planning. Finally, we’ll discuss training approaches and availability specifically, and attendees will leave with ideas for a plan of action for future data training in their libraries.publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9v34x3rrpublicationoai:escholarship.org:ark:/13030/qt4403c0f42021-10-14T13:45:38Zqt4403c0f4Supporting Big Data Research at the University of California, Berkeley: An Ithaka S+R Local ReportFoster, Erin DGlusker, AnnQuigley, Brian2021-10-01Based on interviews with big data researchers at UC Berkeley as part of an Ithaka S+R project, this local report provides insights on researcher practices and challenges in six thematic areas: data collection & processing; analysis: methods, tools, infrastructure; research outputs; collaboration; training; and balancing domain vs data science expertise. The report makes several recommendations based on these findings. A summary post with the recommendations is available at https://update.lib.berkeley.edu/2021/10/04/big-data-as-a-way-of-life/.application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4403c0f4publicationoai:escholarship.org:ark:/13030/qt8479t2nn2021-09-29T12:55:17Zqt8479t2nnCultivating Public Service Competencies in Student Employees: A Case StudyHarrington, Sarah RoseLewis, Nancy OBrown, Nicole E2021-09-27How can we best train student employees for public service roles? At UC Berkeley, as in many academic libraries, a student employee is the first person that a user will see when entering the library; they are the “face of the library.” A positive interaction will set a positive tone for the user’s library experience, while a negative interaction may discourage the user from ever visiting the library again. As such, it is critical to prepare student staff with the competencies to engage positively with library users and feel confident in their roles. This paper shares a case study of a public services training piloted for Access Services student employees at UC Berkeley.public servicescustomer servicetrainingstudent employeesstaff developmentactive learningapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8479t2nnarticlePublic Services Quarterlyvol 17, iss 3, 149-165oai:escholarship.org:ark:/13030/qt2vw807vb2021-07-15T21:07:59Zqt2vw807vbBuilding Legal Literacies for Text Data MiningSamberg, RachaelVollmer, TimothyAlthaus, ScottBamman, DavidBenson, SaraButler, BrandonCate, BethCourtney, Kyle KFlynn, SeanGould, MariaHennesy, CodyDickson Koehl, EleanorPadilla, ThomasReardon, StacySag, MatthewSchofield, Brianna LSenseney, MeganWorthey, Glen2021-07-15text data mininglawpolicydigital humanitiesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2vw807vbmonographoai:escholarship.org:ark:/13030/qt7xx986d52021-06-24T17:12:54Zqt7xx986d5Becoming 'The First Free Town in the Americas': Claiming and Celebrating Blackness in Yanga, VeracruzWanless, DuncanSchneider, Elena2021-04-01Upper DivisionWinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7xx986d5publicationoai:escholarship.org:ark:/13030/qt84n6s7t02021-06-24T17:09:21Zqt84n6s7t0Community Control and Desegregation in East Palo Alto, California, 1958-1986Madhav, TaraPerez, Bernadette2021-04-01Upper DivisionWinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/84n6s7t0publicationoai:escholarship.org:ark:/13030/qt4337w7s32021-06-24T17:03:07Zqt4337w7s3'Know History, Know Self:' Coming Home for Formerly Incarcerated Asian Americans and Pacific IslandersChen, JanieBehbahanian, Laleh2021-04-01Upper DivisionWinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4337w7s3publicationoai:escholarship.org:ark:/13030/qt0nj3g54t2021-06-24T16:56:23Zqt0nj3g54tThailand’s Healthcare, Culture, Media, and COVID-19 Story: A Review of Thailand’s COVID-19 Response and Its Impact on Public Health, Economics, and Citizens’ Personal ExperiencesChinnapha, Jenny LaiEdwards, Penelope2020-10-01Lower divisionWinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0nj3g54tpublicationoai:escholarship.org:ark:/13030/qt74v8z1942021-04-30T14:04:11Zqt74v8z194CIFNAL: A Decade of Collaboration (2006-2016)Potts, Claude, H.2017-10-13CIFNAL, the Collaborative Initiative for French Language Collections, promotes and facilitates the cooperative exchange of ideas and resources between Francophone and North American research libraries. Founded in 2006 with just a few institutions, CIFNAL is the youngest of the expertise groups within the Global Resource Network administered through the Center for Research Libraries (CRL). With a shoestring budget and essentially a volunteer work force, CIFNAL has succeeded where individual libraries or other regional consortia have faltered because of two constants: dedicated librarians and unwavering centralized support of CRL. This presentation provides a short history of the group’s activities over the past decade, highlighting its contributions to digital scholarship, building regional and international alliances, and cultivating relations with information professionals from and outside of the United States. A careful assessment of CIFNAL’s projects, working groups, and publications provides insight as to what might be in store for the future.international library collaborationdigital scholarshiplibrary alliancescollection sharingresource sharingFranceFrancophone worldCenter for Research LibrariesCRLGlobal Resource NetworkCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/74v8z194publicationoai:escholarship.org:ark:/13030/qt307907312021-04-21T15:50:42Zqt30790731Library Staff Morale in the Academic HierarchyGlusker, AnnDyess, BonitaEmmelhainz, CeliaEstrada, Natalia2021-04-20Academic librarians have increasingly gone public with their experiences of low morale and burnout, yet less attention has been paid to the workplace experiencesof library staff. As Kaetrena Davis Kendrick notes in her work on the persistent harm of low morale among librarians, “the cost of silence can be high.” Our research team includes library staff, former library staff, a recent MLS grad and MLIS student, and librarians. Through 34 structured interviews with academic library staff nationwide, we seek to demonstrate how organizational culture, library hierarchies, and management style affect staff morale. In this webinar, we present our findings establishing that efforts to address equity in compensation, provide professional growth opportunities, and create more collegial work environments can all improve staff morale. Finally, wesuggest how you can make changes in your own libraries to assess and improve morale across staff hierarchies.CC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/30790731publicationoai:escholarship.org:ark:/13030/qt7g1322fs2021-04-16T20:49:39Zqt7g1322fsOn Scholarly Book Awards in AnthropologyEmmelhainz, Celia2020-10-01A brief article that explores how and why academic book awards are proliferating, and how anthropology book awards may be used in academic library collecting.book awardsanthropologylibrary sciencecollection developmentprestigeacademic hierarchiesacademic publishingapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7g1322fsarticleANSS Currentsvol 35, iss 2oai:escholarship.org:ark:/13030/qt99k4q2212021-04-16T13:35:05Zqt99k4q221#LibraryStaffLife: Improving Staff Morale in Academic Libraries Glusker, AnnDyess, BonitaEmmelhainz, CeliaEstrada, Natalia2021-04-13Academic librarians have increasingly gone public with their experiences of low morale and burnout, yet less attention has been paid to the workplace experiences of library staff. As Kaetrena Davis Kendrick notes in her work on the persistent harm of low morale in library settings, “the cost of silence can be high.” Our research team includes library staff, former library staff, a recent MLS grad, and librarians. Through 35 structured interviews with academic library staff nationwide, we seek to uncover how organizational culture, library hierarchies, and management style affect staff morale. In this poster, we present our findings establishing that efforts to address equity in compensation, provide professional growth opportunities, and create more collegial work environments can all improve staff morale. Finally, we suggest how you can make changes in your own libraries to assess and improve morale across staff hierarchies.moralelibrary staffrecommendationsCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/99k4q221publicationoai:escholarship.org:ark:/13030/qt7kr0w7hx2021-04-13T20:39:50Zqt7kr0w7hxPlanning an Entry Sequence with Service Design: A Case StudyHarrington, Sarah RChurchill, Veronica2020-11-02How might we plan user-friendly entrances for the library? For this project, we learned about and applied service design tools to an entry experience at an academic library. Service design means working to understand users and applying this understanding to the creation or refinement of services. After learning about service design, we created six user profiles and walked them through different entry scenarios to examine each step. Then we created easy-to-understand graphics to provide library leadership with planning materials.Service designaccess servicesspace and environmentuser experiencedesign thinkingaccess servicesacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7kr0w7hxpublicationoai:escholarship.org:ark:/13030/qt93c6f6472021-03-04T01:00:07Zqt93c6f647Baptism and Reversion in Canon Law (working paper)Sherwood, Jessie2021-03-03application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/93c6f647publicationoai:escholarship.org:ark:/13030/qt1895t5f62021-02-16T18:23:11Zqt1895t5f6International and Areas Studies (IAS) Faculty: Are They Different?Hamed, Mohamed2020-11-17publiceScholarship, University of Californiahttps://escholarship.org/uc/item/1895t5f6publicationoai:escholarship.org:ark:/13030/qt3m46n4j92021-01-22T18:06:11Zqt3m46n4j9HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium Imaging MoviesSpaen, QuicoAsin-Acha, RobertoChettih, Selmaan NMinderer, MatthiasHarvey, Christopher DHochbaum, Dorit S2019-03-20Calcium imaging is a key method in neuroscience for investigating patterns of neuronal activity in vivo. Still, existing algorithms to detect and extract activity signals from calcium-imaging movies have major shortcomings. We introduce the HNCcorr algorithm for cell identification in calcium-imaging datasets that addresses these shortcomings. HNCcorr relies on the combinatorial clustering problem HNC (Hochbaum’s Normalized Cut), which is similar to the Normalized Cut problem of Shi and Malik, a well known problem in image segmentation. HNC identifies cells as coherent clusters of pixels that are highly distinct from the remaining pixels. HNCcorr guarantees a globally optimal solution to the underlying optimization problem as well as minimal dependence on initialization techniques. HNCcorr also uses a new method, called “similarity squared”, for measuring similarity between pixels in calcium-imaging movies. The effectiveness of HNCcorr is demonstrated by its top performance on the Neurofinder cell identification benchmark. We believe HNCcorr is an important addition to the toolbox for analysis of calcium-imaging movies.BRII recipient: HochbaumpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3m46n4j9articleeneurovol 6, iss 2, ENEURO.0304-18.20192373-2822oai:escholarship.org:ark:/13030/qt9hh2x1pg2021-01-13T21:13:52Zqt9hh2x1pgPlanning an Entry Sequence with Service DesignHarrington, Sarah RoseChurchill, Veronica2020-07-21Celebrate the possible with service design! The design of academic libraries is often rooted in the history of the institution. But how might these processes be improved to meet the needs of today’s users? Join us as we discuss our year long journey learning about service design and applying service design tools at UC Berkeley. We will share how we examined the entry sequence from the perspective of various user groups to meet user needs. Ideally service design incorporates user observations and feedback, but we will show you how service design tools and principles can be used even while a library is closed during a pandemic. After this session, you will be ready to embark on your own service design journey.service designuser designservice blueprintscustomer journey mapuser profilesdesign thinkinglibrariesAccess ServicespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9hh2x1pgpublicationoai:escholarship.org:ark:/13030/qt884725t52020-11-05T17:30:18Zqt884725t5Exploring a decision-trigger for maintenance of remotely monitored arsenic-remediation system planned for low-income community in Central Valley, CAShrivatsa, SamyuktaVisswanathan, AartiGadgil, Ashok2020-04-01Lower divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/884725t5publicationoai:escholarship.org:ark:/13030/qt50p3f8md2020-11-05T17:25:31Zqt50p3f8mdWord and Image in Chinese Literati Tradition: Analysis of The Way, a spiritual pathYang, JenniferRussell, Kamala2020-04-01Lower division, winnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/50p3f8mdpublicationoai:escholarship.org:ark:/13030/qt2qc6t0nb2020-10-05T15:44:35Zqt2qc6t0nbTraining Student Employees in Public ServiceHarrington, Sarah Rose2020-10-05How can we teach student employees to interact positively with patrons? At UC Berkeley, Access Services supervisors worked with Reference and Instruction librarians to create a training to better equip student employees to interact with the public and learn basic reference tools. The “Public Services and Effective Referrals Training" teaches student employees how to 1) Apply public service guidelines, 2) Deploy de-escalation techniques, 3) Make effective referrals, 4) Navigate key search tools, and 5) Identify methods for seeking research assistance. The program has been running since 2016, and we have trained over 200 student employees. We believe that all student employees should receive training on these basic tools to excel at their jobs and their studies.public servicestudent assistantsstudent employeestrainingstaff developmentpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2qc6t0nbpublicationoai:escholarship.org:ark:/13030/qt8k31j1j52020-08-25T20:01:18Zqt8k31j1j5Educating the Central Asian Librarian: Considering the International MLIS in KazakhstanEmmelhainz, Celia2020-01-01Why do Central Asian librarians enter the profession, and how do they decide which educational strategies to pursue in developing their careers? Using 13 conversations and 10 qualitative interviews with Kazakh and Kyrgyz librarians, this chapter finds that librarians enter the profession due to personal interest, by happenstance, or for university funding and continue when they perceive an opportunity for career growth as well as salary mobility. Central Asian librarians evaluate their educational options, including local bachelor's degrees; distance education from Russia; MLIS programs in Asia, Europe, or America; and short-term online training, while balancing family responsibilities and career prospects in and outside of librarianship. Prospects for creating a local MLIS or other improved professional training programs are discussed.LibrariansLibrary EducationLibrary ScienceProfessionalizationLibrary EducationCIS CountriesPost-Soviet Central AsiaKazakhstanKyrgyz RepublicRecruitmentRetentionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8k31j1j5publicationoai:escholarship.org:ark:/13030/qt91d9k96z2020-08-10T15:33:48Zqt91d9k96zDigital Blackface: How 21st Century Internet Language Reinforces RacismErinn, WongAcevedo Butcher, Carmen2019-04-01lower divisionhonorable mentionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/91d9k96zpublicationoai:escholarship.org:ark:/13030/qt56h8k5w62020-08-04T20:10:07Zqt56h8k5w6Identity Politics and Cultural Placemaking: The Americanization of Portsmouth SquareJain, DivyaCovey, Catherine2020-04-01WinnerUpper divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/56h8k5w6publicationoai:escholarship.org:ark:/13030/qt7tb144s42020-07-27T20:02:39Zqt7tb144s4The Cowboy in the West Wing: On Western Artworks in the Oval OfficeKersting, SarahPalmer, ChristineBrilliant, Mark2020-04-01Winnerupper divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7tb144s4publicationoai:escholarship.org:ark:/13030/qt34b2g74h2020-07-23T21:43:15Zqt34b2g74hAccept, Accept! Accept?! The Problems, Solutions, and Implications of Digital PrivacyMichele, Makhlouf-CaveroSloan, Ryan2020-04-01https://yesnoperhaps.weebly.com/essay-on-digital-privacy Honorable mentionLower divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/34b2g74hpublicationoai:escholarship.org:ark:/13030/qt33n818d72020-07-23T21:38:27Zqt33n818d7Leserinnen and Enlightenment: Johanna Unzer's Philosophy of WomenCurtis, LouiseSheehan, Jonathan2020-04-01Honorable mentionUpper divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/33n818d7publicationoai:escholarship.org:ark:/13030/qt9k93z4cf2020-07-23T21:23:24Zqt9k93z4cfInventing WestphaliaPingitore, NicholasShagan, EthanMurillo, Raphael2020-07-23WinnerUpper divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9k93z4cfpublicationoai:escholarship.org:ark:/13030/qt0dh4s9j32020-07-23T21:15:01Zqt0dh4s9j3Cultural Variations in the Appraisals of AweChen, Enna YuxuanKeltner, Dacher2020-04-01Upper divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0dh4s9j3publicationoai:escholarship.org:ark:/13030/qt6vm6r2wb2020-06-24T18:31:30Zqt6vm6r2wbMaterials sovereignty: Pathways for shaping nanotechnology designKokai, AkosIles, Alastair2020-03-27People in contemporary industrial societies encounter countless novel materials that did not exist previously, many of which present risks to health and environment. In this article, we build on the concept of “materials sovereignty” as the right of people to use and be surrounded by environmentally benign, non-toxic, and renewing materials in their everyday lives. As a rights-based approach, materials sovereignty may help change the politics of governing materials. We suggest that social movements that explicitly base interventions into design on materials sovereignty may be better able to gain traction in changing industrial production. We consider the case of nanotechnology as a particularly challenging field for social movement intervention. We review several pathways that have been used by social movement organizations in attempts to influence the development of nanomaterials, but which have met with limited success. We more closely examine three participatory pathways through which social movements could intervene more directly into material design: participatory technology assessment, collaboration with industry, and co-design. We identify three key elements of materials sovereignty: participatory knowledge systems, which create multi-directional flows of knowledge and agency; the embedding of citizen voices into design processes; and building accountability systems. Of the pathways we examine here, co-design appears to be the most promising from a theoretical and ethical perspective, but there remain significant institutional and organizational challenges for bringing it into practice.BRII applicant: KokaipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6vm6r2wbarticleElementa: Science of the Anthropocenevol 8, iss 1, 142325-1026oai:escholarship.org:ark:/13030/qt2tf8v7zr2020-06-24T16:56:46Zqt2tf8v7zrSource or Sink? A comparison of Landfire- and FIA-based estimates of change in aboveground live tree carbon in California's forestsHolland, Tim GStewart, WilliamPotts, Matthew D2019-07-05Forests play a central role in addressing climate change, and accurate estimates of forest carbon are critical for the development of actions that reduce emissions from forests and that maximize sequestration by forests. Methodological challenges persist regarding how best to estimate forest carbon stocks and flux at regulatory-relevant scales. Using California, USA as a case study, we compare two approaches to stock-difference forest carbon estimation for aboveground live trees: one based on ground inventories and one on land cover classification of remotely-sensed data. Previous work using ground inventory data from the Forest Inventory and Analysis Program (FIA) showed net aboveground carbon (AGC) sequestration by live trees in California forests, while estimates using land cover classification from the Landscape Fire and Resource Management Planning Tools (Landfire) showed net reductions in live tree AGC over a similar time period. We examined the discrepancy by re-analyzing the FIA inventory data through the lens of a category-change analysis based on Landfire. This analysis showed more than 50% of the live tree AGC in fewer than 4% of Landfire-equivalent categories and that the overwhelming majority (>80%) of forest area did not change height category between measurement periods. Despite the lack of categorical change, the majority of FIA plots increased in both 95th percentile tree height and in live tree AGC. These findings suggest that an approach based on observing categorical changes risks undercounting AGC sequestration resulting from growth and thus overstating the relative importance of AGC reductions that result from disturbances. This would bias AGC flux estimates downward, leading us to validate the conclusion that live trees in California were a net sink of aboveground carbon in the decade ending in 2016. Our findings suggest an inventory-based or hybrid approach is preferable to methods that depend on categorical bins for estimating AGC in disturbance-prone forest ecosystems.BRII applicant: StewartpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2tf8v7zrarticleEnvironmental Research Lettersvol 14, iss 7, 0740081748-9326oai:escholarship.org:ark:/13030/qt73q5b34b2020-06-23T22:33:29Zqt73q5b34bImplicit Standardization in a Minority Language Community: Real-Time Syntactic Change among Hasidic Yiddish WritersBleaman, Isaac L2020-05-29The recent turn to “big data” from social media corpora has enabled sociolinguists to investigate patterns of language variation and change at unprecedented scales. However, research in this paradigm has been slow to address variable phenomena in minority languages, where data scarcity and the absence of computational tools (e.g., taggers, parsers) often present significant barriers to entry. This article analyzes socio-syntactic variation in one minority language variety, Hasidic Yiddish, focusing on a variable for which tokens can be identified in raw text using purely morphological criteria. In non-finite particle verbs, the overt tense marker tsu (cf. English to, German zu) is variably realized either between the preverbal particle and verb (e.g., oyf-tsu-es-n up-to-eat-INF ‘to eat up’; the conservative variant) or before both elements (tsu oyf-es-n to up-eat-INF; the innovative variant). Nearly 38,000 tokens of non-finite particle verbs were extracted from the popular Hasidic Yiddish discussion forum Kave Shtiebel (the ‘coffee room’; kaveshtiebel.com). A mixed-effects regression analysis reveals that despite a forum-wide favoring effect for the innovative variant, users favor the conservative variant the longer their accounts remain open and active. This process of rapid implicit standardization is supported by ethnographic evidence highlighting the spread of language norms among Hasidic writers on the internet, most of whom did not have the opportunity to express themselves in written Yiddish prior to the advent of social media.BRII applicant: BleamanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/73q5b34bpublicationoai:escholarship.org:ark:/13030/qt3ss8f64h2020-06-23T22:30:47Zqt3ss8f64hTopography and human pressure in mountain ranges alter expected species responses to climate changeElsen, Paul RMonahan, William BMerenlender, Adina M2020-04-24ArticleOpen AccessPublished: 24 April 2020Topography and human pressure in mountain ranges alter expected species responses to climate changePaul R. Elsen, William B. Monahan & Adina M. Merenlender Nature Communications volume 11, Article number: 1974 (2020) Cite this article
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AbstractClimate change is leading to widespread elevational shifts thought to increase species extinction risk in mountains. We integrate digital elevation models with a metric of human pressure to examine changes in the amount of intact land area available for species undergoing elevational range shifts in all major mountain ranges globally (n = 1010). Nearly 60% of mountainous area is under intense human pressure, predominantly at low elevations and mountain bases. Consequently, upslope range shifts generally resulted in modeled species at lower elevations expanding into areas of lower human pressure and, due to complex topography, encountering more intact land area relative to their starting position. Such gains were often attenuated at high elevations as land-use constraints diminished and topographic constraints increased. Integrating patterns of topography and human pressure is essential for accurate species vulnerability assessments under climate change, as priorities for protecting, connecting, and restoring mountain landscapes may otherwise be misguided.BRII applicant: MerenlenderpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3ss8f64harticleNature Communicationsvol 11, iss 12041-1723oai:escholarship.org:ark:/13030/qt4kj154592020-06-23T22:04:52Zqt4kj15459Partial migration alters population ecology and food chain length: evidence from a salmonid fishKelson, Suzanne JPower, Mary EFinlay, Jacques CCarlson, Stephanie M2020-02-21Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss , in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O. mykiss . In one stream, we found differences in the frequency of migration‐linked genotypes below and above a waterfall barrier (migratory allele frequency of 60% below vs. 31% above). Below the waterfall, in the migratory‐dominated region, the density of young fish (<1 yr old) was approximately twice that in the resident‐dominated region above the waterfall (0.46 vs. 0.26 individuals/m2, respectively), presumably reflecting the higher fecundity of migratory females. Additionally, there were half as many older fish (>1 yr old) in pools downstream of the waterfall (0.05 vs. 0.13 individuals/m2). In a second stream, between‐year variation in the dominance of migratory vs. resident fish allowed us to explore differences in fish density and size structure through time, and we found a consistent pattern. In brief, when migratory genotypes dominated, we found higher densities of young fish and lower densities of older fish, resulting in a simpler size structure, compared to when resident genotypes dominated. Moreover, large resident trout had a slightly higher trophic position than young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other), quantified with stable isotope data. The difference in fish size structure did not generate trophic cascades. Partial migration is widespread among migratory populations, as is phenotypic divergence between resident and migratory forms, suggesting the potential for widespread ecological effects arising from this common form of intraspecific variation.BRII applicant: CarlsonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4kj15459articleEcospherevol 11, iss 22150-8925 2150-8925oai:escholarship.org:ark:/13030/qt01n1t80p2020-06-23T22:02:39Zqt01n1t80pPatterns of coyote predation on sheep in California: A socio-ecological approach to mapping risk of livestock-predator conflictMcInturff, AlexMiller, Jennifer R. BGaynor, Kaitlyn MBrashares, Justin S2020-04-01Conflict between livestock producers and wild predators is a central driver of large predator declines and simultaneously may imperil the lives and livelihoods of livestock producers. There is a growing recognition that livestock–predator conflict is a socio‐ecological problem, but few case studies exist to guide conflict research and management from this point of view. Here we present a case study of coyote‐sheep predation on a California ranch in which we combine methods from the rapidly growing field of predation risk modeling with participatory mapping of perceptions of predation risk. Our findings reveal an important selection bias that may occur when producer perceptions and decisions are excluded from ecological methods of studying conflict. We further demonstrate how producer inputs, participatory mapping, and ecological modeling of conflict can inform one another in understanding patterns, drivers, and management opportunities for livestock–predator conflict. Finally, we make recommendations for improving the interoperability of ecological and social data about predation risk. Collectively our methods offer a socio‐ecological approach that fills important research gaps and offers guidance to future research.BRII applicant: BrasharespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/01n1t80ppublicationoai:escholarship.org:ark:/13030/qt63s7r6h42020-06-23T21:59:48Zqt63s7r6h4Why Does Therapy Work? An Idiographic Approach to Explore Mechanisms of Change Over the Course of Psychotherapy Using Digital AssessmentsAltman, Allison DiamondShapiro, Lauren AFisher, Aaron J2020-04-24Background and Objective(s): While psychotherapy treatments are largely effective, the processes and mechanisms underlying such positive changes remain somewhat unknown. Focusing on a single participant from a treatment outcome study that used a modular-based cognitive behavior therapy protocol, this article aims to answer this question by identifying changes in specific symptomatology over the course of the treatment. Using quantitative data derived from digital health methodology, we analyzed whether a given therapeutic intervention was related to downstream effects in predicted symptom domains, to assess the accuracy of our interventions.Methods: This case study employed an observational N-of-1 study design. The participant (n = 1) was a female in the age range of 25–35 years. Using digital health data from ambulatory assessment surveys completed prior to and during therapy, separate linear regression analyses were conducted to assess if hypothesized treatment targets reduced after a given module, or intervention.Results: Support was found for some of the hypothesized quantitative changes (e.g., decreases in avoidance after exposures module), yet not for others (e.g., decreases in rumination following the mindfulness module).Conclusion: We present data and results from our analyses to offer an example of a novel design that may allow for a greater understanding of the nature of symptom changes with increased granularity throughout the course of a psychological treatment from the use of digital health tools.BRII applicant: DiamondpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/63s7r6h4publicationoai:escholarship.org:ark:/13030/qt30t653xb2020-06-23T21:57:32Zqt30t653xbSpectrum-Wide Quantum Criticality at the Surface of Class AIII Topological Phases: An "Energy Stack"� of Integer Quantum Hall Plateau TransitionsSbierski, BjornKarcher, Jonas FFoster, Matthew S2020-05-01In the absence of spin-orbit coupling, the conventional dogma of Anderson localization asserts that all states localize in two dimensions, with a glaring exception: the quantum Hall plateau transition (QHPT). In that case, the localization length diverges and interference-induced quantum-critical spatial fluctuations appear at all length scales. Normally, QHPT states occur only at isolated energies; accessing them therefore requires fine-tuning of the electron density or magnetic field. In this paper we show that QHPT states can be realized throughout an energy continuum, i.e., as an “energy stack” of critical states wherein each state in the stack exhibits QHPT phenomenology. The stacking occurs without fine-tuning at the surface of a class AIII topological phase, where it is protected by U(1) and (anomalous) chiral or time-reversal symmetries. Spectrum-wide criticality is diagnosed by comparing numerics to universal results for the longitudinal Landauer conductance and wave function multifractality at the QHPT. Results are obtained from an effective 2D surface field theory and from a bulk 3D lattice model. We demonstrate that the stacking of quantum-critical QHPT states is a robust phenomenon that occurs for AIII topological phases with both odd and even winding numbers. The latter conclusion may have important implications for the still poorly understood logarithmic conformal field theory believed to describe the QHPT.BRII applicant: SbierskipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/30t653xbarticlePhysical Review Xvol 10, iss 22160-3308oai:escholarship.org:ark:/13030/qt1wb7554g2020-06-23T21:54:12Zqt1wb7554gA Tale of Winglets: Evolution of Flight Morphology in Stick InsectsZeng, YuO'Malley, ConnorSinghal, SonalRahim, FaszlyPark, SehoonChen, XinDudley, Robert2020-05-27The evolutionary transition between winglessness and a full-winged morphology requires selective advantage for intermediate forms. Conversely, repeated secondary wing reductions among the pterygotes indicates relaxation of such selection. However, evolutionary trajectories of such transitions are not well-characterized. The stick insects (Phasmatodea) exhibit diverse wing sizes at both interspecific and intersexual levels, and thus provide a system for examining how selection on flight capability, along with other selective forces, drives the evolution of flight-related morphology. Here, we examine variation in relevant morphology for stick insects using data from 1,100+ individuals representing 765 species. Although wing size varies along a continuous spectrum, taxa with either long or miniaturized wings are the most common, whereas those with intermediate-sized wings are relatively rare. In a morphological space defined by wing and body size, the aerodynamically relevant parameter termed wing loading (the average pressure exerted on the air by the wings) varies according to sex-specific scaling laws; volant but also flightless forms are the most common outcomes in both sexes. Using phylogenetically-informed analyses, we show that relative wing size and body size are inversely correlated in long-winged insects regardless of sexual differences in morphology and ecology. These results demonstrate the diversity of flight-related morphology in stick insects, and also provide a general framework for addressing evolutionary coupling between wing and body dimensions. We also find indirect evidence for a “fitness valley” associated with intermediate-sized wings, suggesting relatively rapid evolutionary transitions between wingless and volant forms.BRII applicant: DudleypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1wb7554gpublicationoai:escholarship.org:ark:/13030/qt9tm3n0x62020-06-23T21:19:03Zqt9tm3n0x6Global agricultural economic water scarcityRosa, LorenzoChiarelli, Davide DaniloRulli, Maria CristinaDell'Angelo, JampelD'Odorico, Paolo2020-04-29Water scarcity raises major concerns on the sustainable future of humanity and the conservation of important ecosystem functions. To meet the increasing food demand without expanding cultivated areas, agriculture will likely need to introduce irrigation in croplands that are currently rain-fed but where enough water would be available for irrigation. “Agricultural economic water scarcity” is, here, defined as lack of irrigation due to limited institutional and economic capacity instead of hydrologic constraints. To date, the location and productivity potential of economically water scarce croplands remain unknown. We develop a monthly agrohydrological analysis to map agricultural regions affected by agricultural economic water scarcity. We find these regions account for up to 25% of the global croplands, mostly across Sub-Saharan Africa, Eastern Europe, and Central Asia. Sustainable irrigation of economically water scarce croplands could feed an additional 840 million people while preventing further aggravation of blue water scarcity.BRII applicant: RosapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9tm3n0x6articleScience Advancesvol 6, iss 18, eaaz60312375-2548oai:escholarship.org:ark:/13030/qt77h6w7nd2020-06-23T21:14:17Zqt77h6w7ndHydroclimatic drivers of highly seasonal leptospirosis incidence suggest prominent soil reservoir of pathogenic Leptospira spp. in rural western ChinaCucchi, KarinaLiu, RunyouCollender, Philip ACheng, QuLi, CharlesHoover, Christopher MChang, Howard HLiang, SongYang, ChanghongRemais, Justin V2019-12-26Climate exerts complex influences on leptospirosis transmission, affecting human behavior, zoonotic host population dynamics, and survival of the pathogen in the environment. Here, we describe the spatiotemporal distribution of leptospirosis incidence reported to China’s National Infectious Disease Surveillance System from 2004–2014 in an endemic region in western China, and employ distributed lag models at annual and sub-annual scales to analyze its association with hydroclimatic risk factors and explore evidence for the potential role of a soil reservoir in the transmission of Leptospira spp. More than 97% of the 2,934 reported leptospirosis cases occurred during the harvest season between August and October, and most commonly affected farmers (83%). Using a distributed lag Poisson regression framework, we characterized incidence rate ratios (IRRs) associated with interquartile range increases in precipitation of 3.45 (95% confidence interval 2.57–4.64) over 0-1-year lags, and 1.90 (1.18–3.06) over 0-15-week lags. Adjusting for soil moisture decreased IRRs for precipitation at both timescales (yearly adjusted IRR: 1.05, 0.74–1.49; weekly adjusted IRR: 1.36, 0.72–2.57), suggesting precipitation effects may be mediated through soil moisture. Increased soil moisture was positively associated with leptospirosis at both timescales, suggesting that the survival of pathogenic Leptospira spp. in moist soils may be a critical control on harvest-associated leptospirosis transmission in the study region. These results support the hypothesis that soils may serve as an environmental reservoir and may play a significant yet underrecognized role in leptospirosis transmission.BRII applicant: RemaispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/77h6w7ndarticlePLOS Neglected Tropical Diseasesvol 13, iss 12, e00079681935-2735oai:escholarship.org:ark:/13030/qt3p68g35n2020-06-23T21:12:18Zqt3p68g35nDeflating inflation: the connection (or lack thereof) between decisional and metacognitive processes and visual phenomenologyAbid, Greyson2019-01-01Vision presents us with a richly detailed world. Yet, there is a range of limitations in the processing of visual information, such as poor peripheral resolution and failures to notice things we do not attend. This raises a natural question: How do we seem to see so much when there is considerable evidence indicating otherwise? In an elegant series of studies, Lau and colleagues have offered a novel answer to this long-standing question, proposing that our sense of visual richness is an artifact of decisional and metacognitive deficits. I critically evaluate this proposal and conclude that it rests on questionable presuppositions concerning the relationship between decisional and metacognitive processes, on one hand, and visual phenomenology, on the other.BRII applicant: AbidpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3p68g35narticleNeuroscience of Consciousnessvol 2019, iss 12057-2107oai:escholarship.org:ark:/13030/qt38k2f4s22020-06-23T20:44:18Zqt38k2f4s2Engaging users in the design of an mHealth, text message-based intervention to increase physical activity at a safety-net health care systemAvila-Garcia, PatriciaHernandez-Ramos, RosaNouri, Sarah SCemballi, AnupamaSarkar, UrmimalaLyles, Courtney RAguilera, Adrian2019-12-01ObjectivesText-messaging interventions are a promising approach to increasing physical activity in vulnerable populations. To better inform the development of a text-messaging intervention, we sought to identify barriers and facilitators to using text messaging and engaging in physical activity among patients with diabetes and comorbid depression.Materials and MethodsWe conducted interviews with primary care patients at a safety-net health care system (N = 26). Data were collected at 3 stages, including a focus group (stage 1), and individual interviews (stage 2 and 3). Patients in stage 1 and 2 previously participated in a text-messaging intervention as part of depression treatment. Discussions focused on participant experience of previously using a text-messaging intervention, influences and perceptions of physical activity, and mobile phone use. We analyzed all transcripts for emerging themes.ResultsParticipants were 56.2 years (±9.7); 69.2% were female, 65.4% identified as Hispanic/Latino(a), and 46.2% reported having less than a high school education. All had depression and 61.5% had diabetes. Specific barriers that emerged included low literacy and only basic use of mobile phones in everyday life, in combination with a high prevalence of comorbid health conditions and limited mobility. These were each addressed with a specific content or intervention delivery change in the overall intervention design.ConclusionsConducting a focus group and individual interviews with end users of an mHealth intervention under development has implications for tailoring and modifying components of the content and format to ensure that the final intervention will engage end users most effectively.BRII applicant: AguilerapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/38k2f4s2articleJAMIA Openvol 2, iss 4, 489-4972574-2531oai:escholarship.org:ark:/13030/qt1f59k7nt2020-06-23T20:41:51Zqt1f59k7ntFast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansionsPaulson, Joel AMartin-Casas, MarcMesbah, Ali2019-08-30We present a novel surrogate modeling method that can be used to accelerate the solution of uncertainty quantification (UQ) problems arising in nonlinear and non-smooth models of biological systems. In particular, we focus on dynamic flux balance analysis (DFBA) models that couple intracellular fluxes, found from the solution of a constrained metabolic network model of the cellular metabolism, to the time-varying nature of the extracellular substrate and product concentrations. DFBA models are generally computationally expensive and present unique challenges to UQ, as they entail dynamic simulations with discrete events that correspond to switches in the active set of the solution of the constrained intracellular model. The proposed non-smooth polynomial chaos expansion (nsPCE) method is an extension of traditional PCE that can effectively capture singularities in the DFBA model response due to the occurrence of these discrete events. The key idea in nsPCE is to use a model of the singularity time to partition the parameter space into two elements on which the model response behaves smoothly. Separate PCE models are then fit in both elements using a basis-adaptive sparse regression approach that is known to scale well with respect to the number of uncertain parameters. We demonstrate the effectiveness of nsPCE on a DFBA model of an E. coli monoculture that consists of 1075 reactions and 761 metabolites. We first illustrate how traditional PCE is unable to handle problems of this level of complexity. We demonstrate that over 800-fold savings in computational cost of uncertainty propagation and Bayesian estimation of parameters in the substrate uptake kinetics can be achieved by using the nsPCE surrogates in place of the full DFBA model simulations. We then investigate the scalability of the nsPCE method by utilizing it for global sensitivity analysis and maximum a posteriori estimation in a synthetic metabolic network problem with a larger number of parameters related to both intracellular and extracellular quantities.BRII applicant: MesbahpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1f59k7ntarticlePLOS Computational Biologyvol 15, iss 8, e10073081553-7358oai:escholarship.org:ark:/13030/qt88s2m9h62020-06-23T20:39:48Zqt88s2m9h6Global unsustainable virtual water flows in agricultural tradeRosa, LorenzoChiarelli, Davide DaniloTu, ChengyiRulli, Maria CristinaD'Odorico, Paolo2019-10-22Recent studies have highlighted the reliance of global food production on unsustainable irrigation practices, which deplete freshwater stocks and environmental flows, and consequently impair aquatic ecosystems. Unsustainable irrigation is driven by domestic and international demand for agricultural products. Research on the environmental consequences of trade has often concentrated on the global displacement of pollution and land use, while the effect of trade on water sustainability and the drying of over-depleted watercourses has seldom been recognized and quantified. Here we evaluate unsustainable irrigation water consumption (UWC) associated with global crop production and determine the share of UWC embedded in international trade. We find that, while about 52% of global irrigation is unsustainable, 15% of it is virtually exported, with an average 18% increase between year 2000 and 2015. About 60% of global virtual transfers of UWC are driven by exports of cotton, sugar cane, fruits, and vegetables. One third of UWC in Mexico, Spain, Turkmenistan, South Africa, Morocco, and Australia is associated with demand from the export markets. The globalization of water through trade contributes to running rivers dry, an environmental externality commonly overlooked by trade policies. By identifying the producing and consuming countries that are responsible for unsustainable irrigation embedded in virtual water trade, this study highlights trade links in which policies are needed to achieve sustainable water and food security goals in the coming decades.BRII applicant: RosapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/88s2m9h6articleEnvironmental Research Lettersvol 14, iss 11, 1140011748-9326oai:escholarship.org:ark:/13030/qt2fd766d42020-06-23T20:35:15Zqt2fd766d4Disturbance macroecology: a comparative study of community structure metrics in a high-severity disturbance regimeNewman, Erica AWilber, Mark QKopper, Karen EMoritz, Max AFalk, Donald AMcKenzie, DonHarte, John2020-01-24Macroecological studies have established widespread patterns of species diversity and abundance in ecosystems but have generally restricted their scope to relatively steady‐state systems. As a result, how macroecological metrics are expected to scale in ecosystems that experience natural disturbance regimes is unknown. We examine macroecological patterns in a fire‐dependent forest of Bishop pine (Pinus muricata ). We target two different‐aged stands in a stand‐replacing fire regime: a mature stand with a diverse understory and with no history of major disturbance for at least 40 yr, and one disturbed by a stand‐replacing fire 17 yr prior to measurement. We compare properties of these stands with macroecological predictions from the Maximum Entropy Theory of Ecology (METE ), an information entropy‐based theory that has proven highly successful in predicting macroecological metrics in multiple ecosystems and taxa. Ecological patterns in the mature stand more closely match METE predictions than do data from the more recently disturbed, mid‐seral stage stand. This suggests METE 's predictions are more robust in late‐successional, slowly changing, or steady‐state systems than those in rapid flux with respect to species composition, abundances, and organisms’ sizes. Our findings highlight the need for a macroecological theory that incorporates natural disturbance, perturbations, and ecological dynamics into its predictive capabilities, because most natural systems are not in a steady state.BRII applicant: HartepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2fd766d4articleEcospherevol 11, iss 12150-8925 2150-8925oai:escholarship.org:ark:/13030/qt9m93861w2020-06-23T20:32:41Zqt9m93861wTrauma during humanitarian work: the effects on intimacy, wellbeing and PTSD-symptomsRizkalla, NiveenSegal, Steven P2019-10-22Background: Organizations assisting refugees are over burdened with the Syrian humanitarian catastrophe and encounter diverse difficulties facing the consequences of this massive displacement. Aid-workers experience the horrors of war through their efforts to alleviate suffering of Syrian refugees.Objective: This study of Syrian refugee aid-workers in Jordan examined work-stressors identified as secondary traumatic stress (STS), number of refugees assisted, worker feelings towards the organization, and their associations to PTSD-symptoms, wellbeing and intimacy. It also examined whether self-differentiation, physical health, and physical pain were associated with these variables.Method: Syrian refugee aid-workers (N = 317) in Jordan’s NGOs were surveyed. Univariate statistics and structural equation modeling (SEM) were utilized to test study hypotheses.Results: Increased STS was associated with lower self-differentiation, decreased physical health and increased physical pain, as well as elevated PTSD-symptoms and decreased intimacy. Decreased connection to the NGO was associated with lower self-differentiation, decreased physical health, increased physical pain, and with decreased intimacy and wellbeing. Lower self-differentiation was associated with increased PTSD-symptoms, decreased wellbeing and intimacy. Elevated physical pain was associated with increased PTSD-symptoms, and decreased wellbeing. Diverse mediation effects of physical health, physical pain and self-differentiation were found among the study’s variables.Conclusions: Aid-workers who assist refugees were at risk of physical and mental sequelae as well as suffering from degraded self-differentiation, intimacy and wellbeing. Organizations need to develop prevention policies and tailor interventions to better support their aid-workers while operating in such stressful fieldwork.BRII applicant: RizkalapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9m93861warticleEuropean Journal of Psychotraumatologyvol 10, iss 1, 16790652000-8198 2000-8066oai:escholarship.org:ark:/13030/qt9g99t8362020-06-23T20:17:04Zqt9g99t836On-Farm Diversification in an Agriculturally-Dominated Landscape Positively Influences Specialist PollinatorsGuzman, AideeChase, MarissaKremen, Claire2019-10-15Agricultural practices can either contribute to pollinator decline or provide opportunities to support pollinator communities. At the landscape-scale, agriculture can have negative impacts on pollinators, especially pollinators that specialize on limited floral or nesting resources. While increasing floral resources at the field-scale is positive for pollinator communities, little is known about how it affects specialist bees that depend on a specific pollen source (oligoleges). We studied pollinators on small-scale farms that contrasted in crop diversity (monocultures vs. polycultures), embedded in the intensively managed agriculture region of the San Joaquin Valley in California, to understand how wild bee communities and specialist bees would respond to field-scale diversification practices. We used squash (Cucurbita pepo) as our focal crop, because it is visited by both specialist pollinators, “squash bees” in the genera Peponapis and Xenoglossa, and by generalist bees like those in the genera Apis and Agapostemon. We hypothesized that there would be a greater number of squash bees on monoculture farms, which have abundant squash flowers, than on polyculture farms. Contrary to our predictions, we found that increasing the number of non-squash floral resources at the field-scale in agroecosystems supports a greater abundance of squash bees but has no effect on the diversity of bees visiting squash flowers. This pattern of increased abundance was consistent for other wild bees and the total number of bees (i.e., including honey bees), but not for honey bee abundance alone. Further, the abundance of pollinators increased or remained the same on polyculture farms throughout the morning while decreasing on monoculture farms, suggesting that as squash flowers start to close in midmorning, bees on the monocultures go elsewhere because no other floral resources co-occur. However, they remain on the polycultures where other resources co-occur. Thus, on-farm diversification may be an important refuge for both specialist bees and other pollinator species that are vulnerable to floral resource simplification as a result of development, especially through monoculture agriculture.BRII applicant: GuzmanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9g99t836publicationoai:escholarship.org:ark:/13030/qt9r23322f2020-06-23T20:14:38Zqt9r23322fCaregiver perceptions of child development in rural Madagascar: a cross-sectional studyChung, Esther OFernald, Lia C. HGalasso, EmanuelaRatsifandrihamanana, LisyWeber, Ann M2019-09-11BackgroundHuman capital (the knowledge, skills, and health that accumulate over life) can be optimized by investments in early childhood to promote cognitive and language development. Parents and caregivers play a crucial role in the promotion and support of cognitive development in their children. Thus, understanding caregiver perceptions of a child’s capabilities and attributes, including intelligence, may enhance investments early in life. To explore this question, we asked caregivers to rank their child’s intelligence in comparison with other children in the community, and compared this ranking with children’s scores on an assessment of developmental abilities across multiple domains.MethodsOur study examined cross-sectional data of 3361 children aged 16–42 months in rural Madagascar. Child intelligence, as perceived by their caregiver, was captured using a ladder ranking scale based on the MacArthur Scale for Subjective Social Status. Children’s developmental abilities were assessed using scores from the Ages and Stages Questionnaire: Inventory (ASQ-I), which measures cognitive, language, and socio-emotional development. Ranked percentiles of the ASQ-I were generated within communities and across the whole sample. We created categories of under-estimation, matched, and over-estimation by taking the differences in rankings between caregiver-perceived child intelligence and ASQ-I. Child nutritional status, caregiver belief of their influence on child intelligence, and sociodemographic factors were examined as potential correlates of discordance between the measures using multinomial logistic regressions.ResultsWe found caregiver perceptions of intelligence in Madagascar did not align consistently with the ASQ-I, with approximately 8% of caregivers under-estimating and almost 50% over-estimating their children’s developmental abilities. Child nutritional status, caregiver belief of their influence on child intelligence, caregiver education, and wealth were associated with under- or over-estimation of children’s developmental abilities.ConclusionsOur findings suggest parents may not always have an accurate perception of their child’s intelligence or abilities compared with other children. The results are consistent with the limited literature on parental perceptions of child nutrition, which documents a discordance between caregiver perceptions and objective measures. Further research is needed to understand the common cues caregivers that use to identify child development milestones and how these may differ from researcher-observed measures in low-income settings.BRII applicant: FernaldpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9r23322farticleBMC Public Healthvol 19, iss 11471-2458oai:escholarship.org:ark:/13030/qt9wh8j2jn2020-06-23T20:06:40Zqt9wh8j2jnEarly Childhood Oral Health and Nutrition in Urban and Rural NepalTsang, ChloeSokal-Gutierrez, KarenPatel, PriyaLewis, BrettHuang, DebbieRonsin, KristinaBaral, AshmitaBhatta, AparnaKhadka, NehaaBarkan, HowardGurung, Sidhanta2019-07-10Globalization and urbanization in Nepal have driven a nutritional transition from an agricultural-based diet to an ultra-processed, sugary diet. This study assessed the nutrition and oral health of 836 children age 6 months to 6 years and their families in rural and urban Nepal. Mothers were interviewed about maternal–child oral health and nutrition, and children received dental exams and height and weight measurements. Analyses utilized SPSS statistical software. Most families lived within a 5-minute walk to a store selling ultra-processed snacks and sugary drinks. While most mothers knew sweets caused tooth decay, half of the children were given sweets daily, and 58.2% of children had dental caries. Caries began in the first 2 years and increased in prevalence and severity to age 6, when 74.3% had caries and 20% experienced mouth pain. Despite greater health knowledge and resources among urban mothers, urban children’s increased access to junk food and frequency of consumption was associated with higher prevalence and severity of caries compared to rural children. Severe caries was associated with malnutrition, especially in rural children. Preventive strategies are needed in early childhood to incorporate nutrition and oral health education and dental care into maternal–child health services, and develop policies to prohibit the sale of junk food around schoolsBRII applicant: Sokal-GutierrezpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9wh8j2jnarticleInternational Journal of Environmental Research and Public Healthvol 16, iss 14, 24561660-4601oai:escholarship.org:ark:/13030/qt0k7374sx2020-06-23T20:02:50Zqt0k7374sxInvariant neural responses for sensory categories revealed by the time-varying information for communication callsElie, Julie ETheunissen, Frederic E2019-09-26Although information theoretic approaches have been used extensively in the analysis of the neural code, they have yet to be used to describe how information is accumulated in time while sensory systems are categorizing dynamic sensory stimuli such as speech sounds or visual objects. Here, we present a novel method to estimate the cumulative information for stimuli or categories. We further define a time-varying categorical information index that, by comparing the information obtained for stimuli versus categories of these same stimuli, quantifies invariant neural representations. We use these methods to investigate the dynamic properties of avian cortical auditory neurons recorded in zebra finches that were listening to a large set of call stimuli sampled from the complete vocal repertoire of this species. We found that the time-varying rates carry 5 times more information than the mean firing rates even in the first 100 ms. We also found that cumulative information has slow time constants (100–600 ms) relative to the typical integration time of single neurons, reflecting the fact that the behaviorally informative features of auditory objects are time-varying sound patterns. When we correlated firing rates and information values, we found that average information correlates with average firing rate but that higher-rates found at the onset response yielded similar information values as the lower-rates found in the sustained response: the onset and sustained response of avian cortical auditory neurons provide similar levels of independent information about call identity and call-type. Finally, our information measures allowed us to rigorously define categorical neurons; these categorical neurons show a high degree of invariance for vocalizations within a call-type. Peak invariance is found around 150 ms after stimulus onset. Surprisingly, call-type invariant neurons were found in both primary and secondary avian auditory areas.BRII Applicant: EliepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0k7374sxarticlePLOS Computational Biologyvol 15, iss 9, e10066981553-7358oai:escholarship.org:ark:/13030/qt02q7z4692020-03-31T23:49:37Zqt02q7z469Reading Between the Lines: Using Citations to Understand Anthropologists’ Reading PatternsSturma, MadeleineEmmelhainz, Celia2019-10-16Academic libraries want to collect the materials most useful to researchers, yet how can libraries know how successful they are? While Berkeley’s George and Mary Foster Anthropology Library collects data on which books circulate, it is difficult to evaluate how materials are actually being used to further the discipline of anthropology. In this article, we examine sources cited by our a) faculty members, b) dissertation writers, and c) honors thesis students to better understand how anthropologists read when conducting research. This paper compares materials used across subfields and research levels to highlight patterns in citations within this discipline, leading to new insights that will improve collection development among anthropology librarians.citation analysisanthropologyacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/02q7z469articleQualitative and Quantitative Methods in Librariesvol 8, iss 3, 389--3972241-1925oai:escholarship.org:ark:/13030/qt5j70p2h52020-02-05T22:13:51Zqt5j70p2h5The Impact of Web-Scale Discovery on the Use of Electronic ResourcesNgo, LisaHennesy, CodyKnabe, Ian2019-12-09In 2015, the University of California, Berkeley, launched EBSCO Discovery Service (EDS), a web-scale discovery tool, with a goal of improving visibility and usage of collections. This study applies linear regression analysis to usage data for ebooks, ejournals, and abstracts and indexing (A&I) databases before and after implementation of EDS in order to identify correlations between the discovery layer and usage of library electronic resources across platforms. Our findings diverge from conclusions drawn in the previous literature that indicate that resource use generally increases after a discovery tool is implemented. We examine data from a longer period of time than the previous literature had, looking for statistically significant changes in resource use. The discovery layer at UC Berkeley did not lead to equal increases across platforms, but rather to a complex array of increases and decreases in use according to a variety of factors. Web-scale discoveryEBSCO Discovery ServiceElectronic resourcesAcademic libraryAssessmentUsage dataapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5j70p2h5articleSerials Reviewvol 45, iss 4, 227-2380098-7913 1879-095Xoai:escholarship.org:ark:/13030/qt9523q3nj2020-02-04T23:32:15Zqt9523q3njDemocratizing the Union at UC Berkeley: Lecturers and Librarians in SolidarityPhillips, MargaretEifler, DavidPage, Tiffany Linton2019-01-01This article explores how librarians and lecturers at the University of California, Berkeley, worked together to make their union more participatory in a context of increasing corporatization in public higher education. Written as a case study, we examine this ongoing revitalization process initiated by lecturers in the summer of 2016 and how it transformed librarian activism and bargaining strategy. For context, we also examine the history and unique nature of the University Council–American Federation of Teachers, the union representing both librarians and lecturers. We discuss why librarians had become ambivalent about their union and how an active group of librarians changed the culture in the organization and worked to bring members' voices into the 2018/2019 librarian contract negotiations. Engaging membership and encouraging participation required a group of committed organizers, with the support of paid union staff, to actively seek feedback from members, to communicate regularly, and to organize solidarity events. Throughout this process, the local worked to build coalitions with other campus unions, and members became increasingly aware of the important role unions play in protecting and advancing the mission of a public university and as a site for social justice activism.librariansunionsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9523q3njarticleLibrary Trendsvol 68, iss 2, 343-3671559-0682oai:escholarship.org:ark:/13030/qt7nb1b7882020-01-10T21:19:47Zqt7nb1b788Open Science and Data Management: Introducing Graduate Students to Research Workflows in a Local ContextTeplitzky, SamanthaSackmann, AnnaPowell, Susan2019-12-13The Engineering & Physical Sciences Division of the UC Berkeley Library partners with researchers to support the entire research life cycle. Since 2016, the division’s Science Data Librarian has offered Research Data Management training that covers data management, storage, documentation, and sharing. Based on this established work, division librarians piloted a series of open science workshops in 2019. The Earth & Planetary Sciences (EPS) Department was chosen as the target department for this work. Librarians began by replacing their traditional orientation session, focused on library procedures and resources, with an approach that highlighted local support for open research workflows.publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7nb1b788publicationoai:escholarship.org:ark:/13030/qt3910d0ng2019-12-19T21:44:09Zqt3910d0ngListening to Unaffiliated Users of the Academic LibrarySingh, MonicaEmmelhainz, Celia2019-04-01We know that unaffiliated users access books, reference services, and databases at our libraries, but how do they experience this access? The library science literature reveals a range of ethical concerns around how we serve unaffiliated users, meaning those who are not current students, faculty, or staff. Yet this literature is often based on librarian perspectives rather than on conversations with the unaffiliated users themselves. In this pilot study we interviewed 10 unaffiliated users to better understand their perceptions of a large academic library and how the library fits into their daily habits. Emerging patterns include a respect for the depth of academic collections, an appreciation of how physical spaces shape their campus experience, and a persistent sense of nonbelonging as people who are not students at our university—even if they are affiliated to another institution. In conclusion, we suggest ways that librarians can invite unaffiliated users onto campus as guests in the academic library community.academic librariescommunity usersunaffiliated userscommunity outreachqualitative methodologyrecruitmentnonbelonginglibrary spacesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3910d0ngpublicationoai:escholarship.org:ark:/13030/qt6j73t6662019-12-17T18:30:13Zqt6j73t666Morphological Gender Innovations in Spanish of Genderqueer Speakers / Innovaciones al género morfológico en el español de hablantes genderqueerPapadopoulos, BenjaminDavidson, Justin2019-04-01upper divisionhonorable mention (sociolinguisticsgender in languagegender-neutral languagequeer linguisticsgrammatical gender)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6j73t666publicationoai:escholarship.org:ark:/13030/qt3r17v0n72019-12-17T18:26:42Zqt3r17v0n7“And as to my own Sex”: The Unifying Behaviors, Social Connections, and Values Between Female Stationers in the 17th CenturyDanna, ClaireSorensen, Janet2019-04-01upper divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3r17v0n7publicationoai:escholarship.org:ark:/13030/qt0r66h0gs2019-12-16T23:45:18Zqt0r66h0gsSeasonality of antenatal care attendance, maternal dietary intake, and fetal growth in the VHEMBE birth cohort, South AfricaFahey, Carolyn AChevrier, JonathanCrause, MadeleinObida, MuvhulawaBornman, RianaEskenazi, Brenda2019-09-25Background Seasonality of food availability, physical activity, and infections commonly occurs within rural communities in low and middle-income countries with distinct rainy seasons. To better understand the implications of these regularly occurring environmental stressors for maternal and child health, this study examined seasonal variation in nutrition and health care access of pregnant women and infants in rural South Africa. Methods We analyzed data from the Venda Health Examination of Mothers, Babies and their Environment (VHEMBE) birth cohort study of 752 mother-infant pairs recruited at delivery from August 2012 to December 2013 in the Vhembe District of Limpopo Province, the northernmost region of South Africa. We used truncated Fourier series regression to assess seasonality of antenatal care (ANC) attendance, dietary intake, and birth size. We additionally regressed ANC attendance on daily rainfall values. Models included adjustment for sociodemographic characteristics. Results Maternal ANC attendance, dietary composition, and infant birth size exhibited significant seasonal variation in both unadjusted and adjusted analyses. Adequate frequency of ANC attendance during pregnancy (≥ 4 visits) was highest among women delivering during the gardening season and lowest during the lean (rainy) season. High rainfall during the third trimester was also negatively associated with adequate ANC attendance (adjusted OR = 0.59, 95% CI: 0.40, 0.86). Carbohydrate intake declined during the harvest season and increased during the vegetable gardening and lean seasons, while fat intake followed the opposite trend. Infant birth weight, length, and head circumference z-scores peaked following the gardening season and were lowest after the harvest season. Maternal protein intake and ANC ≤ 12 weeks did not significantly vary by season or rainfall. Conclusions Seasonal patterns were apparent in ANC utilization, dietary intake, and fetal growth in rural South Africa. Interventions to promote maternal and child health in similar settings should consider seasonal factors.BRII recipient: FaheypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0r66h0gsarticlePLOS ONEvol 14, iss 9, e02228881932-6203oai:escholarship.org:ark:/13030/qt7xq845gv2019-12-16T23:42:06Zqt7xq845gvNatural Tolerance to Ischemia and Hypoxemia in Diving Mammals: A ReviewAllen, Kaitlin NVazquez-Medina, Jose Pablo2019-09-20Reperfusion injury follows ischemia/reperfusion events occurring during myocardial infarction, stroke, embolism, and other peripheral vascular diseases. Decreased blood flow and reduced oxygen tension during ischemic episodes activate cellular pathways that upregulate pro-inflammatory signaling and promote oxidant generation. Reperfusion after ischemia recruits inflammatory cells to the vascular wall, further exacerbating oxidant production and ultimately resulting in cell death, tissue injury, and organ dysfunction. Diving mammals tolerate repetitive episodes of peripheral ischemia/reperfusion as part of the cardiovascular adjustments supporting long duration dives. These adjustments allow marine mammals to optimize the use of their body oxygen stores while diving but can result in selectively reduced perfusion to peripheral tissues. Remarkably, diving mammals show no apparent detrimental effects associated with these ischemia/reperfusion events. Here, we review the current knowledge regarding the strategies marine mammals use to suppress inflammation and cope with oxidant generation potentially derived from diving-induced ischemia/reperfusion.BRII recipient: AllenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7xq845gvarticleFrontiers in Physiologyvol 101664-042Xoai:escholarship.org:ark:/13030/qt3wz7633c2019-12-16T23:38:22Zqt3wz7633cA community-based education programme to reduce insecticide exposure from indoor residual spraying in Limpopo, South AfricaEskenazi, BrendaLevine, David IRauch, StephenObida, MuvhulawaCrause, MadeleinBornman, RianaChevrier, Jonathan2019-06-14BackgroundIndoor residual spraying (IRS), the coating of interior walls of houses with insecticides, is common in malaria-endemic areas. While important in malaria control, IRS potentially exposes residents to harmful insecticides. The World Health Organization recommends steps to minimize exposure; however, no programme has focused on educating populations.MethodsA dramatic presentation and song were developed by study personnel and performed by lay performers in order to spread awareness of the importance of IRS and to minimize insecticide exposure. Performances were staged at 16 sprayed villages in the Vhembe District of Limpopo, South Africa, at which 592 attendees completed short questionnaires before and after the performance about behaviors that might limit insecticide exposure. Overall indices of the attendees’ change in knowledge of precautions to take prior to and after spraying to prevent insecticide exposure were analyzed using hierarchical mixed models to assess the effect of the performance on change in participants’ knowledge.ResultsApproximately half of attendees lived in homes that had been sprayed for malaria and 62% were female. Over 90% thought it better to allow IRS prior to the presentation, but knowledge of proper precautions to prevent exposure was low. The proportion answering correctly about proper distance from home during spraying increased from 49.4% pre-performance to 62.0% post-performance (RR = 1.26, 95% CI = 1.13, 1.41), and the proportion reporting correctly about home re-entry interval after spraying increased from 58.5 to 91.1% (RR = 1.54, 95% CI 1.35, 1.77). Attendees improved in their knowledge about precautions to take prior to and after spraying from mean of 57.9% correct to a mean of 69.7% (β = 12.1%, 95% CI 10.9, 13.4). Specifically, increased knowledge in closing cupboards, removing food and bedding from the home, covering immoveable items with plastic, and leading animals away from the home prior to spraying were observed, as was increased knowledge in sweeping the floors, proper disposal of dead insects, and discarding dirty washrags after spraying.ConclusionsA dramatic presentation and song were able to increase the attendees’ knowledge of precautions to take prior to and after spraying in order to limit their insecticide exposure resulting from IRS. This approach to community education is promising and deserves additional study.BRII recipient: EskenazipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3wz7633carticleMalaria Journalvol 18, iss 11475-2875oai:escholarship.org:ark:/13030/qt8t76m7522019-12-16T23:35:33Zqt8t76m752Revealing biases in the sampling of ecological interaction networksde Aguiar, Marcus A.M.Newman, Erica APires, Mathias MYeakel, Justin DBoettiger, CarlBurkle, Laura AGravel, DominiqueGuimaraes, Paulo RO'Donnell, James LPoisot, TimotheeFortin, Marie-JoseeHembry, David H2019-09-02The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling by degree may therefore be common but unintentional in empirical sampling of networks. Conversely, sampling according to module (representing different interaction types or taxa) results in a rather complete view of certain modules, but fails to provide a complete picture of the underlying network. To reduce biases introduced by sampling methods, we recommend that these findings be incorporated into field design considerations for projects aiming to characterize large species interaction networks.BRII recipient: BoettigerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8t76m752articlePeerJvol 7, e75662167-8359oai:escholarship.org:ark:/13030/qt8q23950k2019-12-16T23:31:11Zqt8q23950kKalahari Wildfires Drive Continental Post-Fire Brightening in Sub-Saharan AfricaSaha, Michael VD'Odorico, PaoloScanlon, Todd M2019-05-07Fire can induce long-lived changes to land-surface albedo, an important aspect of the Earth’s energy budget, but the temporal evolution of these anomalies is poorly understood. Due to the widespread presence of fire in Africa, this represents uncertainty in the continental energy budget, which has important implications for regional climate and hydrologic cycling. In this study, we present the first object-based accounting of albedo anomalies induced by larger (>1 km2) individual wildfires in sub-Saharan Africa. We group spatially contiguous wildfire pixels into fire objects and track the albedo anomaly for five years after the burn. We find that albedo anomalies all have the same general temporal signature: An immediate, brief period of darkening followed by persistent brightening. The strongest brightening is found in the Kalahari region while more intense and long-lived initial darkening is found in the Sahel region. The average southern hemisphere albedo anomaly is +1.50 × 10−3 in the year following wildfire, representing a statistically significant negative surface energy balance forcing on a continental scale. This study challenges an existing paradigm surrounding the physical effects of fire on the landscape. Our results suggest that models of albedo that assume a darkening and recovery to baseline are overly simplistic in almost all circumstances. Furthermore, the presumption that immediate darkening is the only meaningful effect on albedo is incorrect for the majority of the African continent.BRII recipient: D'OdoricopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8q23950karticleRemote Sensingvol 11, iss 9, 10902072-4292oai:escholarship.org:ark:/13030/qt8rm3338t2019-10-21T21:42:16Zqt8rm3338tThe emergence of cannabis agriculture frontiers as environmental threatsButsic, VanCarah, Jennifer KBaumann, MatthiasStephens, ConnorBrenner, Jacob C2018-12-05On agricultural frontiers, minimal regulation and potential windfall profits drive opportunistic land use that often results in environmental damage. Cannabis, an increasingly decriminalized agricultural commodity in many places throughout the world, may now be creating new agricultural frontiers. We examined how cannabis frontiers have boomed in northern California, one of the United States' leading production areas. From 2012–2016 cannabis farms increased in number by 58%, cannabis plants increased by 183%, and the total area under cultivation increased by 91%. Growth in number of sites (80%), as well as in site size (56% per site) contributed to the observed expansion. Cannabis expansion took place in areas of high environmental sensitivity, including 80%–116% increases in cultivation sites near high-quality habitat for threatened and endangered salmonid fish species. Production increased by 40% on steep slopes, sites more than doubled near public lands, and increased by 44% in remote locations far from paved roads. Cannabis farm abandonment was modest, and driven primarily by farm size, not location within sensitive environments. To address policy and institutions for environmental protection, we examined state budget allocations for cannabis regulatory programs. These increased six-fold between 2012–2016 but remained very low relative to other regulatory programs. Production may expand on frontiers elsewhere in the world, and our results warn that without careful policy and institutional development these frontiers may pose environmental threats, even in locations with otherwise robust environmental laws and regulatory institutions.BRII recipient: ButsicpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8rm3338tarticleEnvironmental Research Lettersvol 13, iss 12, 1240171748-9326oai:escholarship.org:ark:/13030/qt6qn557vv2019-10-21T21:36:23Zqt6qn557vvThe role of price and convenience in use of oral rehydration salts to treat child diarrhea: A cluster randomized trial in UgandaWagner, ZacharyAsiimwe, John BoscoDow, William HLevine, David I2019-01-24Background Over half a million children die each year of diarrheal illness, although nearly all deaths could be prevented with oral rehydration salts (ORS). The literature on ORS documents both impressive health benefits and persistent underuse. At the same time, little is known about why ORS is underused and what can be done to increase use. We hypothesized that price and inconvenience are important barriers to ORS use and tested whether eliminating financial and access constraints increases ORS coverage. Methods and findings In July of 2016, we recruited 118 community health workers (CHWs; representing 10,384 households) in Central and Eastern Uganda to participate in the study. Study villages were predominantly peri-urban, and most caretakers had no more than primary school education. In March of 2017, we randomized CHWs to one of four methods of ORS distribution: (1) free delivery of ORS prior to illness (free and convenient); (2) home sales of ORS prior to illness (convenient only); (3) free ORS upon retrieval using voucher (free only); and (4) status quo CHW distribution, where ORS is sold and not delivered (control). CHWs offered zinc supplements in addition to ORS in all treatment arms (free in groups 1 and 3 and for sale in group 2), following international treatment guidelines. We used household surveys to measure ORS (primary outcome) and ORS + zinc use 4 weeks after the interventions began (between April and May 2017). We assessed impact using an intention-to-treat (ITT) framework. During follow-up, we identified 2,363 child cases of diarrhea within 4 weeks of the survey (584 in free and convenient [25.6% of households], 527 in convenient only [26.1% of households], 648 in free only [26.8% of households], and 597 in control [28.5% of households]). The share of cases treated with ORS was 77% (448/584) in the free and convenient group, 64% (340/527) in the convenient only group, 74% (447/648) in the free only group, and 56% (335/597) in the control group. After adjusting for potential confounders, instructing CHWs to provide free and convenient distribution increased ORS coverage by 19 percentage points relative to the control group (95% CI 13–26; P < 0.001), 12 percentage points relative to convenient only (95% CI 6–18; P < 0.001), and 2 percentage points (not significant) relative to free only (95% CI −4 to 8; P = 0.38). Effect sizes were similar, but more pronounced, for the use of both ORS and zinc. Limitations include short follow-up period, self-reported outcomes, and limited generalizability. Conclusions Most caretakers of children with diarrhea in low-income countries seek care in the private sector where they are required to pay for ORS. However, our results suggest that price is an important barrier to ORS use and that switching to free distribution by CHWs substantially increases ORS coverage. Switching to free distribution is low-cost, easily scalable, and could substantially reduce child mortality. Convenience was not important in this context.BRII recipient: LevinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6qn557vvarticlePLOS Medicinevol 16, iss 1, e10027341549-1676oai:escholarship.org:ark:/13030/qt4025n4ht2019-10-21T21:32:19Zqt4025n4htProtocol for the evaluation of the population-level impact of Zimbabwe's prevention of mother-to-child HIV transmission program option B+: a community based serial cross-sectional studyKoyuncu, AybukeDufour, Mi-Suk KangMcCoy, Sandra IreneBautista-Arredondo, SergioBuzdugan, RalucaWatadzaushe, ConstanciaDirawo, JeffreyMushavi, AngelaMahomva, AgnesCowan, FrancesPadian, Nancy2019-01-08BackgroundWHO recommends that HIV infected women receive antiretroviral therapy (ART) minimally during pregnancy and breastfeeding (“Option B”), or ideally throughout their lives regardless of clinical stage (“Option B+”) (Coovadia et al., Lancet 379:221–228, 2012). Although these recommendations were based on clinical trials demonstrating the efficacy of ART during pregnancy and breastfeeding, the population-level effectiveness of Option B+ is unknown, as are retention on ART beyond the immediate post-partum period, and the relative impact and cost-effectiveness of Option B+ compared to Option A (Centers for Disease Control and Prevention, Morb Mortal Wkly Rep 62:148–151, 2013; Ahmed et al., Curr Opin HIV AIDS 8:473–488, 2013). To address these issues, we conducted an impact evaluation of Zimbabwe’s prevention of mother to child transmission programme conducted between 2011 and 2018 using serial, community-based cross-sectional serosurveys, which spanned changes in WHO recommendations. Here we describe the rationale for the design and analysis.Methods/designOur method is to survey mother-infant pairs residing in the catchment areas of 157 health facilities randomly selected from 5 of 10 provinces in Zimbabwe. We collect questionnaires, blood samples from mothers and babies for HIV antibody and viral load testing, and verbal autopsies for deceased mothers/babies. Using this approach, we collected data from two previous time points: 2012 (pre-Option A standard of care), 2014 (post-Option A / pre-Option B+) and will collect a third round of data in 2017–18 (post Option B+ implementation) to monitor population-level trends in mother-to-child transmission of HIV (MTCT) and HIV-free infant survival. In addition, we will collect detailed information on facility level factors that may influence service delivery and costs.DiscussionAlthough the efficacy of antiretroviral therapy (ART) during pregnancy and breastfeeding for prevention of mother-to-child transmission of HIV (PMTCT) has been well-documented in randomized trials, little evidence exists on the population-level impact and cost-effectiveness of Option B+ or the influence of the facility on implementation (Siegfried et al., Cochrane Libr 7:CD003510, 2017). This study will provide essential data on these gaps and will provide estimates on retention in care among Option B+ clients after the breastfeeding period.BRII recipient: PadianpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4025n4htarticleBMC Pregnancy and Childbirthvol 19, iss 11471-2393oai:escholarship.org:ark:/13030/qt0f77t3f02019-10-21T21:16:41Zqt0f77t3f0Communicating Climate Change Oceanically: Sea Level Rise Information Increases Mitigation, Inundation, and Global Warming AcceptanceVelautham, LeelaRanney, Michael AndrewBrow, Quinlan S2019-03-22Cognitive impediments and global warming's gradual pace, among other factors, have inhibited some people from detecting climate change's everyday effects. This results in global warming often being perceived as a non-urgent, non-personal, threat that inhibits larger-scale collective action combatting climate change and public will regarding such action. Extreme weather events that global warming causes or exacerbates (e.g., hurricanes, flooding, heat, and droughts), however, are memorable due to their high emotional, social, and economic costs. Sea level rise is an especially salient American issue, given recent heightened storm surges, and the large population-segment who live in or near coastal areas with dangerous flooding risks. In this experiment, we show that providing American participants with U.S.-specific information about the economic and/or geographic/cartological effects and risks of sea level rise results in (a) an increased acceptance of oceanic rise as a phenomenon that is concerning and caused by global warming, and (b) an increased acceptance, in general, of global warming's anthropogenic nature. Communicating sea level rise information also led to (c) a general decrease in nationalism and (d) changes in the perceived effectiveness of mitigation strategies for sea level rise–specifically (d1) a decrease in the perceived effectiveness of constructing sea walls /dikes and (d2) an increase in the perceived effectiveness of phasing out fossil fuel usage. Overall, we find that communicating striking information about this oceanic by-product of global warming is an effective way to motivate acceptance and engagement with the issue of climate change in a reasonably broad manner. The experimental findings replicate, extend, and dovetail with prior experiments by our laboratory, bringing up to six the number of brief interventions (i.e., of roughly 5 or fewer minutes) that have been proven to increase people's science-normative beliefs about global warming. Our laboratory's website, HowGlobalWarmingWorks.org, offers samples of these materials, which additionally include surprising statistics, textual and video explanations of global warming's mechanism, and a contrast of Earth's temperature rise since the 1880's vs. the U.S. stock market rise since then.BRII recipient: RanneypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0f77t3f0articleFrontiers in Communicationvol 42297-900Xoai:escholarship.org:ark:/13030/qt8jk8q1s92019-10-21T21:12:44Zqt8jk8q1s9Cycles of external dependency drive evolution of avian carotenoid networksBadyaev, Alexander VPosner, Alexander BMorrison, Erin SHigginson, Dawn M2019-04-08All organisms depend on input of exogenous compounds that cannot be internally produced. Gain and loss of such dependencies structure ecological communities and drive species’ evolution, yet the evolution of mechanisms that accommodate these variable dependencies remain elusive. Here, we show that historical cycles of gains and losses of external dependencies in avian carotenoid-producing networks are linked to their evolutionary diversification. This occurs because internalization of metabolic controls—produced when gains in redundancy of dietary inputs coincide with increased branching of their derived products—enables rapid and sustainable exploration of an existing network by shielding it from environmental fluctuations in inputs. Correspondingly, loss of internal controls constrains evolution to the rate of the gains and losses of dietary precursors. Because internalization of a network’s controls necessarily bridges diet-specific enzymatic modules within a network, it structurally links local adaptation and continuous evolution even for traits fully dependent on contingent external inputs.BRII recipient: PosnerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8jk8q1s9articleNature Communicationsvol 10, iss 12041-1723oai:escholarship.org:ark:/13030/qt5xd3m2792019-10-21T21:09:07Zqt5xd3m279Shifting Paradigms in the Mechanics of Nectar Extraction and Hummingbird Bill MorphologyRico-Guevara, ARubega, M AHurme, K JDudley, R2019-01-01As functional morphologists, we aim to connect structures, mechanisms, and emergent higher-scale phenomena (e.g., behavior), with the ulterior motive of addressing evolutionary patterns. The fit between flowers and hummingbird bills has long been used as an example of impressive co-evolution, and hence hummingbirds’ foraging behavior and ecological associations have been the subject of intense study. To date, models of hummingbird foraging have been based on the almost two-centuries-old assumption that capillary rise loads nectar into hummingbird tongue grooves. Furthermore, the role of the bill in the drinking process has been overlooked, instead considering it as the mere vehicle with which to traverse the corolla and access the nectar chamber. As a scientific community, we have been making incorrect assumptions about the basic aspects of how hummingbirds extract nectar from flowers. In this article, we summarize recent advances on drinking biomechanics, morphological and ecological patterns, and selective forces involved in the shaping of the hummingbird feeding apparatus, and also address its modifications in a previously unexpected context, namely conspecific and heterospecific fighting. We explore questions such as: how do the mechanics of feeding define the limits and adaptive consequences of foraging behaviors? Which are the selective forces that drive bill and tongue shape, and associated sexually dimorphic traits? And finally, what are the proximate and ultimate causes of their foraging strategies, including exploitative and interference competition? Increasing our knowledge of morphology, mechanics, and diversity of hummingbird feeding structures will have implications for understanding the ecology and evolution of these remarkable animals.BRII recipient: Rico-GuevarapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5xd3m279articleIntegrative Organismal Biologyvol 1, iss 12517-4843oai:escholarship.org:ark:/13030/qt15f2d1332019-10-21T20:52:15Zqt15f2d133New Evidence of Marine Fauna Tropicalization off the Southwestern Iberian Peninsula (Southwest Europe)Encarnacao, JoaoMorais, PedroBaptista, VaniaCruz, JoanaTeodosio, Maria2019-03-27Climate change and the overall increase of seawater temperature are causing a poleward shift in species distribution, which includes a phenomenon described as the tropicalization of temperate regions. This work aims to report the first records of four species off the southwestern Iberian Peninsula, namely, the oceanic puffer Lagocephalus lagocephalus (Linnaeus, 1758), the Madeira rockfish Scorpaena maderensis Valenciennes, 1833, the ornate wrasse Thalassoma pavo (Linnaeus, 1758), and the bearded fireworm Hermodice carunculata (Pallas, 1766). These last three species, along with other occurrences of aquatic fauna and flora along the Portuguese coast, reveal an ongoing process of poleward expansion of several species, which urgently necessitates a comprehensive survey along the entire Iberian Peninsula. The putative origins of these subtropical and tropical species off continental Portugal are discussed, as well as the potential public health problems that two of the four reported species may cause.BRII recipient: MoraispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/15f2d133articleDiversityvol 11, iss 4, 481424-2818oai:escholarship.org:ark:/13030/qt2cq5g6vx2019-10-21T20:34:20Zqt2cq5g6vxInvolving stakeholders in the design of ecological momentary assessment research: An example from smoking cessationSoyster, Peter DFisher, Aaron J2019-05-22Ecological momentary assessment (EMA) is a data collection method that involves repeated sampling of participants’ real-time experience and behavior as they unfold in context. A primary challenge in EMA research is to design surveys that adequately assess constructs of interest while minimizing participant burden. To achieve this balance, researchers must make decisions regarding which constructs should be included and how those constructs should be assessed. To date, a dearth of direction exists for how to best design and carry out EMA studies. The lack of guidelines renders it difficult to systematically compare findings across EMA studies. Study design decisions may be improved by including input from potential research participants (stakeholders). The goal of the present paper is to introduce a general approach for including stakeholders in the development of EMA research design. Rather than suggesting rigid prescriptive guidelines (e.g., the correct number of survey items), we present a systematic and reproducible process through which extant research and stakeholder experience can be leveraged to make design decisions. To that end, we report methods and results for a series of focus group discussions with current tobacco users that were conducted to inform the design of an EMA study aimed at identifying person-specific mechanisms driving tobacco use. We conclude by providing recommendations for item-selection procedures in EMA studies.BRII recipient: SoysterpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2cq5g6vxarticlePLOS ONEvol 14, iss 5, e02171501932-6203oai:escholarship.org:ark:/13030/qt88c5f0t12019-10-21T20:28:32Zqt88c5f0t1Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic GenesDamasco, GabrielShivakumar, Vikram SMisciewicz, Tracy MDaly, Douglas CFine, Paul V. A2019-05-22Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of Burseraceae resins are derived from a variety of terpene and terpenoid chemicals. Although terpene genes have been identified in model plant crops (e.g., Citrus, Arabidopsis), very few genomic resources are available for non-model groups, including the highly diverse Burseraceae family. Here we report the assembly of a leaf transcriptome of Protium copal, an aromatic tree that has a large distribution in Central America, describe the functional annotation of putative terpene biosynthetic genes and compare terpene biosynthetic genes found in P. copal with those identified in other Burseraceae taxa. The genomic resources of Protium copal can be used to generate novel sequencing markers for population genetics and comparative phylogenetic studies, and to investigate the diversity and evolution of terpene genes in the Burseraceae.BRII recipient: FinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/88c5f0t1articleGenesvol 10, iss 5, 3922073-4425oai:escholarship.org:ark:/13030/qt1zh1w4812019-10-21T20:26:05Zqt1zh1w481On the Sparse Structure of Natural Sounds and Natural Images: Similarities, Differences, and Implications for Neural CodingDodds, Eric McVoyDeWeese, Michael Robert2019-06-26Sparse coding models of natural images and sounds have been able to predict several response properties of neurons in the visual and auditory systems. While the success of these models suggests that the structure they capture is universal across domains to some degree, it is not yet clear which aspects of this structure are universal and which vary across sensory modalities. To address this, we fit complete and highly overcomplete sparse coding models to natural images and spectrograms of speech and report on differences in the statistics learned by these models. We find several types of sparse features in natural images, which all appear in similar, approximately Laplace distributions, whereas the many types of sparse features in speech exhibit a broad range of sparse distributions, many of which are highly asymmetric. Moreover, individual sparse coding units tend to exhibit higher lifetime sparseness for overcomplete models trained on images compared to those trained on speech. Conversely, population sparseness tends to be greater for these networks trained on speech compared with sparse coding models of natural images. To illustrate the relevance of these findings to neural coding, we studied how they impact a biologically plausible sparse coding network's representations in each sensory modality. In particular, a sparse coding network with synaptically local plasticity rules learns different sparse features from speech data than are found by more conventional sparse coding algorithms, but the learned features are qualitatively the same for these models when trained on natural images.BRII recipient: DeWeesepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1zh1w481articleFrontiers in Computational Neurosciencevol 131662-5188oai:escholarship.org:ark:/13030/qt5m89z6jf2019-10-21T20:21:13Zqt5m89z6jfThe competitive advantage of a constitutive CAM species over a C
4
grass species under drought and CO
2
enrichmentYu, KailiangD'Odorico, PaoloCollins, Scott LCarr, DavidPorporato, AmilcareAnderegg, William R. LGilhooly, William PWang, LixinBhattachan, AbinashBartlett, MarkHartzell, SamanthaYin, JunHe, YongliLi, WeiTatlhego, MokganediFuentes, Jose D2019-05-17Plants with crassulacean acid metabolism (CAM) are increasing in distribution and abundance in drylands worldwide, but the underlying drivers remain unknown. We investigate the impacts of extreme drought and CO2 enrichment on the competitive relationships between seedlings of Cylindropuntia imbricata (CAM species) and Bouteloua eriopoda (C4 grass), which coexist in semiarid ecosystems across the Southwestern United States. Our experiments under altered water and CO2 water conditions show that C. imbricata positively responded to CO2 enrichment under extreme drought conditions, while B. eriopoda declined from drought stress and did not recover after the drought ended. Conversely, in well‐watered conditions B. eriopoda had a strong competitive advantage on C. imbricata such that the photosynthetic rate and biomass (per individual) of C. imbricata grown with B. eriopoda were lower relative to when growing alone. A meta‐analysis examining multiple plant families across global drylands shows a positive response of CAM photosynthesis and productivity to CO2 enrichment. Collectively, our results suggest that under drought and elevated CO2 concentrations, projected with climate change, the competitive advantage of plant functional groups may shift and the dominance of CAM plants may increase in semiarid ecosystems.BRII recipient: TatlhegopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5m89z6jfarticleEcospherevol 10, iss 5, e027212150-8925 2150-8925oai:escholarship.org:ark:/13030/qt3xx822k32019-10-21T20:13:26Zqt3xx822k3Bovine leukemia virus discovered in human bloodBuehring, Gertrude CDeLaney, AnneShen, HuaMinChu, David LRazavian, NiemaSchwartz, Daniel ADemkovich, Zach RBates, Michael N2019-04-02BackgroundBovine leukemia virus (BLV) infection is widespread in cattle globally and is present in marketed beef and dairy products. Human infection with BLV has been reported in breast and lung cancer tissues and was significantly associated with breast cancer in 3 case-control studies. The purpose of this current research was to determine if BLV is present in human blood cells and if antibodies to BLV are related to blood cell infection.MethodsStandard liquid PCR and Sanger DNA sequencing were used to test for BLV in buffy coat cells (leukocytes and platelets) of blood specimens from 95 self-selected female subjects.Enzyme-linked immunosorbent assay (ELISA) for IgG, IgM, and IgA was used to detect antibodies to BLV in the plasma of the corresponding blood samples.ResultsBLV DNA was detected in the buffy coat cells of blood in 33/95 (38%) of the subjects by PCR and DNA sequencing. IgG antibodies were detected in 30/95(32%), IgM in 55/95(58%), and IgA in 30/95(32%) of the subjects. There was no significant correlation between presence of the antibodies and presence of BLV DNA.ConclusionsThis first report of BLV in human blood raises the question of whether infection of leukocytes could conceivably lead to leukemia as it does in infected cattle. Also, system wide circulation of infected blood cells could facilitate BLV transit to various internal tissues/organs with potential for their infection and subsequent development of cancer. The most likely route of BLV transmission to humans would be zoonotic, as a foodborne infection. Although eradicated from cattle in some countries, BLV still has a high rate of infection in the Americas, the Middle East, and parts of Europe and Asia. This report of BLV in the blood layer containing human leukocytes/platelets adds important information which could be useful to elucidate possible routes of transmission of BLV to humans and to prevent further human infection.BRII recipient: BuehringpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3xx822k3articleBMC Infectious Diseasesvol 19, iss 11471-2334oai:escholarship.org:ark:/13030/qt9p90t88d2019-10-14T18:34:45Zqt9p90t88dUC Berkeley Library Faculty Survey 2018 ReportLi, ChanEdwards, SusanHamed, MohamedHaugan, TorMiller, Becky2019-10-01application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9p90t88dpublicationoai:escholarship.org:ark:/13030/qt8hz6d2b72019-09-23T19:47:09Zqt8hz6d2b7From curation to creation: Transforming paper map collections into research-ready GIS datasetsPowell, Susan2019-04-12How can librarians engage with the concept of collections in new ways? One answer to this question may be expanding the definition of collection management to include active creation and remixing of our collections. Taking on the role of data creator changes the narrative of what libraries do, enables librarians to model metadata creation standards and licensing best practices, and transforms existing analog collections into research-ready data collections. As a GIS and map librarian interested in these issues, I developed a project to scan physical maps from library collections and transform them into a GIS database covering 20th century Mongolia. The project resulted in a useful set of data for researchers, best practices that can be used in other similar projects, and an expanded concept of what it means to curate a geospatial collection.GISdigital humanitiesvectorizationdigitizationMongoliaCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/8hz6d2b7publicationoai:escholarship.org:ark:/13030/qt9bw5w64f2019-07-08T19:24:32Zqt9bw5w64fExtending Europe in Asia: The Spanish Colonial Imprints of the Philippines (1593-1750)Pendse, Liladhar Ramchandra2019-06-25The present work is ongoing research and this presentation was made at the SALALM 2019 Conference in June 2019 in Austin, Texas.The access to the rare originals of the early Spanish colonial imprints of the Philippines remains problematic. The reference librarians often are restricted to directing the students and scholars to the secondary resources that are available both in print and as a part of the digital assets within the North American academic libraries. This introductory article focuses on the select primary source editions including select Spanish language colonial periodicals that are available electronically on the web along the Open Access.Spanish printing in the PhilippinesOpen AccessVirtual CollectionsWeb librarianshippubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9bw5w64fpublicationoai:escholarship.org:ark:/13030/qt4qf2k15d2019-07-01T15:24:04Zqt4qf2k15dLa conciencia evangelizadora del Movimiento Santuario en el caso del East Bay Sanctuary Covenant (1971-1985)Mineiro, AmeliaTarica, Estelle2019-04-01upper divisionhonorable mentionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4qf2k15dpublicationoai:escholarship.org:ark:/13030/qt0s58z6882019-06-25T22:34:44Zqt0s58z688Readers and Authors of Educational Research: A Study of Research Output on K-12 Education PolicyPhillips, Margaret2019-06-02The purpose of this study was to characterize a representative body of research to demonstrate the advantage of disseminating educational research in ways that reach the broadest audience. Using the Education Resources Information Center (ERIC) database, I compiled a set of research findings on a number of broad educational themes. Focusing on journal articles and reports, I examined the public availability of the publications, publication quality as determined by peer review, and authorship. In all, 65% of the journal articles were behind a paywall, and 35% were available either as PDFs or freely available on the publisher website; 61% of the peer-reviewed literature was locked behind a paywall. This study also examined a subset of reports—research studies not published in journals but issued by organizations, think tanks, or policy institutes; 27% of the reports were authored by institutions identified with a neoliberal or free-market ideologyeducational researchlibrary researchbibliographic analysisopen accesspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0s58z688articleSAGE Openvol 9, iss 2, 2158244019853902158-2440 2158-2440oai:escholarship.org:ark:/13030/qt7bp3t4vp2019-06-11T22:09:12Zqt7bp3t4vpThe Invalidation of the Female Ironist in Kierkegaard’s The Seducer’s DiaryZhao, KatherineSmith, Troy Wellington2019-04-01lower divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7bp3t4vppublicationoai:escholarship.org:ark:/13030/qt9gr611nx2019-06-11T22:06:20Zqt9gr611nx“I Gave my Dreams to Liangshan:” The Yi People in the Chinese Literary ImaginationKennerly, JamesFerme, Mariane C2019-04-01upper divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9gr611nxpublicationoai:escholarship.org:ark:/13030/qt83h2s3302019-06-11T22:04:21Zqt83h2s330"That Means Filibuster": Race, Human Rights, and the United Nations Genocide Convention, 1945-1953”Steele, HarrietRobert, Daniel2019-04-01upper divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/83h2s330publicationoai:escholarship.org:ark:/13030/qt440615442019-06-11T21:59:39Zqt44061544Politics, America, and Sex: What Could Go Wrong? The Orange County Right Wing and the Battle over Progressive EducationBianco, EmmaBrilliant, Mark2019-04-01upper divisionwinnerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/44061544publicationoai:escholarship.org:ark:/13030/qt6rx3s46m2019-05-29T17:28:17Zqt6rx3s46mAccuracy of Identity Information and Name Authority RecordsShiraishi, Naomi2019-03-15Name authority controlidentitygendertransgenderapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6rx3s46mmonographoai:escholarship.org:ark:/13030/qt81t2w1gd2019-04-25T20:27:59Zqt81t2w1gdSupporting Research Workflows with Online Collaborative LaTeX Writing ToolsTeplitzky, SamanthaQuigley, BrianSackmann, Anna2019-04-11Science librarians at a major research university have developed a series of LaTeX workshops utilizing online collaborative tools. These sessions allowed us to increase turnout at instruction sessions while also shifting support to patrons across their research lifecycle. By utilizing online collaborative tools to teach the document preparation system, attendees are able to launch their workflow as scholars in their field. This poster will show that the success of this shift in service enables holistic support of the research lifecycle. Learn about the development of these workshops and useful outreach lessons that emerged.application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/81t2w1gdpublicationoai:escholarship.org:ark:/13030/qt296857822019-04-24T20:55:40Zqt29685782Transmission Design and Analysis for Large-Scale Offshore Wind Energy DevelopmentApostolaki-Iosifidou, ElpinikiMccormack, ReginaKempton, WillettMccoy, PaulOzkan, Deniz2019-03-01The offshore wind resource is very large in many coastal regions, over 80,000 MW capacity in the region studied here. However, the resource cannot be utilized unless distant offshore wind generation can be effectively collected and brought to shore. Based on extensive oceanographic, environmental, and shipping data, a realistic wind energy deployment layout is designed with 160 wind power plants each 500 MW. The power collection and transmission infrastructure required to bring this power to shore and connect it to the electricity grid is designed and analyzed. Three types of connection to shore are compared; high voltage AC to the nearest onshore point of interconnection (POI), high voltage DC with voltage-source converter (HVDC-VSC) to the nearest onshore POI, and connecting to an offshore HVDC backbone running parallel to shore that interconnects multiple wind power plants and multiple POIs ashore. The electrical transmission losses are estimated step by step from the wind turbines to the POI. The results show that such a large system can be built with existing technology in near-load resources, and that losses in the HVDC-VSC systems are approximately 1%-2% lower than that in the AC system for a distance about 120 km from shore.BRII recipient: Apostolaki IosifidoupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/29685782articleIEEE Power and Energy Technology Systems Journalvol 6, iss 1, 22-312332-7707oai:escholarship.org:ark:/13030/qt8mx9h38w2019-04-24T18:33:15Zqt8mx9h38wThe sheep look forward: Counterfactuals, dystopias, and ecological science fiction as a social science enterpriseO'Neill, Kate2018-06-15John Brunner’s 1972 novel, The Sheep Look Up, is the story of the year leading up to a global ecological and political catastrophe. Set primarily in the United States in an unspecified near future, The Sheep Look Up tells the story of “death by a thousand cuts”: problem upon problem, malfeasance upon malfeasance, which accumulate, reinforce each other and are met only by a failing political and economic system that ultimately collapses under its own weight. This article reflects on themes and topics of the novel that resonate for social science theorists and teachers in the environmental social sciences, including global environmental politics. First, it provides a type of counterfactual analysis. It opens a window into how the world might have been had certain actions not been taken. Second, it provides a warning: how the world might be if we do not act. Third, it provides a model of how a disastrous transition might unfold as social resilience has been worn down. Looking back on the almost fifty years since the novel was written demonstrates how its scenario was averted through concerted government and societal actions, but the article also points out how Brunner’s work has strong resonance with our present – and at different times in the recent past.BRII recipient: O'NeillpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8mx9h38warticleElementa: Science of the Anthropocenevol 6, iss 1oai:escholarship.org:ark:/13030/qt4060p1jh2019-04-24T18:26:50Zqt4060p1jhPhenotypic and genetic diversity in aposematic Malagasy poison frogs (genus
Mantella
)Klonoski, KarinaBi, KeRosenblum, Erica Bree2019-02-05Intraspecific color variation has long fascinated evolutionary biologists. In species with bright warning coloration, phenotypic diversity is particularly compelling because many factors, including natural and sexual selection, contribute to intraspecific variation. To better understand the causes of dramatic phenotypic variation in Malagasy poison frogs, we quantified genetic structure and color and pattern variation across three closely related species, Mantella aurantiaca, Mantella crocea, and Mantella milotympanum. Although our restriction site‐associated DNA (RAD) sequencing approach identified clear genetic clusters, they do not align with current species designations, which has important conservation implications for these imperiled frogs. Moreover, our results suggest that levels of intraspecific color variation within this group have been overestimated, while species diversity has been underestimated. Within major genetic clusters, we observed distinct patterns of variation including: populations that are phenotypically similar yet genetically distinct, populations where phenotypic and genetic breaks coincide, and populations that are genetically similar but have high levels of within‐population phenotypic variation. We also detected admixture between two of the major genetic clusters. Our study suggests that several mechanisms—including hybridization, selection, and drift—are contributing to phenotypic diversity. Ultimately, our work underscores the need for a reevaluation of how polymorphic and polytypic populations and species are classified, especially in aposematic organisms.BRII recipient: KlonoskipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4060p1jhpublicationoai:escholarship.org:ark:/13030/qt0bt1558v2019-04-24T18:23:34Zqt0bt1558vAccess to environmental health assets across wealth strata: Evidence from 41 low- and middle-income countriesGraham, Jay PKaur, ManeetJeuland, Marc A2018-11-16Introduction Low levels of household access to basic environmental health assets (EHAs)–including technologies such as clean cookstoves and bed nets or infrastructure such as piped water and electricity–in low- and middle-income countries (LMICs) are known to contribute significantly to the global burden of disease. This low access persists despite decades of promotion of many low-cost, life-saving technologies, and is particularly pronounced among poor households. This study aims to characterize variation in access to EHAs among LMIC households as a function of wealth, as defined by ownership of various assets. Methods Demographic and Health Survey (DHS) data from 41 low- and middle-income countries were used to assess household-level access to the following EHAs: 1) improved water supply; 2) piped water supply; 3) improved sanitation; 4) modern cooking fuels; 5) electricity; and 6) bed nets. For comparison, we included access to mobile phones, which is considered a highly successful technology in terms of its penetration into poor households within LMICs. Ownership levels were compared across country-specific wealth quintiles constructed from household assets using bivariate analysis and multivariable linear regression models. Results Access to EHAs was low among the households in the bottom three quintiles of wealth. Access to piped water, modern cooking fuels, electricity and improved sanitation, for example, were all below 50% for households in the bottom three wealth quintiles. Access to certain EHAs such as improved water supply and bed nets increased only slowly with concomitant increases in wealth, while gaps in access to other EHAs varied to a greater degree by wealth quintile. For example, disparities in access between the richest and poorest quintiles were greatest for electricity and improved sanitation. Rural households in all wealth quintiles had much lower levels of access to EHAs, except for bed nets, relative to urban households. Conclusions The findings of this study provide a basis for understanding how EHAs are distributed among poor households in LMICs, elucidate where inequalities in access are particularly pronounced, and point to a need for strategies that better reach the poor, if the global environmental burden of disease is to be reduced.BRII recipient: GrahampubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0bt1558varticlePLOS ONEvol 13, iss 11, e02073391932-6203oai:escholarship.org:ark:/13030/qt53q0r1tk2019-04-24T18:18:38Zqt53q0r1tkThe Atlantic blue crab Callinectes sapidus Rathbun, 1896 expands its non-native distribution into the Ria Formosa lagoon and the Guadiana estuary (SW-Iberian Peninsula, Europe)Morais, PedroGaspar, MiguelGarel, ErwanBaptista, VaniaCruz, JoanaCerveira, InesLeitao, FranciscoTeodosio, Maria Alexandra2019-01-01The Atlantic blue crab Callinectes sapidus Rathbun, 1896 is native in the western Atlantic, however it is a non-indigenous species across Europe since 1900, among other world regions. In this paper, we report the first occurrences of this species in the Ria Formosa lagoon and in the Guadiana estuary (SW-Iberian Peninsula, Europe) which occurred in 2016 and July 2017, respectively. We hypothesize that the introduction of this species into these ecosystems might be due to the expansion of the Guadalquivir estuary population through natural processes (larval advection, active movement), or due to unintended introduction events after being transported aboard fishing boats, or, less likely, through ballast water. Changes in Guadiana’s river flow after the construction of the Alqueva dam might also explain the presence of another non-indigenous species in the Guadiana estuary. The hypotheses presented, regarding the introduction of the Atlantic blue crab into these ecosystems and of its co-occurrence with other decapod species, are framed in a broader context to serve as a future research framework. The use of the Atlantic blue crab as a new fishing resource is also proposed, namely if it is to be used exclusively by local communities and if no deleterious impacts upon other fisheries and the ecosystem occur from this new fishery.BRII recipient: MoraispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/53q0r1tkarticleBioInvasions Recordsvol 8, iss 1, 123-13322421300oai:escholarship.org:ark:/13030/qt19b5c6n42019-01-29T19:36:53Zqt19b5c6n4Bacterial Contamination of Drinking Water in Guadalajara, MexicoRubino, FrancescaCorona, YahairaPerez, Jose Guadalupe JimenezSmith, Charlotte2018-12-27In many regions where drinking water supply is intermittent and unreliable, households adapt by storing water in cisterns or rooftop tanks. Both intermittent supply and stored water can be vulnerable to contamination by microorganisms with deleterious health effects. The Metropolitan Zone of Guadalajara is a rapidly growing urban center with over five million residents where household storage is nearly ubiquitous. This pilot study was conducted in July 2018 to examine the microbiological quality of drinking water in Guadalajara. Samples were tested for free available chlorine residual, total coliform bacteria, and Escherichia coli. A survey on access to water and public perspectives was also conducted. Water exiting rooftop tanks exceeded regulatory limits for total coliform levels in half of the homes studied. Piped water arriving at two homes had total coliform levels that far exceeded regulatory limits. No E. coli were detected in any of the samples. Only 35% of homes had a chlorine residual between the recommended 0.2 and 1.5 mg/L. Many homes reported unpleasant odors and colors. Only 7% of residents drank the piped water. Future studies are needed, especially during April and May when many homes reported a higher disruption to water service.BRII recipient: SmithpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/19b5c6n4articleInternational Journal of Environmental Research and Public Healthvol 16, iss 1, 671660-4601oai:escholarship.org:ark:/13030/qt38d959qf2019-01-29T18:28:15Zqt38d959qfOpen-source food: Nutrition, toxicology, and availability of wild edible greens in the East BayStark, Philip BMiller, DaphneCarlson, Thomas Jde Vasquez, Kristen Rasmussen2019-01-17Significance Foraged leafy greens are consumed around the globe, including in urban areas, and may play a larger role when food is scarce or expensive. It is thus important to assess the safety and nutritional value of wild greens foraged in urban environments. Methods Field observations, soil tests, and nutritional and toxicology tests on plant tissue were conducted for three sites, each roughly 9 square blocks, in disadvantaged neighborhoods in the East San Francisco Bay Area in 2014–2015. The sites included mixed-use areas and areas with high vehicle traffic. Results Edible wild greens were abundant, even during record droughts. Soil at some survey sites had elevated concentrations of lead and cadmium, but tissue tests suggest that rinsed greens of the tested species are safe to eat. Daily consumption of standard servings comprise less than the EPA reference doses of lead, cadmium, and other heavy metals. Pesticides, glyphosate, and PCBs were below detection limits. The nutrient density of 6 abundant species compared favorably to that of the most nutritious domesticated leafy greens. Conclusions Wild edible greens harvested in industrial, mixed-use, and high-traffic urban areas in the San Francisco East Bay area are abundant and highly nutritious. Even grown in soils with elevated levels of heavy metals, tested species were safe to eat after rinsing in tap water. This does not mean that all edible greens growing in contaminated soil are safe to eat—tests on more species, in more locations, and over a broader range of soil chemistry are needed to determine what is generally safe and what is not. But it does suggest that wild greens could contribute to nutrition, food security, and sustainability in urban ecosystems. Current laws, regulations, and public-health guidance that forbid or discourage foraging on public lands, including urban areas, should be revisited.BRII recipient: StarkpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/38d959qfarticlePLOS ONEvol 14, iss 1, e02024501932-6203oai:escholarship.org:ark:/13030/qt8vk0v4wd2019-01-29T18:23:34Zqt8vk0v4wdUnintended pregnancy and subsequent postpartum long-acting reversible contraceptive use in ZimbabweNance, NerissaRalph, LaurenPadian, NancyCowan, FrancesBuzdugan, RalucaMushavi, AngelaMahomva, AgnesMcCoy, Sandra I2018-11-26BackgroundThe postpartum period is an opportune time for contraception adoption, as women have extended interaction with the reproductive healthcare system and therefore more opportunity to learn about and adopt contraceptive methods. This may be especially true for women who experience unintended pregnancy, a key target population for contraceptive programs and programs to eliminate mother-to-child HIV transmission. Among women in Zimbabwe surveyed in 2014, we examined the relationship between pregnancy intention associated with a woman’s most recent pregnancy, and her subsequent postpartum contraceptive use.MethodsIn our analysis we utilized a dataset from a random selection of catchment areas in Zimbabwe to examine the association between pregnancy intention of most recent pregnancy and subsequent postpartum contraceptive use using multinomial logistic regression models. We also explored whether this association differed by women’s HIV status. Finally, we examined the association between pregnancy intention and changes in contraception from the pre- to postpartum periods.ResultsFindings suggest that women who reported that their pregnancy was unintended adopted less modern (all non-traditional) contraceptive methods overall, but adopted long-acting reversible contraception (LARC) more frequently than women reporting an intended pregnancy (OR 1.41; CI 1.18, 1.68). Among HIV-positive women, this relationship was particularly strong (OR 3.12; CI 1.96, 4.97). However, when examining changes in contraceptive use from the pre-pregnancy to the postpartum period, women who had an unintended pregnancy had lower odds of changing to a more effective method postpartum overall (OR 0.71; CI 0.64, 0.79).ConclusionsWe did not find evidence of higher modern method adoption in the postpartum period among women with an unintended pregnancy. However, women who were already on a method in the pre-pregnancy period were catalyzed to move to more effective methods (such as LARC) postpartum. This study provides evidence of low modern (non-traditional) method adoption in general in the postpartum period among a vulnerable sub-population in Zimbabwe (women who experience unintended pregnancy). Simultaneously, however, it shows a relatively greater portion specifically of LARC use among women with an unintended pregnancy. Further research is needed to more closely examine the motivations behind these contraceptive decisions in order to better inform distribution and counseling programs.BRII recipient: McCoypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8vk0v4wdarticleBMC Women's Healthvol 18, iss 11472-6874oai:escholarship.org:ark:/13030/qt1zv0n6sm2019-01-29T17:59:11Zqt1zv0n6smCRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cellsChung, Jennifer EMagis, WendyVu, JonathanHeo, Seok-JinWartiovaara, KirmoWalters, Mark CKurita, RyoNakamura, YukioBoffelli, DarioMartin, David I. KCorn, Jacob EDeWitt, Mark A2019-01-15Sickle Cell Disease and ß-thalassemia, which are caused by defective or deficient adult ß-globin (HBB) respectively, are the most common serious genetic blood diseases in the world. Persistent expression of the fetal ß-like globin, also known as ?-globin, can ameliorate both disorders by serving in place of the adult ß-globin as a part of the fetal hemoglobin tetramer (HbF). Here we use CRISPR-Cas9 gene editing to explore a potential ?-globin silencer region upstream of the δ-globin gene identified by comparison of naturally-occurring deletion mutations associated with up-regulated ?-globin. We find that deletion of a 1.7 kb consensus element or select 350 bp sub-regions from bulk populations of cells increases levels of HbF. Screening of individual sgRNAs in one sub-region revealed three single guides that caused increases in ?-globin expression. Deletion of the 1.7 kb region in HUDEP-2 clonal sublines, and in colonies derived from CD34+ hematopoietic stem/progenitor cells (HSPCs), does not cause significant up-regulation of ?-globin. These data suggest that the 1.7 kb region is not an autonomous ?-globin silencer, and thus by itself is not a suitable therapeutic target for gene editing treatment of ß-hemoglobinopathies.BRII recipient: DeWittpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1zv0n6smarticlePLOS ONEvol 14, iss 1, e02082371932-6203oai:escholarship.org:ark:/13030/qt8qr2q01z2019-01-29T17:53:01Zqt8qr2q01zThe impact of integrating medical assistants and community health workers on diabetes care management in community health centersRodriguez, Hector PFriedberg, Mark WVargas-Bustamante, ArturoChen, XiaoMartinez, Ana ERoby, Dylan H2018-11-20ObjectiveTo compare the impact of implementing team-based diabetes care management involving community health workers (CHWs) vs. medical assistants (MA) in community health centers (CHCs) on diabetes care processes, intermediate outcomes, and patients’ experiences of chronic care.Data sourcesClinical and administrative data (n = 6111) and patient surveys (n = 698) pre-intervention and post-intervention. Surveys (n = 285) and key informant interviews (n = 48) of CHC staff assessed barriers and facilitators of implementation.Study designA three-arm cluster-randomized trial of CHC sites integrating MAs (n = 3) or CHWs (n = 3) for diabetes care management compared control CHC sites (n = 10). Difference-in-difference multivariate regression with exact matching of patients estimated intervention effects.Principal findingsPatients in the CHW intervention arm had improved annual glycated hemoglobin testing (18.5%, p < 0.001), while patients in the MA intervention arm had improved low-density lipoprotein cholesterol control (8.4%, p < 0.05) and reported better chronic care experiences over time (β=7.5, p < 0.001). Except for chronic care experiences (p < 0.05) for patients in the MA intervention group, difference-in-difference estimates were not statistically significant because control group patients also improved over time. Some diabetes care processes improved significantly more for control group patients than intervention group patients. Key informant interviews revealed that immediate patient care issues sometimes crowded out diabetes care management activities, especially for MAs.ConclusionsDiabetes care improved in CHCs integrating CHWs and MAs onto primary care teams, but the improvements were no different than improvements observed among matched control group patients. Greater improvement using CHW and MA team-based approaches may be possible if practice leaders minimize use of these personnel to cover shortages that often arise in busy primary care practices.BRII recipient: RodriguezpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8qr2q01zarticleBMC Health Services Researchvol 18, iss 11472-6963oai:escholarship.org:ark:/13030/qt9pd4x48f2019-01-29T17:48:23Zqt9pd4x48fEffectiveness of a Multimodal Digital Psychotherapy Platform for Adult Depression: A Naturalistic Feasibility StudyMarcelle, Enitan TNolting, LauraHinshaw, Stephen PAguilera, Adrian2019-01-23Background: Although psychotherapy is one of the most efficacious and effective treatments for depression, limited accessibility to trained providers markedly limits access to care. In an attempt to overcome this obstacle, several platforms seeking to provide these services using digital modalities (eg, video, text, and chat) have been developed. However, the use of these modalities individually poses barriers to intervention access and acceptability. Multimodal platforms, comprising those that allow users to select from a number of available modalities, may be able to provide a solution to these concerns.Objective: We aimed to investigate the preliminary effectiveness of providing psychotherapy through a multimodal digital psychotherapy platform. In addition, we aimed to examine differential responses to intervention by gender, self-reported physical health status, and self-reported financial status, as well as how prior exposure to traditional face-to-face psychotherapy affected the effectiveness of a multimodal digital psychotherapy intervention. Finally, we aimed to examine the dose-response effect.Methods: Data were collected from a total of 318 active users of BetterHelp, a multimodal digital psychotherapy platform. Data on physical health status, financial status, and prior exposure to psychotherapy were obtained using self-report measures. Effectiveness was determined by the extent of symptom severity change, which was measured using the Patient Health Questionnaire at Time 1 (time of enrollment) and Time 2 (3 months after enrollment). Intervention dosage was measured as the sum of individual therapist-user interactions across modalities.Results: Depression symptom severity was significantly reduced after the use of the multimodal digital psychotherapy intervention (P<.001). Individuals without prior traditional psychotherapy experience revealed increased improvement after intervention (P=.006). We found no significant dose-response effect of therapy, nor significant differences in outcomes across gender, self-reported financial status, and self-reported physical health status.Conclusions: Users of BetterHelp experienced significantly reduced depression symptom severity after engaging with the platform. Study findings suggest that this intervention is equally effective across gender, self-reported financial status, and self-reported physical health status and particularly effective for individuals without a history of psychotherapy. Overall, study results suggest that multimodal digital psychotherapy is a potentially effective treatment for adult depression; nevertheless, experimental trials are needed. We discuss directions for future research.BRII recipient: MarcellepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9pd4x48farticleJMIR mHealth and uHealthvol 7, iss 1, e109482291-5222oai:escholarship.org:ark:/13030/qt6dw070px2019-01-29T17:30:57Zqt6dw070pxComprehensive innate immune profiling of chikungunya virus infection in pediatric casesMichlmayr, DanielaPak, Theodore RRahman, Adeeb HAmir, El-Ad DavidKim, Eun-YoungKim-Schulze, SeungheeSuprun, MariaStewart, Michael GThomas, Guajira PBalmaseda, AngelWang, LiZhu, JunSuarez-Farinas, MayteWolinsky, Steven MKasarskis, AndrewHarris, Eva2018-08-27Chikungunya virus (CHIKV) is a mosquito‐borne alphavirus that causes global epidemics of debilitating disease worldwide. To gain functional insight into the host cellular genes required for virus infection, we performed whole‐blood RNA‐seq, 37‐plex mass cytometry of peripheral blood mononuclear cells (PBMCs), and serum cytokine measurements of acute‐ and convalescent‐phase samples obtained from 42 children naturally infected with CHIKV. Semi‐supervised classification and clustering of single‐cell events into 57 sub‐communities of canonical leukocyte phenotypes revealed a monocyte‐driven response to acute infection, with the greatest expansions in “intermediate” CD14++CD16+ monocytes and an activated subpopulation of CD14+ monocytes. Increases in acute‐phase CHIKV envelope protein E2 expression were highest for monocytes and dendritic cells. Serum cytokine measurements confirmed significant acute‐phase upregulation of monocyte chemoattractants. Distinct transcriptomic signatures were associated with infection timepoint, as well as convalescent‐phase anti‐CHIKV antibody titer, acute‐phase viremia, and symptom severity. We present a multiscale network that summarizes all observed modulations across cellular and transcriptomic levels and their interactions with clinical outcomes, providing a uniquely global view of the biomolecular landscape of human CHIKV infection.BRII recipient: HarrispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6dw070pxarticleMolecular Systems Biologyvol 14, iss 8, e78621744-4292 1744-4292 1744-4292oai:escholarship.org:ark:/13030/qt5cp0t17z2019-01-03T00:32:12Zqt5cp0t17zMortuary Practices in Late Antique CorinthOtt, Jeremy2019-01-02application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5cp0t17zmonographoai:escholarship.org:ark:/13030/qt8778d29z2018-12-17T23:22:30Zqt8778d29zWhy Promote Foreign Travel Acquisition Trips?Hamed, Mohamed2018-03-10A poster promoting book acquisition trips not only for buying books, but also for other collaboration activities. Middle EastCairo book fairEgyptpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8778d29zpublicationoai:escholarship.org:ark:/13030/qt5210p2nx2018-11-19T23:17:33Zqt5210p2nxVisual Literacy for Libraries: A Practical, Standards-Based GuideBrown, Nicole E.Bussert, KailaHattwig, DeniseMedaille, Ann2016-01-01The importance of images and visual media in today's culture is changing what it means to be literate in the 21st century. Digital technologies have made it possible for almost anyone to create and share visual media. Yet the pervasiveness of images and visual media does not necessarily mean that individuals are able to critically view, use, and produce visual content. The ACRL Visual Literacy Competency Standards for Higher Education were developed to address these distinct characteristics of images and visual media. Based on those standards, this book provides librarians and instructors with the tools, strategies, and confidence to apply visual literacy in a library context. Readers will not only learn about ways to develop students' visual literacy, but also how to use visual materials to make their instruction more engaging. Ideal for the busy librarian who needs ideas, activities, and teaching strategies that are ready to implement, this book: shows how to challenge students to delve into finding images, using images in the research process, interpreting and analyzing images, creating visual communications, and using visual content ethically;provides ready-to-go learning activities for engaging critically with visual materials;offers tools and techniques for increasing one's own visual literacy confidence; and gives strategies for integrating, engaging with and advocating for visual literacy in libraries.visual literacyinformation literacyvisual literacy--study and teachingvisual communicationimagesresearchacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5210p2nxmonographoai:escholarship.org:ark:/13030/qt1kk8c5rm2018-11-16T14:40:14Zqt1kk8c5rmWhere Are They Now? Winners of a Library Prize for Undergraduate Research: A Survey at the University of California, BerkeleyPhillips, MargaretJones, Lynn2018-05-03We conducted a survey of the winners of University of California (UC) Berkeley’s Library Prize for Undergraduate Research (2003-2016) to learn about the long-term impact of undergraduate research projects on students, find out what winners gained from the experience, and compare their careers post-graduation with other students. Seventy-four winners responded and reported increased academic engagement during their undergraduate experience, and demonstrated greater than average academic achievement post-graduation. The winners became more confident of their research skills and their aptitude for post-graduate work as a result of winning. More than 3 times as many prize winners went on to graduate school as the typical UC graduate. We also examined usage statistics of winning papers that had been posted to UC’s open access publishing platform and observed that papers continue to be accessed by the general public years after students graduate.librariesundergraduate researchlibrary prizesawardshigher educationpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1kk8c5rmarticleSAGE Openvol 8, iss 2, 2158244018772622158-2440 2158-2440oai:escholarship.org:ark:/13030/qt4zv0d9482018-11-15T19:34:12Zqt4zv0d948Estimating the elimination feasibility in the 'end game' of control efforts for parasites subjected to regular mass drug administration: Methods and their application to schistosomiasisArakala, ArathiHoover, Christopher MMarshall, John MSokolow, Susanne HDe Leo, Giulio ARohr, Jason RRemais, Justin VGambhir, ManojDobson, Andy P2018-11-12publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4zv0d948articlePLOS Neglected Tropical Diseasesvol 12, iss 11, e00067941935-2735oai:escholarship.org:ark:/13030/qt3b93p5mw2018-11-15T19:29:32Zqt3b93p5mwDeep echocardiography: data-efficient supervised and semi-supervised deep learning towards automated diagnosis of cardiac diseaseMadani, AliOng, Jia RuiTibrewal, AnshulMofrad, Mohammad R. K2018-10-18publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3b93p5mwarticlenpj Digital Medicinevol 1, iss 12398-6352oai:escholarship.org:ark:/13030/qt5mn5d08k2018-11-15T19:20:04Zqt5mn5d08kImproved Diabetes Care Management Through a Text-Message Intervention for Low-Income Patients: Mixed-Methods Pilot StudyWatterson, Jessica LRodriguez, Hector PShortell, Stephen MAguilera, Adrian2018-10-30publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5mn5d08karticleJMIR Diabetesvol 3, iss 4, e152371-4379oai:escholarship.org:ark:/13030/qt4sm8x73j2018-10-30T16:38:24Zqt4sm8x73jPollinator Community Assembly Tracks Changes in Floral Resources as Restored Hedgerows Mature in Agricultural LandscapesKremen, ClaireM'Gonigle, Leithen KPonisio, Lauren C2018-10-25publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4sm8x73jarticleFrontiers in Ecology and Evolutionvol 62296-701Xoai:escholarship.org:ark:/13030/qt3w53j7z02018-10-30T16:37:10Zqt3w53j7z0EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organismsStauffer, WestonSheng, HuanjieLim, Han N2018-10-25publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3w53j7z0articleScientific Reportsvol 8, iss 12045-2322oai:escholarship.org:ark:/13030/qt8sr276v52018-10-30T16:35:24Zqt8sr276v5Parental experience modifies the Mimulus methylomeColicchio, Jack MKelly, John KHileman, Lena C2018-10-12publiceScholarship, University of Californiahttps://escholarship.org/uc/item/8sr276v5articleBMC Genomicsvol 19, iss 11471-2164oai:escholarship.org:ark:/13030/qt05c5k53p2018-10-30T16:33:11Zqt05c5k53pClosing the yield gap while ensuring water sustainabilityRosa, LorenzoRulli, Maria CristinaDavis, Kyle FrankelChiarelli, Davide DaniloPassera, CorradoD'Odorico, Paolo2018-09-24publiceScholarship, University of Californiahttps://escholarship.org/uc/item/05c5k53particleEnvironmental Research Lettersvol 13, iss 10, 1040021748-9326oai:escholarship.org:ark:/13030/qt84x1m84z2018-10-30T16:28:32Zqt84x1m84zCreating correct blur and its effect on accommodationCholewiak, Steven ALove, Gordon DBanks, Martin S2018-09-04publiceScholarship, University of Californiahttps://escholarship.org/uc/item/84x1m84zarticleJournal of Visionvol 18, iss 9, 11534-7362oai:escholarship.org:ark:/13030/qt2xv0t2hs2018-10-30T16:23:48Zqt2xv0t2hsZebra finches identify individuals using vocal signatures unique to each call typeElie, Julie ETheunissen, Frédéric E2018-10-02publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2xv0t2hsarticleNature Communicationsvol 9, iss 12041-1723oai:escholarship.org:ark:/13030/qt56v4r8272018-10-30T16:13:59Zqt56v4r827Human Sperm Rotation is Regulated by Asymmetrically Positioned Flagellar Control UnitsMannowetz, NadjaMiller, Melissa RKenny, Samuel JMansell, Steven AWojcik, MichalZucker, Robert SXu, KeLishko, Polina V2018-02-01publiceScholarship, University of Californiahttps://escholarship.org/uc/item/56v4r827articleBiophysical Journalvol 114, iss 3, 302a00063495oai:escholarship.org:ark:/13030/qt2q8077ph2018-10-30T16:09:11Zqt2q8077phCo-occurrence of ecologically similar species of Hawaiian spiders reveals critical early phase of adaptive radiationCotoras, Darko DBi, KeBrewer, Michael SLindberg, David RProst, StefanGillespie, Rosemary G2018-06-19publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2q8077pharticleBMC Evolutionary Biologyvol 18, iss 11471-2148oai:escholarship.org:ark:/13030/qt51g2k13d2018-09-19T22:36:46Zqt51g2k13dThe Water-Energy Nexus of Hydraulic Fracturing: A Global Hydrologic Analysis for Shale Oil and Gas ExtractionRosa, LorenzoRulli, Maria CristinaDavis, Kyle FrankelD'Odorico, Paolo2018-04-06publiceScholarship, University of Californiahttps://escholarship.org/uc/item/51g2k13darticleEarth's Futurevol 6, iss 5, 745-75623284277oai:escholarship.org:ark:/13030/qt07m8x5hn2018-09-19T22:33:18Zqt07m8x5hnThe potential for phenological mismatch between a perennial herb and its ground-nesting bee pollinatorOlliff-Yang, Rachael LMesler, Michael R2018-07-02publiceScholarship, University of Californiahttps://escholarship.org/uc/item/07m8x5hnarticleAoB PLANTSvol 10, iss 42041-2851oai:escholarship.org:ark:/13030/qt9d48m9fr2018-09-19T22:31:59Zqt9d48m9frModeling the effect of palate shape on the articulatory-acoustics mappingBakst, SarahJohnson, Keith2018-07-01publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9d48m9frarticleThe Journal of the Acoustical Society of Americavol 144, iss 1, EL71-EL750001-4966oai:escholarship.org:ark:/13030/qt6v98995r2018-08-27T19:28:03Zqt6v98995rBroadband Bending of Flexural Waves: Acoustic Shapes and PatternsDarabi, AmirZareei, AhmadAlam, Mohammad-RezaLeamy, Michael J2018-07-25publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6v98995rarticleScientific Reportsvol 8, iss 12045-2322oai:escholarship.org:ark:/13030/qt8fv619312018-08-23T22:58:44Zqt8fv61931Both saccadic and manual responses in the amblyopic eye of strabismics are irreducibly delayedGambacorta, ChristinaDing, JianMcKee, Suzanne PLevi, Dennis M2018-03-29publiceScholarship, University of Californiahttps://escholarship.org/uc/item/8fv61931articleJournal of Visionvol 18, iss 3, 201534-7362oai:escholarship.org:ark:/13030/qt0j97g9n82018-08-08T21:00:52Zqt0j97g9n8Big Data for Big Questions: Assessing the Impact of Non-English Language Sources on Doctoral Research at BerkeleyEdwards, SusanJones, LynnMcGinnis, Scott2017-03-01Even the largest research library can no longer build comprehensive collections from all countries and in all languages. The pressure to justify acquisitions can be great on non-English language materials, which are often low-use in North American universities. Determining the research need for these materials, and assessing how well it is being met, is challenging. This paper analyzes impact by examining the language of cited references in doctoral dissertations at Berkeley, 2008-2015.collection assessmentlibrary sciencepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0j97g9n8publicationoai:escholarship.org:ark:/13030/qt5nk2f2c52018-07-31T17:26:32Zqt5nk2f2c5Over Mary’s Dead Body: Frankenstein, Sexism & SocialismBurke, JuliaJackson, Trevor2018-04-01WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5nk2f2c5publicationoai:escholarship.org:ark:/13030/qt7xn3f1v22018-07-25T20:40:39Zqt7xn3f1v2Privileged Exclusion in Post-Soviet Kazakhstan: Ethnic Return Migration, Citizenship, and the Politics of (Not) BelongingWerner, Cynthia AnnEmmelhainz, CeliaBarcus, Holly2017-12-19This essay explores issues of citizenship and belonging associated with post-Soviet Kazakhstan’s repatriation program. Beginning in 1991, Kazakhstan financed the resettlement of over 944,000 diasporic Kazakhs from nearly a dozen countries, including Mongolia, and encouraged repatriates to become naturalized citizens. Using the concept of privileged exclusion, we argue that repatriated Kazakhs from Mongolia simultaneously belong due to their knowledge of Kazakh language and traditions, yet do not belong due to their lack of linguistic fluency in Russian, the absence of a shared Soviet experience, and limited comfort with the ‘cosmopolitan’ lifestyle that characterizes the new elite in this post-Soviet context.Citizenshipbelongingnation-buildingmigrationKazakhstanKazakhspost-sovietapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7xn3f1v2articleEurope-Asia Studiesvol 69, iss 10, 1557-15830966-8136 1465-3427oai:escholarship.org:ark:/13030/qt72g3j1dn2018-07-13T20:13:20Zqt72g3j1dnBeing there at a distance: connecting the academic library to students who study abroadEmmelhainz, CeliaPukkila, Marilyn R2018-07-05study abroadacademic librarieslibrarians abroadlibrary outreachlibrary liaisonslibrary services for study abroadoff-campus studyColby Collegeapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/72g3j1dnarticleCollege and Research Libraries Newsvol 79, iss 7, 376-3792150-6698oai:escholarship.org:ark:/13030/qt94c8t9sk2018-07-13T17:10:54Zqt94c8t9skSearching for Recent Anthropology and Archaeology PublicationsEmmelhainz, CeliaEstrada, Natalia2018-01-01This article examines where recent books, chapters, articles, and reviews by prominent anthropologists can be found by comparing search results across open access and scholarly databases. Scopus, Web of Science, the International Bibliography of Social Sciences, and Google Scholar all emerge as major resources for finding publications in anthropology and archaeology.open accesssearch strategiesscholarly publicationsfinding anthropology articlesfinding archaeology articlesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/94c8t9skarticleANSS Currentsvol 33, iss 1oai:escholarship.org:ark:/13030/qt38f620fq2018-07-06T17:25:29Zqt38f620fqIncorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservationGuevara Andino, Juan ErnestoPitman, Nigel C. Ater Steege, HansMogollon, HugoCeron, CarlosPalacios, WalterOleas, NoraFine, Paul V. A2017-11-01Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one‐hectare plots in terra firme forests of Ecuadorian Amazon. In these plots, we tagged, collected, and identified every single adult tree with dbh ≥10 cm. These data were combined with a regional community phylogenetic tree to calculate different phylogenetic diversity (PD) metrics in order to create spatial models. We used Loess regression to estimate the spatial variation of taxonomic and phylogenetic beta diversity as well as phylogenetic endemism and evolutionary distinctiveness. We found evidence for the definition of three floristic districts in the Ecuadorian Amazon, supported by both taxonomic and phylogenetic diversity data. Areas with high levels of phylogenetic endemism and evolutionary distinctiveness in Ecuadorian Amazon forests are unprotected. Furthermore, these areas are severely threatened by proposed plans of oil and mining extraction at large scales and should be prioritized in conservation planning for this region.BRII recipient: FinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/38f620fqarticleEcology and Evolutionvol 7, iss 22, 9639-965020457758oai:escholarship.org:ark:/13030/qt0bs9x1p12018-07-06T17:23:13Zqt0bs9x1p1The canon and the mushroomYurchak, Alexei2017-09-01This essay focuses on a paradoxical transformation that happened within Soviet ideological discourse at the very end of perestroika, around 1990–91. The Party’s attempts to revitalize Soviet ideology by returning to the original word of Lenin unexpectedly produced the opposite result. The unquestionable external Truth from which Soviet ideological discourse drew its legitimacy—and that had always been identical with Lenin’s word—suddenly could no longer be known. This shift launched a rapid unraveling of the Soviet communist project. At the center of this unexpected transformation was the search for the true Lenin—a kind of Lenin that Soviet party theorists, bureaucrats, historians, and scientists hoped was still hidden in the midst of his unpublished texts and unknown facts of his biology, life, and death.BRII recipient: YurchakpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0bs9x1p1articleHAU: Journal of Ethnographic Theoryvol 7, iss 2, 165-1982575-1433 2049-1115oai:escholarship.org:ark:/13030/qt6gw6p6sh2018-07-06T17:13:01Zqt6gw6p6shPopulation Genetic Diversity of Quercus ilex subsp. ballota (Desf.) Samp. Reveals Divergence in Recent and Evolutionary Migration Rates in the Spanish DehesasFernandez i Marti, AngelRomero-Rodriguez, CristinaNavarro-Cerrillo, RafaelAbril, NievesJorrin-Novo, JesusDodd, Richard2018-06-07he Spanish dehesas have been severely affected by human activities that date to the prehistoric period and have suffered accelerated decline since the 1980s. Holm oak (Quercus ilex subsp. ballota (Desf.) Samp.) is a key component of this system, and its acorns provide an important food source for wildlife and domesticated livestock. Our earlier work showed structured variation in acorn morphology and biochemistry. Here, we used chloroplast and nuclear microsatellites to detect genetic structure among populations of Q. ilex from the major biogeographic regions of Andalusia. We found high levels of spatial differentiation with chloroplast DNA indicating little seed dispersal among populations. Spatial differentiation was weaker for nuclear DNA, presumably as a result of more widespread pollen dispersal and its larger effective population size. The Baetic Cordillera (Cádiz) population consistently appeared well separated from populations of the northern Sierra Morena, suggesting that the Guadalquivir Valley has played an important role in determining population divergence. This may be, in part, evolutionary, as suggested by chloroplast DNA, and, in part, a result of human-induced population isolation, as Q. ilex has been removed from the Guadalquivir Valley. Evolutionary gene flow rates were greater than contemporary rates, which were limited to unidirectional gene flow from Córdoba to other populations in the Sierra Morena and, surprisingly, to the southern population at Almería. The inconsistency between evolutionary and recent migration rates suggests an effect of anthropogenic activity over the last few generations of Q. ilex.BRII recipient: DoddpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6gw6p6sharticleForestsvol 9, iss 6, 3371999-4907oai:escholarship.org:ark:/13030/qt2f2312t62018-07-06T17:09:04Zqt2f2312t6Indicators of Land Insecurity for Urban Farms: Institutional Affiliation, Investment, and LocationArnold, JoshuaRoge, Paul2018-06-12As urban agriculture (UA) continues to expand in the United States, many practitioners question its continuation in cities with high property values and increased economic incentives for development. Frequently, these pressures make urban farmers anxious about investing resources, time, and energy in land suitable for food production if tenure is insecure. Despite these concerns, UA continues to persist in areas experiencing increased property values and rent-seeking. Based on surveys with over 56 urban farm managers in California, we identify possible indicators of land tenure insecurity for urban farms. Our analysis finds that urban farms with greater land security have more financial and institutional support, and are located in census tracts with higher economic opportunity.BRII recipient: ArnoldpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2f2312t6articleSustainabilityvol 10, iss 6, 19632071-1050oai:escholarship.org:ark:/13030/qt0ct4c4xb2018-07-06T17:06:08Zqt0ct4c4xbNew concepts, models, and assessments of climate-wise connectivityKeeley, Annika T HAckerly, David DCameron, D RichardHeller, Nicole EHuber, Patrick RSchloss, Carrie AThorne, James HMerenlender, Adina M2018-07-01Empirical studies and habitat suitability modeling project significant shifts in species distributions in response to climate change. Because habitat fragmentation can impede species range shifts, wildlife corridors may have increasing importance in enhancing climate resilience for species persistence. While habitat connectivity has been studied for over four decades, the design of connectivity specifically to facilitate species movement in response to climate change is a relatively new challenge. We conducted a systematic review of 116 relevant papers from 1996–2017. Research focused on assessing the utility of habitat connectivity for climate change adaptation by species (N = 29) and modeling and mapping climate-wise connectivity for planning purposes (N = 55). Others addressed fundamental questions of connectivity related to climate adaptation (N = 31). Based on empirical data and computer simulations examining species range shifts in response to climate change at leading edges of current distributions; it is clear that large protected areas connected through linkages, and stepping stones embedded in a permeable matrix promote population persistence and facilitate range expansion. We identified 13 approaches to modeling climate-wise connectivity based on either focal species or landscape structure. When prioritizing areas for connectivity conservation, approaches include focusing on connecting areas of low climate velocity, refugia, climate analogs, or linking current to future suitable habitats. Riparian corridors should be considered in connectivity plans because of their importance as natural movement corridors, climate gradients, and refugia. Guidance is provided on selecting the best methods for connectivity design depending on the objectives, available data, and landscape context. Future research needs to evaluate the functionality of climate-wise connectivity models for facilitating range shifts and compare connectivity outcomes across modeling approaches.BRII recipient: KeeleypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0ct4c4xbarticleEnvironmental Research Lettersvol 13, iss 7, 0730021748-9326oai:escholarship.org:ark:/13030/qt9d50w5vx2018-07-06T17:01:24Zqt9d50w5vxDo incentives undermine intrinsic motivation? Increases in intrinsic motivation within an incentive-based intervention for people living with HIV in TanzaniaCzaicki, Nancy LDow, William HNjau, Prosper FMcCoy, Sandra I2018-06-14Background Cash and in-kind incentives can improve health outcomes in various settings; however, there is concern that incentives may ‘crowd out’ intrinsic motivation to engage in beneficial behaviors. We examined this hypothesis in a randomized trial of food and cash incentives for people living with HIV infection in Tanzania. Methods We analyzed data from 469 individuals randomized to one of three study arms: standard of care, short-term cash transfers, or short-term food assistance. Eligible participants were: 1) ≥18 years old; 2) HIV-infected; 3) food insecure; and 4) initiated antiretroviral therapy (ART) ≤90 days before the study. Food or cash transfers, valued at ~$11 per month and conditional on attending clinic visits, were provided for ≤6 months. Intrinsic motivation was measured at baseline, 6, and 12 months using the autonomous motivation section of the Treatment Self-Regulation Questionnaire (TSRQ). We compared the change in TSRQ score from baseline to 6 and 12 months and the change within study arms. Results The mean intrinsic motivation score was 2.79 at baseline (range: 1–3), 2.91 at 6 months (range: 1–3), and 2.95 at 12 months (range: 2–3), which was 6 months after the incentives had ended. Among all patients, the intrinsic motivation score increased by 0.13 points at 6 months (95% CI (0.09, 0.17), Cohen’s d = 0.29) and 0.19 points at 12 months (95% CI (0.14, 0.24), Cohen’s d = 0.49). Intrinsic motivation also increased within each study group at 6 months: 0.15 points in the food arm (95% CI (0.09, 0.21), Cohen’s d = 0.37), 0.11 points in the cash arm (95% CI (0.05, 0.18), Cohen’s d = 0.25), and 0.08 points in the comparison arm (95% CI (-0.03, 0.19), Cohen’s d = 0.21); findings were similar at 12 months. Increases in motivation were statistically similar between arms at 6 and 12 months. Conclusion Intrinsic motivation for ART adherence increased significantly both overall and within the food and cash incentive arms, even after the incentive period was over. Increases in motivation did not differ by study group. These results suggest that incentive interventions for treatment adherence should not be withheld due to concerns of crowding out intrinsic motivation.BRII recipient: McCoypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9d50w5vxarticlePLOS ONEvol 13, iss 6, e01966161932-6203oai:escholarship.org:ark:/13030/qt9798x18z2018-07-06T16:56:07Zqt9798x18zIncrease in fertility following coal and oil power plant retirements in CaliforniaCasey, Joan AGemmill, AlisonKarasek, DeborahOgburn, Elizabeth LGoin, Dana EMorello-Frosch, Rachel2018-05-02BackgroundFew studies have explored the relationship between air pollution and fertility. We used a natural experiment in California when coal and oil power plants retired to estimate associations with nearby fertility rates.MethodsWe used a difference-in-differences negative binomial model on the incident rate ratio scale to analyze the change in annual fertility rates among California mothers living within 0-5 km and 5-10 km of 8 retired power plants between 2001 and 2011. The difference-in-differences method isolates the portion of the pre- versus post-retirement contrast in the 0-5 km and 5-10 km bins, respectively, that is due to retirement rather than secular trends. We controlled for secular trends with mothers living 10-20 km away. Adjusted models included fixed effects for power plant, proportion Hispanic, Black, high school educated, and aged > 30 years mothers, and neighborhood poverty and educational attainment.ResultsAnalyses included 58,909 live births. In adjusted models, we estimated that after power plant retirement annual fertility rates per 1000 women aged 15–44 years increased by 8 births within 5 km and 2 births within 5-10 km of power plants, corresponding to incident rate ratios of 1.2 (95% CI: 1.1–1.4) and 1.1 (95% CI: 1.0–1.2), respectively. We implemented a negative exposure control by randomly selecting power plants that did not retire and repeating our analysis with those locations using the retirement dates from original 8 power plants. There was no association, suggesting that statewide temporal trends may not account for results.ConclusionsFertility rates among nearby populations appeared to increase after coal and oil power plant retirements. Our study design limited the possibility that our findings resulted from temporal trends or changes in population composition. These results require confirmation in other populations, given known methodological limitations of ecologic study designs.BRII recipient: Morello-FroschpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9798x18zarticleEnvironmental Healthvol 17, iss 11476-069Xoai:escholarship.org:ark:/13030/qt0449f3gd2018-07-06T16:52:43Zqt0449f3gdDrought drives rapid shifts in tropical rainforest soil biogeochemistry and greenhouse gas emissionsO'Connell, Christine SRuan, LeileiSilver, Whendee L2018-04-09Climate change models predict more frequent and severe droughts in the humid tropics. How drought will impact tropical forest carbon and greenhouse gas dynamics is poorly understood. Here we report the effects of the severe 2015 Caribbean drought on soil moisture, oxygen, phosphorus (P), and greenhouse gas emissions in a humid tropical forest in Puerto Rico. Drought significantly decreases inorganic P concentrations, an element commonly limiting to net primary productivity in tropical forests, and significantly increases organic P. High-frequency greenhouse gas measurements show varied impacts across topography. Soil carbon dioxide emissions increase by 60% on slopes and 163% in valleys. Methane (CH4) consumption increases significantly during drought, but high CH4 fluxes post-drought offset this sink after 7 weeks. The rapid response and slow recovery to drought suggest tropical forest biogeochemistry is more sensitive to climate change than previously believed, with potentially large direct and indirect consequences for regional and global carbon cycles.BRII recipient: O'ConnelpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0449f3gdarticleNature Communicationsvol 9, iss 12041-1723oai:escholarship.org:ark:/13030/qt2qn8b7w92018-07-06T16:31:16Zqt2qn8b7w9Renewable energy alternatives to mega hydropower: a case study of Inga 3 for Southern AfricaDeshmukh, RMileva, AWu, G C2018-06-01We assess the feasibility and cost-effectiveness of renewable energy alternatives to Inga 3, a 4.8-GW hydropower project on the Congo River, to serve the energy needs of the host country, the Democratic Republic of Congo (DRC), and the main buyer, South Africa. To account for a key uncertainty in the literature regarding the additional economic impacts of managing variable wind and solar electricity, we built a spatially and temporally detailed power system investment model for South Africa. We find that a mix of wind, solar photovoltaics, and some natural gas is more cost-effective than Inga 3 to meet future demand except in scenarios with pessimistic assumptions about wind technology performance. If a low load growth forecast is used, including Inga 3 in the power mix results in higher system cost across all sensitivities. In our scenarios, the effect of Inga 3 deployment on South African power system cost ranges from an increase of ZAR 4300 (US$ 330) million annually to savings of ZAR 1600 (US$ 120) million annually by 2035. A cost overrun as low as 20% makes the Inga 3 scenarios more expensive in all sensitivity cases. Including time and cost overruns and losses in transmission from DRC to South Africa make Inga 3 an even less attractive investment. For DRC, through analysis of spatial datasets representing technical, physical, and environmental constraints, we find abundant renewable energy potential: 60 GW of solar photovoltaic and 0.6–2.3 GW of wind located close to transmission infrastructure have levelized costs less than US$ 0.07 per kWh, or the anticipated cost of Inga 3 to residential consumers.BRII recipient: WupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2qn8b7w9articleEnvironmental Research Lettersvol 13, iss 6, 0640201748-9326oai:escholarship.org:ark:/13030/qt046265n02018-07-06T16:26:04Zqt046265n0Differences in the reliance on cuticular hydrocarbons as sexual signaling and species discrimination cues in parasitoid waspsBuellesbach, JanVetter, Sebastian GSchmitt, Thomas2018-05-10BackgroundCuticular hydrocarbons (CHC) have been documented to play crucial roles as species- and sex-specific cues in the chemical communication systems of a wide variety of insects. However, whether they are sufficient by themselves as the sole cue triggering sexual behavior as well as preference of con- over heterospecific mating partners is rarely assessed. We conducted behavioral assays in three representative species of parasitoid wasps (Hymenoptera: Pteromalidae) to determine their reliance on CHC as species-specific sexual signaling cues.ResultsWe found a surprising degree of either unspecific or insufficient sexual signaling when CHC are singled out as recognition cues. Most strikingly, the cosmopolitan species Nasonia vitripennis, expected to experience enhanced selection pressure to discriminate against other co-occurring parasitoids, did not discriminate against CHC of a partially sympatric species from another genus, Trichomalopsis sarcophagae. Focusing on the latter species, in turn, it became apparent that CHC are even insufficient as the sole cue triggering conspecific sexual behavior, hinting at the requirement of additional, synergistic sexual cues particularly important in this species. Finally, in the phylogenetically and chemically most divergent species Muscidifurax uniraptor, we intriguingly found both CHC-based sexual signaling as well as species discrimination behavior intact although this species is naturally parthenogenetic with sexual reproduction only occurring under laboratory conditions.ConclusionsOur findings implicate a discrepancy in the reliance on and specificity of CHC as sexual cues in our tested parasitioid wasps. CHC profiles were not sufficient for unambiguous discrimination and preference behavior, as demonstrated by clear cross-attraction between some of our tested wasp genera. Moreover, we could show that only in T. sarcophagae, additional behavioral cues need to be present for triggering natural mating behavior, hinting at an interesting shift in signaling hierarchy in this particular species. This demonstrates the importance of integrating multiple, potentially complementary signaling modalities in future studies for a better understanding of their individual contributions to natural sexual communication behavior.BRII recipient: BuellesbachpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/046265n0articleFrontiers in Zoologyvol 15, iss 11742-9994oai:escholarship.org:ark:/13030/qt6f45w7mz2018-07-06T16:23:38Zqt6f45w7mzMito-nuclear discordance across a recent contact zone for California volesLin, DanaBi, KeConroy, Christopher JLacey, Eileen ASchraiber, Joshua GBowie, Rauri C. K2018-06-01To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi‐permeable. Using mitochondrial cytochrome b sequences and genome‐wide loci developed via ddRAD‐seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5–54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.BRII recipient: LinpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6f45w7mzarticleEcology and Evolutionvol 8, iss 12, 6226-624120457758oai:escholarship.org:ark:/13030/qt4zj8060h2018-07-06T16:21:07Zqt4zj8060hApplying ecological site concepts and state-and-transition models to a grazed riparian rangelandRatcliff, FelixBartolome, JamesMacaulay, LukeSpiegal, SheriWhite, Michael D2018-05-01Ecological sites and state‐and‐transition models are useful tools for generating and testing hypotheses about drivers of vegetation composition in rangeland systems. These models have been widely implemented in upland rangelands, but comparatively, little attention has been given to developing ecological site concepts for rangeland riparian areas, and additional environmental criteria may be necessary to classify riparian ecological sites. Between 2013 and 2016, fifteen study reaches on five creeks were studied at Tejon Ranch in southern California. Data were collected to describe the relationship between riparian vegetation composition, environmental variables, and livestock management; and to explore the utility of ecological sites and state‐and‐transition models for describing riparian vegetation communities and for creating hypotheses about drivers of vegetation change. Hierarchical cluster analysis was used to classify the environmental and vegetation data (15 stream reaches × 4 years) into two ecological sites and eight community phases that comprised three vegetation states. Classification and regression tree (CART) analysis was used to determine the influence of abiotic site variables, annual precipitation, and cattle activity on vegetation clusters. Channel slope explained the greatest amount of variation in vegetation clusters; however, soil texture, geology, watershed size, and elevation were also selected as important predictors of vegetation composition. The classification tree built with this limited set of abiotic predictor variables explained 90% of the observed vegetation clusters. Cattle grazing and annual precipitation were not linked to qualitative differences in vegetation. Abiotic variables explained almost all of the observed riparian vegetation dynamics—and the divisions in the CART analysis corresponded roughly to the ecological sites—suggesting that ecological sites are well‐suited for understanding and predicting change in this highly variable system. These findings support continued development of riparian ecological site concepts and state‐and‐transition models to aid decision making for conservation and management of rangeland riparian areas.BRII recipient: RatcliffpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4zj8060harticleEcology and Evolutionvol 8, iss 10, 4907-491820457758oai:escholarship.org:ark:/13030/qt5799b4gj2018-07-06T16:08:51Zqt5799b4gjDetermining the scope of attacks on health in four governorates of Syria in 2016: Results of a field surveillance programHaar, Rohini JRisko, Casey BSingh, SonalRayes, DianaAlbaik, AhmadAlnajar, MohammedKewara, MazenClouse, EmilyBaker, EliseRubenstein, Leonard S2018-04-24Violent attacks on and interferences with hospitals, ambulances, health workers, and patients during conflict destroy vital health services during a time when they are most needed and undermine the long-term capacity of the health system. In Syria, such attacks have been frequent and intense and represent grave violations of the Geneva Conventions, but the number reported has varied considerably. A systematic mechanism to document these attacks could assist in designing more protection strategies and play a critical role in influencing policy, promoting justice, and addressing the health needs of the population.BRII applicant: HaarpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5799b4gjarticlePLOS Medicinevol 15, iss 4, e10025591549-1676oai:escholarship.org:ark:/13030/qt1v02m28f2018-07-06T16:04:34Zqt1v02m28fTGF-β1/CD105 signaling controls vascular network formation within growth factor sequestering hyaluronic acid hydrogelsBrowne, ShaneJha, Amit KAmeri, KuroshMarcus, Sivan GYeghiazarians, YeremHealy, Kevin E2018-03-22Cell-based strategies for the treatment of ischemic diseases are at the forefront of tissue engineering and regenerative medicine. Cell therapies purportedly can play a key role in the neovascularization of ischemic tissue; however, low survival and poor cell engraftment with the host vasculature following implantation limits their potential to treat ischemic diseases. To overcome these limitations, we previously developed a growth factor sequestering hyaluronic acid (HyA)-based hydrogel that enhanced transplanted mouse cardiosphere-derived cell survival and formation of vasculature that anastomosed with host vessels. In this work, we examined the mechanism by which HyA hydrogels presenting transforming growth factor beta-1 (TGF-β1) promoted proliferation of more clinically relevant human cardiosphere-derived cells (hCDC), and their formation of vascular-like networks in vitro. We observed hCDC proliferation and enhanced formation of vascular-like networks occurred in the presence of TGF-β1. Furthermore, production of nitric oxide (NO), VEGF, and a host of angiogenic factors were increased in the presence of TGF-β1. This response was dependent on the co-activity of CD105 (Endoglin) with the TGF-βR2 receptor, demonstrating its role in the process of angiogenic differentiation and vascular organization of hCDC. These results demonstrated that hCDC form vascular-like networks in vitro, and that the induction of vascular networks by hCDC within growth factor sequestering HyA hydrogels was mediated by TGF-β1/CD105 signaling.BRII applicant: HealypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1v02m28farticlePLOS ONEvol 13, iss 3, e01946791932-6203oai:escholarship.org:ark:/13030/qt1pq6w9c32018-07-02T21:26:51Zqt1pq6w9c3Access to public drinking water fountains in Berkeley, California: a geospatial analysisAvery, Dylan CSmith, Charlotte D2018-01-24BACKGROUND:In January 2015, Berkeley, California became the first city in the Unites States to impose a tax on sugar-sweetened beverages. The tax is intended to discourage purchase of sugary beverages and promote consumption of healthier alternatives such as tap water. The goal of the study was to assess the condition of public drinking water fountains and determine if there is a difference in access to clean, functioning fountains based on race or socio-economic status.METHODS:A mobile-GIS App was created to locate and collect data on existing drinking water fountains in Berkeley, CA. Demographic variables related to race and socio-economic status (SES) were acquired from the US Census - American Community Survey database. Disparities in access to, or condition of drinking water fountains relative to demographics was explored using spatial analyses. Spatial statistical-analysis was performed to estimate demographic characteristics of communities near the water fountains and logistic regression was used to examine the relationship between household median income or race and condition of fountain.RESULTS:Although most fountains were classified as functioning, some were dirty, clogged, or both dirty and clogged. No spatial relationships between demographic characteristics and fountain conditions were observed.DISCUSSION:All geo-located data and a series of maps were provided to the City of Berkeley and the public.CONCLUSIONS:The geo-database created as an outcome of this study is useful for prioritizing maintenance of existing fountains and planning the locations of future fountains. The methodologies used for this study could be applied to a wide variety of asset inventory and assessment projects such as clinics or pharmaceutical dispensaries, both in developed and developing countries.BRII Recipient: SmithpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1pq6w9c3articleBMC Public Healthvol 18, iss 11471-2458oai:escholarship.org:ark:/13030/qt8bq915502018-06-22T22:28:44Zqt8bq91550Fuzhou Shipyard at Fujian Province: Early Divergence in Late Qing ModernizationDuan, LiLazopoulos, George2014-04-012014 WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8bq91550publicationoai:escholarship.org:ark:/13030/qt7md156rf2018-06-07T21:26:38Zqt7md156rfThe Girls Who Were Never Born: A Study of Sex-Selection and Healthcare Professionals in IndiaJagannatha, ShubhaWald, Margi2018-04-01WinnerLower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7md156rfpublicationoai:escholarship.org:ark:/13030/qt3gz750tw2018-06-07T21:24:41Zqt3gz750twFrankenfood: The Misunderstood Monster of the GMO DebateBukhari, HaroonRyan, Sloan2018-04-01Honorable MentionLower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3gz750twpublicationoai:escholarship.org:ark:/13030/qt2974s4sw2018-06-07T21:14:49Zqt2974s4swA Multi-layered Approach to Anglo-Dutch RelationsSmelser, KristinaLewandoski, Julia2018-04-01WinnerLower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2974s4swpublicationoai:escholarship.org:ark:/13030/qt6440g7012018-06-07T18:45:14Zqt6440g701The Social and Political Organizing of Guatemalan Refugees in Mexico and their Campaign for Return: 1980 to 1992Plummer, EmilyBallenger, Stephanie2018-04-01WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6440g701publicationoai:escholarship.org:ark:/13030/qt1mv9z4xd2018-06-07T18:42:19Zqt1mv9z4xdDecapitating the AcademieTobias, RosenGrimaldo Grigsby, Darcy2018-04-01Honorable MentionUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1mv9z4xdpublicationoai:escholarship.org:ark:/13030/qt8d97r4022018-06-07T18:37:09Zqt8d97r402On the Road to Damascus: Searching for New Socialisms in East Germany's 1983 LutherjahrSloan, BenjaminJackson, Trevor2018-04-01Honorable MentionUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8d97r402publicationoai:escholarship.org:ark:/13030/qt4bw948bp2018-06-07T18:31:44Zqt4bw948bpGentrification in San Francisco: No One Right AnswerEscobar, MariaLarkin, Michael2017-04-01Honorable MentionLower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4bw948bppublicationoai:escholarship.org:ark:/13030/qt9sg5t66n2018-06-07T18:30:26Zqt9sg5t66nResonance, Radicalism, and the Death Penalty: A Framing Analysis of the Anti-Death Penalty Movement, 1965-2014Marnie, LoweMorrill, CalvinLauren, Edelman2018-04-01WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9sg5t66npublicationoai:escholarship.org:ark:/13030/qt9nf8t9v52018-06-07T18:27:55Zqt9nf8t9v5Sympathy for the Loss of a Comrade: Black Citizenship and the 1873 Fort Stockton "Mutiny"Eskow, NicholasWilkie, Laurie2018-04-01WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9nf8t9v5publicationoai:escholarship.org:ark:/13030/qt734058x12018-05-24T20:11:13Zqt734058x1Accés Obert: Modeling Open Access in CataloniaPotts, Claude H.2017-06-05For the past decade, Spain has been a European leader in the transformation to open access publishing. About 70 percent of Spanish journals publish freely online — far higher than world averages. Conversations with two of Spain's foremost scholarly communication experts describe the conditions that have been conducive to academic openness in the region of Catalonia in particular. Among those conditions are stable public funding, an effective consortial library infrastructure, and supportive intellectual environments.open accessscholarly publishingSpainCataloniaOApublic knowledgeacademic opennessAccesso AbiertoCRISpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/734058x1publicationoai:escholarship.org:ark:/13030/qt6250q4532018-04-30T17:55:48Zqt6250q453GIS Historical Map Project and MetadataShiraishi, NaomiLin, Haiqing2018-03-21Metadata is important in making digital humanity research more discoverable and accessible. For geospatial resources, there are different metadata standards available, but no one standard can cover all materials. Some specialized projects may need experienced technical service librarians’ help for creating effective metadata.This research aims to examine the functional requirements of metadata services for digital humanities research by analyzing a GIS project involving East Asian historical maps. Historical maps are unique in that they may not fit into current geospatial metadata standards well and this is where technical services librarians can utilize their knowledge and experience of historical resources. By exploring some metadata solutions, we intend to demonstrate the role of controlled vocabulary as a means to improving the access to and usability of spatial data. We suggest that digital humanities researchers create metadata for their GIS projects collaboratively with technical services librarians.GIShistorical mapsJapanese mapsmetadataapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6250q453publicationoai:escholarship.org:ark:/13030/qt198472pc2018-04-26T19:15:18Zqt198472pcSeasonal Reproduction in Vertebrates: Melatonin Synthesis, Binding, and Functionality Using Tinbergen’s Four QuestionsviviD, DaxBentley, George E2018-03-13One of the many functions of melatonin in vertebrates is seasonal reproductive timing. Longer nights in winter correspond to an extended duration of melatonin secretion. The purpose of this review is to discuss melatonin synthesis, receptor subtypes, and function in the context of seasonality across vertebrates. We conclude with Tinbergen’s Four Questions to create a comparative framework for future melatonin research in the context of seasonal reproduction.BRII recipient: viviDpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/198472pcarticleMoleculesvol 23, iss 3oai:escholarship.org:ark:/13030/qt9sp4f5br2018-04-24T22:11:31Zqt9sp4f5brSearch Chinese Government Resources for Geographic NamesTang, Stella S2018-03-21This is a poster presented on March 21, 2018 in Washington, D.C at the Annual Meeting of the Council on East Asian Libraries (a Committee of the Association for Asian Studies). Chinese government department websites were introduced for verification and identification of the current Chinese place names.Chinese place namesChinese government resourcesMinistry of Civil Affairs of the People's Republic of ChinaNational Administrative Division Information Search PlatformNational Bureau of Statistics of the People's Republic of Chinaadministrative divisions codeChinese place name changes reportapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9sp4f5brpublicationoai:escholarship.org:ark:/13030/qt6g7630k22018-04-23T22:15:37Zqt6g7630k2Spatial characterization of long-term hydrological change in the Arkavathy watershed adjacent to Bangalore, IndiaPenny, GopalSrinivasan, VeenaDronova, IrynaLele, SharachchandraThompson, Sally2018-01-24The complexity and heterogeneity of human water use over large spatial areas and decadal timescales can impede the understanding of hydrological change, particularly in regions with sparse monitoring of the water cycle. In the Arkavathy watershed in southern India, surface water inflows to major reservoirs decreased over a 40-year period during which urbanization, groundwater depletion, modification of the river network, and changes in agricultural practices also occurred. These multiple, interacting drivers combined with limited hydrological monitoring make attribution of the causes of diminishing water resources in the watershed challenging and impede effective policy responses. To mitigate these challenges, we developed a novel, spatially distributed dataset to understand hydrological change by characterizing the residual trends in surface water extent that remain after controlling for precipitation variations and comparing the trends with historical land use maps to assess human drivers of change. Using an automated classification approach with subpixel unmixing, we classified water extent in nearly 1700 man-made lakes, or tanks, in Landsat images from 1973 to 2010. The classification results compared well with a reference dataset of water extent of tanks (R2 = 0.95). We modeled the water extent of 42 clusters of tanks in a multiple regression on simple hydrological covariates (including precipitation) and time. Inter-annual variability in precipitation accounted for 63 % of the predicted variability in water extent. However, precipitation did not exhibit statistically significant trends in any part of the watershed. After controlling for precipitation variability, we found statistically significant temporal trends in water extent, both positive and negative, in 13 of the clusters. Based on a water balance argument, we inferred that these trends likely reflect a non-stationary relationship between precipitation and watershed runoff. Independently of precipitation, water extent increased in a region downstream of Bangalore, likely due to increased urban effluents, and declined in the northern portion of the Arkavathy. Comparison of the drying trends with land use indicated that they were most strongly associated with irrigated agriculture, sourced almost exclusively by groundwater. This suggests that groundwater abstraction was a major driver of hydrological change in this watershed. Disaggregating the watershed-scale hydrological response via remote sensing of surface water bodies over multiple decades yielded a spatially resolved characterization of hydrological change in an otherwise poorly monitored watershed. This approach presents an opportunity to understand hydrological change in heavily managed watersheds where surface water bodies integrate upstream runoff and can be delineated using satellite imagery.BRII recipient: ThompsonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6g7630k2articleHydrology and Earth System Sciencesvol 22, iss 1, 595-6101607-7938oai:escholarship.org:ark:/13030/qt0x60d3kz2018-04-23T22:06:35Zqt0x60d3kzAncient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvementWales, NathanAkman, MelisWatson, Ray H. BSanchez Barreiro, FatimaSmith, Bruce DGremillion, Kristen JGilbert, M. Thomas PBlackman, Benjamin K2018-02-13Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in‐depth gene‐based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.BRII recipient: WalespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0x60d3kzpublicationoai:escholarship.org:ark:/13030/qt4pv4w77j2018-04-23T22:02:47Zqt4pv4w77jComparative genetics of invasive populations of walnut aphid,
Chromaphis juglandicola
, and its introduced parasitoid,
Trioxys pallidus
, in CaliforniaAndersen, Jeremy CMills, Nicholas J2018-01-01Coevolution may be an important component of the sustainability of importation biological control, but how frequently introduced natural enemies coevolve with their target pests is unclear. Here we explore whether comparative population genetics of the invasive walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, provide insights into the localized breakdown of biological control services in walnut orchards in California. We found that sampled populations of C. juglandicolaexhibited higher estimates of genetic differentiation (FST) than co‐occurring populations of T. pallidus. In contrast, estimates of both the inbreeding coefficient (GIS) and contemporary gene flow were higher for T. pallidus than for C. juglandicola. We also found evidence of reciprocal outlier loci in some locations, but none showed significant signatures of selection. Synthesis and applications. Understanding the importance of coevolutionary interactions for the sustainability of biological control remains an important and understudied component of biological control research. Given the observed differences in gene flow and genetic differentiation among populations of T. pallidus and C. juglandicola, we suspect that temporary local disruption of biological control services may occur more frequently than expected while remaining stable at broader regional scales. Further research that combines genomewide single nucleotide polymorphism genotyping with measurements of phenotypic traits is needed to provide more conclusive evidence of whether the occurrence of outlier loci that display significant signatures of selection can be interpreted as evidence of the presence of a geographic mosaic of coevolution in this system.BRII recipient: AndersenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4pv4w77jarticleEcology and Evolutionvol 8, iss 1, 801-81120457758oai:escholarship.org:ark:/13030/qt9zm9r5b52018-04-23T21:22:53Zqt9zm9r5b5Choosing a Future Shoreline for the San Francisco Bay: Strategic Coastal Adaptation Insights from Cost EstimationHirschfeld, DaniellaHill, Kristina E2017-09-04 In metropolitan regions made up of multiple independent jurisdictions, adaptation to increased coastal flooding due to sea level rise requires coordinated strategic planning of the physical and organizational approaches to be adopted. Here, we explore a flexible method for estimating physical adaptation costs along the San Francisco Bay shoreline. Our goal is to identify uncertainties that can hinder cooperation and decision-making. We categorized shoreline data, estimated the height of exceedance for sea level rise scenarios, and developed a set of unit costs for raising current infrastructure to meet future water levels. Using these cost estimates, we explored critical strategic planning questions, including shoreline positions, design heights, and infrastructure types. For shoreline position, we found that while the shortest line is in fact the least costly, building the future shoreline at today’s transition from saltwater to freshwater vegetation is similar in cost but allows for the added possibility of conserving saltwater wetlands. Regulations requiring a specific infrastructure design height above the water level had a large impact on physical construction costs, increasing them by as much as 200%. Finally, our results show that the costs of raising existing walls may represent 70% to 90% of the total regional costs, suggesting that a shift to earthen terraces and levees will reduce adaptation costs significantly.BRII recipient: HirschfeldpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9zm9r5b5articleJournal of Marine Science and Engineeringvol 5, iss 3oai:escholarship.org:ark:/13030/qt46v489xk2018-04-23T19:08:11Zqt46v489xkGermanium as a scalable sacrificial layer for nanoscale protein patterningLu, BochaoMaharbiz, Michel M2018-04-06We demonstrate the use of germanium (Ge) films as water-soluble features that allow the patterning of proteins onto surfaces with commonly used organic solvents. This technique is scalable for manufacturing and is compatible with nano- and microfabrication processes, including standard lithography. We use Ge as a sacrificial layer to mask and protect areas of the substrate during surface functionalization. Since Ge dissolves in 0.35% hydrogen peroxide (H2O2) in water but not in organic solvents, Ge can be removed after patterning without significantly affecting protein activities. In this paper, we present examples of protein patterning with two different techniques. We show that 50 nm thick Ge layers can be completely removed in 10 min without residues and, importantly, nanoscale resolution and misalignment can be achieved with conventional photolithography equipment. Both biotin and streptavidin maintain ~80% and >50% activity after 10 min and 360 min incubation in 0.35% H2O2, respectively. Lastly, the process can be used to functionalize sidewalls with proteins, a capability of recent interest for cell-cell adhesion studies.BRII recipient: MaharbizpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/46v489xkarticlePLOS ONEvol 13, iss 4, e01950621932-6203oai:escholarship.org:ark:/13030/qt8zf032pq2018-04-23T18:58:40Zqt8zf032pqReal-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity buildingPomerantz, AaronPenafiel, NicolasArteaga, AlejandroBustamante, LucasPichardo, FrankColoma, Luis ABarrio-Amoros, Cesar LSalazar-Valenzuela, DavidProst, Stefan2018-04-01BackgroundAdvancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field.FindingsWe demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding.ConclusionsOverall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.BRII recipient: PomerantzpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8zf032pqarticleGigaSciencevol 7, iss 42047-217Xoai:escholarship.org:ark:/13030/qt6tj4j37c2018-04-23T18:49:28Zqt6tj4j37cOptical characterization of surface adlayers and their compositional demixing at the nanoscaleXiang, LiminWojcik, MichalKenny, Samuel JYan, RuiMoon, SeonahLi, WanXu, Ke2018-04-12Under ambient conditions, the behavior of a solid surface is often dominated by a molecularly thin adsorbed layer (adlayer) of small molecules. Here we develop an optical approach to unveil the nanoscale structure and composition of small-molecule adlayers on glass surfaces through spectrally resolved super-resolution microscopy. By recording the images and emission spectra of millions of individual solvatochromic molecules that turn fluorescent in the adlayer phase, we obtain ~30 nm spatial resolution and achieve concurrent measurement of local polarity. This allows us to establish that the adlayer dimensionality gradually increases through a sequence of 0D (nanodroplets), 1D (nano-lines), and 2D (films) for liquids of increasing polarity. Moreover, we find that in adlayers, a solution of two miscible liquids spontaneously demixes into nanodroplets of different compositions that correlate strongly with droplet size and location. We thus reveal unexpectedly rich structural and compositional behaviors of surface adlayers at the nanoscale.BRII recipient: XupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6tj4j37carticleNature Communicationsvol 9, iss 12041-1723oai:escholarship.org:ark:/13030/qt3gv7k8md2018-04-23T18:46:31Zqt3gv7k8mdSea Level Rise Impacts on Wastewater Treatment Systems Along the U.S. CoastsHummel, Michelle ABerry, Matthew SStacey, Mark T2018-04-13As sea levels rise, coastal communities will experience more frequent and persistent nuisance flooding, and some low‐lying areas may be permanently inundated. Critical components of lifeline infrastructure networks in these areas are also at risk of flooding, which could cause significant service disruptions that extend beyond the flooded zone. Thus, identifying critical infrastructure components that are exposed to sea level rise is an important first step in developing targeted investment in protective actions and enhancing the overall resilience of coastal communities. Wastewater treatment plants are typically located at low elevations near the coastline to minimize the cost of collecting consumed water and discharging treated effluent, which makes them particularly susceptible to coastal flooding. For this analysis, we used geographic information systems to assess the exposure of wastewater infrastructure to various sea level rise projections at the national level. We then estimated the number of people who would lose wastewater services, which could be more than five times as high as previous predictions of the number of people at risk of direct flooding due to sea level rise. We also performed a regional comparison of wastewater exposure to marine and groundwater flooding in the San Francisco Bay Area. Overall, this analysis highlights the widespread exposure of wastewater infrastructure in the United States and demonstrates that local disruptions to infrastructure networks may have far‐ranging impacts on areas that do not experience direct flooding.BRII recipient: HummelpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3gv7k8mdpublicationoai:escholarship.org:ark:/13030/qt74g239b32018-04-23T18:43:21Zqt74g239b3Sodium ion channel alkaloid resistance does not vary with toxicity in aposematic Dendrobates poison frogs: An examination of correlated trait evolutionYuan, Michael LWang, Ian J2018-03-13Spatial heterogeneity in the strength or agents of selection can lead to geographic variation in ecologically important phenotypes. Many dendrobatid frogs sequester alkaloid toxins from their diets and often exhibit fixed mutations at NaV1.4, a voltage-gated sodium ion channel associated with alkaloid toxin resistance. Yet previous studies have noted an absence of resistance mutations in individuals from several species known to sequester alkaloid toxins, suggesting possible intraspecific variation for alkaloid resistance in these species. Toxicity and alkaloid profiles vary substantially between populations in several poison frog species (genus Dendrobates) and are correlated with variation in a suite of related traits such as aposematic coloration. If resistance mutations are costly, due to alterations of channel gating properties, we expect that low toxicity populations will have reduced frequencies and potentially even the loss of resistance alleles. Here, we examine whether intraspecific variation in toxicity in three dendrobatid frogs is associated with intraspecific variation in alleles conferring toxin resistance. Specifically, we examine two species that display marked variation in toxicity throughout their native ranges (Dendrobates pumilio and D. granuliferus) and one species with reduced toxicity in its introduced range (D. auratus). However, we find no evidence for population-level variation in alkaloid resistance at NaV1.4. In fact, contrary to previous studies, we found that alkaloid resistance alleles were not absent in any populations of these species. All three species exhibit fixed alkaloid resistance mutations throughout their ranges, suggesting that these mutations are maintained even when alkaloid sequestration is substantially reduced.BRII recipient: WangpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/74g239b3articlePLOS ONEvol 13, iss 3, e01942651932-6203oai:escholarship.org:ark:/13030/qt0vw151702018-04-20T22:58:49Zqt0vw15170The impact of land ownership, firefighting, and reserve status on fire probability in CaliforniaStarrs, Carlin FrancesBustic, VanStephens, ConnorStewart, William2018-02-28The extent of wildfires in the western United States is increasing, but how land ownership, firefighting, and reserve status influence fire probability is unclear. California serves as a unique natural experiment to estimate the impact of these factors, as ownership is split equally between federal and non-federal landowners; there is a relatively large proportion of reserved lands where extractive uses are prohibited and fire suppression is limited; and land ownership and firefighting responsibility are purposefully not always aligned. Panel Poisson regression techniques and pre-regression matching were used to model changes in annual fire probability from 1950–2015 on reserve and non-reserve lands on federal and non-federal ownerships across four vegetation types: forests, rangelands, shrublands, and forests without commercial species. Fire probability was found to have increased over time across all 32 categories. A marginal effects analysis showed that federal ownership and firefighting was associated with increased fire probability, and that the difference in fire probability on federal versus non-federal lands is increasing over time. Ownership, firefighting, and reserve status, played roughly equal roles in determining fire probability, and were found to have much greater influence than average maximum temperature (°C) during summer months (June, July, August), average annual precipitation (cm), and average annual topsoil moisture content by volume, demonstrating the critical role these factors play in western fire regimes and the importance of including them in future analysis focused on understanding and predicting wildfire in the Western United States.BRII recipient: StewartpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0vw15170articleEnvironmental Research Lettersvol 13oai:escholarship.org:ark:/13030/qt8p71s6122018-04-10T19:40:28Zqt8p71s612Following the Yik Yak: Using Social Media Observations to Understand Student Needs on College CampusesEmmelhainz, CeliaRigby, Miriam2017-07-12What can social media tell us about our patrons? We look at Yik Yak through the lens of library ethnography, suggesting that anonymous social media can reveal not only complaints and commentary about library services and spaces, but also uncover students’ emotional and social experience with research and study space. Looking at social media posts on Yik Yak, we uncover common threads of social dynamics, expectations of quiet space, and frustration with studying, all of which increase our understanding of student experiences in US and international libraries.library assessmentacademic librariessocial medialibrary ethnographyuser experienceapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8p71s612publicationoai:escholarship.org:ark:/13030/qt1sg5c62t2018-03-15T17:25:12Zqt1sg5c62tComparative genetics of invasive populations of walnut aphid,
Chromaphis juglandicola
, and its introduced parasitoid,
Trioxys pallidus
, in CaliforniaAndersen, Jeremy CMills, Nicholas J2018-01-01Coevolution may be an important component of the sustainability of importation biological control, but how frequently introduced natural enemies coevolve with their target pests is unclear. Here we explore whether comparative population genetics of the invasive walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, provide insights into the localized breakdown of biological control services in walnut orchards in California. We found that sampled populations of C. juglandicola exhibited higher estimates of genetic differentiation (F
ST) than co-occurring populations of T. pallidus. In contrast, estimates of both the inbreeding coefficient (G
IS) and contemporary gene flow were higher for T. pallidus than for C. juglandicola. We also found evidence of reciprocal outlier loci in some locations, but none showed significant signatures of selection. Synthesis and applications. Understanding the importance of coevolutionary interactions for the sustainability of biological control remains an important and understudied component of biological control research. Given the observed differences in gene flow and genetic differentiation among populations of T. pallidus and C. juglandicola, we suspect that temporary local disruption of biological control services may occur more frequently than expected while remaining stable at broader regional scales. Further research that combines genomewide single nucleotide polymorphism genotyping with measurements of phenotypic traits is needed to provide more conclusive evidence of whether the occurrence of outlier loci that display significant signatures of selection can be interpreted as evidence of the presence of a geographic mosaic of coevolution in this system.BRII recipient: AndersenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1sg5c62tarticleEcology and Evolutionvol 8, iss 1, 801-81120457758oai:escholarship.org:ark:/13030/qt59j5f9sp2018-03-06T22:13:09Zqt59j5f9spSupporting the expatriate social scientist: Faculty research and information access in post-Soviet KazakhstanEmmelhainz, Celia2015-06-17Librarians in America and Europe find that social scientists rely heavily on journal articles, specialized data, and feedback from colleagues in directing their research. This project uses 21 ethnographic interviews with librarians, students, and faculty at “Atameken University” in post-Soviet Kazakhstan to explore how social scientists adjust such research habits to a context of distant information sources and limited access. By developing technological adaptations to the local context, expatriate scholars can surmount most barriers to access—and yet librarians are then less able to effectively support research. Increased access to information and skilled librarians remains essential for Eurasian universities seeking to support world-class research in the developing world.Central Asiaexpatriate facultyresearch barrierssocial scientistsworkaroundsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/59j5f9sppublicationoai:escholarship.org:ark:/13030/qt45c0g6182018-01-30T21:31:36Zqt45c0g618Brahms’s Piano Exercise Mode and the Politics of Friendship (excerpt)Serbanescu-Martin, TheodoraMathew, Nicholas2017-04-012017 WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/45c0g618publicationoai:escholarship.org:ark:/13030/qt4ps1c0g92018-01-24T22:47:21Zqt4ps1c0g9Warm Grief: Uncanny Narratives of Trauma and Kinship in Oh Jung-hee's The Yard of ChildhoodLee, JulieKwon, Youngmin2017-04-01Honorable MentionUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4ps1c0g9publicationoai:escholarship.org:ark:/13030/qt87s7308h2018-01-24T22:40:11Zqt87s7308hAcross Three Oceans: Shipwrecks as Early Modern Globalismde Santiago, RamonTrever, Lisa2016-12-01WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/87s7308hpublicationoai:escholarship.org:ark:/13030/qt27r8h2jc2018-01-24T17:22:22Zqt27r8h2jcCross-boundary subsidy cascades from oil palm degrade distant tropical forestsLuskin, Matthew ScottBrashares, Justin SIckes, KalanSun, I-FangFletcher, ChristineWright, S. JosephPotts, Matthew D2017-12-20Native species that forage in farmland may increase their local abundances thereby affecting adjacent ecosystems within their landscape. We used two decades of ecological data from a protected primary rainforest in Malaysia to illutrate how subsidies from neighboring oil palm plantations triggered powerful secondary ‘cascading’ effects on natural habitats located >1.3 km away. We found (i) oil palm fruit drove 100-fold increases in crop-raiding native wild boar (Sus scrofa), (ii) wild boar used thousands of understory plants to construct birthing nests in the pristine forest interior, and (iii) nest building caused a 62% decline in forest tree sapling density over the 24-year study period. The long-term, landscape-scale indirect effects from agriculture suggest its full ecological footprint may be larger in extent than is currently recognized. Cross-boundary subsidy cascades may be widespread in both terrestrial and marine ecosystems and present significant conservation challenges.BRII recipient: PottspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/27r8h2jcarticleNature Communicationsvol 8, iss 12041-1723oai:escholarship.org:ark:/13030/qt2dv5b3p02018-01-23T19:06:33Zqt2dv5b3p0Death, injury and disability from kinetic impact projectiles in crowd-control settings: a systematic reviewHaar, Rohini JIacopino, VincentRanadive, NikhilDandu, MadhaviWeiser, Sheri D2017-12-05Objective We conducted a systematic review of the available literature on deaths, injuries and permanent disability from rubber and plastic bullets, as well as from bean bag rounds, shot pellets and other projectiles used in arrests, protests and other contexts from 1 January 1990 until 1 June 2017.Data sources PubMed, Scopus, JSTOR and grey literature.Data synthesis We report on descriptive statistics as well as data on injury severity, permanent disability and death. We analysed potential risk factors for injury severity, including the site of impact, firing distance and access to medical care.Results Of 3228 identified articles, 26 articles met inclusion criteria. These articles included injury data on 1984 people, 53 of whom died as a result of their injuries. 300 people suffered permanent disability. Deaths and permanent disability often resulted from strikes to the head and neck (49.1% of deaths and 82.6% of permanent disabilities). Of the 2135 injuries in those who survived their injuries, 71% were severe, injuries to the skin and to the extremities were most frequent. Anatomical site of impact, firing distance and timely access to medical care were correlated with injury severity and risk of disability.Conclusions Kinetic impact projectiles (KIPs), often called rubber or plastic bullets, are used commonly in crowd-control settings. We find that these projectiles have caused significant morbidity and mortality during the past 27 years, much of it from penetrative injuries and head, neck and torso trauma. Given their inherent inaccuracy, potential for misuse and associated health consequences of severe injury, disability and death, KIPs do not appear to be appropriate weapons for use in crowd-control settings. There is an urgent need to establish international guidelines on the use of crowd-control weapons to prevent unnecessary injuries and deaths.BRII recipient: IacopinopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2dv5b3p0articleBMJ Openvol 7, iss 12, e0181542044-6055 2044-6055oai:escholarship.org:ark:/13030/qt5f21j3nk2018-01-23T19:03:05Zqt5f21j3nkThe canon and the mushroomYurchak, Alexei2017-09-01This essay focuses on a paradoxical transformation that happened within Soviet ideological discourse at the very end of perestroika, around 1990–91. The Party’s attempts to revitalize Soviet ideology by returning to the original word of Lenin unexpectedly produced the opposite result. The unquestionable external Truth from which Soviet ideological discourse drew its legitimacy—and that had always been identical with Lenin’s word—suddenly could no longer be known. This shift launched a rapid unraveling of the Soviet communist project. At the center of this unexpected transformation was the search for the true Lenin—a kind of Lenin that Soviet party theorists, bureaucrats, historians, and scientists hoped was still hidden in the midst of his unpublished texts and unknown facts of his biology, life, and death.BRII recipient: YurchakpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5f21j3nkarticleHAU: Journal of Ethnographic Theoryvol 7, iss 2, 165-1982049-1115oai:escholarship.org:ark:/13030/qt6nv9m4752018-01-23T18:59:15Zqt6nv9m475Revisiting Ecosystem Services: Assessment and Valuation as Starting Points for Environmental PoliticsJadhav, AdamAnderson, SharolynDyer, Michael J. BSutton, Paul C2017-09-28The paradigm of ecosystem services (ES) and the methods of monetary valuation have become boundary objects, spanning disciplines and earning particular purchase in policy circles. However, the notion of ES and ES valuation have also been subjected to multiple critiques, ranging from their varying precision to the potential for neoliberalization of nature. This paper does not attempt to refute such critiques but rather revisits the potentials of the ES paradigm and the specific method of benefit transfer valuation for their utility as a form of environmental politics and sustainability practice. We find they have particular relevance in contexts where “data” are not readily available or are not legible to policy makers as well as where the imperative of “development” remains ideological. We argue for ES assessment and, specifically, rapid ES valuation as a first-pass tactic to inform evaluation of potentially environmentally degrading projects or environmental management. We demonstrate this using a simple benefit transfer analysis to offer an initial evaluation of (wet) landscape ES in a lightly touched estuary in Karnataka, India, where a state-backed proposal to develop an industrial shipping port is gathering steam. While we recognize and do not categorically reject critiques of the ES paradigm, we nonetheless argue for valuation as a starting point for politics that highlight and make visible ES benefits and users implicated by “development” and other kinds of environmental change.BRII recipient: JadhavpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6nv9m475articleSustainabilityvol 9, iss 10, 17552071-1050oai:escholarship.org:ark:/13030/qt29d680652018-01-23T17:27:57Zqt29d68065Response of Gilthead Seabream (Sparus aurata L., 1758) Larvae to Nursery Odor Cues as Described by a New Set of Behavioral IndexesMorais, PedroParra, Maria PBaptista, VaniaRibeiro, LauraPousao-Ferreira, PedroTeodosio, Maria A2017-10-13Temperate marine fish larvae use a series of environmental cues (e.g., olfactory, hearing, visual) to mediate the selection of nursery habitats. However, habitat selection may vary according to individuals' physiological condition. Therefore, this study aimed to determine the ability of gilthead seabream (Sparus aurata L., 1758) larvae to utilize natural odor cues to locate nursery habitats along ontogeny and to examine how it varies with individual's physiological condition. The hypothesis being tested is that S. aurata larvae prefer coastal rocky reefs as nursery areas, but they might use coastal lagoons as nursery grounds—ecosystems known for their productivity—if under starvation conditions, as a compensatory mechanism to avoid slow growth or even death. A choice-chamber experiment was used to investigate the behavioral responses of satiated and starved laboratory-reared S. aurata larvae, along ontogeny (pre-flexion, flexion, post-flexion), to water collected in a coastal artificial rocky reef and a coastal lagoon. The physiological condition of S. aurata larvae was determined by analyzing several biochemical condition indices. Complementarily, a new set of four preference indexes were developed—Choice-Chamber Preference Indexes—and discussed to provide a clear measure of the behavioral changes of a species along ontogeny by balancing all the behavioral choices made during the experimental trials, including the unresponsive behavior. A developmental threshold was identified at 24 days post-hatching, before which insufficient swimming capability disabled responsive behavior. Beyond this threshold, post-flexion larvae preferred rocky coastal water over lagoon water, even if under starvation conditions or poor physiological condition, despite the fact that the unresponsive behavior was largely predominant. S. aurata larvae displayed a cautionary behavioral strategy, so the compensatory mechanisms to ensure metapopulation stability and resilience have to rely on their feeding plasticity and on being a batch-spawning species (i.e., diversified bet-hedging strategy) to compensate the lack of apparent behavioral plasticity.BRII recipient: MoraispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/29d68065articleFrontiers in Marine Sciencevol 42296-7745oai:escholarship.org:ark:/13030/qt0jk3f7qp2018-01-22T17:22:47Zqt0jk3f7qpMothers' labor market choices and child development outcomes in ChileReynolds, Sarah AFernald, Lia C.H.Behrman, Jere R2017-12-01This paper examines associations between labor market participation of Chilean mothers and the cognitive, language, and socio-economic development of their children. Using a nationally-representative sample of 3-year-old children, we test if mothers’ work intensity in the two previous years is associated with child development outcomes; data were collected in 2010 when children were one year old, and again in 2012, when they were three years old. We find that children who were three years old with mothers who worked for higher fractions of their children’s lives in the previous two years perform significantly better on all tests (cognitive, language, socio-emotional) than children whose mothers had worked less, while controlling for baseline test performance. These main effects did not remain significant with the inclusion of a wide range of socio-economic, demographic control variables, however. Our results were similarly null when using an IV analysis or a propensity score matching approach. We provide descriptive information on theoretical pathways by which maternal work may influence child development. Though several of these pathways (e.g. preschool, toys, maternal stress) seem to be associated with both maternal work and child development outcomes, the pathways are not sufficiently strong to generate an association between maternal work and child development. We conclude that Chilean mothers’ employment in early childhood generally does not have an effect on child development.BRII recipient: ReynoldspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0jk3f7qppublicationoai:escholarship.org:ark:/13030/qt26c1f2z12018-01-22T17:11:12Zqt26c1f2z1Microbial community-level regulation explains soil carbon responses to long-term litter manipulationsGeorgiou, KaterinaAbramoff, Rose ZHarte, JohnRiley, William JTorn, Margaret S2017-10-31Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity, mediated by changes in plant inputs. Many microbial models of soil organic carbon (SOC) decomposition have been proposed recently to advance prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the source of these problems in four archetypal models and propose a density-dependent formulation of microbial turnover, motivated by community-level interactions, that limits population sizes and reduces oscillations. We compare model predictions to 24 long-term C-input field manipulations and identify key benchmarks. The proposed formulation reproduces soil C responses to long-term C-input changes and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to recent microbial models. This study provides a simple modification to improve microbial models for inclusion in Earth System Models.BRII recipient: GeorgioupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/26c1f2z1articleNature Communicationsvol 8, iss 12041-1723oai:escholarship.org:ark:/13030/qt38g364r92018-01-22T17:08:28Zqt38g364r9Incorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservationGuevara Andino, Juan ErnestoPitman, Nigel C. Ater Steege, HansMogollon, HugoCeron, CarlosPalacios, WalterOleas, NoraFine, Paul V. A2017-11-01Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one-hectare plots in terra firme forests of Ecuadorian Amazon. In these plots, we tagged, collected, and identified every single adult tree with dbh ≥10 cm. These data were combined with a regional community phylogenetic tree to calculate different phylogenetic diversity (PD) metrics in order to create spatial models. We used Loess regression to estimate the spatial variation of taxonomic and phylogenetic beta diversity as well as phylogenetic endemism and evolutionary distinctiveness. We found evidence for the definition of three floristic districts in the Ecuadorian Amazon, supported by both taxonomic and phylogenetic diversity data. Areas with high levels of phylogenetic endemism and evolutionary distinctiveness in Ecuadorian Amazon forests are unprotected. Furthermore, these areas are severely threatened by proposed plans of oil and mining extraction at large scales and should be prioritized in conservation planning for this region.BRII recipient: FinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/38g364r9articleEcology and Evolutionvol 7, iss 22, 9639-965020457758oai:escholarship.org:ark:/13030/qt2xk7d6vh2018-01-22T17:04:47Zqt2xk7d6vhDevelopment of Single-Copy Nuclear Intron Markers for Species-Level Phylogenetics: Case Study with Paullinieae (Sapindaceae)Chery, Joyce GSass, ChodonSpecht, Chelsea D2017-09-01Premise of the study:We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline.Methods and Results:Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a “pseudoreference” closer to the lineage of interest. Several filters are applied to meet the criteria of single-copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single-copy nuclear intron markers for Paullinieae.Conclusions:This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.BRII recipient: SasspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2xk7d6vharticleApplications in Plant Sciencesvol 5, iss 9, 17000512168-0450oai:escholarship.org:ark:/13030/qt5bc7b8072018-01-20T00:23:00Zqt5bc7b807Composite likelihood method for inferring local pedigreesKo, AmyNielsen, Rasmus2017-08-21Pedigrees contain information about the genealogical relationships among individuals and are of fundamental importance in many areas of genetic studies. However, pedigrees are often unknown and must be inferred from genetic data. Despite the importance of pedigree inference, existing methods are limited to inferring only close relationships or analyzing a small number of individuals or loci. We present a simulated annealing method for estimating pedigrees in large samples of otherwise seemingly unrelated individuals using genome-wide SNP data. The method supports complex pedigree structures such as polygamous families, multi-generational families, and pedigrees in which many of the member individuals are missing. Computational speed is greatly enhanced by the use of a composite likelihood function which approximates the full likelihood. We validate our method on simulated data and show that it can infer distant relatives more accurately than existing methods. Furthermore, we illustrate the utility of the method on a sample of Greenlandic Inuit.BRII recipient: KopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5bc7b807articlePLOS Geneticsvol 13, iss 8, e10069631553-7404oai:escholarship.org:ark:/13030/qt8zf664562018-01-20T00:20:38Zqt8zf66456Given enough eyeballs, all bugs are shallow? Revisiting Eric Raymond with bug bounty programsMaillart, ThomasZhao, MingyiGrossklags, JensChuang, John2017-10-13Bug bounty programs offer a modern way for organizations to crowdsource their software security, and for security researchers to be fairly rewarded for the vulnerabilities they find. However, little is known on the incentives set by bug bounty programs – how they drive engagement and new bug discoveries. This article provides an empirical investigation of the strategic interactions among the managers and participants of bug bounty programs, as well as the intermediation by bug bounty platforms. We find that for a given bug bounty program, each security researcher can only expect to discover a bounded number of bugs. This result offers a validation step to a theory brought forth early on by Brady et al. This theory proposes that each security researcher inspecting a piece of software offers a unique environment of skills and mindset, which is amenable to the discovery of bugs that others may not be able to uncover. Bug bounty programs indeed benefit from the engagement of large crowds of researchers. Conversely, security researchers benefit greatly from searching for bugs in multiple bug bounty programs. However, we find that following a strong front-loading effect, newly launched programs attract researchers at the expense of older programs: the probability of finding bugs decays as ∼1/t0.4∼1/t0.4 after the launch of a program, even though bugs found later yield on average higher rewards. Our results lead us to formulate three recommendations for organizing bug bounty programs and platforms: (i) organize enrollment, mobility, and renewal of security researchers across bounty programs, (ii) highlight and organize programs for front-loading, and (iii) organize fluid market transactions to reduce uncertainty and thus reduce incentives for security researchers to sell on the black market.BRII recipient: ChuangpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8zf66456publicationoai:escholarship.org:ark:/13030/qt8403d95v2018-01-20T00:16:54Zqt8403d95vNorthern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated GenesHanna, Zachary RHenderson, James BWall, Jeffrey DEmerling, Christopher AFuchs, JeromeRunckel, CharlesMindell, David PBowie, Rauri C. KDeRisi, Joseph LDumbacher, John P2017-10-01We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106nt. We calculated the genome-wide fixation index (F
ST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.BRII recipient: HannapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8403d95varticleGenome Biology and Evolutionvol 9, iss 10, 2522-25451759-6653oai:escholarship.org:ark:/13030/qt6bk3c4cw2018-01-19T22:46:31Zqt6bk3c4cwMaintaining Traditions: A Qualitative Study of Early Childhood Caries Risk and Protective Factors in an Indigenous CommunityLevin, AnaSokal-Gutierrez, KarenHargrave, AnitaFunsch, ElizabethHoeft, Kristin2017-08-11In lower middle-income economies (LMIE), the nutrition transition from traditional diets to sugary foods and beverages has contributed to widespread early childhood dental caries. This qualitative study explores perceived risk and protective factors, and overall experiences of early childhood nutrition and oral health in indigenous Ecuadorian families participating in a community-based oral health and nutrition intervention. Dental exams of 698 children age 6 months through 6 years determined each child’s caries burden. A convenience sample of 18 “outlier” families was identified: low-caries children with ≤2 carious teeth vs. high-caries children with ≥10 carious teeth. Semi-structured in-depth interviews with parents/caregivers explored the child’s diet, dental habits, and family factors related to nutrition and oral health. Interviews were transcribed and thematically analyzed using grounded theory. In the high-caries families, proximity to highway and stores, consumption of processed-food, and low parental monitoring of child behavior were identified as risk factors for ECC (early childhood caries). In the low-caries families, protective factors included harvesting and consuming food from the family farm, remote geography, and greater parental monitoring of child behavior. The study results suggest that maintaining traditional family farms and authoritative parenting to avoid processed foods/drinks and ensure tooth brushing could improve early childhood nutrition and oral health.BRII recipient: Sokal-GutierrezpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6bk3c4cwarticleInternational Journal of Environmental Research and Public Healthvol 14, iss 8, 9071660-4601oai:escholarship.org:ark:/13030/qt11c5f6pm2018-01-19T22:44:19Zqt11c5f6pmVegetation Development in a Tidal Marsh Restoration Project during a Historic Drought: A Remote Sensing ApproachChapple, DylanDronova, Iryna2017-08-10Tidal wetland restoration efforts can be challenging to monitor in the field due to unstable local conditions and poor site access. However, understanding how restored systems evolve over time is essential for future management of their ecological benefits, many of which are related to vegetation dynamics. Physical attributes, such as elevation and distance to channel play important roles in governing vegetation expansion in developing tidal wetlands. However, in Mediterranean ecosystems, drought years, wet years, and their resulting influence on salinity levels may also play a crucial role in determining the trajectory of restoration projects, but the influence of weather variability on restoration outcomes is not well-understood. Here, we use object-based image analysis (OBIA) and change analysis of high-resolution IKONOS and WorldView-2 satellite imagery to explore whether mean annual rates of change from mudflat to vegetation are lower during drought years with higher salinity (2011–2015) compared to years with lower salinity (2009–2011) at a developing restoration site in California's San Francisco Bay. We found that vegetation increased at a mean rate of 1,979 m2/year during California's historic drought, 10.4 times slower than the rate of 20,580 m2/year between 2009 and 2011 when the state was not in drought. Vegetation was significantly concentrated in areas closer to channel edges, where salinity stress is ameliorated, and the magnitude of the effect increased in the 2015 image. In our image analysis, we found that different distributions of water, mud, and algae between years led to different segmentation settings for each set of images, highlighting the need for more robust and reproducible OBIA strategies in complex wetlands. Our results demonstrate that adaptive monitoring efforts in variable climates should take into account the influence of weather on tidal wetland ecosystems, and that high-resolution remote sensing can be an effective means of assessing these dynamics.BRII recipient: ChapplepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/11c5f6pmarticleFrontiers in Marine Sciencevol 42296-7745oai:escholarship.org:ark:/13030/qt8jk5j27v2018-01-19T22:40:53Zqt8jk5j27vEncoding and Decoding Models in Cognitive ElectrophysiologyHoldgraf, Christopher RRieger, Jochem WMicheli, CristianoMartin, StephanieKnight, Robert TTheunissen, Frederic E2017-09-26Cognitive neuroscience has seen rapid growth in the size and complexity of data recorded from the human brain as well as in the computational tools available to analyze this data. This data explosion has resulted in an increased use of multivariate, model-based methods for asking neuroscience questions, allowing scientists to investigate multiple hypotheses with a single dataset, to use complex, time-varying stimuli, and to study the human brain under more naturalistic conditions. These tools come in the form of “Encoding” models, in which stimulus features are used to model brain activity, and “Decoding” models, in which neural features are used to generated a stimulus output. Here we review the current state of encoding and decoding models in cognitive electrophysiology and provide a practical guide toward conducting experiments and analyses in this emerging field. Our examples focus on using linear models in the study of human language and audition. We show how to calculate auditory receptive fields from natural sounds as well as how to decode neural recordings to predict speech. The paper aims to be a useful tutorial to these approaches, and a practical introduction to using machine learning and applied statistics to build models of neural activity. The data analytic approaches we discuss may also be applied to other sensory modalities, motor systems, and cognitive systems, and we cover some examples in these areas. In addition, a collection of Jupyternotebooks is publicly available as a complement to the material covered in this paper, providing code examples and tutorials for predictive modeling in python. The aim is to provide a practical understanding of predictive modeling of human brain data and to propose best-practices in conducting these analyses.BRII recipient: TheunissenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8jk5j27varticleFrontiers in Systems Neurosciencevol 111662-5137oai:escholarship.org:ark:/13030/qt8g13c4h22018-01-19T16:41:42Zqt8g13c4h2Patterns and dynamics of vegetation recovery following grazing cessation in the California golden trout habitatNussle, SebastienMatthews, Kathleen RCarlson, Stephanie M2017-07-01In 1978, the Golden Trout Wilderness area was established to protect the California golden trout (Oncorhynchus mykiss aguabonita)—a vulnerable subspecies of the rainbow trout that is endemic to California—and its habitat, which is currently restricted to a few streams within high-elevation meadows in the Sierra Nevada Mountain Range. Because of the deleterious effects of livestock grazing on riparian vegetation in the golden trout habitat (occurring since the 1800s), meadow restoration activities were initiated in 1991, including cattle exclusion. There has been renewed discussion about re-opening these public lands to livestock grazing, and impact assessment studies are needed to inform decision makers about the potential consequences. Thus, we estimated the recovery potential of the golden trout habitat by measuring the height of riparian vegetation within areas that have been grazed vs. closed to grazing (“rested”) since 1991. We found that cattle exclusion is effective at favoring riparian vegetation growth, but that vegetation recovery from grazing could take several decades in these sensitive habitats as some “rested” areas have yet to recover to full vegetation height, even after 25 yr of rest.BRII recipient: CarlsonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8g13c4h2articleEcospherevol 8, iss 7, e0188021508925oai:escholarship.org:ark:/13030/qt93z5q9m62018-01-19T16:38:31Zqt93z5q9m6Charting the circuit QED design landscape using optimal control theoryGoerz, Michael HMotzoi, FelixWhaley, K. BirgittaKoch, Christiane P2017-09-18With recent improvements in coherence times, superconducting transmon qubits have become a promising platform for quantum computing. They can be flexibly engineered over a wide range of parameters, but also require us to identify an efficient operating regime. Using state-of-the-art quantum optimal control techniques, we exhaustively explore the landscape for creation and removal of entanglement over a wide range of design parameters. We identify an optimal operating region outside of the usually considered strongly dispersive regime, where multiple sources of entanglement interfere simultaneously, which we name the quasi-dispersive straddling qutrits regime. At a chosen point in this region, a universal gate set is realized by applying microwave fields for gate durations of 50 ns, with errors approaching the limit of intrinsic transmon coherence. Our systematic quantum optimal control approach is easily adapted to explore the parameter landscape of other quantum technology platforms.BRII recipient: WhaleypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/93z5q9m6articlenpj Quantum Informationvol 3, iss 12056-6387oai:escholarship.org:ark:/13030/qt0zt776122018-01-18T17:02:24Zqt0zt77612Bovine leukemia virus linked to breast cancer in Australian women and identified before breast cancer developmentBuehring, Gertrude CShen, Hua MinSchwartz, Daniel ALawson, James S2017-06-22Bovine leukemia virus (BLV), a common virus of cattle globally, was believed for decades not to infect humans. More recent techniques (in situ PCR and DNA sequencing) enabled detection of BLV in human breast tissue, and determination of its significant association with breast cancer in a US population. Using similar techniques to study 96 Australian women, we report here detection of retrotranscribed BLV DNA in breast tissue of 40/50(80%) of women with breast cancer versus 19/46(41%) of women with no history of breast cancer, indicating an age-adjusted odds ratio and confidence interval of 4.72(1.71–13.05). These results corroborate the findings of the previous study of US women with an even higher odds ratio for the Australian population. For 48 of the subjects, paired breast tissue samples, removed 3–10 years apart in two unrelated procedures, were available. For 23/31 (74%) of these, in which the first specimen was diagnosed as nonmalignant (benign or premalignant) and the second as malignant, BLV was already present in benign breast tissue years 3–10 years before the malignancy was diagnosed. This is consistent with the supposition of a causative temporal relationship between BLV infection and subsequent development of cancer.BRII recipient: BuehringpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0zt77612articlePLOS ONEvol 12, iss 6, e01793671932-6203oai:escholarship.org:ark:/13030/qt0ff6s8rz2018-01-18T16:57:55Zqt0ff6s8rzMolecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagenMadani, AliGarakani, KiavashMofrad, Mohammad R. K2017-06-30Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. In this study, we explore the collagen binding mechanism of the multi-modular cell wall anchored collagen adhesin (CNA) in Staphylococcus aureus and examine how applied mechanical forces can modulate adhesion ability. The common structural-functional elements and domain organization of CNA are present across over 50 genera of bacteria. Through the use of molecular dynamics models and normal mode analysis, we shed light on the CNA’s structural and conformational dynamics and its interactions with collagen that lead to collagen binding. Our results suggest that the linker region, CNA165-173, acts as a hinge exhibiting bending, extensional, and torsional modes of structural flexibility and its residues are key in the interaction of the CNA-collagen complex. Steered molecular dynamics simulations were conducted with umbrella sampling. During the course of these simulations, the ‘locking’ latch from the CNA N2 domain was dissociated from its groove in the CNA N1 domain, implying the importance of the latch for effective ligand binding. Finally, we observed that the binding efficiency of the CNA N1-N2 domains to collagen decreases greatly with increasing tensile force application to the collagen peptides. Thus, CNA and similar adhesins might preferentially bind to sites in which collagen fibers are cleaved, such as in wounded, injured, or inflamed tissues, or in which the collagenous tissue is less mature. As alternative techniques for control of bacterial infection are in-demand due to the rise of bacterial antibiotic resistance, results from our computational studies with respect to the mechanoregulation of the collagen binding site may inspire new therapeutics and engineering solutions by mechanically preventing colonization and/or further pathogenesis.BRII recipient: MadanipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0ff6s8rzarticlePLOS ONEvol 12, iss 6, e01796011932-6203oai:escholarship.org:ark:/13030/qt07n440x72018-01-18T16:53:50Zqt07n440x7Cellobiose Consumption Uncouples Extracellular Glucose Sensing and Glucose Metabolism in
Saccharomyces cerevisiaeChomvong, KulikaBenjamin, Daniel INomura, Daniel KCate, Jamie H. DZhou, Jizhong2017-08-08Glycolysis is central to energy metabolism in most organisms, and is highly regulated to enable optimal growth. In the yeast Saccharomyces cerevisiae, feedback mechanisms that control flux through glycolysis span transcriptional control to metabolite levels in the cell. Using a cellobiose consumption pathway, we decoupled glucose sensing from carbon utilization, revealing new modular layers of control that induce ATP consumption to drive rapid carbon fermentation. Alterations of the beta subunit of phosphofructokinase (PFK2), H+-plasma membrane ATPase (PMA1), and glucose sensors (SNF3, RGT2) revealed the importance of coupling extracellular glucose sensing to manage ATP levels in the cell. Controlling the upper bound of cellular ATP levels may be a general mechanism used to regulate energy levels in cells, via a regulatory network that can be uncoupled from ATP concentrations under perceived starvation conditions.BRII recipient: CatepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/07n440x7articlemBiovol 8, iss 4, e00855-172150-7511oai:escholarship.org:ark:/13030/qt81w992n72018-01-18T16:50:02Zqt81w992n7The Battle of Worldviews: A Case Study of Liver Fluke Infection in Khon Kaen, ThailandSamiphak, SaraSyme, S. Leonard2017-08-10Control efforts to reduce infection from the parasitic flatworm Opisthorchis viverrini have progressed through understanding the epidemiology of Opisthorchis viverrini, antiparasitic drug developments, technological innovations, health education promoting cooking of fish, and improved hygienic defecation. Yet the problem persists. The case study method was used to examine the fundamental cause of the liver fluke infection problem. Evidence shows that the liver fluke–infected population does not care about living a long life. For them, suffering and death are simply a part of life, and expected. Thus, the cause(s) leading to death is not important. They believe morally bad actions, and predetermined fate associated with kamma in Buddhism, play a big role whether or not one is infected with the liver fluke. Health interventions may be made more effective if they take into account the liver fluke–infected population’s worldviews about ethics, morality, life, and death. We researchers should not feel concerned only about medically determined causes of death.BRII recipient: SymepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/81w992n7articleJournal of Evidence-Based Complementary & Alternative Medicinevol 22, iss 4, 902-9082156-5872 2156-5899oai:escholarship.org:ark:/13030/qt752311942018-01-17T20:37:57Zqt75231194Thinking through Visualizations: Critical Data Literacy Using RemittancesEmmelhainz, CeliaPappas, ErinSeale, Maura2016-09-30[Chapter excerpt] "We aim to situate and critically interrogate the increasingly privileged role of data within library and information literacy outreach on college and university campuses. Following a brief discussion of data in a college context, we provide a lesson plan that adapts critical information literacy and critical data librarianship to draw entirely on open data... we ask librarian and students together to consider a series of interrelated questions and activities. This lesson plan is focused on the topic of remittances to the Philippines, but it could be adapted to any topic for which World Bank data is available..."[for the two-volume series] Critical pedagogy incorporates inclusive and reflective teaching for aims of social justice; it provides mechanisms for students to evaluate their social, political, and economic standing, and to question societal norms and how these norms perpetuate societal injustices. Teaching librarians have long incorporated social justice into their work, but focused interest in critical library pedagogy has grown rapidly in recent years. In two volumes, the Critical Library Pedagogy Handbook works to make critical pedagogy more accessible for library educators, examining both theory and practice...data literacydata visualizationlibrary instructiondata librarianshipcritical library pedagogycritlibteaching data literacy in the libraryapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/75231194publicationoai:escholarship.org:ark:/13030/qt1c3230k32018-01-17T19:05:50Zqt1c3230k3Morphometrics in Developmental Neurobiology: Quantitative Analysis of Growth Cone Motility in VivoAnoukh, SohalJames, HaManuel, ZhuFayha, LakhaniKavitha, ThiagaraganLauren, OlzewskiRaagav, MonakrishnanTamira, Elul2017-07-12In order for the nervous system to function properly, neurons in the brain must establish specific connections during embryonic development. Formation of neuronal circuits involves axons extending from cell bodies and navigating through diverse tissues to reach their targets in the brain. Once axons reach their target tissues, they arborize and make synaptic connections. Axon pathfinding is driven by dynamic motility behaviors expressed by terminal growth cones at the tips of the axons. Here, we applied morphometrics to determine quantitative values for six morphological and motility parameters for growth cones of optic axons navigating through the optic tract of a living brain preparation from a Xenopus laevis tadpole. Our results demonstrate an increase in length, decrease in width, increase in perimeter, decrease in area, increase in number of filopodia, and a decrease in number of lamellipodia, of the growth cones in the optic tract. Therefore, optic axonal growth cones become less circular and more elongated and protrusive during their navigation through the optic tract. Quantitatively deconstructing parameters of growth cone motility is necessary to determine molecular, cellular, and biophysical mechanisms of axon pathfinding, and to formulate computational analyses of developing neuronal connectivity in the brain.BRII recipien: ElulpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1c3230k3publicationoai:escholarship.org:ark:/13030/qt7hm8n8jg2018-01-17T18:52:59Zqt7hm8n8jgDressmakers show enhanced stereoscopic visionChopin, AdrienLevi, Dennis MBavelier, Daphne2017-06-13The ability to estimate the distance of objects from one’s self and from each other is fundamental to a variety of behaviours from grasping objects to navigating. The main cue to distance, stereopsis, relies on the slight offsets between the images derived from our left and right eyes, also termed disparities. Here we ask whether the precision of stereopsis varies with professional experience with precise manual tasks. We measured stereo-acuities of dressmakers and non-dressmakers for both absolute and relative disparities. We used a stereoscope and a computerized test removing monocular cues. We also measured vergence noise and bias using the Nonius line technique. We demonstrate that dressmakers’ stereoscopic acuities are better than those of non-dressmakers, for both absolute and relative disparities. In contrast, vergence noise and bias were comparable in the two groups. Two non-exclusive mechanisms may be at the source of the group difference we document: (i) self-selection or the fact that stereo-vision is functionally important to become a dressmaker, and (ii) plasticity, or the fact that training on demanding stereovision tasks improves stereo-acuity.BRII recipient: ChopinpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7hm8n8jgarticleScientific Reportsvol 7, iss 12045-2322oai:escholarship.org:ark:/13030/qt7g05c07g2018-01-17T16:34:20Zqt7g05c07gStimulating Parenting Practices in Indigenous and Non-Indigenous Mexican CommunitiesKnauer, HeatherOzer, EmilyDow, WilliamFernald, Lia2017-12-25Parenting may be influenced by ethnicity; marginalization; education; and poverty. A critical but unexamined question is how these factors may interact to compromise or support parenting practices in ethnic minority communities. This analysis examined associations between mothers’ stimulating parenting practices and a range of child-level (age; sex; and cognitive and socio-emotional development); household-level (indigenous ethnicity; poverty; and parental education); and community-level (economic marginalization and majority indigenous population) variables among 1893 children ages 4–18 months in poor; rural communities in Mexico. We also explored modifiers of associations between living in an indigenous community and parenting. Key findings were that stimulating parenting was negatively associated with living in an indigenous community or family self-identification as indigenous (β = −4.25; SE (Standard Error) = 0.98; β = −1.58; SE = 0.83 respectively). However; living in an indigenous community was associated with significantly more stimulating parenting among indigenous families than living in a non-indigenous community (β = 2.96; SE = 1.25). Maternal education was positively associated with stimulating parenting only in indigenous communities; and household crowding was negatively associated with stimulating parenting only in non-indigenous communities. Mothers’ parenting practices were not associated with child sex; father’s residential status; education; or community marginalization. Our findings demonstrate that despite greater community marginalization; living in an indigenous community is protective for stimulating parenting practices of indigenous mothers.BRII recipient: FernaldpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7g05c07garticleInternational Journal of Environmental Research and Public Healthvol 15, iss 1, 291660-4601oai:escholarship.org:ark:/13030/qt256389042018-01-12T22:05:27Zqt25638904Beyond the one-shot: Intensive workshops as a platform for engaging the library in digital humanitiesPowell, SusanKong, Nicole Ningning2017-07-10This article explores how librarian participation as instructors in week-long intensive classes—a common workshop format in digital humanities (DH)—can advance a variety of library objectives, while also uniquely supporting the DH community. Intensive workshops fall between the one-shot session and credit course formats more commonly found in library instruction. Drawing on case studies from Geographic Information Systems (GIS) instruction at DH institutes at the University of California Berkeley and Purdue University, the authors explore the origins of librarian involvement, course topics, pedagogy, and library services. Based on their instruction experiences in the DH summer institutes and student surveys, the authors argue that intensive instruction workshops provide a good potential platform for library involvement in DH.Digital humanitiesinformation literacyintensive instructionlibrariespedagogyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/25638904articleCollege and Undergraduate Librariesvol 24, iss 2-4, 516-5311545-2530oai:escholarship.org:ark:/13030/qt4p95v5d82018-01-12T20:38:05Zqt4p95v5d8Serial dependence in the perception of attractivenessXia, YeLeib, Allison YamanashiWhitney, David2016-12-22The perception of attractiveness is essential for choices of food, object, and mate preference. Like perception of other visual features, perception of attractiveness is stable despite constant changes of image properties due to factors like occlusion, visual noise, and eye movements. Recent results demonstrate that perception of low-level stimulus features and even more complex attributes like human identity are biased towards recent percepts. This effect is often called serial dependence. Some recent studies have suggested that serial dependence also exists for perceived facial attractiveness, though there is also concern that the reported effects are due to response bias. Here we used an attractiveness-rating task to test the existence of serial dependence in perceived facial attractiveness. Our results demonstrate that perceived face attractiveness was pulled by the attractiveness level of facial images encountered up to 6 s prior. This effect was not due to response bias and did not rely on the previous motor response. This perceptual pull increased as the difference in attractiveness between previous and current stimuli increased. Our results reconcile previously conflicting findings and extend previous work, demonstrating that sequential dependence in perception operates across different levels of visual analysis, even at the highest levels of perceptual interpretation.BRII recipient: Xiaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4p95v5d8articleJournal of Visionvol 16, iss 15, 281534-7362oai:escholarship.org:ark:/13030/qt77m6j50d2018-01-12T20:35:35Zqt77m6j50dSerial dependence promotes object stability during occlusionLiberman, AlinaZhang, KathyWhitney, David2016-12-22Object identities somehow appear stable and continuous over time despite eye movements, disruptions in visibility, and constantly changing visual input. Recent results have demonstrated that the perception of orientation, numerosity, and facial identity is systematically biased (i.e., pulled) toward visual input from the recent past. The spatial region over which current orientations or face identities are pulled by previous orientations or identities, respectively, is known as the continuity field, which is temporally tuned over the past several seconds (Fischer & Whitney, 2014). This perceptual pull could contribute to the visual stability of objects over short time periods, but does it also address how perceptual stability occurs during visual discontinuities? Here, we tested whether the continuity field helps maintain perceived object identity during occlusion. Specifically, we found that the perception of an oriented Gabor that emerged from behind an occluder was significantly pulled toward the random (and unrelated) orientation of the Gabor that was seen entering the occluder. Importantly, this serial dependence was stronger for predictable, continuously moving trajectories, compared to unpredictable ones or static displacements. This result suggests that our visual system takes advantage of expectations about a stable world, helping to maintain perceived object continuity despite interrupted visibility.BRII recipient: Zhangapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/77m6j50darticleJournal of Visionvol 16, iss 15, 161534-7362oai:escholarship.org:ark:/13030/qt37x979bp2018-01-12T20:30:42Zqt37x979bpNucleoid and cytoplasmic localization of small RNAs in
Escherichia coliSheng, HuanjieStauffer, Weston THussein, RazikaLin, ChrisLim, Han N2017-01-23Bacterial small RNAs (sRNAs) regulate protein production by binding to mRNAs and altering their translation and degradation. sRNAs are smaller than most mRNAs but larger than many proteins. Therefore it is uncertain whether sRNAs can enter the nucleoid to target nascent mRNAs. Here, we investigate the intracellular localization of sRNAs transcribed from plasmids in Escherichia coliusing RNA fluorescent in-situ hybridization. We found that sRNAs (GlmZ, OxyS, RyhB and SgrS) have equal preference for the nucleoid and cytoplasm, and no preferential localization at the cell membrane. We show using the gfp mRNA (encoding green fluorescent protein) that non-sRNAs can be engineered to have different proportions of nucleoid and cytoplasmic localization by altering their length and/or translation. The same localization as sRNAs was achieved by decreasing gfp mRNA length and translation, which suggests that sRNAs and other RNAs may enter the densely packed DNA of the nucleoid if they are sufficiently small. We also found that the Hfq protein, which binds sRNAs, minimally affects sRNA localization. Important implications of our findings for engineering synthetic circuits are: (i) sRNAs can potentially bind nascent mRNAs in the nucleoid, and (ii) localization patterns and distribution volumes of sRNAs can differ from some larger RNAs.BRII recipient: ShengpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/37x979bparticleNucleic Acids Researchvol 45, iss 5, gkx0230305-1048 1362-4962oai:escholarship.org:ark:/13030/qt3px582132018-01-12T20:27:51Zqt3px58213Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibianWang, Ian JShaffer, H. Bradley2017-07-01The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow, in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field-ecological studies. However, empirical assessments of the concordance between direct field-ecological and indirect population genetic studies of the same populations are uncommon in the literature. In this study, we investigate genetic isolation, rates of dispersal, and population sizes for the endangered California tiger salamander, Ambystoma californiense, across multiple breeding seasons in an intact vernal pool network. We then compare our molecular results to a previously published study based on multiyear, mark–recapture data from the same breeding sites. We found that field and genetic estimates of population size were only weakly correlated, but dispersal rates were remarkably congruent across studies and methods. In fact, dispersal probability functions derived from genetic data and traditional field-ecological data were a significant match, suggesting that either method can be used effectively to assess population connectivity. These results provide one of the first explicit tests of the correspondence between landscape genetic and field-ecological approaches to measuring functional population connectivity and suggest that even single-year genetic samples can return biologically meaningful estimates of natural dispersal and gene flow.BRII recipient: WangpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3px58213articleEvolutionary Applicationsvol 10, iss 6, 630-63917524571oai:escholarship.org:ark:/13030/qt93s1033j2018-01-12T20:24:31Zqt93s1033jThe perceived stability of scenes: serial dependence in ensemble representationsManassi, MauroLiberman, AlinaChaney, WesleyWhitney, David2017-05-16We are continuously surrounded by a noisy and ever-changing environment. Instead of analyzing all the elements in a scene, our visual system has the ability to compress an enormous amount of visual information into ensemble representations, such as perceiving a forest instead of every single tree. Still, it is unclear why such complex scenes appear to be the same from moment to moment despite fluctuations, noise, and discontinuities in retinal images. The general effects of change blindness are usually thought to stabilize scene perception, making us unaware of minor inconsistencies between scenes. Here, we propose an alternative, that stable scene perception is actively achieved by the visual system through global serial dependencies: the appearance of scene gist is sequentially dependent on the gist perceived in previous moments. To test this hypothesis, we used summary statistical information as a proxy for “gist” level, global information in a scene. We found evidence for serial dependence in summary statistical representations. Furthermore, we show that this kind of serial dependence occurs at the ensemble level, where local elements are already merged into global representations. Taken together, our results provide a mechanism through which serial dependence can promote the apparent consistency of scenes over time.BRII recipient: ManassipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/93s1033jarticleScientific Reportsvol 7, iss 12045-2322oai:escholarship.org:ark:/13030/qt0j45s0dp2018-01-12T20:21:15Zqt0j45s0dpListening to Communities: Mixed-Method Study of the Engagement of Disadvantaged Mothers and Pregnant Women With Digital Health TechnologiesGuendelman, SylviaBroderick, AndrewMlo, HmellisaGemmill, AlisonLindeman, David2017-07-05Background: US health care providers are increasingly demanding patient engagement with digital health technologies to enroll in care, access personal health information, communicate with providers, and monitor their own health. Such engagement may be difficult for disadvantaged populations who may have limited health literacy, time constraints, or competing priorities.Objective: We aimed to understand the extent of adoption and use of digital health tools and to identify key perceived psychological motivators of technology use among disadvantaged first-time pregnant women and mothers of young children.Methods: We recruited women from health organizations serving low-income communities in the Midwest and on the East and West coasts. A total of 92 women participated in 14 focus groups. During each session, we administered worksheets that measured 3 utilization outcomes: the number of recent Web-based health-seeking activities, current use of digital health-management practices (eg, accessing personal health information, communicating with providers, and scheduling appointments), and potential adoption of digital health-management tools among low users or nonusers. Responses to the worksheets and to a pre-focus group survey on demographics, technology access, and motivators of use were examined to create user profiles. Separate regression models identified the motivators (eHealth literacy, internal health orientation, and trust in digital information) associated with these outcomes. Qualitative data were incorporated to illustrate the worksheet responses. Results: Whereas 97% of the participants reported that they had searched for health information on the Internet in the past year, 42% did not engage in digital health-management practices. Among the low users and nonusers, 49% expressed interest in future adoption of digital health tools. Web-based health information-seeking activities were associated with digital health-management practices (P<.001). When controlling for covariates, eHealth literacy was positively correlated with the number of Web-based health-seeking activities (beta=.03, 95% CI 0.00-0.07). However, an internal health orientation was a much stronger correlate of digital health-management practices (beta=.13, 95% CI 0.02-0.24), whereas trust in digital information increased the odds of potential adoption (vs no adoption) in adjusted models (OR 5.21, 95% CI 0.84-32.53). Demographic characteristics were not important drivers of digital health use and few differences distinguished use among mothers and pregnant women.Conclusions: Seeking health information on the Internet may be an important gateway toward engaging in digital health-management practices. Notably, different consumer motivators influence digital health tool use. The relative contributions of each must be explored to design tools and interventions that enhance competencies for the management of self and child health among disadvantaged mothers and pregnant women. Unless we address disparities in digital health tool use, benefits from their use will accrue predominantly to individuals with the resources and skills to use technology effectively.BRII recipient: GuendelmanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0j45s0dparticleJournal of Medical Internet Researchvol 19, iss 7, e2401438-8871oai:escholarship.org:ark:/13030/qt7s69r1hf2018-01-12T20:15:34Zqt7s69r1hfClimate change, collections and the classroom: using big data to tackle big problemsLacey, Eileen AHammond, Talisin TWalsh, Rachel EBell, Kayce CEdwards, Scott VEllwood, Elizabeth RGuralnick, RobertIckert-Bond, Stefanie MMast, Austin RMcCormack, John EMonfils, Anna KSoltis, Pamela SSoltis, Douglas ECook, Joseph A2017-05-22Preparing students to explore, understand, and resolve societal challenges such as global climate change is an important task for evolutionary and ecological biologists that will require novel and innovative pedagogical approaches. Recent calls to reform undergraduate science education emphasize the importance of engaging students in inquiry-driven, active, and authentic learning experiences. We believe that the vast digital resources (i.e., “big data”) associated with natural history collections provide invaluable but underutilized opportunities to create such experiences for undergraduates in biology. Here, we describe an online, open-access educational module that we have developed that harnesses the power of collections-based information to introduce students to multiple conceptual and analytical elements of climate change, evolutionary, and ecological biology research. The module builds upon natural history specimens and data collected over the span of nearly a century in Yosemite National Park, California, to guide students through a series of exercises aimed at testing hypotheses regarding observed differences in response to climate change by two closely related and partially co-occurring species of chipmunks. The content of the module can readily be modified to meet the pedagogical goals and instructional levels of different courses while the analytical strategies outlined can be adapted to address a wide array of questions in evolutionary and ecological biology. In sum, we believe that specimen-based natural history data represent a powerful platform for reforming undergraduate instruction in biology. Because these efforts will result in citizens who are better prepared to understand complex biological relationships, the benefits of this approach to undergraduate education will have widespread benefits to society.BRII recipient: LaceypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7s69r1hfarticleEvolution: Education and Outreachvol 10, iss 11936-6426 1936-6434oai:escholarship.org:ark:/13030/qt2cd010v52018-01-11T18:29:02Zqt2cd010v5Solution nuclear magnetic resonance spectroscopy on a nanostructured diamond chipKehayias, P.Jarmola, A.Mosavian, N.Fescenko, I.Benito, F. MLaraoui, A.Smits, J.Bougas, L.Budker, D.Neumann, A.Brueck, S. R. JAcosta, V. M2017-08-04Sensors using nitrogen-vacancy centers in diamond are a promising tool for small-volume nuclear magnetic resonance (NMR) spectroscopy, but the limited sensitivity remains a challenge. Here we show nearly two orders of magnitude improvement in concentration sensitivity over previous nitrogen-vacancy and picoliter NMR studies. We demonstrate NMR spectroscopy of picoliter-volume solutions using a nanostructured diamond chip with dense, high-aspect-ratio nanogratings, enhancing the surface area by 15 times. The nanograting sidewalls are doped with nitrogen-vacancies located a few nanometers from the diamond surface to detect the NMR spectrum of roughly 1 pl of fluid lying within adjacent nanograting grooves. We perform 1H and 19F nuclear magnetic resonance spectroscopy at room temperature in magnetic fields below 50 mT. Using a solution of CsF in glycerol, we determine that 4 ± 2 × 1012 19F spins in a 1 pl volume can be detected with a signal-to-noise ratio of 3 in 1 s of integration.BRII recipient: JarmolapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2cd010v5articleNature Communicationsvol 8, iss 12041-1723oai:escholarship.org:ark:/13030/qt00c995sw2018-01-11T18:24:39Zqt00c995swOpportunities and Constraints in Characterizing Landscape Distribution of an Invasive Grass from Very High Resolution Multi-Spectral ImageryDronova, IrynaSpotswood, Erica NSuding, Katharine N2017-05-30Understanding spatial distributions of invasive plant species at early infestation stages is critical for assessing the dynamics and underlying factors of invasions. Recent progress in very high resolution remote sensing is facilitating this task by providing high spatial detail over whole-site extents that are prohibitive to comprehensive ground surveys. This study assessed the opportunities and constraints to characterize landscape distribution of the invasive grass medusahead (Elymus caput-medusae) in a ∼36.8 ha grassland in California, United States from 0.15m-resolution visible/near-infrared aerial imagery at the stage of late spring phenological contrast with dominant grasses. We compared several object-based unsupervised, single-run supervised and hierarchical approaches to classify medusahead using spectral, textural, and contextual variables. Fuzzy accuracy assessment indicated that 44–100% of test medusahead samples were matched by its classified extents from different methods, while 63–83% of test samples classified as medusahead had this class as an acceptable candidate. Main sources of error included spectral similarity between medusahead and other green species and mixing of medusahead with other vegetation at variable densities. Adding texture attributes to spectral variables increased the accuracy of most classification methods, corroborating the informative value of local patterns under limited spectral data. The highest accuracy across different metrics was shown by the supervised single-run support vector machine with seven vegetation classes and Bayesian algorithms with three vegetation classes; however, their medusahead allocations showed some “spillover” effects due to misclassifications with other green vegetation. This issue was addressed by more complex hierarchical approaches, though their final accuracy did not exceed the best single-run methods. However, the comparison of classified medusahead extents with field segments of its patches overlapping with survey transects indicated that most methods tended to miss and/or over-estimate the length of the smallest patches and under-estimate the largest ones due to classification errors. Overall, the study outcomes support the potential of cost-effective, very high-resolution sensing for the site-scale detection of infestation hotspots that can be customized to plant phenological schedules. However, more accurate medusahead patch delineation in mixed-cover grasslands would benefit from testing hyperspectral data and using our study’s framework to inform and constrain the candidate vegetation classes in heterogeneous locations.BRII recipient: DronovapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/00c995swarticleFrontiers in Plant Sciencevol 81664-462Xoai:escholarship.org:ark:/13030/qt8h35g5rn2018-01-11T18:20:40Zqt8h35g5rnConvergent evolution of Y chromosome gene content in fliesMahajan, ShivaniBachtrog, Doris2017-10-04Sex-chromosomes have formed repeatedly across Diptera from ordinary autosomes, and X-chromosomes mostly conserve their ancestral genes. Y-chromosomes are characterized by abundant gene-loss and an accumulation of repetitive DNA, yet the nature of the gene repertoire of fly Y-chromosomes is largely unknown. Here we trace gene-content evolution of Y-chromosomes across 22 Diptera species, using a subtraction pipeline that infers Y genes from male and female genome, and transcriptome data. Few genes remain on old Y-chromosomes, but the number of inferred Y-genes varies substantially between species. Young Y-chromosomes still show clear evidence of their autosomal origins, but most genes on old Y-chromosomes are not simply remnants of genes originally present on the proto-sex-chromosome that escaped degeneration, but instead were recruited secondarily from autosomes. Despite almost no overlap in Y-linked gene content in different species with independently formed sex-chromosomes, we find that Y-linked genes have evolved convergent gene functions associated with testis expression. Thus, male-specific selection appears as a dominant force shaping gene-content evolution of Y-chromosomes across fly species.BRII recipient: BachtrogpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8h35g5rnarticleNature Communicationsvol 8, iss 12041-1723oai:escholarship.org:ark:/13030/qt3v78s2rc2018-01-11T17:23:17Zqt3v78s2rcAdolescents' Perspectives on Personalized E-Feedback in the Context of Health Risk Behavior Screening for Primary Care: Qualitative StudyZieve, Garret GRichardson, Laura PKatzman, KatherineSpielvogle, HeatherWhitehouse, SandyMcCarty, Carolyn A2017-07-20Background: Electronic health screening tools for primary care present an opportunity to go beyond data collection to provide education and feedback to adolescents in order to motivate behavior change. However, there is limited research to guide feedback message development.Objective: The aim of this study was to explore youth perceptions of and preferences for receiving personalized feedback for multiple health risk behaviors and reinforcement for health promoting behaviors from an electronic health screening tool for primary care settings, using qualitative methodology.Methods: In total, 31 adolescents aged 13-18 years completed the screening tool, received the electronic feedback, and subsequently participated in individual, semistructured, qualitative interviews lasting approximately 60 min. Participants were queried about their overall impressions of the tool, perceptions regarding various types of feedback messages, and additional features that would help motivate health behavior change. Using thematic analysis, interview transcripts were coded to identify common themes expressed across participants.Results: Overall, the tool was well-received by participants who perceived it as a way to enhance—but not replace—their interactions with providers. They appreciated receiving nonjudgmental feedback from the tool and responded positively to information regarding the consequences of behaviors, comparisons with peer norms and health guidelines, tips for behavior change, and reinforcement of healthy choices. A small but noteworthy minority of participants dismissed the peer norms as not real or relevant and national guidelines as not valid or reasonable. When prompted for possible adaptations to the tool, adolescents expressed interest in receiving follow-up information, setting health-related goals, tracking their behaviors over time, and communicating with providers electronically between appointments.Conclusions: Adolescents in this qualitative study desired feedback that validates their healthy behavior choices and supports them as independent decision makers by neutrally presenting health information, facilitating goal setting, and offering ongoing technological supports.BRII recipient: ZievepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3v78s2rcarticleJournal of Medical Internet Researchvol 19, iss 7, e2611438-8871oai:escholarship.org:ark:/13030/qt45r438sc2018-01-11T17:06:05Zqt45r438scImproving the Measurement of Shared Cultural Schemas with Correlational Class Analysis: Theory and MethodBoutyline, Andrei2017-01-01Measurement of shared cultural schemas is a central methodological challenge for the sociology of culture. Relational Class Analysis (RCA) is a recently developed technique for identifying such schemas in survey data. However, existing work lacks a clear definition of such schemas, which leaves RCA’s accuracy largely unknown. Here, I build on the theoretical intuitions behind RCA to arrive at this definition. I demonstrate that shared schemas should result in linear dependencies between survey rows—the relationship usually measured with Pearson’s correlation. I thus modify RCA into a “Correlational Class Analysis” (CCA). When I compare the methods using a broad set of simulations, results show that CCA is reliably more accurate at detecting shared schemas than RCA, even in scenarios that substantially violate CCA’s assumptions. I find no evidence of theoretical settings where RCA is more accurate. I then revisit a previous RCA analysis of the 1993 General Social Survey musical tastes module. Whereas RCA partitioned these data into three schematic classes, CCA partitions them into four. I compare these results with a multiple-groups analysis in structural equation modeling and find that CCA’s partition yields greatly improved model fit over RCA. I conclude with a parsimonious framework for future work.BRII recipient: BoutylinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/45r438scarticleSociological Sciencevol 4, 353-39323306696oai:escholarship.org:ark:/13030/qt8jw4w84k2018-01-11T16:53:11Zqt8jw4w84kThe centrality of social ties to climate migration and mental healthTorres, Jacqueline MCasey, Joan A2017-07-06Climate change-related hazards and disasters, known to adversely impact physical and mental health outcomes, are also expected to result in human migration above current levels. Environmentally-motivated migration and displacement may lead to the disruption of existing social ties, with potentially adverse consequences for mobile populations as well as their family members who remain in places of origin. We propose that the disruption of social ties is a key mechanism by which climate-related migration may negatively impact mental health, in particular. Existing social ties may provide social and material resources that buffer mental health stressors related to both prolonged and acute climate events. Preparation for such events may also strengthen these same ties and protect mental health. Communities may leverage social ties, first to mitigate climate change, and second, to adapt and rebuild post-disaster in communities of origin. Additionally, social ties can inform migration decisions and destinations. For example, scholars have found that the drought-motivated adaptive migration of West African Fulbe herders only occurred because of the long-term development of social networks between migrants and non-migrants through trade and seasonal grazing. On the other hand, social ties do not always benefit mental health. Some migrants, including those from poor regions or communities with no formal safety net, may face considerable burden to provide financial and emotional resources to family members who remain in countries of origin. In destination communities, migrants often face significant social marginalization. Therefore, policies and programs that aim to maintain ongoing social ties among migrants and their family and community members may be critically important in efforts to enhance population resilience and adaptation to climate change and to improve mental health outcomes. Several online platforms, like Refugee Start Force, serve to integrate refugees by connecting migrants directly to people and services in destination communities. These efforts may increasingly draw upon novel technologies to support and maintain social networks in the context of population mobility due to climatic and other factors.BRII recipient: CaseypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8jw4w84karticleBMC Public Healthvol 17, iss 11471-2458oai:escholarship.org:ark:/13030/qt4j24p6g52018-01-11T16:48:25Zqt4j24p6g5An Intervention Using Gamification to Increase Human Immunodeficiency Virus and Sexually Transmitted Infection Screening Among Young Men Who Have Sex With Men in California: Rationale and Design of Stick To ItMejia, Christopher MAcland, DanielBuzdugan, RalucaGrimball, RevaNatoli, LaurenMcGrath, Mark RKlausner, Jeffrey DMcCoy, Sandra I2017-07-17Background: In the United States, young men who have sex with men (YMSM) remain disproportionately affected by human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs). Although routine HIV/STI screening is pivotal to the timely diagnosis of HIV and STIs, initiation of appropriate treatment, and reduced onward disease transmission, repeat screening is underused. Novel interventions that incorporate elements of games, an approach known as gamification, have the potential to increase routinization of HIV/STI screening among YMSM.Objective: The study aims to test the hypothesis that an incentive-based intervention that incorporates elements of gamification can increase routine HIV/STI screening among YMSM in California.Methods: The study consists of a formative research phase to develop the intervention and an implementation phase where the intervention is piloted in a controlled research setting. In the formative research phase, we use an iterative development process to design the intervention, including gathering information about the feasibility, acceptability, and expected effectiveness of potential game elements (eg, points, leaderboards, rewards). These activities include staff interviews, focus group discussions with members of the target population, and team meetings to strategize and develop the intervention. The final intervention is called Stick To It and consists of 3 components: (1) online enrollment, (2) Web-based activities consisting primarily of quizzes and a countdown “timer” to facilitate screening reminders, and (3) in-person activities that occur at 2 sexual health clinics. Participants earn points through the Web-based activities that are then redeemed for chances to win various prizes during clinic visits. The pilot study is a quasi-experimental study with a minimum of 60 intervention group participants recruited at the clinics, at community-based events, and online. We will compare outcomes in the intervention group with a historical control group consisting of individuals meeting the inclusion criteria who attended study clinics in the 12 months prior to intervention implementation. Eligible participants in the pilot study (1) are 18 to 26 years old, (2) were born or identify as male, 3) report male sexual partners, and 4) have a zip code of residence within defined areas in the vicinity of 1 of the 2 implementation sites. The primary outcome is repeat HIV/STI screening within 6 months.Results: This is an ongoing research study with initial results expected in the fourth quarter of 2017.Conclusions: We will develop and pilot test a gamification intervention to encourage YMSM to be regularly screened for HIV/STIs. The results from this research will provide preliminary evidence about the potential effectiveness of using gamification to amplify health-related behavioral change interventions. Further, the research aims to determine the processes that are essential to developing and implementing future health-related gamification interventions.BRII recipient: McCoypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4j24p6g5articleJMIR Research Protocolsvol 6, iss 7, e1401929-0748oai:escholarship.org:ark:/13030/qt6x07z2882018-01-11T16:42:59Zqt6x07z288Herbivores alter plant-wind interactions by acting as a point mass on leaves and by removing leaf tissueKothari, Adit RBurnett, Nicholas P2017-09-01In nature, plants regularly interact with herbivores and with wind. Herbivores can wound and alter the structure of plants, whereas wind can exert aerodynamic forces that cause the plants to flutter or sway. While herbivory has many negative consequences for plants, fluttering in wind can be beneficial for plants by facilitating gas exchange and loss of excess heat. Little is known about how herbivores affect plant motion in wind. We tested how the mass of an herbivore resting on a broad leaf of the tulip tree Liriodendron tulipifera, and the damage caused by herbivores, affected the motion of the leaf in wind. For this, we placed mimics of herbivores on the leaves, varying each herbivore's mass or position, and used high-speed video to measure how the herbivore mimics affected leaf movement and reconfiguration at two wind speeds inside a laboratory wind tunnel. In a similar setup, we tested how naturally occurring herbivore damage on the leaves affected leaf movement and reconfiguration. We found that the mass of an herbivore resting on a leaf can change that leaf's orientation relative to the wind and interfere with the ability of the leaf to reconfigure into a smaller, more streamlined shape. A large herbivore load slowed the leaf's fluttering frequency, while naturally occurring damage from herbivores increased the leaf's fluttering frequency. We conclude that herbivores can alter the physical interactions between wind and plants by two methods: (1) acting as a point mass on the plant while it is feeding and (2) removing tissue from the plant. Altering a plant's interaction with wind can have physical and physiological consequences for the plant. Thus, future studies of plants in nature should consider the effect of herbivory on plant–wind interactions, and vice versa.BRII recipient: BurnettpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6x07z288articleEcology and Evolutionvol 7, iss 17, 6884-689320457758oai:escholarship.org:ark:/13030/qt10k4x3bg2018-01-10T22:43:05Zqt10k4x3bgAutomated Text Messaging as an Adjunct to Cognitive Behavioral Therapy for Depression: A Clinical TrialAguilera, AdrianBruehlman-Senecal, EmmaDemasi, OriannaAvila, Patricia2017-05-08Background: Cognitive Behavioral Therapy (CBT) for depression is efficacious, but effectiveness is limited when implemented in low-income settings due to engagement difficulties including nonadherence with skill-building homework and early discontinuation of treatment. Automated messaging can be used in clinical settings to increase dosage of depression treatment and encourage sustained engagement with psychotherapy.Objectives: The aim of this study was to test whether a text messaging adjunct (mood monitoring text messages, treatment-related text messages, and a clinician dashboard to display patient data) increases engagement and improves clinical outcomes in a group CBT treatment for depression. Specifically, we aim to assess whether the text messaging adjunct led to an increase in group therapy sessions attended, an increase in duration of therapy attended, and reductions in Patient Health Questionnaire-9 item (PHQ-9) symptoms compared with the control condition of standard group CBT in a sample of low-income Spanish speaking Latino patients.Methods: Patients in an outpatient behavioral health clinic were assigned to standard group CBT for depression (control condition; n=40) or the same treatment with the addition of a text messaging adjunct (n=45). The adjunct consisted of a daily mood monitoring message, a daily message reiterating the theme of that week’s content, and medication and appointment reminders. Mood data and qualitative responses were sent to a Web-based platform (HealthySMS) for review by the therapist and displayed in session as a tool for teaching CBT skills.Results: Intent-to-treat analyses on therapy attendance during 16 sessions of weekly therapy found that patients assigned to the text messaging adjunct stayed in therapy significantly longer (median of 13.5 weeks before dropping out) than patients assigned to the control condition (median of 3 weeks before dropping out; Wilcoxon-Mann-Whitney z=−2.21, P=.03). Patients assigned to the text messaging adjunct also generally attended more sessions (median=6 sessions) during this period than patients assigned to the control condition (median =2.5 sessions), but the effect was not significant (Wilcoxon-Mann-Whitney z=−1.65, P=.10). Both patients assigned to the text messaging adjunct (B=−.29, 95% CI −0.38 to −0.19, z=−5.80, P<.001) and patients assigned to the control conditions (B=−.20, 95% CI −0.32 to −0.07, z=−3.12, P=.002) experienced significant decreases in depressive symptom severity over the course of treatment; however, the conditions did not significantly differ in their degree of symptom reduction.Conclusions: This study provides support for automated text messaging as a tool to sustain engagement in CBT for depression over time. There were no differences in depression outcomes between conditions, but this may be influenced by low follow-up rates of patients who dropped out of treatment.BRII recipient: AguilerapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/10k4x3bgarticleJournal of Medical Internet Researchvol 19, iss 5, e1481438-8871oai:escholarship.org:ark:/13030/qt3k0071k62018-01-10T22:35:46Zqt3k0071k6From Sea to Plate: The Role of Fish in a Sustainable DietSeto, KatherineFiorella, Kathryn J2017-03-16In the most recent U.S. Dietary Guidelines, the USDA Advisory Committee recommended for the first time the inclusion of sustainability considerations (DGA Committee, 2015). Since the U.S. Dietary Guidelines provide standards for nutrition and targets for federal and state food programs, explicitly incorporating sustainability would advance considerably discussions of food system sustainability (Merrigan et al., 2015). However, despite broad public support, sustainability 80 concerns were ultimately jettisoned from the 2015–2020 Guidelines (Secretary Vilsack and Burwell, 2015; US Department of Health and Human Services and US Department of Agriculture, 2015; Wood-Wright, 2016). Though much of the concern around incorporating sustainability has focused on animal agriculture, the sectors most heavily impacted by sustainability policies are arguably fisheries and aquaculture. Fish have been promoted as a sustainability strategy, providing nutritious alternatives to resource intensive livestock and poultry, and a concern, given the decline of many global fish stocks (Worm et al., 2006; Health Council of the Netherlands, 2011; FAO, 2014). Yet, we regularly overlook the origins and implications of this decline due to fragmented notions of our food resources. Resources that originate in our oceans, rivers, and lakes are almost entirely omitted in our conceptions of a sustainable food system.To understand the trade-offs from food production and consumption to sustainability, we must extend our understanding of food resources to conceive of fishery, agricultural, and livestock systems as integrally linked. Our failure to do so thus far has led to a disjointed understanding of our food system, contributed to inequalities in food access, and exacerbated overexploitation and environmental degradation. We argue here that fishery resources are of particular concern for sustainability yet often omitted in conceptions of our food system, and that such disjointed notions of food resources limit our ability to foster sustainable diets (Farmery et al., 2017).BRII recipient: SetopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3k0071k6articleFrontiers in Marine Sciencevol 42296-7745oai:escholarship.org:ark:/13030/qt1816t1wn2018-01-10T22:32:07Zqt1816t1wnComparative Autonomic Responses to Diagnostic Interviewing between Individuals with GAD, MDD, SAD and Healthy ControlsDiamond, Allison EFisher, Aaron J2017-01-11Dysregulation of the autonomic nervous system (ANS) has been well documented in individuals diagnosed with a range of psychological disorders, including generalized anxiety disorder (GAD) and major depressive disorder (MDD). Moreover, these disorders both confer an increased risk of cardiovascular disease—which may relate to increased sympathetic and decreased parasympathetic tone. Extant research has indicated a reduction in autonomic flexibility in GAD, and while reduced flexibility has also been seen in MDD, the specific physiological alterations have been more difficult to categorize due to methodological limitations, including high co-morbidity rates with anxiety disorders. Prior studies have largely assessed autonomic functioning in stress paradigms or at the trait level, yet to date, no research has investigated the ANS during a diagnostic interview, a ubiquitous task employed in both research and clinical settings. In this study we sought to identify physiological differences in both branches of the ANS across diagnostic categories in the context of a diagnostic interview. Participants (n = 82) were administered a structured clinical interview, during which heart rate (HR), respiratory sinus arrhythmia (RSA) and pre-ejection period (PEP) were recorded in participants carrying a diagnosis of GAD (n = 34), MDD (n = 22), Social Anxiety Disorder (SAD; n = 15) and healthy controls (n = 27). Person-specific linear regression models were employed to assess the level and slope for HR, RSA and PEP throughout the course of the interview. A multivariate analysis of variance (MANOVA) model was conducted to baseline differences in HR, RSA and PEP between diagnostic groups. Multiple regression models were then conducted to differences in slope of HR, RSA and PEP throughout the course of the interview amongst diagnostic groups, including both suppression and worry as moderators. Results indicated significant increases in RSA throughout the interview in MDD (p = 0.01) compared to healthy controls. Worry itself was found to be a more significant predictor of both decreased PEP (p = 0.02) and increased HR (p = 0.05). Suppression exhibited a dampening effect on individuals with worry and GAD, whereby those who suppressed had dampened HR responsiveness compared to those who did not suppress. These findings are consistent with existing literature supporting a decreased autonomic flexibility in certain psychological disorders, as well as indicate distinct physiological differences across certain transdiagnostic features of mood and anxiety disorders.BRII recipient: DiamondpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1816t1wnarticleFrontiers in Human Neurosciencevol 101662-5161oai:escholarship.org:ark:/13030/qt2f87d09w2018-01-10T22:30:31Zqt2f87d09wHealth impacts of chemical irritants used for crowd control: a systematic review of the injuries and deaths caused by tear gas and pepper sprayHaar, Rohini JIacopino, VincentRanadive, NikhilWeiser, Sheri DDandu, Madhavi2017-10-19Chemical irritants used in crowd control, such as tear gases and pepper sprays, are generally considered to be safe and to cause only transient pain and lacrimation. However, there are numerous reports that use and misuse of these chemicals may cause serious injuries. We aimed to review documented injuries from chemical irritants to better understand the morbidity and mortality associated with these weapons.BRII recipient: HaarpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2f87d09warticleBMC Public Healthvol 17, iss 11471-2458oai:escholarship.org:ark:/13030/qt96c6j4t92018-01-10T22:28:28Zqt96c6j4t9Graphene-enabled electron microscopy and correlated super-resolution microscopy of wet cellsWojcik, MichalHauser, MargaretLi, WanMoon, SeonahXu, Ke2015-06-11The application of electron microscopy to hydrated biological samples has been limited by high-vacuum operating conditions. Traditional methods utilize harsh and laborious sample dehydration procedures, often leading to structural artefacts and creating difficulties for correlating results with high-resolution fluorescence microscopy. Here, we utilize graphene, a single-atom-thick carbon meshwork, as the thinnest possible impermeable and conductive membrane to protect animal cells from vacuum, thus enabling high-resolution electron microscopy of wet and untreated whole cells with exceptional ease. Our approach further allows for facile correlative super-resolution and electron microscopy of wet cells directly on the culturing substrate. In particular, individual cytoskeletal actin filaments are resolved in hydrated samples through electron microscopy and well correlated with super-resolution results.BRII recipient: XupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/96c6j4t9articleNature Communicationsvol 6, 73842041-1723oai:escholarship.org:ark:/13030/qt9dk8f2v22018-01-10T22:28:14Zqt9dk8f2v2The Phytopathogen Pseudomonas syringae pv. tomato DC3000 Has Three High-Affinity Iron-Scavenging Systems Functional under Iron Limitation Conditions but Dispensable for PathogenesisJones, A. MWildermuth, M. C2011-03-25High-affinity iron scavenging through the use of siderophores is a well-established virulence determinant in mammalian pathogenesis. However, few examples have been reported for plant pathogens. Here, we use a genetic approach to investigate the role of siderophores in Pseudomonas syringae pv. tomato DC3000 (DC3000) virulence in tomato. DC3000, an agronomically important pathogen, has two known siderophores for high-affinity iron scavenging, yersiniabactin and pyoverdin, and we uncover a third siderophore, citrate, required for growth when iron is limiting. Though growth of a DC3000 triple mutant unable to either synthesize or import these siderophores is severely restricted in iron-limited culture, it is fully pathogenic. One explanation for this phenotype is that the DC3000 triple mutant is able to directly pirate plant iron compounds such as heme/hemin or iron-nicotianamine, and our data indicate that DC3000 can import iron-nicotianamine with high affinity. However, an alternative explanation, supported by data from others, is that the pathogenic environment of DC3000 (i.e., leaf apoplast) is not iron limited but is iron replete, with available iron of >1 μM. Growth of the triple mutant in culture is restored to wild-type levels by supplementation with a variety of iron chelates at >1 μM, including iron(III) dicitrate, a dominant chelate of the leaf apoplast. This suggests that lower-affinity iron import would be sufficient for DC3000 iron nutrition in planta and is in sharp contrast to the high-affinity iron-scavenging mechanisms required in mammalian pathogenesis. High-affinity iron scavenging through the use of siderophores is a well-established virulence determinant in mammalian pathogenesis. However, few examples have been reported for plant pathogens. Here, we use a genetic approach to investigate the role of siderophores in Pseudomonas syringae pv. tomato DC3000 (DC3000) virulence in tomato. DC3000, an agronomically important pathogen, has two known siderophores for high-affinity iron scavenging, yersiniabactin and pyoverdin, and we uncover a third siderophore, citrate, required for growth when iron is limiting. Though growth of a DC3000 triple mutant unable to either synthesize or import these siderophores is severely restricted in iron-limited culture, it is fully pathogenic. One explanation for this phenotype is that the DC3000 triple mutant is able to directly pirate plant iron compounds such as heme/hemin or iron-nicotianamine, and our data indicate that DC3000 can import iron-nicotianamine with high affinity. However, an alternative explanation, supported by data from others, is that the pathogenic environment of DC3000 (i.e., leaf apoplast) is not iron limited but is iron replete, with available iron of >1 μM. Growth of the triple mutant in culture is restored to wild-type levels by supplementation with a variety of iron chelates at >1 μM, including iron(III) dicitrate, a dominant chelate of the leaf apoplast. This suggests that lower-affinity iron import would be sufficient for DC3000 iron nutrition in planta and is in sharp contrast to the high-affinity iron-scavenging mechanisms required in mammalian pathogenesis. BRII recipient: Wildermuth (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9dk8f2v2articleJournal of Bacteriologyvol 193, iss 11, 2767-27750021-9193oai:escholarship.org:ark:/13030/qt9p6542z82018-01-10T22:28:05Zqt9p6542z8The Interaction of Deworming, Improved Sanitation, and Household Flooring with Soil-Transmitted Helminth Infection in Rural BangladeshBenjamin-Chung, JadeNazneen, ArifaHalder, Amal KHaque, RashidulSiddique, AbdullahUddin, Muhammed SalahKoporc, KimArnold, Benjamin FHubbard, Alan EUnicomb, LeanneLuby, Stephen PAddiss, David GColford, John M2015-12-01The combination of deworming and improved sanitation or hygiene may result in greater reductions in soil-transmitted helminth (STH) infection than any single intervention on its own. We measured STH prevalence in rural Bangladesh and assessed potential interactions among deworming, hygienic latrines, and household finished floors.BRII recipient: Benjamin-ChungpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9p6542z8articlePLOS Neglected Tropical Diseasesvol 9, iss 12, e00042561935-2735oai:escholarship.org:ark:/13030/qt4jm368z32018-01-10T22:27:49Zqt4jm368z3Invasion of non-native grasses causes a drop in soil carbon storage in California grasslandsKoteen, Laura EBaldocchi, Dennis DHarte, John2011-10-01Vegetation change can affect the magnitude and direction of global climate change via its effect on carbon cycling among plants, the soil and the atmosphere. The invasion of non-native plants is a major cause of land cover change, of biodiversity loss, and of other changes in ecosystem structure and function. In California, annual grasses from Mediterranean Europe have nearly displaced native perennial grasses across the coastal hillsides and terraces of the state. Our study examines the impact of this invasion on carbon cycling and storage at two sites in northern coastal California. The results suggest that annual grass invasion has caused an average drop in soil carbon storage of 40 Mg/ha in the top half meter of soil, although additional mechanisms may also contribute to soil carbon losses. We attribute the reduction in soil carbon storage to low rates of net primary production in non-native annuals relative to perennial grasses, a shift in rooting depth and water use to primarily shallow sources, and soil respiratory losses in non-native grass soils that exceed production rates. These results indicate that even seemingly subtle land cover changes can significantly impact ecosystem functions in general, and carbon storage in particular.BRII recipient: KoteenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4jm368z3articleEnvironmental Research Lettersvol 6, iss 4, 0440011748-9326oai:escholarship.org:ark:/13030/qt3xj2c5612018-01-10T22:27:34Zqt3xj2c561Dyon condensation in topological Mott insulatorsCho, Gil YoungXu, CenkeMoore, Joel EKim, Yong Baek2012-11-28We consider quantum phase transitions out of topological Mott insulators in which the ground state of the fractionalized excitations (fermionic spinons) is topologically non-trivial. The spinons in topological Mott insulators are coupled to an emergent compact U(1) gauge field with a so-called 'axion' term. We study the confinement transitions from the topological Mott insulator to broken symmetry phases, which may occur via the condensation of dyons. Dyons carry both 'electric' and 'magnetic' charges, and arise naturally in this system because the monopoles of the emergent U(1) gauge theory acquire gauge charge due to the axion term. It is shown that the dyon condensate, in general, induces simultaneous current and bond orders. To demonstrate this, we study the confined phase of the topological Mott insulator on the cubic lattice. When the magnetic transition is driven by dyon condensation, we identify the bond order as valence bond solid order and the current order as scalar spin chirality order. Hence, the confined phase of the topological Mott insulator is an exotic phase where the scalar spin chirality and the valence bond order coexist and appear via a single transition. We discuss the implications of our results for generic models of topological Mott insulators.BRII recipient: MoorepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3xj2c561articleNew Journal of Physicsvol 14, iss 11, 1150301367-2630oai:escholarship.org:ark:/13030/qt34j6d6kj2018-01-10T22:27:13Zqt34j6d6kjCodeHint: dynamic and interactive synthesis of code snippetsGalenson, JoelReames, PhilipBodik, RastislavHartmann, BjornSen, Koushik2014-05-31There are many tools that help programmers find code fragments, but most are inexpressive and rely on static information. We present a new technique for synthesizing code that is dynamic (giving accurate results and allowing programmers to reason about concrete executions), easy-to-use (supporting a wide range of correctness specifications), and interactive (allowing users to refine the candidate code snippets). Our implementation, which we call CodeHint, generates and evaluates code at runtime and hence can synthesize real-world Java code that involves I/O, reflection, native calls, and other advanced language features. We have evaluated CodeHint in two user studies and show that its algorithms are efficient and that it improves programmer productivity by more than a factor of two.BRII recipient: Bodik (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/34j6d6kjpublicationoai:escholarship.org:ark:/13030/qt1nc449cf2018-01-10T22:25:59Zqt1nc449cfFlowering time evolution is independent of serpentine tolerance in the California floraSchneider, Adam2017-04-01Comparative phylogenetic tests have been only recently applied to the many hypotheses about the role ultramafic (serpentine) soils play in the evolution and ecology of regional floras. An association between serpentine tolerance and early flowering has been observed at microevolutionary scales but not yet tested broadly across angiosperms. I used both hypothesis testing (phylogenetically independent contrasts) and model-selection approaches to compare published data of serpentine tolerance with flowering time using phylogenetic trees representing 24 clades of plants representing 27 genera and 17 families. A total of 126 independent contrasts revealed no significant difference in flowering times across all clades or within any one clade except for the Thelypodieae, in which flowering time of serpentine-tolerant lineages was later. Similarly, an Ornstein-Uhlenbeck model with one optimal flowering time was preferred over a model with separate optima depending on serpentine tolerance in nearly all genera. A phylogenetically un-corrected ANOVA found that serpentine-tolerant species have an earlier distribution of flowering times compared to both endemic and non-tolerant species, and median flowering times of non-tolerant species show a bimodal distribution. Therefore, I conclude that the long-term evolutionary responses of flowering time in a lineage that becomes tolerant of serpentine are variable across genera, with no significant overall bias toward earlier or later flowering. However, given that close relatives of serpentine-tolerant lineages tend to also flower relatively early, early flowering time may serve as an exaptation for serpentine tolerance. In combination with previously published ecotype studies, these results illustrate the eco-evolutionary scale dependence of flowering time.BRII recipient: SchneiderpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1nc449cfarticleEcospherevol 8, iss 4, e0176721508925oai:escholarship.org:ark:/13030/qt9vv862ms2017-11-08T22:22:13Zqt9vv862msTrends in Open Educational Resources in the Earth Sciences: Emerging Roles for the Academic LibraryTeplitzky, SamanthaWarren, Mea2017-10-24Students have cited the cost of textbooks and other class materials as a barrier to majoring in certain subjects, often in the sciences where costs are most prohibitive. In an effort to curb the high cost of textbooks on students, many universities are investigating the promotion and adoption of Open Educational Resources (OERs). These are free or low-cost materials such as textbooks or other resources that can be used as class material. This poster will examine the state of OERs in the Earth Sciences and give suggestions for adoption of OERs. Many institutions have concerns about the quality of materials for educational purposes and also encounter a lack of support for widespread adoption of many open resource materials. However, we will highlight a number of sources for high quality materials, many of which have already been adopted for use. There are also ways to use less expensive resources in your class without sacrificing quality, such as using popular geology books that cover core concepts instead of the typical textbook. This poster will examine current trends in OERs and present case studies demonstrating the use of OERs in the Earth Sciences at institutions who have supported the practice, as well as the possibilities for future use at other institutions with currently available resources. Survey data of librarians involved in OER efforts will be presented, as well as ideas of how your library can help you in adopting OERs in your classroom through licensing, support, and promotion.application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9vv862mspublicationoai:escholarship.org:ark:/13030/qt9mm6s1bs2017-11-07T02:34:51Zqt9mm6s1bsAssess, Annotate, Export: Quick Recipes for Archiving Your Personal Digital LifeEmmelhainz, CeliaWittenberg, Jamie2018-01-01Book information: "Scholars and scrapbookers alike need your help with saving their most important digital content. But how do you translate your professional knowledge as a librarian or archivist into practical skills that novices can apply to their own projects? The Complete Guide to Personal Archiving will show you the way, helping you break down archival concepts and best practices into teachable solutions for your patrons’ projects. Whether it’s a researcher needing to cull their most important email correspondence, or an empty-nester transferring home movies and photographs to more easily shared and mixed digital formats, this book will show you how to offer assistance, providing explanations of common terms in plain language; quick, non-technical solutions . . . guidance on how to archive Facebook posts and other social media . . . and additional resources for digging deep into personal digital archiving."personal digital archivingself-archivingdigital archivesrecords managementsocial media archives document managementcomputer file organizationbackupsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9mm6s1bspublicationoai:escholarship.org:ark:/13030/qt2mq851m02017-10-24T20:36:40Zqt2mq851m0Behavioral Expectations for the Mommy Librarian: The Successful Reference Transaction as Emotional LaborEmmelhainz, CeliaPappas, ErinSeale, Maura2017-10-01emotional laborreference librarianshipfeminist librarianshipaffective laborRUSA guidelinesreference servicesprofessional librariansbehavioral guidelineslibrarian statusethic of careapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2mq851m0publicationoai:escholarship.org:ark:/13030/qt7nt0d6bt2017-07-20T19:40:52Zqt7nt0d6btNo Legacy || Literatura Electrónica [academic poster for a library exhibition] Hamilton, AishaHennesy, CodyLie, StephanieOrtega, ÉlikaPotts, ClaudeSaum-Pascual, Alex2016-10-01The library exhibition No Legacy || Literatura Electrónica
at the University of California, Berkeley (March-September 2016) showcases eighteen works of electronic literature in Spanish, Portuguese, Catalan, and English, along with rare print works from Latin America, Spain, and Portugal. To address the unique challenges of exhibiting vintage interactive digital works on this scale in the century-old Doe Library, we collaborated with a team including members from ten campus units, with broad national and international support. In this poster we will illustrate how we forged new communities across the digital humanities to install an exhibit that bridges print and digital literary histories.The University Library selected and prepared print works for the exhibit, coordinated the digital user experience, upgraded facilities, provided IT support, and co-designed the exhibit with faculty curators from UC Berkeley and the University of Kansas. The Berkeley Center for New Media brought in a visiting artist to teach the course Archive, Install, Restore in Fall 2015 where undergraduate and graduate students designed and fabricated furniture to house the exhibit computers. To revive a work from a twenty-five year old 3.5” floppy disk the Digital Collections Unit in the Bancroft Library performed digital forensics and built a custom PC to meet the outdated system requirements in an exhibit-safe environment. The exhibit team also worked closely with the artists and authors to maintain the integrity of works that were originally created for a networked environment that no longer exists.The poster was presented at the Digital Frontiers conference in Houston in October 2016, the DH Faire at UC Berkeley in April 2017, and the Digital Initiatives Symposium at the University of San Diego in May 2017.http://nolegacy.berkeley.eduDigital HumanitiesElectronic Literature (E-Lit)Post-digitalLiterary archaeologyLibrary exhibitionsLatin AmericaSpainPortugalpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7nt0d6btpublicationoai:escholarship.org:ark:/13030/qt04q2f4232017-06-12T23:38:22Zqt04q2f423Evading Dam-Nation: Land Use History of the Lower Cosumnes River Watershed, ca. 1820-2016Johnson, MichelainaSahlins, PeterKlein, Kerwin Lee2017-06-112017 WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/04q2f423publicationoai:escholarship.org:ark:/13030/qt0wt5d3m62017-06-06T19:06:54Zqt0wt5d3m6An Examination of Forced Marriages and their Impact Under the Khmer RougeCong, StephanieEdwards, Penelope2016-12-01Honorable Mention 2017Lower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0wt5d3m6publicationoai:escholarship.org:ark:/13030/qt2885j9cm2017-06-06T19:03:23Zqt2885j9cm"Victory or not, we know this to be our duty": Pan-Islam in Early Revolutionary IranMousavi, BitaLaqueur, Thomas W.2017-04-012017 Honorable MentionUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2885j9cmpublicationoai:escholarship.org:ark:/13030/qt36s587v32017-06-06T18:56:13Zqt36s587v3Housewives Save the City from the "Cement Octopus"! Women's Activism in the San Francisco Freeway Revolts, 1955-1967Germain, JustinSahlins, Peter2017-04-012017 WinnerUpper Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/36s587v3publicationoai:escholarship.org:ark:/13030/qt00q8z1322017-05-17T16:49:21Zqt00q8z132"The River of Revenge": The Tension Between Farmers and the Federal Government in the Tula Valley, Mexico, 1992-2014Johnson, MichelainaPalomino, Pablo2014-12-012015 WinnerLower Divisionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/00q8z132publicationoai:escholarship.org:ark:/13030/qt7zz1t4hv2017-03-17T19:17:30Zqt7zz1t4hvInclusive, Participatory, and Research-Driven Approaches to Strategic Planning in Academic LibrariesQuigley, BrianEifler, DavidLoo, Jeffery L.2017-04-01Which strategic planning approaches can motivate academic library staff to adopt new organizational structures and adapt to emerging library paradigms? Over the past 10 years, the library at a major research university has undertaken three separate strategic planning initiatives employing significantly different approaches. Each approach has shaped the library and its relationship to the campus community in positive ways. This poster will show that academic libraries have several options for engaging in strategic planning including inclusive, participatory, and research-driven options that can suit different institutional time and resource constraints.In our first strategic planning initiative, we conducted a lengthy and highly inclusive process to educate library staff about emerging issues and inspire them to generate creative ideas from which library administration prioritized and implemented strategic directions. Our next planning initiative facilitated an expeditious self-study in which two core teams completed environmental scans and developed ideas for new service models and librarian roles. In our most recent planning initiative, liaison librarians conducted research-driven assessments of academic departments’ internal reviews to identify new services that addressed emerging faculty and student needs. Common threads among these approaches were their inclusiveness, the participation of diverse library staff to build internal expertise, and a systematic examination of the data on local contexts in order to promote the successful implementation of new initiatives.However, these approaches varied dramatically. Our comparison of these three strategic planning initiatives based on factors of participatory and inclusive information gathering techniques, research-driven methods, plan validation and implementation, time and resource constraints, outcomes, and challenges will show how these factors can be adapted in different institutional contexts.Important principles learned from the three strategic planning initiatives include:- staff participation, input, and buy-in are essential for successful implementation of new ideas, and there are a range of ways in which these can be achieved;- success depends on the time and resources committed to socializing and implementing identified priorities;- communication about strategic plans is a critical success factor - it needs to be early and frequent, coherent and two-way, evidence-based, and widespread through multiple channels- idea generation can be framed as research exercises to foster an open approach; this may be achieved through brainstorming, literature reviews, surveys, focus groups, or environmental scans;- strategic planning should be iterative, inclusive, and systematic, building upon priorities identified in one’s past strategic plans as well as those of peer institutions; and-early and intentional consultation with faculty is crucial for significant changes.strategic planningacademic librariesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7zz1t4hvpublicationoai:escholarship.org:ark:/13030/qt88g0t92f2017-02-10T20:03:48Zqt88g0t92fMicrobiological Evaluation of Household Drinking Water Treatment in Rural China Shows Benefits of Electric Kettles: A Cross-Sectional StudyCohen, AlasdairTao, YongLuo, QingZhong, GemeiRomm, JeffColford, John MRay, Isha2015-09-30In rural China ~607 million people drink boiled water, yet little is known about prevailing household water treatment (HWT) methods or their effectiveness. Boiling, the most common HWT method globally, is microbiologically effective, but household air pollution (HAP) from burning solid fuels causes cardiovascular and respiratory disease, and black carbon emissions exacerbate climate change. Boiled water is also easily re-contaminated. Our study was designed to identify the HWT methods used in rural China and to evaluate their effectiveness.Methods: We used a geographically stratified cross-sectional design in rural Guangxi Province to collect survey data from 450 households in the summer of 2013. Household drinking water samples were collected and assayed for Thermotolerant Coliforms (TTC), and physicochemical analyses were conducted for village drinking water sources. In the winter of 2013–2104, we surveyed 120 additional households and used remote sensors to corroborate self-reported boiling data.Findings: Our HWT prevalence estimates were: 27.1% boiling with electric kettles, 20.3% boiling with pots, 34.4% purchasing bottled water, and 18.2% drinking untreated water (for these analyses we treated bottled water as a HWT method). Households using electric kettles had the lowest concentrations of TTC (73% lower than households drinking untreated water). Multilevel mixed-effects regression analyses showed that electric kettles were associated with the largest Log10TTC reduction (-0.60, p<0.001), followed by bottled water (-0.45, p<0.001) and pots (-0.44, p<0.01). Compared to households drinking untreated water, electric kettle users also had the lowest risk of having TTC detected in their drinking water (risk ratio, RR = 0.49, 0.34–0.70, p<0.001), followed by bottled water users (RR = 0.70, 0.53–0.93, p<0.05) and households boiling with pots (RR = 0.74, 0.54–1.02, p = 0.06).Conclusion: As far as we are aware, this is the first HWT-focused study in China, and the first to quantify the comparative advantage of boiling with electric kettles over pots. Our results suggest that electric kettles could be used to rapidly expand safe drinking water access and reduce HAP exposure in rural China.BRI recipient: RaypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/88g0t92farticlePLOS ONEvol 10, iss 9, e01384511932-6203oai:escholarship.org:ark:/13030/qt2w4028422017-01-25T19:20:19Zqt2w402842Discrimination between competing model structures of biological systems in the presence of population heterogeneityMartin-Casas, MarcMesbah, Ali2016-01-01Computational models are useful for quantitative elucidation of the dynamical behavior of biological systems. Oftentimes, several competing models (i.e., hypotheses) are proposed to describe the underlying molecular mechanisms of a biological system. Selecting the most representative model is imperative for obtaining meaningful quantitative insights into the dynamics of the system of interest. However, discrimination between competing models poses a significant challenge due to heterogeneity that is intrinsic to biological systems. This paper demonstrates the effectiveness of a probabilistic approach to optimal experiment design for model discrimination in the presence of time-invariant, cell-to-cell differences within a cell population. The JAK2/STAT5 signaling pathway, which is involved in proliferation and differentiation of hematopoietic stem cells, is used as a case study.BRII recipient: Martin-CasaspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2w402842publicationoai:escholarship.org:ark:/13030/qt8sq6m1c12017-01-23T20:34:53Zqt8sq6m1c1Development of a Blue Emitting Calcium-Aluminate PhosphorKim, DooryKim, Han-EolKim, Chang-Hong2016-09-20We report methodological advances that enhance the phosphorescence efficiency of a blue-emitting calcium aluminate phosphor (CaAl2O4: Eu2+, Nd3+). The investigation of long-persistence blue-emitting phosphors is highly desirable due to their promising applications, such as white LEDs; however, the development of highly efficient blue-emitting phosphors is still challenging. Here, we have quantitatively characterized the phosphorescence properties of the blue-emitting phosphor CaAl2O4:Eu2+, Nd3+ with various compositions and directly related these properties to the quality of its luminescence. We optimized the composition of the activator Eu2+ and the co-activator Nd3+, the doping conditions with alkaline earth metals, alkali metals, and Si to create crystallographic distortions and, finally, the flux conditions to find the best parameters for bright and persistent blue-emitting phosphors. Our research has identified several doping compositions with good to excellent performance, with which we have demonstrated bright and persistent phosphors with afterglow characteristics superior to those of conventional phosphors.BRII recipient: KimpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8sq6m1c1articlePLOS ONEvol 11, iss 9, e01629201932-6203oai:escholarship.org:ark:/13030/qt7m93t1zz2017-01-20T00:44:13Zqt7m93t1zzRegulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAsSoheilypour, MMofrad, M.R.K.2016-11-02Export of messenger ribonucleic acids (mRNAs) into the cytoplasm is a fundamental step in gene regulation processes, which is meticulously quality controlled by highly efficient mechanisms in eukaryotic cells. Yet, it remains unclear how the aberrant mRNAs are recognized and retained inside the nucleus. Using a new modelling approach for complex systems, namely the agent-based modelling (ABM) approach, we develop a minimal model of the mRNA quality control (QC) mechanism. Our results demonstrate that regulation of the affinity of RNA-binding proteins (RBPs) to export receptors along with the weak interaction between the nuclear basket protein (Mlp1 or Tpr) and RBPs are the minimum requirements to distinguish and retain aberrant mRNAs. Our results show that the affinity between Tpr and RBPs is optimized to maximize the retention of aberrant mRNAs. In addition, we demonstrate how the length of mRNA affects the QC process. Since longer mRNAs spend more time in the nuclear basket to form a compact conformation and initiate their export, nuclear basket proteins could more easily capture and retain them inside the nucleus.BRII recipient: SoheilypourpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7m93t1zzarticleScientific Reportsvol 6oai:escholarship.org:ark:/13030/qt0sz4x3d42017-01-19T19:17:39Zqt0sz4x3d4sFlt Multivalent Conjugates Inhibit Angiogenesis and Improve Half-Life In VivoAltiok, Eda IBrowne, ShaneKhuc, EmilyMoran, Elizabeth PQiu, FangfangZhou, KeluSantiago-Ortiz, Jorge LMa, Jian-xingChan, Matilda FHealy, Kevin E2016-06-03Current anti-VEGF drugs for patients with diabetic retinopathy suffer from short residence time in the vitreous of the eye. In order to maintain biologically effective doses of drug for inhibiting retinal neovascularization, patients are required to receive regular monthly injections of drug, which often results in low patient compliance and progression of the disease. To improve the intravitreal residence time of anti-VEGF drugs, we have synthesized multivalent bioconjugates of an anti-VEGF protein, soluble fms-like tyrosine kinase-1 (sFlt) that is covalently grafted to chains of hyaluronic acid (HyA), conjugates that are termed mvsFlt. Using a mouse corneal angiogenesis assay, we demonstrate that covalent conjugation to HyA chains does not decrease the bioactivity of sFlt and that mvsFlt is equivalent to sFlt at inhibiting corneal angiogenesis. In a rat vitreous model, we observed that mvsFlt had significantly increased intravitreal residence time compared to the unconjugated sFlt after 2 days. The calculated intravitreal half-lives for sFlt and mvsFlt were 3.3 and 35 hours, respectively. Furthermore, we show that mvsFlt is more effective than the unconjugated form at inhibiting retinal neovascularization in an oxygen-induced retinopathy model, an effect that is most likely due to the longer half-life of mvsFlt in the vitreous. Taken together, our results indicate that conjugation of sFlt to HyA does not affect its affinity for VEGF and this conjugation significantly improves drug half-life. These in vivo results suggest that our strategy of multivalent conjugation could substantially improve upon drug half-life, and thus the efficacy of currently available drugs that are used in diseases such as diabetic retinopathy, thereby improving patient quality of life.BRII recipient: SiemonspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0sz4x3d4articlePLOS ONEvol 11, iss 6, e01559901932-6203oai:escholarship.org:ark:/13030/qt0c0813fg2017-01-19T17:30:20Zqt0c0813fgRisk factors for differential outcome following directly observed treatment (DOT) of slum and non-slum tuberculosis patients: a retrospective cohort studySnyder, Robert EMarlow, Mariel APhuphanich, Melissa ERiley, Lee WMaciel, Ethel Leonor Noia2016-09-20Brazil’s National Tuberculosis Control Program seeks to improve tuberculosis (TB) treatment in vulnerable populations. Slum residents are more vulnerable to TB due to a variety of factors, including their overcrowded living conditions, substandard infrastructure, and limited access to healthcare compared to their non-slum dwelling counterparts. Directly observed treatment (DOT) has been suggested to improve TB treatment outcomes among vulnerable populations, but the program’s differential effectiveness among urban slum and non-slum residents is not known.Methods: We retrospectively compared the impact of DOT on TB treatment outcome in residents of slum and non-slum census tracts in Rio de Janeiro reported to the Brazilian Notifiable Disease Database in 2010. Patient residential addresses were geocoded to census tracts from the 2010 Brazilian Census, which were identified as slum (aglomerados subnormais -AGSN) and non-slum (non-AGSN) by the Census Bureau. Homeless and incarcerated cases as well as those geocoded outside the city’s limits were excluded from analysis.Results: In 2010, 6,601 TB cases were geocoded within Rio de Janeiro; 1,874 (27.4 %) were residents of AGSN, and 4,794 (72.6 %) did not reside in an AGSN area. DOT coverage among AGSN cases was 35.2 % (n = 638), while the coverage in non-AGSN cases was 26.2 % (n = 1,234). Clinical characteristics, treatment, follow-up, cure, death and abandonment were similar in both AGSN and non-AGSN TB patients. After adjusting for covariates, AGSN TB cases on DOT had 1.67 (95 % CI: 1.17, 2.4) times the risk of cure, 0.61 (95 % CI: 0.41, 0.90) times the risk of abandonment, and 0.1 (95 % CI: 0.01, 0.77) times the risk of death from TB compared to non-AGSN TB cases not on DOT.Conclusion: While DOT coverage was low among TB cases in both AGSN and non-AGSN communities, it had a greater impact on TB cure rate in AGSN than in non-AGSN populations in the city of Rio de Janeiro.BRII recipient: SnyderpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0c0813fgarticleBMC Infectious Diseasesvol 16, iss 11471-2334oai:escholarship.org:ark:/13030/qt8f7218mq2017-01-18T18:32:42Zqt8f7218mqA figure gamePrice, Jason J2016-10-31This piece inhabits the history of anthropology in a nonteleological way to index (and advocate for) the joyfulness in prefiguration.[Due to unique formatting, this article is currently only available in PDF. – Eds.]BRII recipient: PricepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8f7218mqarticleHAU: Journal of Ethnographic Theoryvol 6, iss 2, 345-3872049-1115oai:escholarship.org:ark:/13030/qt9qm236r82017-01-03T18:34:56Zqt9qm236r8LSD1 Interacts with Zfp516 to Promote UCP1 Transcription and Brown Fat ProgramSambeat, AudreyGulyaeva, OlgaDempersmier, JonTharp, Kevin M.Stahl, AndreasPaul, Sarah M.Sul, Hei Sook2016-06-01Zfp516, a brown fat (BAT)-enriched and cold-inducible transcription factor, promotes transcription of UCP1 and other BAT-enriched genes for non-shivering thermogenesis. Here, we identify lysine-specific demethylase 1 (LSD1) as a direct binding partner of Zfp516. We show that, through interaction with Zfp516, LSD1 is recruited to UCP1 and other BAT-enriched genes, such as PGC1α, to function as a coactivator by demethylating H3K9. We also show that LSD1 is induced during brown adipogenesis and that LSD1 and its demethylase activity is required for the BAT program. Furthermore, we show that LSD1 ablation in mice using Myf5-Cre alters embryonic BAT development. Moreover, BAT-specific deletion of LSD1 via the use of UCP1-Cre impairs the BAT program and BAT development, making BAT resemble WAT, reducing thermogenic activity and promoting obesity. Finally, we demonstrate an in vivo requirement of the Zfp516-LSD1 interaction for LSD1 function in BAT gene activation.BRII recipient: SulpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9qm236r8articleCell Reportsvol 15, iss 11, 2536-254922111247oai:escholarship.org:ark:/13030/qt07c8x8892017-01-03T18:30:18Zqt07c8x889The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube FormationWeichsel, JulianGeissler, Phillip L2016-07-06The necessary biophysical conditions for the formation of tubular membrane protrusions by polymerizing actin filament bundles have not yet been fully understood. For this reason we introduce a novel grand canonical simulation model that describes stochastic polymerization of filaments against a fluctuating fluid membrane, while only considering a minimum set of biological proteins. Although still relatively simple and highly tractable, our model explicitly accounts for thermal fluctuations of membrane and filaments, stochastic and quantized polymerization dynamics at the filament tip, cooperativity of multiple filaments, and steric interactions between all model constituents in a physically realistic way. This approach enables us to go well beyond previous static zero-temperature theoretical considerations to filament bundling and explore the physical origins of membrane tube formation dynamics on length and time scales that are currently inaccessible to both experiments and atomistically detailed simulations. Our results suggest a membrane mediated dynamical transition from single filaments to cooperatively growing bundles as an important dynamical bottleneck to tubular protrusion.BRII recipient: GeisslerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/07c8x889articlePLOS Computational Biologyvol 12, iss 7, e10049821553-7358oai:escholarship.org:ark:/13030/qt0zv3d7662017-01-03T18:25:30Zqt0zv3d766Kinetic Study of Acetone-Butanol-Ethanol Fermentation in Continuous CultureBuehler, Edward AMesbah, Ali2016-08-03Acetone-butanol-ethanol (ABE) fermentation by clostridia has shown promise for industrial-scale production of biobutanol. However, the continuous ABE fermentation suffers from low product yield, titer, and productivity. Systems analysis of the continuous ABE fermentation will offer insights into its metabolic pathway as well as into optimal fermentation design and operation. For the ABE fermentation in continuous Clostridium acetobutylicum culture, this paper presents a kinetic model that includes the effects of key metabolic intermediates and enzymes as well as culture pH, product inhibition, and glucose inhibition. The kinetic model is used for elucidating the behavior of the ABE fermentation under the conditions that are most relevant to continuous cultures. To this end, dynamic sensitivity analysis is performed to systematically investigate the effects of culture conditions, reaction kinetics, and enzymes on the dynamics of the ABE production pathway. The analysis provides guidance for future metabolic engineering and fermentation optimization studies.BRII recipient: MesbahpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0zv3d766articlePLOS ONEvol 11, iss 8, e01582431932-6203oai:escholarship.org:ark:/13030/qt1pt8b5dj2017-01-03T18:22:15Zqt1pt8b5djThe Sapir-Whorf Hypothesis and Probabilistic Inference: Evidence from the Domain of ColorCibelli, EmilyXu, YangAusterweil, Joseph LGriffiths, Thomas LRegier, Terry2016-07-19The Sapir-Whorf hypothesis holds that our thoughts are shaped by our native language, and that speakers of different languages therefore think differently. This hypothesis is controversial in part because it appears to deny the possibility of a universal groundwork for human cognition, and in part because some findings taken to support it have not reliably replicated. We argue that considering this hypothesis through the lens of probabilistic inference has the potential to resolve both issues, at least with respect to certain prominent findings in the domain of color cognition. We explore a probabilistic model that is grounded in a presumed universal perceptual color space and in language-specific categories over that space. The model predicts that categories will most clearly affect color memory when perceptual information is uncertain. In line with earlier studies, we show that this model accounts for language-consistent biases in color reconstruction from memory in English speakers, modulated by uncertainty. We also show, to our knowledge for the first time, that such a model accounts for influential existing data on cross-language differences in color discrimination from memory, both within and across categories. We suggest that these ideas may help to clarify the debate over the Sapir-Whorf hypothesis.BRII recipient:RegierpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1pt8b5djarticlePLOS ONEvol 11, iss 7, e01587251932-6203oai:escholarship.org:ark:/13030/qt4gj4s3fp2017-01-03T18:14:20Zqt4gj4s3fpSimulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortiumDavies, NeilField, DawnGavaghan, DavidHolbrook, Sally JPlanes, SergeTroyer, MatthiasBonsall, MichaelClaudet, JoachimRoderick, GeorgeSchmitt, Russell JZettler, Linda AmaralBerteaux, VeroniqueBossin, Herve CCabasse, CharlotteCollin, AntoineDeck, JohnDell, TonyDunne, JenniferGates, RuthHarfoot, MikeHench, James LHopuare, MaraniaKirch, PatrickKotoulas, GeorgiosKosenkov, AlexKusenko, AlexLeichter, James JLenihan, HunterMagoulas, AntoniosMartinez, NeoMeyer, ChrisStoll, BenoitSwalla, BillieTartakovsky, Daniel MMurphy, Hinano TeavaiTuryshev, SlavaValdvinos, FernandaWilliams, RichWood, Spencer2016-03-17Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.BRII recipient: DaviespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4gj4s3fparticleGigaSciencevol 5, iss 12047-217Xoai:escholarship.org:ark:/13030/qt57k7f8pr2017-01-03T18:10:55Zqt57k7f8prIntravital Imaging Reveals Dynamics of Lymphangiogenesis and ValvulogenesisKang, Gyeong JinEcoiffier, TatianaTruong, TanYuen, DonLi, GuangyuLee, NaraeZhang, LiweiChen, Lu2016-01-20Lymphatic research signifies a field of rapid progression in recent years. Though lymphatic dysfunction has been found in a myriad of disorders, to date, few effective treatments are available for lymphatic diseases. It is therefore urgent to develop new experimental approaches and therapeutic protocols. The cornea offers an ideal site for lymphatic research due to its transparent nature, accessible location, and lymphatic-free but –inducible features. Moreover, we have recently discovered that corneal lymphatic vessels develop luminal valves as lymphangiogenesis proceeds. This tissue thus provides an optimal tool to study both lymphangiogenesis and valvulogenesis upon a pathological insult. In this paper, we show that the modified Prox-1-GFP mice carrying wildtype C57BL/6 background provide a valuable tool for intravital imaging of corneal lymphatic vessels and valves and can be used to study pathological lymphangiogenesis induced by various insults. Further, we demonstrate the multifaceted dynamics of lymphangiogenesis and valvulogenesis associated with transplantation, from the initiation to regression phases, and report several novel and critical phenomena and mechanisms that cannot be detected by conventional ex vivo approaches. Further investigation holds the great potential for divulging new mechanisms and therapeutic strategies for lymphangiogenesis and lymphangiogenesis-related diseases at various stages and inside or outside the eye.BRII recipient: KangpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/57k7f8prarticleScientific Reportsvol 6, 194592045-2322oai:escholarship.org:ark:/13030/qt6tp124pq2017-01-03T18:05:38Zqt6tp124pqDevelopment of a Conceptual Model and Survey Instrument to Measure Conscientious Objection to Abortion ProvisionHarris, Laura FlorenceAwoonor-Williams, John KokuGerdts, CaitlinGil Urbano, LauraGonzalez Velez, Ana CristinaHalpern, JodiPrata, NdolaBaffoe, Peter2016-10-13Conscientious objection to abortion, clinicians’ refusal to perform legal abortions because of their religious or moral beliefs, has been the subject of increasing debate among bioethicists, policymakers, and public health advocates in recent years. Conscientious objection policies are intended to balance reproductive rights and clinicians’ beliefs. However, in practice, clinician objection can act as a barrier to abortion access–impinging on reproductive rights, and increasing unsafe abortion and related morbidity and mortality. There is little information about conscientious objection from a medical or public health perspective. A quantitative instrument is needed to assess prevalence of conscientious objection and to provide insight on its practice. This paper describes the development of a survey instrument to measure conscientious objection to abortion provision.Methods: A literature review, and in-depth formative interviews with stakeholders in Colombia were used to develop a conceptual model of conscientious objection. This model led to the development of a survey, which was piloted, and then administered, in Ghana.Results: The model posits three domains of conscientious objection that form the basis for the survey instrument: 1) beliefs about abortion and conscientious objection; 2) actions related to conscientious objection and abortion; and 3) self-identification as a conscientious objector.Conclusions: The instrument is intended to be used to assess prevalence among clinicians trained to provide abortions, and to gain insight on how conscientious objection is practiced in a variety of settings. Its results can inform more effective and appropriate strategies to regulate conscientious objection.BRII recipient: NdolapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6tp124pqarticlePLOS ONEvol 11, iss 10, e01643681932-6203oai:escholarship.org:ark:/13030/qt0pf4g18f2017-01-03T18:00:11Zqt0pf4g18fResurrection of the genus Aphyllon for New World broomrapes (Orobanche s.l., Orobanchaceae)Schneider, Adam C2016-12-09Recent phylogenetic studies support a monophyletic clade of New World broomrapes (Orobanche sects. Gymnocaulis and Nothaphyllon) sister to the Old World genus Phelipanche. I place the New World taxa in the genus Aphyllon, propose 21 new combinations, and provide a list of currently accepted taxa.BRII recipient: SchneiderpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0pf4g18farticlePhytoKeysvol 75, 107-1181314-2003 1314-2011oai:escholarship.org:ark:/13030/qt9zq3c8662017-01-03T17:54:49Zqt9zq3c866Genetic Evidence of Contemporary Dispersal of the Intermediate Snail Host of Schistosoma japonicum: Movement of an NTD Host Is Facilitated by Land Use and Landscape ConnectivityHead, Jennifer RChang, HowardLi, QunnaHoover, Christopher MWilke, ThomasClewing, CatharinaCarlton, Elizabeth JLiang, SongLu, DingZhong, BoRemais, Justin V2016-12-15In China, human schistosomiasis is caused by infection with the parasitic blood fluke Schistosoma japonicum, which requires snail hosts as a lifecycle intermediary. Snail control efforts have been a key component of China’s schistosomiasis control program, which has reduced human infections from 11 million in the 1950s to approximately 115,000 today. However, schistosomiasis has re-emerged in some areas, and the range of areas infested by or suitable for snail hosts is expanding. Understanding how the physical structure of the environment influences snail migration could aid in understanding how intermediate host mobility contributes to persistence and/or re-emergence of schistosomiasis. Within the 29 sites sampled for snail hosts, we estimated that between 14–33% of snails were recent migrants from another site, and above average inter-site migration rates occurred between sites separated by up to 44 km. Greater landscape connectivity was associated with increased recent migration rates. Connectivity models considering land use patterns explained the largest proportion of the variance in migration rates between sites. An increase in the number of irrigation channels leading into the site was associated with an increase in a site’s propensity to both attract migrant snails and retain snails. Our findings have important implications for understanding and responding to the geographic spread of schistosomiasis.BRII recipient: RemaispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9zq3c866articlePLOS Neglected Tropical Diseasesvol 10, iss 12, e00051511935-2735oai:escholarship.org:ark:/13030/qt05g2068h2016-12-23T20:06:26Zqt05g2068hElectricity reform and sustainable development in ChinaWilliams, James HKahrl, Fredrich2008-10-01Reducing the environmental impact of supplying electricity is a key to China's sustainable development, and a focus of both domestic and international concerns with greenhouse gas emissions. The environmental performance of the electricity sector is strongly affected by its institutional arrangements: regulatory frameworks, wholesale markets, pricing mechanisms, planning and coordination, and enforcement and incentive mechanisms. These arrangements are set to change as electricity reforms inaugurated in 2002, but sidetracked by several years of supply shortages, are being resumed. In this paper we examine the impact of electricity reform on environmental sustainability by analyzing case studies of four environmental initiatives in the electricity sector: retirement of inefficient generators, installation of pollution control equipment, renewable energy development, and efforts to promote energy efficiency. We find that implementation of these policies falls short of objectives for two main underlying reasons: conflicting priorities between central and provincial governments, and ineffective regulation. Sustainability will be best served not by redoubling short-term supply-oriented, market-based reforms, but by better aligning central and provincial government incentives, and by developing competent, independent regulation at the provincial level. China's central government and sub-national governments in industrialized countries can both contribute to the latter goal.BRII recipient: KahrlpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/05g2068harticleEnvironmental Research Lettersvol 3, iss 4, 0440091748-9326oai:escholarship.org:ark:/13030/qt2pr8x5bm2016-12-23T20:03:42Zqt2pr8x5bmRecognition of the Hyaloperonospora parasitica effector ATR13 triggers resistance against oomycete, bacterial, and viral pathogensRentel, M. CLeonelli, L.Dahlbeck, D.Zhao, B.Staskawicz, B. J2008-01-15Phytopathogenic oomycetes cause some of the most devastating diseases affecting agricultural crops. Hyaloperonospora parasitica is a native oomycete pathogen of Arabidopsis and is related to other oomycete phytopathogens that include several species of Phytophthora, including the causal agent of potato late blight. Recently, four oomycete effector genes have been isolated, and several oomycete genomes have been sequenced. We have developed an efficient and genetically amenable system to test putative effector genes using the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. The H. parasitica effector protein ATR13 was delivered via P. syringae by fusing the ATR13 gene with the avrRpm1 type three secretion signal peptide, a bacterial sequence that allows transfer of proteins into the host cell through the bacterial type III secretion system. We also inserted ATR13 into the genome of the turnip mosaic virus, a single-stranded RNA virus. Our results show that delivery of ATR13 via the bacterial or viral pathogen triggers defense responses in plants containing the cognate resistance protein RPP13Nd, which restricts proliferation of both pathogens. Hence, recognition of ATR13 by RPP13 initiates defense responses that are effective against oomycete, bacterial and viral pathogens, pointing to a common defense mechanism. We have characterized regions of the RPP13Nd resistance protein that are essential for effector recognition and/or downstream signaling, using transient coexpression in Nicotiana benthamiana.BRII recipient: Staskawicz (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2pr8x5bmarticleProceedings of the National Academy of Sciencesvol 105, iss 3, 1091-10960027-8424 1091-6490oai:escholarship.org:ark:/13030/qt6825b8572016-12-23T20:02:48Zqt6825b857A review of the endemic Hawaiian Drosophilidae and their host plantsMagnacca, Karl NFoote, DavidO'Grady, Patrick M2008-03-17The Hawaiian Drosophilidae is one of the best examples of rapid speciation in nature. Nearly 1,000 species of endemicdrosophilids have evolved in situ in Hawaii since a single colonist arrived over 25 million years ago. A number of mech-anisms, including ecological adaptation, sexual selection, and geographic isolation, have been proposed to explain theevolution of this hyperdiverse group of species. Here, we examine the known ecological associations of 326 species ofendemic Hawaiian Drosophilidae in light of the phylogenetic relationships of these species. Our analysis suggests thatthe long-accepted belief of strict ecological specialization in this group does not hold for all taxa. While many specieshave a primary host plant family, females will also oviposit on non-preferred host plant taxa. Host shifting is fairly com-mon in some groups, especially the grimshawi and modified mouthparts species groups of Drosophila, and the Scapto-myza subgenus Elmomyza. Associations with types of substrates (bark, leaves, flowers) are more evolutionarilyconserved than associations with host plant families. These data not only give us insight into the role ecology has playedin the evolution of this large group, but can help in making decisions about the management of rare and endangered hostplants and the insects that rely upon them for survival.BRII recipient: O'Grady (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6825b857articleZootaxaiss 1728oai:escholarship.org:ark:/13030/qt7gt9d8s42016-12-23T20:01:51Zqt7gt9d8s4Climate Change and the Future of California's Endemic FloraLoarie, Scott R.Carter, Benjamin E.Hayhoe, KatharineMcMahon, SeanMoe, RichardKnight, Charles A.Ackerly, David D.2008-06-25The flora of California, a global biodiversity hotspot, includes 2387 endemic plant taxa. With anticipated climate change, we project that up to 66% will experience >80% reductions in range size within a century. These results are comparable with other studies of fewer species or just samples of a region's endemics. Projected reductions depend on the magnitude of future emissions and on the ability of species to disperse from their current locations. California's varied terrain could cause species to move in very different directions, breaking up present-day floras. However, our projections also identify regions where species undergoing severe range reductions may persist. Protecting these potential future refugia and facilitating species dispersal will be essential to maintain biodiversity in the face of climate change.BRII recipient: AckerlypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7gt9d8s4articlePLoS ONEvol 3, iss 6oai:escholarship.org:ark:/13030/qt8jq969xq2016-12-23T20:00:52Zqt8jq969xqHow students learn from multiple contexts and definitions: Proper time as a coordination classLevrini, OliviadiSessa, Andrea A2008-04-23This article provides an empirical analysis of a single classroom episode in which students reveal difficulties with the concept of proper time in special relativity but slowly make progress in improving their understanding. The theoretical framework used is “coordination class theory,” which is an evolving model of concepts and conceptual change. The paper will focus on showing to what extent and in what sense most of the conditions and events in the data corpus seem understandable from the point of view of coordination class theory. In addition, however, some extensions of the theory are implicated, although we argue that they are “natural” extensions, improvements that extend, but do not threaten, the core theory. In particular, we observe students articulately aligning different ways of determining proper time, and we conjecture, more generally, that such a process is strongly consistent with coordination class theory and likely to be productive in other cases of conceptual change. The empirical analysis is explicitly connected to the general issue of theories and theory development in studies of conceptual change.BRII recipient: diSessapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8jq969xqarticlePhysical Review Special Topics - Physics Education Researchvol 4, iss 11554-9178oai:escholarship.org:ark:/13030/qt0gf0h2m32016-12-23T19:59:35Zqt0gf0h2m3Quantitative Detection of Schistosoma japonicum Cercariae in Water by Real-Time PCRHung, Yuen WaiRemais, Justin2008-11-18In China alone, an estimated 30 million people are at risk of schistosomiasis, caused by the Schistosoma japonicum parasite. Disease has re-emerged in several regions that had previously attained transmission control, reinforcing the need for active surveillance. The environmental stage of the parasite is known to exhibit high spatial and temporal variability, and current detection techniques rely on a sentinel mouse method which has serious limitations in obtaining data in both time and space. Here we describe a real-time PCR assay to quantitatively detect S. japonicum cercariae in laboratory samples and in natural water that has been spiked with known numbers of S. japonicum. Multiple primers were designed and assessed, and the best performing set, along with a TaqMan probe, was used to quantify S. japonicum. The resulting assay was selective, with no amplification detected for Schistosoma mansoni, Schistosoma haematobium, avian schistosomes nor organisms present in non-endemic surface water samples. Repeated samples containing various concentrations of S. japonicum cercariae showed that the real-time PCR method had a strong linear correlation (R2 = 0.921) with light microscopy counts, and the detection limit was below the DNA equivalent of half of one cercaria. Various cercarial concentrations spiked in 1 liter of natural water followed by a filtration process produced positive detection from 93% of samples analyzed. The real-time PCR method performed well quantifying the relative concentrations of various spiked samples, although the absolute concentration estimates exhibited high variance across replicated samples. Overall, the method has the potential to be applied to environmental water samples to produce a rapid, reliable assay for cercarial location in endemic areas.BRII recipient: RemaispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0gf0h2m3articlePLoS Neglected Tropical Diseasesvol 2, iss 11, e3371935-2735oai:escholarship.org:ark:/13030/qt8k05x4v12016-12-23T19:58:29Zqt8k05x4v1Connectivity sustains disease transmission in environments with low potential for endemicity: modelling schistosomiasis with hydrologic and social connectivitiesGurarie, D.Seto, E. Y.W.2008-09-09Social interaction and physical interconnections between populations can influence the spread of parasites. The role that these pathways play in sustaining the transmission of parasitic diseases is unclear, although increasingly realistic metapopulation models are being used to study how diseases persist in connected environments. We use a mathematical model of schistosomiasis transmission for a distributed set of heterogeneous villages to show that the transport of parasites via social (host movement) and environmental (parasite larvae movement) pathways has consequences for parasite control, spread and persistence. We find that transmission can be sustained regionally throughout a group of connected villages even when individual village conditions appear not to support endemicity. Optimum transmission is determined by an interplay between different transport pathways, and not necessarily by those that are the most dispersive (e.g. disperse social contacts may not be optimal for transmission). We show that the traditional targeting of villages with high infection, without regard to village interconnections, may not lead to optimum control. These findings have major implications for effective disease control, which needs to go beyond considering local variations in disease intensity, to also consider the degree to which populations are interconnected.BRII recipient: Seto (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/8k05x4v1articleJournal of The Royal Society Interfacevol 6, iss 35, 495-5081742-5689 1742-5662oai:escholarship.org:ark:/13030/qt9sj6b7212016-12-23T19:57:31Zqt9sj6b721Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifaunaFuchs, JeromePons, Jean-MarcGoodman, Steven MBretagnolle, VincentMelo, MartimBowie, Rauri CCurrie, DavidSafford, RogerVirani, Munir ZThomsett, SimonHija, AlawiCruaud, CorinnePasquet, Eric2008-01-01The island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (Otus: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa.Results:Our analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles Otus insularis is genetically closer to the South-East Asian endemic O. sunia than to species from the Comoros and Madagascar. The Pemba Scops-owls O. pembaensis, often considered closely related to, if not conspecific with O. rutilus of Madagascar, is instead closely related to the African mainland O. senegalensis. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (O. sunia). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, O. pembaensis diverged from O. senegalensis about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages.Conclusion:Our analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species.BRII recipient: FuchspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9sj6b721articleBMC Evolutionary Biologyvol 8, iss 1, 1971471-2148oai:escholarship.org:ark:/13030/qt6w1351v42016-12-23T19:56:17Zqt6w1351v4Determination of the evaporation coefficient of D2ODrisdell, W. SCappa, C. DSmith, J. DSaykally, R. JCohen, R. C2008-11-20The evaporation rate of D2O has been determined by Raman thermometry of a droplet train (12–15 μm diameter) injected into vacuum (~10-5 torr). The cooling rate measured as a function of time in vacuum was fit to a model that accounts for temperature gradients between the surface and the core of the droplets, yielding an evaporation coefficient (γe) of 0.57±0.06. This is nearly identical to that found for H2O (0.62±0.09) using the same experimental method and model, and indicates the existence of a kinetic barrier to evaporation. The application of a recently developed transition-state theory (TST) model suggests that the kinetic barrier is due to librational and hindered translational motions at the liquid surface, and that the lack of an isotope effect is due to competing energetic and entropic factors. The implications of these results for cloud and aerosol particles in the atmosphere are discussed.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6w1351v4articleAtmospheric Chemistry and Physicsvol 8, iss 22, 6699-67061680-7324oai:escholarship.org:ark:/13030/qt5fn834bb2016-12-23T19:55:22Zqt5fn834bbProduction and detection of atomic hexadecapole at Earth's magnetic fieldAcosta, V. MAuzinsh, M.Gawlik, W.Grisins, P.Higbie, J. MJackson Kimball, D. FKrzemien, L.Ledbetter, M. PPustelny, S.Rochester, S. MYashchuk, V. VBudker, D.2008-07-15Optical magnetometers measure magnetic fields with extremely high precision and without cryogenics. However, at geomagnetic fields, important for applications from landmine removal to archaeology, they suffer from nonlinear Zeeman splitting, leading to systematic dependence on sensor orientation. We present experimental results on a method of eliminating this systematic error, using the hexadecapole atomic polarization moment. In particular, we demonstrate selective production of the atomic hexadecapole moment at Earth’s magnetic field and verify its immunity to nonlinear Zeeman splitting. This technique promises to eliminate directional errors in all-optical atomic magnetometers, potentially improving their measurement accuracy by several orders of magnitude.BRII recipient: BudkerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5fn834bbarticleOptics Expressvol 16, iss 15, 114231094-4087oai:escholarship.org:ark:/13030/qt6x8497t62016-12-23T19:31:40Zqt6x8497t6Parking infrastructure: energy, emissions, and automobile life-cycle environmental accountingChester, MikhailHorvath, ArpadMadanat, Samer2010-07-01The US parking infrastructure is vast and little is known about its scale and environmental impacts. The few parking space inventories that exist are typically regionalized and no known environmental assessment has been performed to determine the energy and emissions from providing this infrastructure. A better understanding of the scale of US parking is necessary to properly value the total costs of automobile travel. Energy and emissions from constructing and maintaining the parking infrastructure should be considered when assessing the total human health and environmental impacts of vehicle travel. We develop five parking space inventory scenarios and from these estimate the range of infrastructure provided in the US to be between 105 million and 2 billion spaces. Using these estimates, a life-cycle environmental inventory is performed to capture the energy consumption and emissions of greenhouse gases, CO, SO2, NOX, VOC (volatile organic compounds), and PM10 (PM: particulate matter) from raw material extraction, transport, asphalt and concrete production, and placement (including direct, indirect, and supply chain processes) of space construction and maintenance. The environmental assessment is then evaluated within the life-cycle performance of sedans, SUVs (sports utility vehicles), and pickups. Depending on the scenario and vehicle type, the inclusion of parking within the overall life-cycle inventory increases energy consumption from 3.1 to 4.8 MJ by 0.1–0.3 MJ and greenhouse gas emissions from 230 to 380 g CO2e by 6–23 g CO2e per passenger kilometer traveled. Life-cycle automobile SO2 and PM10 emissions show some of the largest increases, by as much as 24% and 89% from the baseline inventory. The environmental consequences of providing the parking spaces are discussed as well as the uncertainty in allocating paved area between parking and roadways.BRII recipient: ChesterpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6x8497t6articleEnvironmental Research Lettersvol 5, iss 3, 0340011748-9326oai:escholarship.org:ark:/13030/qt246136st2016-12-23T19:23:24Zqt246136stA capping-independent function of MePCE in stabilizing 7SK snRNA and facilitating the assembly of 7SK snRNPXue, Y.Yang, Z.Chen, R.Zhou, Q.2009-11-11The 7SK snRNP represents a major reservoir of activity where P-TEFb, a general transcription factor key for RNA polymerase II elongation, can be withdrawn to promote gene expression, cell growth and development. Within this complex, 7SK snRNA is a central scaffold that coordinates key protein–protein interactions and maintains P-TEFb in an inactive state. Although the stability of 7SK directly affects the amount of active P-TEFb in vivo, relatively little is known about how it is maintained and how the 7SK methylphosphate capping enzyme MePCE and LARP7, a La-related protein associated with the 3′-poly(U) of 7SK, contribute to this process. Here, we show that 7SK is capped by the LARP7-free MePCE and in probably a co-transcriptional manner prior to its sequestration into 7SK snRNP. However, upon interacting with LARP7 within 7SK snRNP, MePCE loses its capping activity, probably due to the occlusion of its catalytic center by LARP7. Despite its lack of capping activity in 7SK snRNP, MePCE displays a capping-independent function to promote the LARP7–7SK interaction, which in turn stabilizes 7SK and facilitates the assembly of a stable MePCE–LARP7–7SK subcomplex. Our data indicate that MePCE and LARP7 act cooperatively to stabilize 7SK and maintain the integrity of 7SK snRNP.BRII recipient: ZhoupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/246136starticleNucleic Acids Researchvol 38, iss 2, 360-3690305-1048 1362-4962oai:escholarship.org:ark:/13030/qt29r3426k2016-12-23T19:22:28Zqt29r3426kAvian Incubation Inhibits Growth and Diversification of Bacterial Assemblages on EggsShawkey, Matthew DFirestone, Mary KBrodie, Eoin LBeissinger, Steven R2009-02-19Microbial infection is a critical source of mortality for early life stages of oviparous vertebrates, but parental defenses against infection are less well known. Avian incubation has been hypothesized to reduce the risk of trans-shell infection by limiting microbial growth of pathogenic bacteria on eggshells, while enhancing growth of commensal or beneficial bacteria that inhibit or competitively exclude pathogens. We tested this hypothesis by comparing bacterial assemblages on naturally incubated and experimentally unincubated eggs at laying and late incubation using a universal 16S rRNA microarray containing probes for over 8000 bacterial taxa. Before treatment, bacterial assemblages on individual eggs from both treatment groups were dissimilar to one another, as measured by clustering in non-metric dimensional scaling (NMDS) ordination space. After treatment, assemblages of unincubated eggs were similar to one another, but those of incubated eggs were not. Furthermore, assemblages of unincubated eggs were characterized by high abundance of six indicator species while incubated eggs had no indicator species. Bacterial taxon richness remained static on incubated eggs, but increased significantly on unincubated eggs, especially in several families of Gram-negative bacteria. The relative abundance of individual bacterial taxa did not change on incubated eggs, but that of 82 bacterial taxa, including some known to infect the interior of eggs, increased on unincubated eggs. Thus, incubation inhibits all of the relatively few bacteria that grow on eggshells, and does not appear to promote growth of any bacteria.BRII recipient: BeissingerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/29r3426karticlePLoS ONEvol 4, iss 2, e45221932-6203oai:escholarship.org:ark:/13030/qt8jh438bb2016-12-23T19:21:23Zqt8jh438bbGlobal warming potential of pavementsSantero, Nicholas JHorvath, Arpad2009-09-01Pavements comprise an essential and vast infrastructure system supporting our transportation network, yet their impact on the environment is largely unquantified. Previous life-cycle assessments have only included a limited number of the applicable life-cycle components in their analysis. This research expands the current view to include eight different components: materials extraction and production, transportation, onsite equipment, traffic delay, carbonation, lighting, albedo, and rolling resistance. Using global warming potential as the environmental indicator, ranges of potential impact for each component are calculated and compared based on the information uncovered in the existing research. The relative impacts between components are found to be orders of magnitude different in some cases. Context-related factors, such as traffic level and location, are also important elements affecting the impacts of a given component. A strategic method for lowering the global warming potential of a pavement is developed based on the concept that environmental performance is improved most effectively by focusing on components with high impact potentials. This system takes advantage of the fact that small changes in high-impact components will have more effect than large changes in low-impact components.BRII recipient: SanteropubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8jh438bbarticleEnvironmental Research Lettersvol 4, iss 3, 0340111748-9326oai:escholarship.org:ark:/13030/qt6rq2959b2016-12-23T19:18:56Zqt6rq2959bDramatic declines in neotropical salamander populations are an important part of the global amphibian crisisRovito, S. MParra-Olea, G.Vasquez-Almazan, C. RPapenfuss, T. JWake, D. B2009-02-09We document major declines of many species of salamanders at several sites in Central America and Mexico, with emphasis on the San Marcos region of Guatemala, one of the best studied and most diverse salamander communities in the Neotropics. Profound declines of several formerly abundant species, including 2 apparent extinctions, are revealed. Terrestrial microhabitat specialists at mid- to high elevations have declined more than microhabitat generalists. These terrestrial microhabitat specialists have largely disappeared from multiple sites in western Guatemala, including in well-protected areas, suggesting that the phenomenon cannot be explained solely by localized habitat destruction. Major declines in southern Mexican plethodontid salamanders occurred in the late 1970s to early 1980s, concurrent with or preceding many reported frog declines. The species in decline comprise several major evolutionary lineages of tropical salamanders, underscoring that significant portions of the phylogenetic diversity of Neotropical salamanders are at risk. Our results highlight the urgent need to document and understand Neotropical salamander declines as part of the larger effort to conserve global amphibian diversity.BRII recipient: Wake (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6rq2959barticleProceedings of the National Academy of Sciencesvol 106, iss 9, 3231-32360027-8424 1091-6490oai:escholarship.org:ark:/13030/qt7pk093zv2016-12-23T19:18:03Zqt7pk093zvLeveraging Rural Energy Investment for Parasitic Disease Control: Schistosome Ova Inactivation and Energy Co-Benefits of Anaerobic Digesters in Rural ChinaRemais, JustinChen, LinSeto, Edmund2009-03-18Cooking and heating remain the most energy intensive activities among the world's poor, and thus improved access to clean energies for these tasks has been highlighted as a key requirement of attaining the major objectives of the UN Millennium Development Goals. A move towards clean energy technologies such as biogas systems (which produce methane from human and animal waste) has the potential to provide immediate benefits for the control of neglected tropical diseases. Here, an assessment of the parasitic disease and energy benefits of biogas systems in Sichuan Province, China, is presented, highlighting how the public health sector can leverage the proliferation of rural energy projects for infectious disease control. Methodology/Findings: First, the effectiveness of biogas systems at inactivating and removing ova of the human parasite Schistosoma japonicum is experimentally evaluated. Second, the impact of biogas infrastructure on energy use and environmental quality as reported by surveyed village populations is assessed, as is the community acceptance of the technology. No viable eggs were recovered in the effluent collected weekly from biogas systems for two months following seeding with infected stool. Less than 1% of ova were recovered viable from a series of nylon bags seeded with ova, a 2-log removal attributable to biochemical inactivation. More than 90% of Ascaris lumbricoides ova (used as a proxy for S. japonicum ova) counted at the influent of two biogas systems were removed in the systems when adjusted for system residence time, an approximate 1-log removal attributable to sedimentation. Combined, these inactivation/removal processes underscore the promise of biogas infrastructure for reducing parasite contamination resulting from nightsoil use. When interviewed an average of 4 years after construction, villagers attributed large changes in fuel usage to the installation of biogas systems. Household coal usage decreased by 68%, wood by 74%, and crop waste by 6%. With reported energy savings valued at roughly 600 CNY per year, 2–3 years were required to recoup the capital costs of biogas systems. In villages without subsidies, no new biogas systems were implemented. Conclusions: Sustainable strategies that integrate rural energy needs and sanitation offer tremendous promise for long-term control of parasitic diseases, while simultaneously reducing energy costs and improving quality of life. Government policies can enhance the financial viability of such strategies by introducing fiscal incentives for joint sanitation/sustainable energy projects, along with their associated public outreach and education programs.BRII recipient: SetopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7pk093zvarticlePLoS ONEvol 4, iss 3, e48561932-6203oai:escholarship.org:ark:/13030/qt0mk723052016-12-23T19:06:56Zqt0mk72305Returning home: forced conscription, reintegration, and mental health status of former abductees of the Lord's Resistance Army in northern UgandaPham, Phuong NVinck, PatrickStover, Eric2009-01-01Since the late 1980s, the Lord's Resistance Army (LRA), a spiritualist rebel group in northern Uganda, has killed and mutilated thousands of civilians and abducted an estimated 52,000 to 75,000 people to serve as soldiers, porters, and sex slaves for its commanders. This study examines the types of violence to which former abductees have been exposed and the extent to which these acts have affected their psychological well-being.Methods:This is a cross-sectional study of 2,875 individuals selected through a multi-stage stratified cluster sampling design conducted in 8 districts of northern Uganda. Multivariate logistic regressions were performed with symptoms for Post-traumatic Stress Disorder (PTSD) and depression as the main outcome measures.Results:One-third of the respondents (33%) self-reported having experienced abduction (49% among the Acholi, the largest tribal group in northern Uganda). Over half (56%) of all the respondents and over two-thirds of those who experienced abduction met the criteria for symptoms of post-traumatic stress disorder (PTSD). Multivariate analysis shows that several factors increased the risk of former LRA abductees developing symptoms of PTSD. These factors included gender (females were more susceptible than males), being a member of the Acholi ethnic group, participating in or witnessing a cumulative number of traumatic events, and encountering difficulties re-integrating into communities after abduction. Factors associated with increased risk of meeting criteria for symptoms of depression included older age of males at the time of abduction, lower score on social relationship scale, high incidence of general traumatic event exposure, high incidence of forced acts of violence, and problems reintegrating into communities after abduction.Conclusion:Abduction and forced conscription of civilians has affected the psychological well-being of a significant number of northern Ugandans. The sources of psychological trauma are multiple, ranging from witnessing to being forced to commit violent acts, and compounded by prolonged exposure to violence, often for months or years. Community-based mental health care services and reintegration programs are needed to facilitate the reintegration of former abductees back into their communities.BRII recipient: PhampubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0mk72305articleBMC Psychiatryvol 9, iss 1, 231471-244Xoai:escholarship.org:ark:/13030/qt1nx1c4sx2016-12-23T19:03:39Zqt1nx1c4sxAirborne observations of total RONO2: new constraints on the yield and lifetime of isoprene nitratesPerring, A. EBertram, T. HWooldridge, P. JFried, A.Heikes, B. GDibb, J.Crounse, J. DWennberg, P. OBlake, N. JBlake, D. RBrune, W. HSingh, H. BCohen, R. C2009-02-23Formation of isoprene nitrates (INs) is an important free radical chain termination step ending production of ozone and possibly affecting formation of secondary organic aerosol. Isoprene nitrates also represent a potentially large, unmeasured contribution to OH reactivity and are a major pathway for the removal of nitrogen oxides from the atmosphere. Current assessments indicate that formation rates of isoprene nitrates are uncertain to a factor of 2–3 and the subsequent fate of isoprene nitrates remains largely unconstrained by laboratory, field or modeling studies. Measurements of total alkyl and multifunctional nitrates (ΣANs), NO2, total peroxy nitrates (ΣPNs), HNO3, CH2O, isoprene and other VOC were obtained from the NASA DC-8 aircraft during summer 2004 over the continental US during the INTEX-NA campaign. These observations represent the first characterization of ΣANs over a wide range of land surface types and in the lower free troposphere. ΣANs were a significant, 12–20%, fraction of NOy throughout the experimental domain and ΣANs were more abundant when isoprene was high. We use the observed hydrocarbon species to calculate the relative contributions of ΣAN precursors to their production. These calculations indicate that isoprene represents at least three quarters of the ΣAN source in the summertime continental boundary layer of the US. An observed correlation between ΣANs and CH2O is used to place constraints on nitrate yields from isoprene oxidation, atmospheric lifetimes of the resulting nitrates and recycling efficiencies of nitrates during subsequent oxidation. We find reasonable fits to the data using sets of production rates, lifetimes and recycling efficiencies of INs as follows (4.4%, 16 h, 97%), (8%, 2.5 h, 79%) and (12%, 95 min, 67%). The analysis indicates that the lifetime of ΣANs as a pool of compounds is considerably longer than the lifetime of the individual isoprene nitrates to reaction with OH, implying that the organic nitrate functionality is at least partially maintained through a second oxidation cycle.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1nx1c4sxarticleAtmospheric Chemistry and Physicsvol 9, iss 4, 1451-14631680-7324oai:escholarship.org:ark:/13030/qt6p01751j2016-12-23T19:02:33Zqt6p01751jNitrogen oxide chemistry in an urban plume: investigation of the chemistry of peroxy and multifunctional organic nitrates with a Lagrangian modelPerez, I. MLaFranchi, B. WCohen, R. C2009-12-16Air quality in the outflow from urban centers affects millions of people, as well as, natural and managed ecosystems downwind. In locations where there are large sources of biogenic VOCs downwind of urban centers, the outflow is characterized by a high VOC reactivity due to biogenic emissions and low NOx. However most field and chamber studies have focused on limiting cases of high NOx or of near zero NOx. Recent measurements of a wide suite of VOCs, O3 and meteorological parameters at several locations within the Sacramento urban plume have provided a detailed benchmark for testing our understanding of chemistry in a plume transitioning from high NOx to low NOx and high VOC reactivity. As an additional simplification, the strong mountain valley circulation in the region makes this urban plume a physical realization of a nearly idealized Lagrangian plume. Here, we describe a model of this plume. We use a Lagrangian model representing chemistry based on the Master Chemical Mechanism (MCM) v3.1 along with mixing and deposition. We discuss the effects of entrainment of background air, the branching ratio for the production of isoprene nitrates and the effects of soil NOx emissions on the composition of the evolving plume. The model predicts that after 2–3 h of chemical processing only 45% of the peroxynitrates (ΣPNs) are PAN and that most (69%) RONO2 are secondary alkyl nitrate products of the reaction of OH with RONO2. We find the model is more consistent with the observations if: a) the yield of ΣPNs from large and multi-functional aldehydes is close to zero; and b) the reaction between OH and RONO2 produces multifunctional nitrates as opposed to either HNO3 or NO2 as is typical in most currently adopted reaction mechanisms. Model results also show that adding NOx emissions throughout the transect increases the available NOx in the downwind regions, but modeled ozone concentrations were little affected by the increased NOx.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6p01751jarticleAtmospheric Chemistry and Physics Discussionsvol 9, iss 6, 27099-271651680-7375oai:escholarship.org:ark:/13030/qt6mm126v92016-12-23T19:01:39Zqt6mm126v9Memory suppression is an active process that improves over childhoodPaz-Alonso, PedroGhetti, Simona GhettiMatlen, Bryan JAnderson, Michael CBunge, Silvia A2009-01-01We all have memories that we prefer not to think about. The ability to suppress retrieval of unwanted memories has been documented in behavioral and neuroimaging research using the Think/No-Think (TNT) paradigm with adults. Attempts to stop memory retrieval are associated with increased activation of lateral prefrontal cortex (PFC) and concomitant reduced activation in medial temporal lobe (MTL) structures. However, the extent to which children have the ability to actively suppress their memories is unknown. This study investigated memory suppression in middle childhood using the TNT paradigm. Forty children aged 8–12 and 30 young adults were instructed either to remember (Think) or suppress (No-Think) the memory of the second word of previously studied word-pairs, when presented with the first member as a reminder. They then performed two different cued recall tasks, testing their memory for the second word in each pair after the TNT phase using the same first studied word within the pair as a cue (intra-list cue) and also an independent cue (extra-list cue). Children exhibited age-related improvements in memory suppression from age 8 to 12 in both memory tests, against a backdrop of overall improvements in declarative memory over this age range. These findings suggest that memory suppression is an active process that develops during late childhood, likely due to an age-related refinement in the ability to engage PFC to down-regulate activity in areas involved in episodic retrieval.BRII recipient: Paz-AlonsopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6mm126v9articleFrontiers in Human Neurosciencevol 316625161oai:escholarship.org:ark:/13030/qt4rw2m3h02016-12-23T18:59:50Zqt4rw2m3h0Arabidopsis GH3.12 (PBS3) Conjugates Amino Acids to 4-Substituted Benzoates and Is Inhibited by SalicylateOkrent, R. ABrooks, M. DWildermuth, M. C2009-02-02Salicylate (SA, 2-hydroxybenzoate) is a phytohormone best known for its role as a critical mediator of local and systemic plant defense responses. In response to pathogens such as Pseudomonas syringae, SA is synthesized and activates widespread gene expression. In gh3.12/pbs3 mutants of Arabidopsis thaliana, induced total SA accumulation is significantly compromised as is SA-dependent gene expression and plant defense. AtGH3 subfamily I and II members have been shown to conjugate phytohormone acyl substrates to amino acids in vitro, with this role supported by in planta analyses. Here we sought to determine the in vitro biochemical activity and kinetic properties of GH3.12/avrPphB susceptible 3 (PBS3), a member of the uncharacterized AtGH3 subfamily III. Using a novel high throughput adenylation assay, we characterized the acyl substrate preference of PBS3. We found PBS3 favors 4-substituted benzoates such as 4-aminobenzoate and 4-hydroxybenzoate, with moderate activity on benzoate and no observed activity with 2-substituted benzoates. Similar to known GH3 enzymes, PBS3 catalyzes the conjugation of specific amino acids (e.g. Glu) to its preferred acyl substrates. Kinetic analyses indicate 4-aminobenzoate and 4-hydroxybenzoate are preferred acyl substrates as PBS3 exhibits both higher affinities (apparent Km
= 153 and 459 μm, respectively) and higher catalytic efficiencies (k
cat
/Km
= 0.0179 and 0.0444 μm–1 min–1, respectively) with these acyl substrates compared with benzoate (apparent Km
= 867 μm, k
cat/Km
= 0.0046 μm–1 min–1). Notably, SA specifically and reversibly inhibits PBS3 activity with an IC50 of 15 μm. This suggests a general mechanism for the rapid, reversible regulation of GH3 activity and small molecule cross-talk. For PBS3, this may allow for coordination of flux through diverse chorismate-derived pathways.BRII recipient: Wildermuth (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4rw2m3h0articleJournal of Biological Chemistryvol 284, iss 15, 9742-97540021-9258 1083-351Xoai:escholarship.org:ark:/13030/qt03m9p72w2016-12-23T18:58:51Zqt03m9p72wProper accounting for time increases crop-based biofuels' greenhouse gas deficit versus petroleumO'Hare, MPlevin, R JMartin, J IJones, A DKendall, AHopson, E2009-04-01The global warming intensities of crop-based biofuels and fossil fuels differ not only in amount but also in their discharge patterns over time. Early discharges, for example, from market-mediated land use change, will have created more global warming by any time in the future than later discharges, owing to the slow decay of atmospheric CO2. A spreadsheet model of this process, BTIME, captures this important time pattern effect using the Bern CO2 decay model to allow fuels to be compared for policy decisions on the basis of their real warming effects with a variety of user-supplied parameter values. The model also allows economic discounting of climate effects extended far into the future. Compared to approaches that simply sum greenhouse gas emissions over time, recognizing the physics of atmospheric CO2 decay significantly increases the deficit relative to fossil fuel of any biofuel causing land use change.BRII recipient: O'HarepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/03m9p72warticleEnvironmental Research Lettersvol 4, iss 2, 0240011748-9326oai:escholarship.org:ark:/13030/qt7g35t34j2016-12-23T18:57:03Zqt7g35t34jEpicormic sprout development in pruned coast redwood: pruning severity, genotype, and sprouting characteristicsO'Hara, Kevin LBerrill, John-Pascal2009-01-01• Young coast redwood (Sequoia sempervirens (D. Don.) Endl.) trees were pruned to various heights to examine the effect of pruning severity on epicormic sprouting. Seven separate stands were used with as many as six treatments per stand in coastal Humboldt County, California, USA.• Epicormic sprout development was affected by pruning severity but primarily at the most severe pruning treatments that removed all but the branches in the top 15% of tree height. Less severe treatments produced sprouts but the number and size of these sprouts were comparable to unpruned trees.• Natural clonal patterns were also used to explore patterns of sprouting between genotypes. Linear mixed-effects models were developed to predict sprouting frequency as a function of pruning severity while accounting for the nested data structure (i.e., stem sections sampled nested within genotypes within treatments within sites).• Comparing variances attributed to each of these random effects indicated that at any level of pruning severity, differences in epicormic sprouting between genotypes and sites expressed soon after pruning had disappeared after six growing seasons. Epicormic branches were more common two years after pruning than six years indicating many branches were dying. Branches were more common in the middle of the pruned bole, possibly because of competition from basal sprouts and the expanding tree crown.BRII recipient: O'Hara (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7g35t34jarticleAnnals of Forest Sciencevol 66, iss 4, 409-4091286-4560 1297-966Xoai:escholarship.org:ark:/13030/qt5x56w52m2016-12-23T18:55:29Zqt5x56w52mQuantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)Leache, A. DKoo, M. SSpencer, C. LPapenfuss, T. JFisher, R. NMcGuire, J. A2009-07-22Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG−1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.BRII recipient: McGuire (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5x56w52marticleProceedings of the National Academy of Sciencesvol 106, iss 30, 12418-124230027-8424 1091-6490oai:escholarship.org:ark:/13030/qt40f1940m2016-12-23T18:54:26Zqt40f1940mThe Nicaraguan Pediatric Dengue Cohort Study: Study Design, Methods, Use of Information Technology, and Extension to Other Infectious DiseasesKuan, G.Gordon, A.Aviles, W.Ortega, O.Hammond, S. NElizondo, D.Nunez, A.Coloma, J.Balmaseda, A.Harris, E.2009-05-12Dengue is a mosquito-borne viral disease that is a major public health problem worldwide. In 2004, the Pediatric Dengue Cohort Study was established in Managua, Nicaragua, to study the natural history and transmission of dengue in children. Here, the authors describe the study design, methods, and results from 2004 to 2008. Initially, 3,721 children 2–9 years of age were recruited through door-to-door visits. Each year, new children aged 2 years are enrolled in the study to maintain the age structure. Children are provided with medical care through the study, and data from each medical visit are recorded on systematic study forms. All participants presenting with suspected dengue or undifferentiated fever are tested for dengue by virologic, serologic, and molecular biologic assays. Yearly blood samples are collected to detect inapparent dengue virus infections. Numerous information and communications technologies are used to manage study data, track samples, and maintain quality control, including personal data assistants, barcodes, global information systems, and fingerprint scans. Close collaboration with the Nicaraguan Ministry of Health and use of almost entirely local staff are essential components for success. This study is providing critical data on the epidemiology and transmission of dengue in the Americas needed for future vaccine trials.BRII recipient: Gordon (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/40f1940marticleAmerican Journal of Epidemiologyvol 170, iss 1, 120-1290002-9262 1476-6256oai:escholarship.org:ark:/13030/qt4c5835802016-12-23T18:52:43Zqt4c583580Global Pyrogeography: the Current and Future Distribution of WildfireKrawchuk, Meg AMoritz, Max AParisien, Marc-AndreVan Dorn, JeffHayhoe, Katharine2009-04-08Climate change is expected to alter the geographic distribution of wildfire, a complex abiotic process that responds to a variety of spatial and environmental gradients. How future climate change may alter global wildfire activity, however, is still largely unknown. As a first step to quantifying potential change in global wildfire, we present a multivariate quantification of environmental drivers for the observed, current distribution of vegetation fires using statistical models of the relationship between fire activity and resources to burn, climate conditions, human influence, and lightning flash rates at a coarse spatiotemporal resolution (100 km, over one decade). We then demonstrate how these statistical models can be used to project future changes in global fire patterns, highlighting regional hotspots of change in fire probabilities under future climate conditions as simulated by a global climate model. Based on current conditions, our results illustrate how the availability of resources to burn and climate conditions conducive to combustion jointly determine why some parts of the world are fire-prone and others are fire-free. In contrast to any expectation that global warming should necessarily result in more fire, we find that regional increases in fire probabilities may be counter-balanced by decreases at other locations, due to the interplay of temperature and precipitation variables. Despite this net balance, our models predict substantial invasion and retreat of fire across large portions of the globe. These changes could have important effects on terrestrial ecosystems since alteration in fire activity may occur quite rapidly, generating ever more complex environmental challenges for species dispersing and adjusting to new climate conditions. Our findings highlight the potential for widespread impacts of climate change on wildfire, suggesting severely altered fire regimes and the need for more explicit inclusion of fire in research on global vegetation-climate change dynamics and conservation planning.BRII recipient: MoritzpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4c583580articlePLoS ONEvol 4, iss 4, e51021932-6203oai:escholarship.org:ark:/13030/qt80v7t10v2016-12-23T18:51:22Zqt80v7t10vHost structural carbohydrate induces vector transmission of a bacterial plant pathogenKilliny, N.Almeida, R. P. P2009-12-15Many insect-borne pathogens have complex life histories because they must colonize both hosts and vectors for successful dissemination. In addition, the transition from host to vector environments may require changes in gene expression before the pathogen's departure from the host. Xylella fastidiosa is a xylem-limited plant-pathogenic bacterium transmitted by leafhopper vectors that causes diseases in a number of economically important plants. We hypothesized that factors of host origin, such as plant structural polysaccharides, are important in regulating X. fastidiosa gene expression and mediating vector transmission of this pathogen. The addition of pectin and glucan to a simple defined medium resulted in dramatic changes in X. fastidiosa's phenotype and gene-expression profile. Cells grown in the presence of pectin became more adhesive than in other media tested. In addition, the presence of pectin and glucan in media resulted in significant changes in the expression of several genes previously identified as important for X. fastidiosa's pathogenicity in plants. Furthermore, vector transmission of X. fastidiosa was induced in the presence of both polysaccharides. Our data show that host structural polysaccharides mediate gene regulation in X. fastidiosa, which results in phenotypic changes required for vector transmission. A better understanding of how vector-borne pathogens transition from host to vector, and vice versa, may lead to previously undiscovered disease-control strategies.BRII recipient: Almeida (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/80v7t10varticleProceedings of the National Academy of Sciencesvol 106, iss 52, 22416-224200027-8424 1091-6490oai:escholarship.org:ark:/13030/qt9m1403g82016-12-23T18:50:19Zqt9m1403g8Tripping points: barriers and bargaining chips on the road to CopenhagenJinnah, SikinaBushey, DouglasMunoz, MiquelKulovesi, Kati2009-07-01This letter aims to help scholars and practitioners alike prepare for the 15th Conference of the Parties (COP15) to the United Nations Framework Convention on Climate Change (UNFCCC), to be held in Copenhagen in December 2009, by providing a bird's eye view of the increasingly complex terrain of the global climate negotiations. It identifies and explains the most important and contentious 'tripping points' for reaching any agreement on a post-2012 framework, by explaining the primary barriers among countries to reaching consensus and the bargaining chips that countries may draw upon to get there. Namely, the letter details the contours of the ongoing debates on: developed and developing country mitigation; reducing emissions from deforestation and forest degradation (REDD); technology transfer; adaptation; and finance.BRII recipient: BusheypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9m1403g8articleEnvironmental Research Lettersvol 4, iss 3, 0340031748-9326oai:escholarship.org:ark:/13030/qt91g0m1wr2016-12-23T18:46:32Zqt91g0m1wrSpatial analysis of plague in California: niche modeling predictions of the current distribution and potential response to climate changeHolt, Ashley CSalkeld, Daniel JFritz, Curtis LTucker, James RGong, Peng2009-01-01Plague, caused by the bacterium Yersinia pestis, is a public and wildlife health concern in California and the western United States. This study explores the spatial characteristics of positive plague samples in California and tests Maxent, a machine-learning method that can be used to develop niche-based models from presence-only data, for mapping the potential distribution of plague foci. Maxent models were constructed using geocoded seroprevalence data from surveillance of California ground squirrels (Spermophilus beecheyi) as case points and Worldclim bioclimatic data as predictor variables, and compared and validated using area under the receiver operating curve (AUC) statistics. Additionally, model results were compared to locations of positive and negative coyote (Canis latrans) samples, in order to determine the correlation between Maxent model predictions and areas of plague risk as determined via wild carnivore surveillance.Results:Models of plague activity in California ground squirrels, based on recent climate conditions, accurately identified case locations (AUC of 0.913 to 0.948) and were significantly correlated with coyote samples. The final models were used to identify potential plague risk areas based on an ensemble of six future climate scenarios. These models suggest that by 2050, climate conditions may reduce plague risk in the southern parts of California and increase risk along the northern coast and Sierras.Conclusion:Because different modeling approaches can yield substantially different results, care should be taken when interpreting future model predictions. Nonetheless, niche modeling can be a useful tool for exploring and mapping the potential response of plague activity to climate change. The final models in this study were used to identify potential plague risk areas based on an ensemble of six future climate scenarios, which can help public managers decide where to allocate surveillance resources. In addition, Maxent model results were significantly correlated with coyote samples, indicating that carnivore surveillance programs will continue to be important for tracking the response of plague to future climate conditions.BRII recipient: HoltpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/91g0m1wrarticleInternational Journal of Health Geographicsvol 8, iss 1, 381476-072Xoai:escholarship.org:ark:/13030/qt82p8593k2016-12-23T18:44:25Zqt82p8593kConserved Amino Acid Sequence Features in the α Subunits of MoFe, VFe, and FeFe NitrogenasesGlazer, Alexander NKechris, Katerina J2009-07-03This study examines the structural features and phylogeny of the α subunits of 69 full-length NifD (MoFe subunit), VnfD (VFe subunit), and AnfD (FeFe subunit) sequences. Methodology/Principal Findings: The analyses of this set of sequences included BLAST scores, multiple sequence alignment, examination of patterns of covariant residues, phylogenetic analysis and comparison of the sequences flanking the conserved Cys and His residues that attach the FeMo cofactor to NifD and that are also conserved in the alternative nitrogenases. The results show that NifD nitrogenases fall into two distinct groups. Group I includes NifD sequences from many genera within Bacteria, including all nitrogen-fixing aerobes examined, as well as strict anaerobes and some facultative anaerobes, but no archaeal sequences. In contrast, Group II NifD sequences were limited to a small number of archaeal and bacterial sequences from strict anaerobes. The VnfD and AnfD sequences fall into two separate groups, more closely related to Group II NifD than to Group I NifD. The pattern of perfectly conserved residues, distributed along the full length of the Group I and II NifD, VnfD, and AnfD, confirms unambiguously that these polypeptides are derived from a common ancestral sequence.Conclusions/Significance:There is no indication of a relationship between the patterns of covariant residues specific to each of the four groups discussed above that would give indications of an evolutionary pathway leading from one type of nitrogenase to another. Rather the totality of the data, along with the phylogenetic analysis, is consistent with a radiation of Group I and II NifDs, VnfD and AnfD from a common ancestral sequence. All the data presented here strongly support the suggestion made by some earlier investigators that the nitrogenase family had already evolved in the last common ancestor of the Archaea and Bacteria.BRII recipient: GlazerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/82p8593karticlePLoS ONEvol 4, iss 7, e61361932-6203oai:escholarship.org:ark:/13030/qt4kw1826n2016-12-23T18:41:32Zqt4kw1826nScientific and social challenges for the management of fire-prone wildland-urban interfacesGill, A MalcolmStephens, Scott L2009-09-01At their worst, fires at the rural–urban or wildland–urban interface cause tragic loss of human lives and homes, but mitigating these fire effects through management elicits many social and scientific challenges. This paper addresses four interconnected management challenges posed by socially disastrous landscape fires. The issues concern various assets (particularly houses, human life and biodiversity), fuel treatments, and fire and human behaviours. The topics considered are: 'asset protection zones'; 'defensible space' and urban fire spread in relation to house ignition and loss; 'stay-or-go' policy and the prediction of time available for safe egress and the possible conflict between the creation of defensible space and wildland management objectives. The first scientific challenge is to model the effective width of an asset protection zone of an urban area. The second is to consider the effect of vegetation around a house, potentially defensible space, on fire arrival at the structure. The third scientific challenge is to present stakeholders with accurate information on rates of spread, and where the fire front is located, so as to allow them to plan safe egress or preparation time in their particular circumstances. The fourth scientific challenge is to be able to predict the effects of fires on wildland species composition. Associated with each scientific challenge is a social challenge: for the first two scientific challenges the social challenge is to co-ordinate fuel management within and between the urban and rural or wildland sides of the interface. For the third scientific challenge, the social challenge is to be aware of, and appropriately use, fire danger information so that the potential for safe egress from a home can be estimated most accurately. Finally, the fourth social challenge is to for local residents of wildland–urban interfaces with an interest in biodiversity conservation to understand the effects of fire regimes on biodiversity, thereby assisting hard-pressed wildland managers to make informed choices.BRII recipient: StephenspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4kw1826narticleEnvironmental Research Lettersvol 4, iss 3, 0340141748-9326oai:escholarship.org:ark:/13030/qt4q9305jm2016-12-23T18:37:03Zqt4q9305jmOrganic nitrate and secondary organic aerosol yield from NO3 oxidation of beta-pinene evaluated using a gas-phase kinetics/aerosol partitioning modelFry, J. LKiendler-Scharr, A.Rollins, A. WWooldridge, P. JBrown, S. SFuchs, H.Dube, W.Mensah, A.dal Maso, M.Tillmann, R.Dorn, H.-P.Brauers, T.Cohen, R. C2009-02-23The yields of organic nitrates and of secondary organic aerosol (SOA) particle formation were measured for the reaction NO3+β-pinene under dry and humid conditions in the atmosphere simulation chamber SAPHIR at Research Center Jülich. These experiments were conducted at low concentrations of NO3 (NO3+N2O5<10 ppb) and β-pinene (peak~15 ppb), with no seed aerosol. SOA formation was observed to be prompt and substantial (~50% mass yield under both dry conditions and at 60% RH), and highly correlated with organic nitrate formation. The observed gas/aerosol partitioning of organic nitrates can be simulated using an absorptive partitioning model to derive an estimated vapor pressure of the condensing nitrate species of pvap~5×10−6 Torr (6.67×10−4 Pa), which constrains speculation about the oxidation mechanism and chemical identity of the organic nitrate. Once formed the SOA in this system continues to evolve, resulting in measurable aerosol volume decrease with time. The observations of high aerosol yield from NOx-dependent oxidation of monoterpenes provide an example of a significant anthropogenic source of SOA from biogenic hydrocarbon precursors. Estimates of the NO3+β-pinene SOA source strength for California and the globe indicate that NO3 reactions with monoterpenes are likely an important source (0.5–8% of the global total) of organic aerosol on regional and global scales.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4q9305jmarticleAtmospheric Chemistry and Physicsvol 9, iss 4, 1431-14491680-7324oai:escholarship.org:ark:/13030/qt1js2r71v2016-12-23T18:35:19Zqt1js2r71vThe Modulation Transfer Function for Speech IntelligibilityElliott, Taffeta MTheunissen, Frederic E2009-03-06We systematically determined which spectrotemporal modulations in speech are necessary for comprehension by human listeners. Speech comprehension has been shown to be robust to spectral and temporal degradations, but the specific relevance of particular degradations is arguable due to the complexity of the joint spectral and temporal information in the speech signal. We applied a novel modulation filtering technique to recorded sentences to restrict acoustic information quantitatively and to obtain a joint spectrotemporal modulation transfer function for speech comprehension, the speech MTF. For American English, the speech MTF showed the criticality of low modulation frequencies in both time and frequency. Comprehension was significantly impaired when temporal modulations <12 Hz or spectral modulations <4 cycles/kHz were removed. More specifically, the MTF was bandpass in temporal modulations and low-pass in spectral modulations: temporal modulations from 1 to 7 Hz and spectral modulations <1 cycles/kHz were the most important. We evaluated the importance of spectrotemporal modulations for vocal gender identification and found a different region of interest: removing spectral modulations between 3 and 7 cycles/kHz significantly increases gender misidentifications of female speakers. The determination of the speech MTF furnishes an additional method for producing speech signals with reduced bandwidth but high intelligibility. Such compression could be used for audio applications such as file compression or noise removal and for clinical applications such as signal processing for cochlear implants.BRII recipient: ElliottpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1js2r71varticlePLoS Computational Biologyvol 5, iss 3, e10003021553-7358oai:escholarship.org:ark:/13030/qt56w2n3db2016-12-23T18:34:27Zqt56w2n3dbLaser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulatorsChandran, D.Inada, N.Hather, G.Kleindt, C. KWildermuth, M. C2009-12-14To elucidate host processes and components required for the sustained growth and reproduction of the obligate biotrophic fungus Golovinomyces orontii on Arabidopsis thaliana, laser microdissection was used to isolate cells at the site of infection at 5 days postinfection for downstream global Arabidopsis expression profiling. Site-specific profiling increased sensitivity dramatically, allowing us to identify specific host processes, process components, and their putative regulators hidden in previous whole-leaf global expression analyses. For example, 67 transcription factors exhibited altered expression at the powdery mildew (PM) infection site, with subsets of these playing known or inferred roles in photosynthesis, cold/dehydration responses, defense, auxin signaling, and the cell cycle. Using integrated informatics analyses, we constructed putative regulatory networks for a subset of these processes and provided strong support for host cell cycle modulation at the PM infection site. Further experimentation revealed induced host endoreduplication occurred exclusively at the infection site and led us to identify MYB3R4 as a transcriptional regulator of this process. Induced endoreduplication was abrogated in myb3r4 mutants, and G. orontii growth and reproduction were reduced. This suggests that, by increasing gene copy number, localized endoreduplication serves as a mechanism to meet the enhanced metabolic demands imposed by the fungus, which acquires all its nutrients from the plant host.BRII recipient: Wildermuth (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/56w2n3dbarticleProceedings of the National Academy of Sciencesvol 107, iss 1, 460-4650027-8424 1091-6490oai:escholarship.org:ark:/13030/qt89n5w05t2016-12-23T18:33:26Zqt89n5w05tControl of Stochastic Gene Expression by Host Factors at the HIV PromoterBurnett, John CMiller-Jensen, KathrynShah, Priya SArkin, Adam PSchaffer, David V2009-01-09The HIV promoter within the viral long terminal repeat (LTR) orchestrates many aspects of the viral life cycle, from the dynamics of viral gene expression and replication to the establishment of a latent state. In particular, after viral integration into the host genome, stochastic fluctuations in viral gene expression amplified by the Tat positive feedback loop can contribute to the formation of either a productive, transactivated state or an inactive state. In a significant fraction of cells harboring an integrated copy of the HIV-1 model provirus (LTR-GFP-IRES-Tat), this bimodal gene expression profile is dynamic, as cells spontaneously and continuously flip between active (Bright) and inactive (Off) expression modes. Furthermore, these switching dynamics may contribute to the establishment and maintenance of proviral latency, because after viral integration long delays in gene expression can occur before viral transactivation. The HIV-1 promoter contains cis-acting Sp1 and NF-κB elements that regulate gene expression via the recruitment of both activating and repressing complexes. We hypothesized that interplay in the recruitment of such positive and negative factors could modulate the stability of the Bright and Off modes and thereby alter the sensitivity of viral gene expression to stochastic fluctuations in the Tat feedback loop. Using model lentivirus variants with mutations introduced in the Sp1 and NF-κB elements, we employed flow cytometry, mRNA quantification, pharmacological perturbations, and chromatin immunoprecipitation to reveal significant functional differences in contributions of each site to viral gene regulation. Specifically, the Sp1 sites apparently stabilize both the Bright and the Off states, such that their mutation promotes noisy gene expression and reduction in the regulation of histone acetylation and deacetylation. Furthermore, the NF-κB sites exhibit distinct properties, with κB site I serving a stronger activating role than κB site II. Moreover, Sp1 site III plays a particularly important role in the recruitment of both p300 and RelA to the promoter. Finally, analysis of 362 clonal cell populations infected with the viral variants revealed that mutations in any of the Sp1 sites yield a 6-fold higher frequency of clonal bifurcation compared to that of the wild-type promoter. Thus, each Sp1 and NF-κB site differentially contributes to the regulation of viral gene expression, and Sp1 sites functionally “dampen” transcriptional noise and thereby modulate the frequency and maintenance of this model of viral latency. These results may have biomedical implications for the treatment of HIV latency.BRII recipient: SchafferpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/89n5w05tarticlePLoS Pathogensvol 5, iss 1, e10002601553-7374oai:escholarship.org:ark:/13030/qt7hw979gf2016-12-23T18:32:29Zqt7hw979gfMethyl chavicol: characterization of its biogenic emission rate, abundance, and oxidation products in the atmosphereBouvier-Brown, N. CGoldstein, A. HWorton, D. RMatross, D. MGilman, J. BKuster, W. CWelsh-Bon, D.Warneke, C.de Gouw, J. ACahill, T. MHolzinger, R.2009-03-23We report measurements of ambient atmospheric mixing ratios for methyl chavicol and determine its biogenic emission rate. Methyl chavicol, a biogenic oxygenated aromatic compound, is abundant within and above Blodgett Forest, a ponderosa pine forest in the Sierra Nevada Mountains of California. Methyl chavicol was detected simultaneously by three in-situ instruments – a gas chromatograph with mass spectrometer detector (GC-MS), a proton transfer reaction mass spectrometer (PTR-MS), and a thermal desorption aerosol GC-MS (TAG) – and found to be abundant within and above Blodgett Forest. Methyl chavicol atmospheric mixing ratios are strongly correlated with 2-methyl-3-buten-2-ol (MBO), a light- and temperature-dependent biogenic emission from the ponderosa pine trees at Blodgett Forest. Scaling from this correlation, methyl chavicol emissions account for 4–68% of the carbon mass emitted as MBO in the daytime, depending on the season. From this relationship, we estimate a daytime basal emission rate of 0.72–10.2 μgCg−1 h−1, depending on needle age and seasonality. We also present the first observations of its oxidation products (4-methoxybenzaldehyde and 4-methyoxy benzene acetaldehyde) in the ambient atmosphere. Methyl chavicol is a major essential oil component of many plant species. This work suggests that methyl chavicol plays a significant role in the atmospheric chemistry of Blodgett Forest, and potentially other sites, and should be included explicitly in both biogenic volatile organic carbon emission and atmospheric chemistry models.BRII recipient: Bouvier-BrownpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7hw979gfarticleAtmospheric Chemistry and Physicsvol 9, iss 6, 2061-20741680-7324oai:escholarship.org:ark:/13030/qt1bb7p5tn2016-12-23T18:31:38Zqt1bb7p5tnThe role of an e+e− linear collider in the study of cosmic dark matterBattaglia, M2009-10-16The potential of a high energy, high luminosity e+e− linear collider in the study of a weakly interacting massive new particle as a cosmic dark matter candidate is reviewed, with special emphasis on supersymmetric scenarios. Results of detailed simulation studies for supersymmetric neutralino dark matter indicate that the accuracy from linear collider data of sufficient energy may allow us to infer the dark matter relic density to accuracies comparable to those already obtained from the study of cosmic microwave background and other astrophysical data, thus providing a powerful test on the nature of dark matter by combining results from particle colliders with satellite and direct detection experiment data.BRII recipient: BattagliapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1bb7p5tnarticleNew Journal of Physicsvol 11, iss 10, 1050251367-2630oai:escholarship.org:ark:/13030/qt6fv8d6bd2016-12-23T18:27:03Zqt6fv8d6bdEvaluation of a pre-existing, 3-year household water treatment and handwashing intervention in rural GuatemalaArnold, B.Arana, B.Mausezahl, D.Hubbard, A.Colford, J. M2009-07-02Background The promotion of household water treatment and handwashing with soap has led to large reductions in child diarrhoea in randomized efficacy trials. Currently, we know little about the health effectiveness of behaviour-based water and hygiene interventions after the conclusion of intervention activities.Methods We present an extension of previously published design (propensity score matching) and analysis (targeted maximum likelihood estimation) methods to evaluate the behavioural and health impacts of a pre-existing but non-randomized intervention (a 3-year, combined household water treatment and handwashing campaign in rural Guatemala). Six months after the intervention, we conducted a cross-sectional cohort study in 30 villages (15 intervention and 15 control) that included 600 households, and 929 children <5 years of age.Results The study design created a sample of intervention and control villages that were comparable across more than 30 potentially confounding characteristics. The intervention led to modest gains in confirmed water treatment behaviour [risk difference = 0.05, 95% confidence interval (CI) 0.02–0.09]. We found, however, no difference between the intervention and control villages in self-reported handwashing behaviour, spot-check hygiene conditions, or the prevalence of child diarrhoea, clinical acute lower respiratory infections or child growth.Conclusions To our knowledge this is the first post-intervention follow-up study of a combined household water treatment and handwashing behaviour change intervention, and the first post-intervention follow-up of either intervention type to include child health measurement. The lack of child health impacts is consistent with unsustained behaviour adoption. Our findings highlight the difficulty of implementing behaviour-based household water treatment and handwashing outside of intensive efficacy trials.BRII recipient: Arnold (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6fv8d6bdarticleInternational Journal of Epidemiologyvol 38, iss 6, 1651-16610300-5771 1464-3685oai:escholarship.org:ark:/13030/qt0nb4v63p2016-12-23T18:26:05Zqt0nb4v63pNonlinear magneto-optical rotation in the presence of a radio-frequency fieldZigdon, T.Wilson-Gordon, A. DGuttikonda, S.Bahr, E. JNeitzke, O.Rochester, S. MBudker, D.2010-11-22We report measurements of nonlinear magneto-optical rotation (NMOR) for the D2 line of 87Rb atoms in an antirelaxation-coated vapor cell in the presence of a radio-frequency (rf) field. The experimental NMOR signals as a function of rf field frequency for various rf field powers are compared to a theoretical model based on the density-matrix formalism. The comparison between experiment and theory enables understanding of the ground-state atomic spin polarization dynamics, illustrated using plots of the probability distribution of the atomic angular momentum.BRII recipient: RochesterpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0nb4v63particleOptics Expressvol 18, iss 25, 254941094-4087oai:escholarship.org:ark:/13030/qt8b9541sn2016-12-23T17:17:43Zqt8b9541snOperational approaches to managing forests of the future in Mediterranean regions within a context of changing climatesStephens, Scott LMillar, Constance ICollins, Brandon M2010-04-01Many US forest managers have used historical ecology information to assist in the development of desired conditions. While there are many important lessons to learn from the past, we believe that we cannot rely on past forest conditions to provide us with blueprints for future management. To respond to this uncertainty, managers will be challenged to integrate adaptation strategies into plans in response to changing climates. Adaptive strategies include resistance options, resilience options, response options, and realignment options. Our objectives are to present ideas that could be useful in developing plans under changing climates that could be applicable to forests with Mediterranean climates. We believe that managing for species persistence at the broad ecoregion scale is the most appropriate goal when considering the effects of changing climates. Such a goal relaxes expectations that current species ranges will remain constant, or that population abundances, distribution, species compositions and dominances should remain stable. Allowing fundamental ecosystem processes to operate within forested landscapes will be critical. Management and political institutions will have to acknowledge and embrace uncertainty in the future since we are moving into a time period with few analogs and inevitably, there will be surprises.BRII recipient: StephenspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8b9541snarticleEnvironmental Research Lettersvol 5, iss 2, 0240031748-9326oai:escholarship.org:ark:/13030/qt1xp822kk2016-12-23T17:12:40Zqt1xp822kkChannel Characterization for 700 MHz DSRC Vehicular CommunicationSevlian, RaffiChun, CarlTan, IanBahai, AhmadLaberteaux, Ken2010-01-01Adapting OFDM for vehicular communication requires extensive knowledge of anticipated multipath and Doppler environments. We present a GPS-enabled channel sounding system built and used to conduct a channel measurement campaign. Tests conducted at the 700 MHz band in and around downtown Ann Arbor, Michigan, explored various vehicle-to-vehicle and vehicle-to-roadside channel scenarios. The measured channel metrics are used to quantify the effects on guard interval, packet duration, and subcarrier spacing for a functional OFDM system at 700 MHz. This paper is one of the first to present vehicular-based channel-modeling results from measured data in the 700 MHz band.BRII recipient: ChunpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1xp822kkarticleJournal of Electrical and Computer Engineeringvol 2010, 1-92090-0147 2090-0155oai:escholarship.org:ark:/13030/qt9223t06g2016-12-23T17:11:39Zqt9223t06gThe role of fire in the competitive dynamics of coast redwood forestsRamage, B. SO'Hara, K. LCaldwell, B. T2010-12-01Fire is a major component of the disturbance regime and a critical determinant of competitive outcomes in many ecosystems. In forests dominated by coast redwood (Sequoia sempervirens), fire was frequent and ubiquitous prior to European settlement, but fires have been exceedingly small and rare over the last 70–80 years because of aggressive fire prevention and suppression policies. As a result, many aspects of redwood fire ecology remain poorly understood. However, in 2008 a single storm ignited numerous fires throughout the redwood region, providing a rare opportunity to conduct replicated fire effects research. One year post-fire, we investigated competitive dynamics by quantifying bole survival and basal sprouting, for redwood and associated species, at four field sites that spanned much of the latitudinal range of redwood and encompassed (1) second-growth and old-growth stands, (2) burned and unburned areas, and (3) a wide range of fire severities. We employed a mixed effects analytical framework and found that: (1) the probability of bole survival was greater for redwood than for its primary competitor (tanoak; Notholithocarpus densiflorus), (2) this divergence was much more pronounced at higher fire severities, and (3) tanoak exhibited a slight advantage in terms of post-fire basal sprouting, but the dominance of tanoak basal sprouts in burned areas was reduced relative to unburned areas. For many disturbance types in many ecosystems, the empirical data necessary for effective management decisions are lacking, and studies incorporating vegetative tree regeneration are especially scarce. Our work demonstrates the importance of utilizing unique field research opportunities to test current theories, while unequivocally documenting that fires of all severities increased the abundance of redwood relative to tanoak, and that higher severity fires more strongly favored redwood.BRII recipient: O'HarapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9223t06garticleEcospherevol 1, iss 6, art202150-8925oai:escholarship.org:ark:/13030/qt95f2m3nx2016-12-23T17:09:48Zqt95f2m3nxEntanglement spectra of critical and near-critical systems in one dimensionPollmann, FMoore, J E2010-02-26The entanglement spectrum of a pure state of a bipartite system is the full set of eigenvalues of the reduced density matrix obtained from tracing out one part. Such spectra are known in several cases to contain important information beyond that in the entanglement entropy. This paper studies the entanglement spectrum for a variety of critical and near-critical quantum lattice models in one dimension, chiefly by the infinite time evolving block decimation (iTEBD) numerical method, which enables both integrable and non-integrable models to be studied. We find that the distribution of eigenvalues in the entanglement spectra agrees with an approximate result derived by Calabrese and Lefevre to an accuracy of a few per cent for all models studied. This result applies whether the correlation length is intrinsic or generated by the finite matrix size accessible in iTEBD. For the transverse Ising model, the known exact results from Peschel and Eisler for the entanglement spectrum are used to confirm the validity of the iTEBD approach. For more general models, no exact result is available but the iTEBD results directly test the hypothesis that all moments of the reduced density matrix are determined by a single parameter.BRII recipient: MoorepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/95f2m3nxarticleNew Journal of Physicsvol 12, iss 2, 0250061367-2630oai:escholarship.org:ark:/13030/qt6c31v4qs2016-12-23T17:08:33Zqt6c31v4qsChloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomesOliver, Melvin JMurdock, Andrew GMishler, Brent DKuehl, Jennifer VBoore, Jeffrey LMandoli, Dina FEverett, Karin DWolf, Paul GDuffy, Aaron MKarol, Kenneth G2010-01-01Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant.Results:The Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered.Conclusions:Although the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.BRII recipient: MishlerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6c31v4qsarticleBMC Genomicsvol 11, iss 1, 1431471-2164oai:escholarship.org:ark:/13030/qt4fk4p35q2016-12-23T17:06:47Zqt4fk4p35qFunctional Toxicogenomics: Mechanism-Centered ToxicologyNorth, MatthewVulpe, Chris D2010-11-24Traditional toxicity testing using animal models is slow, low capacity, expensive and assesses a limited number of endpoints. Such approaches are inadequate to deal with the increasingly large number of compounds found in the environment for which there are no toxicity data. Mechanism-centered high-throughput testing represents an alternative approach to meet this pressing need but is limited by our current understanding of toxicity pathways. Functional toxicogenomics, the global study of the biological function of genes on the modulation of the toxic effect of a compound, can play an important role in identifying the essential cellular components and pathways involved in toxicity response. The combination of the identification of fundamental toxicity pathways and mechanism-centered targeted assays represents an integrated approach to advance molecular toxicology to meet the challenges of toxicity testing in the 21st century.BRII recipient: NorthpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4fk4p35qarticleInternational Journal of Molecular Sciencesvol 11, iss 12, 4796-48131422-0067oai:escholarship.org:ark:/13030/qt0c88q9hc2016-12-23T17:04:36Zqt0c88q9hcComplete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineagesKarol, Kenneth GArumuganathan, KathiravetpillaiBoore, Jeffrey LDuffy, Aaron MEverett, Karin DHall, John DHansen, SKuehl, Jennifer VMandoli, Dina FMishler, Brent DOlmstead, Richard GRenzaglia, Karen SWolf, Paul G2010-01-01Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats.Results:We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes.Conclusions:Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.BRII recipient: MishlerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0c88q9hcarticleBMC Evolutionary Biologyvol 10, iss 1, 3211471-2148oai:escholarship.org:ark:/13030/qt0ns972052016-12-23T17:02:44Zqt0ns97205Interannual variability in soil nitric oxide emissions over the United States as viewed from spaceHudman, R. CRussell, A. RValin, L. CCohen, R. C2010-10-20We examine the interannual variability in the NO2 column over North America measured by the Ozone Monitoring Instrument (OMI) in 2005–2008. By comparison to a model of soil NOx emissions driven by the North American Regional Reanalysis precipitation and 0–10 cm soil temperature fields, we show the source of this observed interannual variability over much of the central United States in June is fertilizer application. We find that dry, warm conditions followed by convective precipitation induces pulsed emissions of NOx over the agricultural Great Plains. In June 2006 we infer a 50% increase in soil NOx emission and a 30% increase in the tropospheric NO2 column relative to the June 2005–2008 mean. In a case-study of fertilized corn and soybean fields over SE South Dakota, we find an associated rain-induced pulsing event reaching 4.6×1015 molec cm−2, equivalent to a surface concentration of ~2 ppbv. We calculate that soil NOx emissions resulted in a mean daily maximum 8-h ozone enhancement over the agricultural Great Plains of 5 ppbv in June 2006 (with predicted events reaching 16 ppbv) compared with a mean enhancement of 3 ppbv for soil NOx in the years 2005–2008.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0ns97205articleAtmospheric Chemistry and Physicsvol 10, iss 20, 9943-99521680-7324oai:escholarship.org:ark:/13030/qt5dg9z1dx2016-12-23T16:58:38Zqt5dg9z1dxLimits of quantum speedup in photosynthetic light harvestingHoyer, StephanSarovar, MohanWhaley, K. Birgitta2010-06-30It has been suggested that excitation transport in photosynthetic light-harvesting complexes features speedups analogous to those found in quantum algorithms. Here we compare the dynamics in these light-harvesting systems to the dynamics of quantum walks, in order to elucidate the limits of such quantum speedups. For the Fenna–Matthews–Olson complex of green sulfur bacteria, we show that while there is indeed speedup at short times, this is short lived (70 fs) despite longer-lived (ps) quantum coherence. Remarkably, this timescale is independent of the details of the decoherence model. More generally, we show that the distinguishing features of light-harvesting complexes not only limit the extent of quantum speedup but also reduce the rates of diffusive transport. These results suggest that quantum coherent effects in biological systems are optimized for efficiency or robustness rather than the more elusive goal of quantum speedup.BRII recipient: HoyerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5dg9z1dxarticleNew Journal of Physicsvol 12, iss 6, 0650411367-2630oai:escholarship.org:ark:/13030/qt6tq6f00v2016-12-23T16:54:37Zqt6tq6f00vDiagnostic Accuracy of a Rapid Influenza Test for Pandemic Influenza A H1N1Gordon, AubreeVidea, ElsaSaborío, SairaLópez, RogerKuan, GuillerminaBalmaseda, AngelHarris, Eva2010-04-28With the current influenza A H1N1 pandemic (H1N1pdm), it is extremely important that clinicians can quickly and accurately identify influenza cases. Methodology/Principal Findings: To investigate the performance of the QuickVue Influenza A+B rapid test, we conducted a prospective study of the diagnostic accuracy of the QuickVue Influenza A+B test compared to real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for influenza A H1N1pdm in Nicaraguan children aged 2 to 14 years. Rapid test sensitivity and specificity compared to real-time RT-PCR were 64.1% (95% CI 53.5, 73.9) and 98.3% (95.0, 99.6), respectively. Agreement between the two tests was 86.4% (95% CI 81.7, 90.3), and kappa was calculated to be 0.67 (95% CI 0.56, 0.76). Performance of the rapid test varied by day of presentation, with a sensitivity of 41.7% (95% CI 22.1, 63.4) for samples from children presenting on the day of symptom onset and a sensitivity of 72.1% (95% CI 59.9, 82.3) for samples from children presenting one or more days post-symptom onset. Conclusions/Significance: We found that the rapid test performed with moderate sensitivity and high specificity. Test performance varied by day of onset, with lower sensitivity on the day of symptom onset.BRII recipient: GordonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6tq6f00varticlePLoS ONEvol 5, iss 4, e103641932-6203oai:escholarship.org:ark:/13030/qt65v512ph2016-12-23T16:47:27Zqt65v512phAccounting for the water impacts of ethanol productionFingerman, Kevin RTorn, Margaret SO'Hare, Michael HKammen, Daniel M2010-01-01Biofuels account for 1–2% of global transportation fuel and their share is projected to continue rising, with potentially serious consequences for water resources. However, current literature does not present sufficient spatial resolution to characterize this localized effect. We used a coupled agro-climatic and life cycle assessment model to estimate the water resource impacts of bioenergy expansion scenarios at a county-level resolution. The study focused on the case of California, with its range of agroecological conditions, water scarcity, and aggressive alternative fuel incentive policies. Life cycle water consumption for ethanol production in California is up to 1000 times that of gasoline due to a cultivation phase that consumes over 99% of life cycle water use for agricultural biofuels. This consumption varies by up to 60% among different feedstocks and by over 350% across regions in California. Rigorous policy analysis requires spatially resolved modeling of water resource impacts and careful consideration of the various metrics that might act to constrain technology and policy options.BRII recipient: FingermanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/65v512pharticleEnvironmental Research Lettersvol 5, iss 1, 0140201748-9326oai:escholarship.org:ark:/13030/qt07m8c5zs2016-12-22T23:46:13Zqt07m8c5zsPopulation Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage FormationSimmons, Sheri LDiBartolo, GenevieveDenef, Vincent JGoltsman, Daniela S. AliagaThelen, Michael PBanfield, Jillian F2008-07-22Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.BRII recipient: SimmonspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/07m8c5zsarticlePLoS Biologyvol 6, iss 7, e1771545-7885oai:escholarship.org:ark:/13030/qt6nc0j9vp2016-12-22T23:44:57Zqt6nc0j9vpThe control of reproductive physiology and behavior by gonadotropin-inhibitory hormoneUbuka, T.McGuire, N. LCalisi, R. MPerfito, N.Bentley, G. E2008-04-19Gonadotropin-releasing hormone (GnRH) controls the reproductive physiology and behavior of vertebrates by stimulating synthesis and release of gonadotropin from the pituitary gland. In 2000, another hypothalamic neuropeptide, gonadotropin-inhibitory hormone (GnIH), was discovered in quail and found to be an inhibiting factor for gonadotropin release. GnIH homologs are present in the brains of vertebrates, including birds, mammals, amphibians, and fish. These peptides, categorized as RF amide-related peptides (RFRPs), possess a characteristic LPXRF-amide (X = L or Q) motif at their C-termini. GnIH/RFRP precursor mRNA encodes a polypeptide that is possibly cleaved into three mature peptides in birds and two in mammals. The names of these peptides are GnIH, GnIH-related peptide-1 (GnIH-RP-1) and GnIH-RP-2 in birds, and RFRP-1 and RFRP-3 in mammals. GnIH/RFRP is synthesized in neurons of the paraventricular nucleus of the hypothalamus in birds and the dorsomedial hypothalamic area in mammals. GnIH neurons project to the median eminence, thus providing a functional neuroanatomical infrastructure to regulate anterior pituitary function. In quail, GnIH inhibits gonadal activity by decreasing synthesis and release of gonadotropin. The widespread distribution of GnIH/RFRP immunoreactive fibers in all animals tested suggests various actions within the brain. In accordance, GnIH/RFRP receptor mRNA is also expressed widely in the brain and the pituitary. GnIH/RFRP immunoreactive axon terminals are in probable contact with GnRH neurons in birds and mammals, and we recently demonstrated expression of GnIH receptor mRNA in GnRH-I and GnRH-II neurons in European starlings. Thus, GnIH/RFRP may also inhibit gonadotropin synthesis and release by inhibiting GnRH neurons in addition to having direct actions on the pituitary gland. Intracerebroventricular administration of GnIH/RFRP further inhibits reproductive behaviors in songbirds and rodents, possibly via direct actions on the GnRH system. The expression of GnIH/RFRP is regulated by melatonin which is an internal indicator of day length in vertebrates. Stress stimuli also regulate the expression of GnIH/RFRP in songbirds and rodents. Accordingly, GnIH/RFRP may serve as a transducer of environmental information and social interactions into endogenous physiology and behavior of the animal. Recently, it was shown that GnIH/RFRP and its receptor are also expressed in the gonads of birds, rodents and primates. In sum, the existing data suggest that GnIH/RFRP is an important mediator of reproductive function acting at the level of the brain, pituitary, and the gonad in birds and mammals.BRII recipient: Ubuka (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6nc0j9vparticleIntegrative and Comparative Biologyvol 48, iss 5, 560-5691540-7063 1557-7023oai:escholarship.org:ark:/13030/qt0wp2t4rr2016-12-22T23:42:21Zqt0wp2t4rrNeural correlates of tic severity and cognitive control in children with Tourette syndromeBaym, C. LCorbett, B. AWright, S. BBunge, S. A2007-12-03Tourette syndrome (TS) is a neurodevelopmental disorder characterized by involuntary motor and phonic tics. It is hypothesized that excess dopamine leads to an imbalance in the pathways through the basal ganglia, resulting in unchecked movements via thalamic disinhibition. It has been unclear whether TS is associated with cognitive control deficits as well as pure motor control deficits, or whether cognitive deficits are associated with the presence of comorbid conditions. Furthermore, little is known about the neural underpinnings of TS in childhood, prior to the long-term effects of medication on brain function. Here, children with TS and typically developing children performed a cognitive control task during event-related fMRI data acquisition. The study included 18 native English-speaking 7–13-year-old children with TS (M = 10.42; 15 males), and 19 healthy, age-matched native English-speaking volunteers (M = 10.33; 11 males). The task involved three separate manipulations of cognitive control. Behaviourally, higher tic severity was correlated with slower task performance on the most demanding task conditions. Neurally, higher tic severity was associated with enhanced activation of dopaminergic nuclei (substantia nigra/ventral tegmental area) and cortical, striatal and thalamic regions in the direct pathway. Heightened tic severity was also associated with greater engagement of the subthalamic nucleus area, suggestive of a compensatory mechanism. Overall, patients engaged left prefrontal cortex more strongly than typicals during task performance. These data suggest that children aged 7–13 unmedicated for TS exhibit increased activation in the direct pathway through the basal ganglia, as well as increased compensatory activation in prefrontal cortex and the subthalamic nucleus.BRII recipient: Bunge (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/0wp2t4rrarticleBrainvol 131, iss 1, 165-1790006-8950 1460-2156oai:escholarship.org:ark:/13030/qt6sr7z3322016-12-22T22:36:06Zqt6sr7z332Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast AsiaChe, J.Zhou, W.-W.Hu, J.-S.Yan, F.Papenfuss, T. JWake, D. BZhang, Y.-P.2010-07-19Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological history of the earth can be viewed from a biological perspective. Our analysis of a concatenated dataset comprising four nuclear gene sequences of Paini revealed two main radiations, corresponding to the genera Nanorana (I) and Quasipaa (II). Five distinct clades are recognized: Tibetan plateau clade (I-1), Himalaya clade (I-2), environs of Himalaya–Tibetan plateau clade (I-3), South China clade (II-1), and Indochina clade (II-2). This pattern of relationships highlights the significance of geography in shaping evolutionary history. Building on our molecular dating, ancestral region reconstruction, and distributional patterns, we hypothesize a distinct geographic and climatic transition in Asia beginning in the Oligocene and intensifying in the Miocene; this stimulated rapid diversification of Paini. Vicariance explains species formation among major lineages within Nanorana. Dispersal, in contrast, plays an important role among Quasipaa, with the southern Chinese taxa originating from Indochina. Our results support the tectonic hypothesis that an uplift in the Himalaya–Tibetan plateau region resulting from crustal thickening and lateral extrusion of Indochina occurred synchronously during the transition between Oligocene and Miocene in reaction to the Indo-Asian collision. The phylogenetic history of Paini illuminates critical aspects of the timing of geological events responsible for the current geography of Southeast Asia.BRII recipient: Wake (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6sr7z332articleProceedings of the National Academy of Sciencesvol 107, iss 31, 13765-137700027-8424 1091-6490oai:escholarship.org:ark:/13030/qt6dh685jm2016-12-22T22:35:04Zqt6dh685jmEvaluation of statistical methods for normalization and differential expression in mRNA-Seq experimentsBullard, James HPurdom, ElizabethHansen, Kasper DDudoit, Sandrine2010-01-01High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generated by the sequencers. We provide a detailed evaluation of statistical methods for normalization and differential expression (DE) analysis of Illumina transcriptome sequencing (mRNA-Seq) data.Results:We compare statistical methods for detecting genes that are significantly DE between two types of biological samples and find that there are substantial differences in how the test statistics handle low-count genes. We evaluate how DE results are affected by features of the sequencing platform, such as, varying gene lengths, base-calling calibration method (with and without phi X control lane), and flow-cell/library preparation effects. We investigate the impact of the read count normalization method on DE results and show that the standard approach of scaling by total lane counts (e.g., RPKM) can bias estimates of DE. We propose more general quantile-based normalization procedures and demonstrate an improvement in DE detection.Conclusions:Our results have significant practical and methodological implications for the design and analysis of mRNA-Seq experiments. They highlight the importance of appropriate statistical methods for normalization and DE inference, to account for features of the sequencing platform that could impact the accuracy of results. They also reveal the need for further research in the development of statistical and computational methods for mRNA-Seq.BRII recipient: DudoitpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6dh685jmarticleBMC Bioinformaticsvol 11, iss 1, 941471-2105oai:escholarship.org:ark:/13030/qt4dj5d3q22016-12-22T22:33:54Zqt4dj5d3q2Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered LizardsBrandley, Matthew CWang, YuezhaoGuo, XianguangNieto Montes de Oca, AdrianFeria Ortiz, ManuelHikida, TsutomuOta, Hidetoshi2010-06-30Oceanic islands are well known for harboring diverse species assemblages and are frequently the basis of research on adaptive radiation and neoendemism. However, a commonly overlooked role of some islands is their function in preserving ancient lineages that have become extinct everywhere else (paleoendemism). The island archipelago of Bermuda is home to a single species of extant terrestrial vertebrate, the endemic skink Plestiodon (formerly Eumeces) longirostris. The presence of this species is surprising because Bermuda is an isolated, relatively young oceanic island approximately 1000 km from the eastern United States. Here, we apply Bayesian phylogenetic analyses using a relaxed molecular clock to demonstrate that the island of Bermuda, although no older than two million years, is home to the only extant representative of one of the earliest mainland North American Plestiodon lineages, which diverged from its closest living relatives 11.5 to 19.8 million years ago. This implies that, within a short geological time frame, mainland North American ancestors of P. longirostris colonized the recently emergent Bermuda and the entire lineage subsequently vanished from the mainland. Thus, our analyses reveal that Bermuda is an example of a “life raft” preserving millions of years of unique evolutionary history, now at the brink of extinction. Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard.BRII recipient: BrandleypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4dj5d3q2articlePLoS ONEvol 5, iss 6, e113751932-6203oai:escholarship.org:ark:/13030/qt6139r6w42016-12-22T22:32:59Zqt6139r6w4Lethal Antibody Enhancement of Dengue Disease in Mice Is Prevented by Fc ModificationBalsitis, Scott JWilliams, Katherine LLachica, RubenFlores, DianaKyle, Jennifer LMehlhop, ErinJohnson, SydDiamond, Michael SBeatty, P. RobertHarris, Eva2010-02-12Immunity to one of the four dengue virus (DV) serotypes can increase disease severity in humans upon subsequent infection with another DV serotype. Serotype cross-reactive antibodies facilitate DV infection of myeloid cells in vitro by promoting virus entry via Fcγ receptors (FcγR), a process known as antibody-dependent enhancement (ADE). However, despite decades of investigation, no in vivo model for antibody enhancement of dengue disease severity has been described. Analogous to human infants who receive anti-DV antibodies by transplacental transfer and develop severe dengue disease during primary infection, we show here that passive administration of anti-DV antibodies is sufficient to enhance DV infection and disease in mice using both mouse-adapted and clinical DV isolates. Antibody-enhanced lethal disease featured many of the hallmarks of severe dengue disease in humans, including thrombocytopenia, vascular leakage, elevated serum cytokine levels, and increased systemic viral burden in serum and tissue phagocytes. Passive transfer of a high dose of serotype-specific antibodies eliminated viremia, but lower doses of these antibodies or cross-reactive polyclonal or monoclonal antibodies all enhanced disease in vivo even when antibody levels were neutralizing in vitro. In contrast, a genetically engineered antibody variant (E60-N297Q) that cannot bind FcγR exhibited prophylactic and therapeutic efficacy against ADE-induced lethal challenge. These observations provide insight into the pathogenesis of antibody-enhanced dengue disease and identify a novel strategy for the design of therapeutic antibodies against dengue.BRII recipient: HarrispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6139r6w4articlePLoS Pathogensvol 6, iss 2, e10007901553-7374oai:escholarship.org:ark:/13030/qt4pb8q90q2016-12-22T22:31:44Zqt4pb8q90qTaxonomic review of the Pterostichini and Loxandrini fauna of New Caledonia (Coleoptera, Carabidae)Will, Kipling2011-11-16The generic-level taxa included in Pterostichini and Loxandrini from New Caledonia are reviewed and a key to genera and species provided. Two new genera are described, Paniestichus and Abacophrastus, with the following new species: Paniestichus subsolianus, Abacophrastus millei, Abacophrastus chapes, Abacophrastus carnifex, Abacophrastus hobbit, Abacophrastus megalops, Abacophrastus reflexus and Abacophrastus bellorum. Abacoleptus curtus new species, is described. Notonomus irideus and Notonomus savesi are moved to Prosopogmus. Four new species of Prosopogmus are described: Prosopogmus koghisensis, Prosopogmus lescheni, Prosopogmus fortis and Prosopogmus aoupiniensis. Homalosoma griseolum is moved to Sphodrosomus. Cerabilia is newly recorded from New Caledonia and the genus is moved from Platynini to Loxandrini and therefore is the first report of Loxandrini from New Caledonia. An apparent adventive from Australia, Darodilia, is newly reported from New Caledonia.BRII recipient: WillpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4pb8q90qarticleZooKeysvol 147, 337-3971313-2970 1313-2989oai:escholarship.org:ark:/13030/qt6zj492jg2016-12-22T22:30:47Zqt6zj492jgA Real-Time PCR Antibiogram for Drug-Resistant SepsisWaldeisen, John RWang, TimMitra, DebkishoreLee, Luke P2011-12-02Current molecular diagnostic techniques for susceptibility testing of septicemia rely on genotyping for the presence of known resistance cassettes. This technique is intrinsically vulnerable due to the inability to detect newly emergent resistance genes. Traditional phenotypic susceptibility testing has always been a superior method to assay for resistance; however, relying on the multi-day growth period to determine which antimicrobial to administer jeopardizes patient survival. These factors have resulted in the widespread and deleterious use of broad-spectrum antimicrobials. The real-time PCR antibiogram, described herein, combines universal phenotypic susceptibility testing with the rapid diagnostic capabilities of PCR. We have developed a procedure that determines susceptibility by monitoring pathogenic load with the highly conserved 16S rRNA gene in blood samples exposed to different antimicrobial drugs. The optimized protocol removes heme and human background DNA from blood, which allows standard real-time PCR detection systems to be employed with high sensitivity (<100 CFU/mL). Three strains of E. coli, two of which were antimicrobial resistant, were spiked into whole blood and exposed to three different antibiotics. After real-time PCR-based determination of pathogenic load, a ΔCt<3.0 between untreated and treated samples was found to indicate antimicrobial resistance (P<0.01). Minimum inhibitory concentration was determined for susceptible bacteria and pan-bacterial detection was demonstrated with 3 Gram-negative and 2 Gram-positive bacteria. Species identification was performed via analysis of the hypervariable amplicons. In summary, we have developed a universal diagnostic phenotyping technique that assays for the susceptibility of drug-resistant septicemia with the speed of PCR. The real-time PCR antibiogram achieves detection, susceptibility testing, minimum inhibitory concentration determination, and identification in less than 24 hours.BRII recipient: WaldeisenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6zj492jgarticlePLoS ONEvol 6, iss 12, e285281932-6203oai:escholarship.org:ark:/13030/qt1v63c73t2016-12-22T22:29:54Zqt1v63c73tHigh Genetic Diversity Despite the Potential for Stepping-Stone Colonizations in an Invasive Species of Gecko on Moorea, French PolynesiaTonione, Maria AReeder, NatalieMoritz, Craig C2011-11-02Invasive species often have reduced genetic diversity, but the opposite can be true if there have been multiple introductions and genetic admixture. Reduced diversity is most likely soon after establishment, in remote locations, when there is lower propagule pressure and with stepping-stone colonizations. The common house gecko (Hemidactylus frenatus) was introduced to Moorea, French Polynesia in the remote eastern Pacific within the last two decades and accordingly is expected to exhibit low diversity. In contrast, we show that H. frenatus on Moorea has exceptionally high genetic diversity, similar to that near the native range in Asia and much higher than reported for other Pacific island reptiles. The high diversity in this recently founded population likely reflects extensive genetic admixture in source population(s) and a life history that promotes retention of diversity. These observations point to the importance of understanding range-wide dynamics of genetic admixture in highly invasive species.BRII recipient: TonionepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1v63c73tarticlePLoS ONEvol 6, iss 11, e268741932-6203oai:escholarship.org:ark:/13030/qt1bx5h2242016-12-22T22:29:04Zqt1bx5h224A New Basal Caniform (Mammalia: Carnivora) from the Middle Eocene of North America and Remarks on the Phylogeny of Early CarnivoransTomiya, Susumu2011-09-14Despite a long history of research, the phylogenetic origin and initial diversification of the mammalian crown-group Carnivora remain elusive. Well-preserved fossil materials of basal carnivorans are essential for resolving these issues, and for constraining the timing of the carnivoran origin, which constitutes an important time-calibration point in mammalian phylogenetics. Methodology/Principal Findings: A new carnivoramorphan from the middle Eocene of southern California, Lycophocyon hutchisoni, is described. The new taxon exhibits stages of dental and basicranial evolution that are intermediate between earlier carnivoramorphans and the earliest representatives of canoid carnivorans. The evolutionary affinity of the new taxon was determined by a cladistic analysis of previously-published and newly-acquired morphological data for 30 Paleogene carnivoramorphans. The most-parsimonious trees identified L. hutchisoni as a basal caniform carnivoran, and placed (1) Tapocyon robustus, Quercygale angustidens, “Miacis” sylvestris, “M.” uintensis, and “M.” gracilis inside or outside the Carnivora, (2) nimravids within the Feliformia, and (3) the amphicyonid Daphoenus outside the crown-group Canoidea. Parsimony reconstructions of ancestral character states suggest that loss of the upper third molars and development of well-ossified entotympanics that are firmly fused to the basicranium (neither condition is observed in L. hutchisoni) are not associated with the origin of the Carnivora as traditionally thought, but instead occurred independently in the Caniformia and the Feliformia. A discriminant analysis of the estimated body weight and dental ecomorphology predicted a mesocarnivorous diet for L. hutchisoni, and the postcranial morphology suggests a scansorial habit. Conclusions/Significance: Lycophocyon hutchisoni illuminates the morphological evolution of early caniforms leading to the origin of crown-group canoids. Considerable uncertainty remains with respect to the phylogenetic origin of the Carnivora. The minimum date of caniform-feliform divergence is provisionally suggested to be either 47 million years ago or 38 million years ago, depending on the position of “Miacis” sylvestris within or outside the Carnivora, respectively.BRII recipient: TomiyapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1bx5h224articlePLoS ONEvol 6, iss 9, e241461932-6203oai:escholarship.org:ark:/13030/qt94b839xc2016-12-22T22:27:21Zqt94b839xcInternal versus external determinants of Schistosoma japonicum transmission in irrigated agricultural villagesSpear, R C2011-07-13Currently schistosomiasis transmission has been suppressed to low levels in many historically endemic areas of China by widespread use of praziquantel in human and bovine populations and application of niclosamide for snail control. However, re-emergent transmission has signalled the need for sustainable interventions beyond these repeated chemical interventions. To take advantage of ongoing investment in rural infrastructure, an index of schistosomiasis transmission potential is needed to identify villages where environmental modifications would be particularly effective. Based on a retrospective analysis of data from 10 villages in Sichuan Province, an index linked to the basic reproductive number is shown to have promise in meeting this need. However, a lack of methods for estimating the spatial components of the proposed metric and for estimating the import of cercariae and miracidia from neighbouring villages leads to significant uncertainty in its estimation. These findings suggest a priority effort to develop methods for measuring the free-swimming forms of the parasite in surface waters. This need is underscored by the high cost and limited sensitivity of current methods for diagnosing human infection and mounting evidence of the inadequacy of snail surveys to identify environments supporting low levels of transmission.BRII recipient: Spear (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/94b839xcarticleJournal of The Royal Society Interfacevol 9, iss 67, 272-2821742-5689 1742-5662oai:escholarship.org:ark:/13030/qt7dj8t8h82016-12-22T22:25:17Zqt7dj8t8h8New Method for Parameter Estimation in Probabilistic Models: Minimum Probability FlowSohl-Dickstein, JaschaBattaglino, Peter BDeWeese, Michael R2011-11-21Fitting probabilistic models to data is often difficult, due to the general intractability of the partition function. We propose a new parameter fitting method, minimum probability flow (MPF), which is applicable to any parametric model. We demonstrate parameter estimation using MPF in two cases: a continuous state space model, and an Ising spin glass. In the latter case, MPF outperforms current techniques by at least an order of magnitude in convergence time with lower error in the recovered coupling parameters.BRII recipient: DeWeese (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7dj8t8h8articlePhysical Review Lettersvol 107, iss 220031-9007 1079-7114oai:escholarship.org:ark:/13030/qt3t34n8vz2016-12-22T20:03:33Zqt3t34n8vzOccurrence of Grapevine Leafroll-Associated Virus Complex in Napa ValleySharma, Abhineet MWang, JinboDuffy, SiobainZhang, SimingWong, Michelle KRashed, ArashCooper, Monica LDaane, Kent MAlmeida, Rodrigo P. P2011-10-19Grapevine leafroll disease (GLD) is caused by a complex of several virus species (grapevine leafroll-associated viruses, GLRaV) in the family Closteroviridae. Because of its increasing importance, it is critical to determine which species of GLRaV is predominant in each region where this disease is occurring. A structured sampling design, utilizing a combination of RT-PCR based testing and sequencing methods, was used to survey GLRaVs in Napa Valley (California, USA) vineyards (n = 36). Of the 216 samples tested for GLRaV-1, -2, -3, -4, -5, and -9, 62% (n = 134) were GLRaV positive. Of the positives, 81% (n = 109) were single infections with GLRaV-3, followed by GLRaV-2 (4%, n = 5), while the remaining samples (15%, n = 20) were mixed infections of GLRaV-3 with GLRaV-1, 2, 4, or 9. Additionally, 468 samples were tested for genetic variants of GLRaV-3, and of the 65% (n = 306) of samples positive for GLRaV-3, 22% were infected with multiple GLRaV-3 variants. Phylogenetic analysis utilizing sequence data from the single infection GLRaV-3 samples produced seven well-supported GLRaV-3 variants, of which three represented 71% of all GLRaV-3 positive samples in Napa Valley. Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples. Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley. Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events.BRII recipient: AlmeidapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3t34n8vzarticlePLoS ONEvol 6, iss 10, e262271932-6203oai:escholarship.org:ark:/13030/qt0qh9q9sm2016-12-22T20:02:17Zqt0qh9q9smInferring Social Network Structure from Bacterial Sequence DataPlucinski, Mateusz MStarfield, RichardAlmeida, Rodrigo P. P2011-08-01Using DNA sequence data from pathogens to infer transmission networks has traditionally been done in the context of epidemics and outbreaks. Sequence data could analogously be applied to cases of ubiquitous commensal bacteria; however, instead of inferring chains of transmission to track the spread of a pathogen, sequence data for bacteria circulating in an endemic equilibrium could be used to infer information about host contact networks. Here, we show—using simulated data—that multilocus DNA sequence data, based on multilocus sequence typing schemes (MLST), from isolates of commensal bacteria can be used to infer both local and global properties of the contact networks of the populations being sampled. Specifically, for MLST data simulated from small-world networks, the small world parameter controlling the degree of structure in the contact network can robustly be estimated. Moreover, we show that pairwise distances in the network—degrees of separation—correlate with genetic distances between isolates, so that how far apart two individuals in the network are can be inferred from MLST analysis of their commensal bacteria. This result has important consequences, and we show an example from epidemiology: how this result could be used to test for infectious origins of diseases of unknown etiology.BRII Recipient: PlucinskipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0qh9q9smarticlePLoS ONEvol 6, iss 8, e226851932-6203oai:escholarship.org:ark:/13030/qt7ft8k5032016-12-22T20:01:11Zqt7ft8k503Genome-Wide Functional Profiling Reveals Genes Required for Tolerance to Benzene Metabolites in YeastNorth, MatthewTandon, Vickram JThomas, ReubenLoguinov, AlexGerlovina, InnaHubbard, Alan EZhang, LuopingSmith, Martyn TVulpe, Chris D2011-08-30Benzene is a ubiquitous environmental contaminant and is widely used in industry. Exposure to benzene causes a number of serious health problems, including blood disorders and leukemia. Benzene undergoes complex metabolism in humans, making mechanistic determination of benzene toxicity difficult. We used a functional genomics approach to identify the genes that modulate the cellular toxicity of three of the phenolic metabolites of benzene, hydroquinone (HQ), catechol (CAT) and 1,2,4-benzenetriol (BT), in the model eukaryote Saccharomyces cerevisiae. Benzene metabolites generate oxidative and cytoskeletal stress, and tolerance requires correct regulation of iron homeostasis and the vacuolar ATPase. We have identified a conserved bZIP transcription factor, Yap3p, as important for a HQ-specific response pathway, as well as two genes that encode putative NAD(P)H:quinone oxidoreductases, PST2 and YCP4. Many of the yeast genes identified have human orthologs that may modulate human benzene toxicity in a similar manner and could play a role in benzene exposure-related disease.BRII recipient: NorthpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7ft8k503articlePLoS ONEvol 6, iss 8, e242051932-6203oai:escholarship.org:ark:/13030/qt84j7n6pd2016-12-22T20:00:04Zqt84j7n6pdPredictors for reproductive isolation in a ring species complex following genetic and ecological divergencePereira, Ricardo JMonahan, William BWake, David B2011-01-01Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI.Results:By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI.Conclusions:These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.BRII recipient: WakepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/84j7n6pdarticleBMC Evolutionary Biologyvol 11, iss 1, 1941471-2148oai:escholarship.org:ark:/13030/qt8z50r52s2016-12-22T19:58:31Zqt8z50r52sPaternal Smoking and Risk of Childhood Acute Lymphoblastic Leukemia: Systematic Review and Meta-AnalysisLiu, RuilingZhang, LuopingMcHale, Cliona MHammond, S. Katharine2011-01-01Objective. To investigate the association between paternal smoking and childhood acute lymphoblastic leukemia (ALL). Method. We identified 18 published epidemiologic studies that reported data on both paternal smoking and childhood ALL risk. We performed a meta-analysis and analyzed dose-response relationships on ALL risk for smoking during preconception, during pregnancy, after birth, and ever smoking. Results. The summary odds ratio (OR) of childhood ALL associated with paternal smoking was 1.11 (95% Confidence Interval (CI): 1.05–1.18, %) during any time period, 1.25 (95% CI: 1.08–1.46, %) preconception; 1.24 (95% CI: 1.07–1.43, %) during pregnancy, and 1.24 (95% CI: 0.96–1.60, %) after birth, with a dose-response relationship between childhood ALL and paternal smoking preconception or after birth. Conclusion. The evidence supports a positive association between childhood ALL and paternal ever smoking and at each exposure time period examined. Future epidemiologic studies should assess paternal smoking during well-defined exposure windows and should include biomarkers to assess smoking exposure and toxicological mechanisms.BRII recipient: LiupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8z50r52spublicationoai:escholarship.org:ark:/13030/qt8jn2809m2016-12-22T19:57:20Zqt8jn2809mRestaurant and Bar Owners' Exposure to Secondhand Smoke and Attitudes Regarding Smoking Bans in Five Chinese CitiesLiu, RuilingHammond, S. KatharineHyland, AndrewTravers, Mark JYang, YanNan, YiFeng, GuozeLi, QiangJiang, Yuan2011-05-12Despite the great progress made towards smoke-free environments, only 9% of countries worldwide mandate smoke-free restaurants and bars. Smoking was generally not regulated in restaurants and bars in China before 2008. This study was designed to examine the public attitudes towards banning smoking in these places in China. A convenience sample of 814 restaurants and bars was selected in five Chinese cities and all owners of these venues were interviewed in person by questionnaire in 2007. Eighty six percent of current nonsmoking subjects had at least one-day exposure to secondhand smoke (SHS) at work in the past week. Only 51% of subjects knew SHS could cause heart disease. Only 17% and 11% of subjects supported prohibiting smoking completely in restaurants and in bars, respectively, while their support for restricting smoking to designated areas was much higher. Fifty three percent of subjects were willing to prohibit or restrict smoking in their own venues. Of those unwilling to do so, 82% thought smoking bans would reduce revenue, and 63% thought indoor air quality depended on ventilation rather than smoking bans. These results showed that there was support for smoking bans among restaurant or bar owners in China despite some knowledge gaps. To facilitate smoking bans in restaurants and bars, it is important to promote health education on specific hazards of SHS, provide country-specific evidence on smoking bans and hospitality revenues, and disseminate information that restricting smoking and ventilation alone cannot eliminate SHS hazards.BRII recipient: LiupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8jn2809marticleInternational Journal of Environmental Research and Public Healthvol 8, iss 12, 1520-15331660-4601oai:escholarship.org:ark:/13030/qt84g5z2nd2016-12-22T18:52:56Zqt84g5z2ndComparative Analysis of Chromosome Counts Infers Three Paleopolyploidies in the MolluscaHallinan, N. MLindberg, D. R2011-08-22The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If the branches of a phylogeny on which a whole-genome duplication (WGD) occurred could be identified before genome sequencing, taxa could be selected that provided a better assessment of that genome duplication. Here, we describe a likelihood model in which the number of chromosomes in a genome evolves according to a Markov process with one rate of chromosome duplication and loss that is proportional to the number of chromosomes in the genome and another stochastic rate at which every chromosome in the genome could duplicate in a single event. We compare the maximum likelihoods of a model in which the genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, to determine if a model with WGDs is a good fit for the data. Once it has been determined that the data does fit the WGD model, we infer the phylogenetic position of paleopolyploidies by calculating the posterior probability that a WGD occurred on each branch of the taxon tree. Here, we apply this model to a molluscan tree represented by 124 taxa and infer three putative WGD events. In the Gastropoda, we identify a single branch within the Hypsogastropoda and one of two branches at the base of the Stylommatophora. We also identify one or two branches near the base of the Cephalopoda.BRII recipient: Lindberg (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/84g5z2ndarticleGenome Biology and Evolutionvol 3, iss 0, 1150-11631759-6653oai:escholarship.org:ark:/13030/qt3hv0s6732016-12-22T18:51:55Zqt3hv0s673Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of AfricaFuchs, JeromeFjeldsa, JonBowie, Rauri C2011-01-01The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (Phyllastephus debilis) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies albigula (green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies rabai (grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (Phyllastrephus debilis) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages.Results:We found significant biometric differences between the lowland (rabai) and montane (albigula) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago.Our coalescent analyses suggest that limited gene flow, mostly from the subspecies rabai to albigula, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of rabai further inland.Conclusion:The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend albigula be elevated to species rank.BRII recipient: BowiepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3hv0s673articleBMC Evolutionary Biologyvol 11, iss 1, 1171471-2148oai:escholarship.org:ark:/13030/qt77j3w46w2016-12-22T18:50:33Zqt77j3w46wSOA from limonene: role of NO3 in its generation and degradationFry, J. LKiendler-Scharr, A.Rollins, A. WBrauers, T.Brown, S. SDorn, H.-P.Dube, W. PFuchs, H.Mensah, A.Rohrer, F.Tillmann, R.Wahner, A.Wooldridge, P. JCohen, R. C2011-04-28The formation of organic nitrates and secondary organic aerosol (SOA) were monitored during the NO3 + limonene reaction in the atmosphere simulation chamber SAPHIR at Research Center Jülich. The 24-h run began in a purged, dry, particle-free chamber and comprised two injections of limonene and oxidants, such that the first experiment measured SOA yield in the absence of seed aerosol, and the second experiment yields in the presence of 10 μg m−3 seed organic aerosol. After each injection, two separate increases in aerosol mass were observed, corresponding to sequential oxidation of the two limonene double bonds. Analysis of the measured NO3, limonene, product nitrate concentrations, and aerosol properties provides mechanistic insight and constrains rate constants, branching ratios and vapor pressures of the products. The organic nitrate yield from NO3 + limonene is ≈30%. The SOA mass yield was observed to be 25–40%. The first injection is reproduced by a kinetic model. PMF analysis of the aerosol composition suggests that much of the aerosol mass results from combined oxidation by both O3 and NO3, e.g., oxidation of NO3 + limonene products by O3. Further, later aerosol nitrate mass seems to derive from heterogeneous uptake of NO3 onto unreacted aerosol alkene.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/77j3w46warticleAtmospheric Chemistry and Physicsvol 11, iss 8, 3879-38941680-7324oai:escholarship.org:ark:/13030/qt11m5b4622016-12-22T18:49:30Zqt11m5b462On the Geometry of Almost Fitzpatrick, Sean2011-01-01BRII recipient: FitzpatrickpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/11m5b462articleISRN Geometryvol 2011, 1-122090-6315oai:escholarship.org:ark:/13030/qt5538z09q2016-12-22T18:43:18Zqt5538z09qLong-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations AloneDuBay, Kateri HBothma, Jacques PGeissler, Phillip L2011-09-29Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations.BRII recipient: GeisslerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5538z09qarticlePLoS Computational Biologyvol 7, iss 9, e10021681553-7358oai:escholarship.org:ark:/13030/qt9mk306gv2016-12-22T18:42:17Zqt9mk306gvGlobal and regional effects of the photochemistry of CH3O2NO2: evidence from ARCTASBrowne, E. CPerring, A. EWooldridge, P. JApel, E.Hall, S. RHuey, L. GMao, J.Spencer, K. MClair, J. M. St.Weinheimer, A. JWisthaler, A.Cohen, R. C2011-05-06Using measurements from the NASA Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) experiment, we show that methyl peroxy nitrate (CH3O2NO2) is present in concentrations of ~5–15 pptv in the springtime arctic upper troposphere. We investigate the regional and global effects of CH3O2NO2 by including its chemistry in the GEOS-Chem 3-D global chemical transport model. We find that at temperatures below 240 K inclusion of CH3O2NO2 chemistry results in decreases of up to ~20 % in NOx, ~20 % in N2O5, ~5 % in HNO3, ~2 % in ozone, and increases in methyl hydrogen peroxide of up to ~14 %. Larger changes are observed in biomass burning plumes lofted to high altitude. Additionally, by sequestering NOx at low temperatures, CH3O2NO2 decreases the cycling of HO2 to OH, resulting in a larger upper tropospheric HO2 to OH ratio. These results may impact some estimates of lightning NOx sources as well as help explain differences between models and measurements of upper tropospheric composition.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9mk306gvarticleAtmospheric Chemistry and Physicsvol 11, iss 9, 4209-42191680-7324oai:escholarship.org:ark:/13030/qt2b79r1r12016-12-22T18:41:15Zqt2b79r1r1Genetic Population Structure of Tectura paleacea: Implications for the Mechanisms Regulating Population Structure in Patchy Coastal HabitatsBegovic, EminaLindberg, David R2011-04-07The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda) belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California – Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb) sequences were obtained from 20 individuals (10 per year) from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC) biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation efforts in near shore marine environments.BRII recipient: BegovicpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2b79r1r1articlePLoS ONEvol 6, iss 4, e184081932-6203oai:escholarship.org:ark:/13030/qt7w69k06f2016-12-22T18:40:11Zqt7w69k06fEssential Requirements for Robust Signaling in Hfq Dependent Small RNA NetworksAdamson, David NLim, Han N2011-08-18Bacteria possess networks of small RNAs (sRNAs) that are important for modulating gene expression. At the center of many of these sRNA networks is the Hfq protein. Hfq's role is to quickly match cognate sRNAs and target mRNAs from among a large number of possible combinations and anneal them to form duplexes. Here we show using a kinetic model that Hfq can efficiently and robustly achieve this difficult task by minimizing the sequestration of sRNAs and target mRNAs in Hfq complexes. This sequestration can be reduced by two non-mutually exclusive kinetic mechanisms. The first mechanism involves heterotropic cooperativity (where sRNA and target mRNA binding to Hfq is influenced by other RNAs bound to Hfq); this cooperativity can selectively decrease singly-bound Hfq complexes and ternary complexes with non-cognate sRNA-target mRNA pairs while increasing cognate ternary complexes. The second mechanism relies on frequent RNA dissociation enabling the rapid cycling of sRNAs and target mRNAs among different Hfq complexes; this increases the probability the cognate ternary complex forms before the sRNAs and target mRNAs degrade. We further demonstrate that the performance of sRNAs in isolation is not predictive of their performance within a network. These findings highlight the importance of experimentally characterizing duplex formation in physiologically relevant contexts with multiple RNAs competing for Hfq. The model will provide a valuable framework for guiding and interpreting these experiments.BRII recipient: AdamsonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7w69k06farticlePLoS Computational Biologyvol 7, iss 8, e10021381553-7358oai:escholarship.org:ark:/13030/qt7312970m2016-12-22T18:38:58Zqt7312970mExtraordinary epitaxial alignment of graphene islands on Au(111)Wofford, Joseph MStarodub, ElenaWalter, Andrew LNie, ShuBostwick, AaronBartelt, Norman CThuermer, KonradRotenberg, EliMcCarty, Kevin FDubon, Oscar D2012-05-07Pristine, single-crystalline graphene displays a unique collection of remarkable electronic properties that arise from its two-dimensional, honeycomb structure. Using in situ low-energy electron microscopy, we show that when deposited on the (111) surface of Au carbon forms such a structure. The resulting monolayer, epitaxial film is formed by the coalescence of dendritic graphene islands that nucleate at a high density. Over 95% of these islands can be identically aligned with respect to each other and to the Au substrate. Remarkably, the dominant island orientation is not the better lattice-matched 30° rotated orientation but instead one in which the graphene [01] and Au [011] in-plane directions are parallel. The epitaxial graphene film is only weakly coupled to the Au surface, which maintains its reconstruction under the slightly p-type doped graphene. The linear electronic dispersion characteristic of free-standing graphene is retained regardless of orientation. That a weakly interacting, non-lattice matched substrate is able to lock graphene into a particular orientation is surprising. This ability, however, makes Au(111) a promising substrate for the growth of single crystalline graphene films.BRII recipient: DubonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7312970marticleNew Journal of Physicsvol 14, iss 5, 0530081367-2630oai:escholarship.org:ark:/13030/qt43q3k2222016-12-22T18:37:35Zqt43q3k222A new species of Lesticus Dejean, 1828 (Coleoptera, Carabidae) from the Finisterre Range, Papua New Guinea and a key to the genera of pterostichine-like Harpalinae of New GuineaWill, KiplingKavanaugh, David2012-11-29Lesticus finisterrae (Carabidae: Pterostichini) sp. n. (type locality: Finisterre Range, Papua New Guinea), is described and characters to differentiate it from other “Trigonotomi” species are given. A key to the genera of pterostichine-like Harpalinae of the island, including all genera of Morionini, Cratocerini, Drimostomatini, Abacetini, Loxandrini and Pterostichini, is provided. The genus Rhytisternus (Pterostichini) is for the first time reported from New Guinea, represented by the likely adventive species Rhytisternus laevis (Macleay). The previously unknown male of Stegazopteryx ivimkaensis Will (Drimostomatini) is described.BRII recipient: WillpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/43q3k222articleZooKeysvol 246, 27-371313-2970 1313-2989oai:escholarship.org:ark:/13030/qt0tc179sc2016-12-22T18:36:17Zqt0tc179scDarwin Core: An Evolving Community-Developed Biodiversity Data StandardWieczorek, JohnBloom, DavidGuralnick, RobertBlum, StanDoring, MarkusGiovanni, RenatoRobertson, TimVieglais, David2012-01-06Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.BRII recipient: WieczorekpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0tc179scarticlePLoS ONEvol 7, iss 1, e297151932-6203oai:escholarship.org:ark:/13030/qt7r57m8gp2016-12-22T18:07:36Zqt7r57m8gpThe Ontogenetic Osteohistology of Tenontosaurus tillettiWerning, Sarah2012-03-28Tenontosaurus tilletti is an ornithopod dinosaur known from the Early Cretaceous (Aptian-Albian) Cloverly and Antlers formations of the Western United States. It is represented by a large number of specimens spanning a number of ontogenetic stages, and these specimens have been collected across a wide geographic range (from central Montana to southern Oklahoma). Here I describe the long bone histology of T. tilletti and discuss histological variation at the individual, ontogenetic and geographic levels. The ontogenetic pattern of bone histology in T. tilletti is similar to that of other dinosaurs, reflecting extremely rapid growth early in life, and sustained rapid growth through sub-adult ontogeny. But unlike other iguanodontians, this dinosaur shows an extended multi-year period of slow growth as skeletal maturity approached. Evidence of termination of growth (e.g., an external fundamental system) is observed in only the largest individuals, although other histological signals in only slightly smaller specimens suggest a substantial slowing of growth later in life. Histological differences in the amount of remodeling and the number of lines of arrested growth varied among elements within individuals, but bone histology was conservative across sampled individuals of the species, despite known paleoenvironmental differences between the Antlers and Cloverly formations. The bone histology of T. tilletti indicates a much slower growth trajectory than observed for other iguanodontians (e.g., hadrosaurids), suggesting that those taxa reached much larger sizes than Tenontosaurus in a shorter time.BRII recipient: WerningpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7r57m8gparticlePLoS ONEvol 7, iss 3, e335391932-6203oai:escholarship.org:ark:/13030/qt77h634v02016-12-22T18:06:32Zqt77h634v0A note on the Wehrheim-Woodward categoryWeinstein, Alan2012-02-01Wehrheim and Woodward have shown how to embed all the canonical relations between symplectic manifolds into a category in which the composition is the usual one when transversality and embedding assumptions are satisfied. A morphism in their category is an equivalence class of composable sequences of canonical relations, with composition given by concatenation. In this note, we show that every such morphism is represented by a sequence consisting of just two relations, one of them a reduction and the other a coreduction.BRII recipient: WeinsteinpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/77h634v0articleJournal of Geometric Mechanicsvol 3, iss 4, 507-5151941-4889oai:escholarship.org:ark:/13030/qt8wv1x1xj2016-12-22T18:05:29Zqt8wv1x1xjDissociation of Immune Responses from Pathogen Colonization Supports Pattern Recognition in C. elegansTwumasi-Boateng, KwameShapira, Michael2012-04-13Caenorhabditis elegans has been used for over a decade to characterize signaling cascades controlling innate immune responses. However, what initiates these responses in the worm has remained elusive. To gain a better understanding of the initiating events we delineated genome-wide immune responses to the bacterial pathogen Pseudomonas aeruginosa in worms heavily-colonized by the pathogen versus worms visibly not colonized. We found that infection responses in both groups were identical, suggesting that immune responses were not correlated with colonization and its associated damage. Quantitative RT-PCR measurements further showed that pathogen secreted factors were not able to induce an immune response, but exposure to a non-pathogenic Pseudomonas species was. These findings raise the possibility that the C.elegans immune response is initiated by recognition of microbe-associated molecular patterns. In the absence of orthologs of known pattern recognition receptors, C. elegans may rely on novel mechanisms, thus holding the potential to advance our understanding of evolutionarily conserved strategies for pathogen recognition.BRII recipient: ShapirapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8wv1x1xjarticlePLoS ONEvol 7, iss 4, e354001932-6203oai:escholarship.org:ark:/13030/qt4fp5w5js2016-12-22T18:04:40Zqt4fp5w5jsAn age-dependent reversal in the protective capacities of JNK signaling shortens Caenorhabditis elegans lifespanTwumasi-Boateng, KwameWang, Tim WTsai, LindaLee, Kuang-HuiSalehpour, AliBhat, SudarshanTan, Man-WahShapira, Michael2012-08-01Stress-activated protein kinase (SAPK) pathways are evolutionarily conserved signaling modules that orchestrate protective responses to adverse environmental conditions. However, under certain conditions, their activation can be deleterious. Thus, activation of the c-Jun N-terminal kinase (JNK) SAPK pathway exacerbates a diverse set of pathologies, many of which are typical of old age. The contexts determining whether the outcome of JNK signaling is protective or detrimental are not fully understood. Here, we show that the age of an animal defines such a context. The Caenorhabditis elegans JNK homolog, KGB-1, provides protection from heavy metals and protein folding stress in developing animals. However, we found that with the onset of adulthood, KGB-1 activity becomes detrimental, reducing stress resistance and lifespan. Genetic analyses coupled with fluorescent imaging linked this phenotypic switch to age-dependent antagonistic modulation of DAF-16/FOXO: KGB-1 activation enhanced DAF-16 nuclear localization and transcriptional activity during development but decreased it in adults. Epistasis analyses showed that DAF-16 was necessary and sufficient to explain some of the kgb-1-dependent detrimental phenotypes, but not all. The identification of early adulthood as a point following which the contribution of KGB-1 activity reverses from beneficial to detrimental sheds new light on the involvement of JNK signaling in age-related pathologies. Furthermore, the age-dependent reversal has intriguing implications for our understanding of aging.BRII recipient: Shapira (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4fp5w5jsarticleAging Cellvol 11, iss 4, 659-66714749718oai:escholarship.org:ark:/13030/qt7742x8rp2016-12-22T18:03:39Zqt7742x8rpA Marine Stem-Tetrapod from the Devonian of Western North AmericaSwartz, Brian2012-03-20The origin of terrestrial vertebrates represents one of the major evolutionary and ecological transformations in the history of life, and the established timing and environment of this transition has recently come under scrutiny. The discovery and description of a well-preserved fossil sarcopterygian (fleshy-limbed vertebrate) from the Middle Devonian of Nevada helps to refine and question aspects of the temporal and anatomical framework that underpins the tetrapod condition. This new taxon, Tinirau clackae, demonstrates that substantial parallelism pervaded the early history of stem-tetrapods, raises additional questions about when digited sarcopterygians first evolved, and further documents that incipient stages of the terrestrial appendicular condition began when sarcopterygians still retained their median fins and occupied aquatic habitats.BRII recipient: SwartzpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7742x8rparticlePLoS ONEvol 7, iss 3, e336831932-6203oai:escholarship.org:ark:/13030/qt305129g62016-12-22T18:02:53Zqt305129g6How safe is mist netting? evaluating the risk of injury and mortality to birdsSpotswood, Erica NGoodman, Kari RoeschCarlisle, JayCormier, Rene LHumple, Diana LRousseau, JoseGuers, Susan LBarton, Gina G2012-02-011. The capture of birds using mist nets is a widely utilized technique for monitoring avian populations. While the method is assumed to be safe, very few studies have addressed how frequently injuries and mortalities occur and the associated risks have not been formally evaluated.2. We quantified the rates of mortality and injury at 22 banding organizations in the United States and Canada and used capture data from five organizations to determine what kinds of incidents occur most frequently. Analyses focused on passerines and near-passerines, but other groups were included. We evaluated whether body mass, age, sex, mist net mesh size, month and time of day or frequency of capture are related to the risk or type of incident. We also compared the recapture histories over time between birds that were injured and those that were never injured for 16 species.3. The average rate of injury was 0·59%, while mortality was 0·23%. Birds captured frequently were less at risk to incident. Body mass was positively correlated with incident and larger birds were at greater risk to predation, leg injuries, broken legs, internal bleeding and cuts, while smaller birds were more prone to stress, tangling-related injuries and wing strain. Rates of incident varied among species, with some at greater risk than others. We found no evidence for increased mortality over time of injured birds compared with uninjured birds.4. We provide the first comprehensive evaluation of the risks associated with mist netting. Our results indicate that (1) injury and mortality rates below one percent can be achieved during mist netting and (2) injured birds are likely to survive in comparable numbers to uninjured birds after release. While overall risks are low, this study identified vulnerable species and traits that may increase a bird’s susceptibility to incident that should be considered in banding protocols aimed at minimizing injury and mortality. Projects using mist nets should monitor their performance and compare their results to those of other organizations.BRII recipient: Spotswood (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/305129g6articleMethods in Ecology and Evolutionvol 3, iss 1, 29-382041210Xoai:escholarship.org:ark:/13030/qt6fs2f5rw2016-12-22T18:01:35Zqt6fs2f5rwMolecules and fossils reveal punctuated diversification in Caribbean "faviid"� coralsSchwartz, Sonja ABudd, Ann FCarlon, David B2012-01-01Even with well-known sampling biases, the fossil record is key to understanding macro-evolutionary patterns. During the Miocene to Pleistocene in the Caribbean Sea, the fossil record of scleractinian corals shows a remarkable period of rapid diversification followed by massive extinction. Here we combine a time-calibrated molecular phylogeny based on three nuclear introns with an updated fossil stratigraphy to examine patterns of radiation and extinction in Caribbean corals within the traditional family Faviidae.Results:Concatenated phylogenetic analysis showed most species of Caribbean faviids were monophyletic, with the exception of two Manicina species. The time-calibrated tree revealed the stem group originated around the closure of the Tethys Sea (17.0 Ma), while the genus Manicina diversified during the Late Miocene (8.20 Ma), when increased sedimentation and productivity may have favored free-living, heterotrophic species. Reef and shallow water specialists, represented by Diploria and Favia, originate at the beginning of the Pliocene (5 – 6 Ma) as the Isthmus of Panama shoaled and regional productivity declined.Conclusions:Later origination of the stem group than predicted from the fossil record corroborates the hypothesis of morphological convergence in Diploria and Favia genera. Our data support the rapid evolution of morphological and life-history traits among faviid corals that can be linked to Mio-Pliocene environmental changes.BRII recipient: SchwartzpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6fs2f5rwarticleBMC Evolutionary Biologyvol 12, iss 1, 1231471-2148oai:escholarship.org:ark:/13030/qt5qw5f58b2016-12-22T18:00:30Zqt5qw5f58bScience and the Large Hadron Collider: a probe into instrumentation, periodization and classificationRoy, Arpita2012-09-05On September 19, 2008, the Large Hadron Collider (LHC) at CERN, Switzerland, began the world’s highest energy experiments as a probe into the structure of matter and forces of nature. Just nine days after the gala start-up, an explosion occurred in the LHC tunnel that brought the epic collider to a complete standstill. In light of the catastrophic incident that disrupted the operation of the LHC, the paper investigates the relation of temporality to the cycle of work in science, and raises the question: What kind of methodological value should we ascribe to events such as crises or breakdowns? Drawing upon and integrating classical anthropological themes with two and a half years of fieldwork at the LHC particle accelerator complex, the paper explores how the incident in September, which affected the instrument, acquaints us with the distribution of work in the laboratory. The incident discloses that the organization of science is not a homogenous ensemble, but marked by an enormous diversity of tasks and personnel, at the heart of which lies the opposition of theory and practice, or pure and applied. This opposition not only forms the source and sanction of the intricate division of labor found in high-energy physics, but also provides a satisfactory answer to every question involving the interface of experimental science and engineering skill.BRII recipient: Roy (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5qw5f58barticleDialectical Anthropologyvol 36, iss 3-4, 291-3160304-4092 1573-0786oai:escholarship.org:ark:/13030/qt83t5r33q2016-12-22T17:59:37Zqt83t5r33qSpecies Differentiation on a Dynamic Landscape: Shifts in Metapopulation Genetic Structure Using the Chronology of the Hawaiian ArchipelagoRoderick, George KCroucher, Peter J. PVandergast, Amy GGillespie, Rosemary G2012-05-15Species formation during adaptive radiation often occurs in the context of a changing environment. The establishment and arrangement of populations, in space and time, sets up ecological and genetic processes that dictate the rate and pattern of differentiation. Here, we focus on how a dynamic habitat can affect genetic structure, and ultimately, differentiation among populations. We make use of the chronology and geographical history provided by the Hawaiian archipelago to examine the initial stages of population establishment and genetic divergence. We use data from a set of 6 spider lineages that differ in habitat affinities, some preferring low elevation habitats with a longer history of connection, others being more specialized for high elevation and/or wet forest, some with more general habitat affinities. We show that habitat preferences associated with lineages are important in ecological and genetic structuring. Lineages that have more restricted habitat preferences are subject to repeated episodes of isolation and fragmentation as a result of lava flows and vegetation succession. The initial dynamic set up by the landscape translates over time into discrete lineages. Further work is needed to understand how genetic changes interact with a changing set of ecological interactions amongst a shifting mosaic of landscapes to achieve species formation.BRII recipient: Roderick (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/83t5r33qarticleEvolutionary Biologyvol 39, iss 2, 192-2060071-3260 1934-2845oai:escholarship.org:ark:/13030/qt0p36c0v42016-12-22T17:57:56Zqt0p36c0v4Epidemiologic Features of Vulvovaginal Candidiasis among Reproductive-Age Women in IndiaRathod, Sujit DKlausner, Jeffrey DKrupp, KarlReingold, Arthur LMadhivanan, Purnima2012-01-01Vulvovaginal candidiasis is characterized by curd-like vaginal discharge and itching, and is associated with considerable health and economic costs. Materials and Methods. We examined the incidence, prevalence, and risk factors for vulvovaginal candidiasis among a cohort of 898 women in south India. Participants completed three study visits over six months, comprised of a structured interview and a pelvic examination. Results. The positive predictive values for diagnosis of vulvovaginal candidiasis using individual signs or symptoms were low (<19%). We did not find strong evidence for associations between sociodemographic characteristics and the prevalence of vulvovaginal candidiasis. Women clinically diagnosed with bacterial vaginosis had a higher prevalence of vulvovaginal candidiasis (Prevalence 12%, 95% CI 8.2, 15.8) compared to women assessed to be negative for bacterial vaginosis (Prevalence 6.5%, 95% 5.3, 7.6); however, differences in the prevalence of vulvovaginal candidiasis were not observed by the presence or absence of laboratory-confirmed bacterial vaginosis. Conclusions. For correct diagnosis of vulvovaginal candidiasis, laboratory confirmation of infection with Candida is necessary as well as assessment of whether the discharge has been caused by bacterial vaginosis. Studies are needed of women infected with Candida yeast species to determine the risk factors for yeast’s overgrowth.BRII recipient: RathodpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0p36c0v4publicationoai:escholarship.org:ark:/13030/qt6961v0bp2016-12-22T17:56:47Zqt6961v0bpCallose plug deposition patterns vary in pollen tubes of Arabidopsis thaliana ecotypes and tomato speciesQin, PengTing, DylanShieh, AndrewMcCormick, Sheila2012-01-01The pollen grain contains the male gametophyte that extends a pollen tube that grows through female tissues in order to deliver sperm to the embryo sac for double fertilization. Growing pollen tubes form periodic callose plugs that are thought to block off the older parts of the tube and maintain the cytoplasm near the growing tip. The morphology of callose plugs and the patterns of their deposition were previously shown to vary among species, but variation within a species had not been examined. We therefore systematically examined callose plug deposition in Arabidopsis thaliana ecotypes, tested for heritability using reciprocal crosses between ecotypes that had differing deposition patterns, and investigated the relationship between callose plugs and pollen tube growth rate. We also surveyed callose plug deposition patterns in different species of tomato.Results:We used in vitro grown pollen tubes of 14 different A. thaliana ecotypes and measured the distance from the pollen grain pore to the first callose plug (termed first interval). This distance varied among Arabidopsis ecotypes and in some cases even within an ecotype. Pollen tubes without a callose plug were shorter than those with a callose plug, and tubes with a callose plug near the grain were, on average, longer than those with the first callose plug farther from the grain. Variations in the first callose plug position were also observed between different species of tomato.Conclusions:We showed that the position of the first callose plug varied among Arabidopsis ecotypes and in tomato species, and that callose plug deposition patterns were heritable. These findings lay a foundation for mapping genes that regulate callose plug deposition or that determine pollen tube length or growth rate.BRII recipient: McCormickpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6961v0bparticleBMC Plant Biologyvol 12, iss 1, 1781471-2229oai:escholarship.org:ark:/13030/qt43k5z7t22016-12-22T17:54:37Zqt43k5z7t2On the observed response of ozone to NOx and VOC reactivity reductions in San Joaquin Valley California 1995-presentPusede, S. ECohen, R. C2012-09-17We describe the effects of nitrogen oxide (NOx) and organic reactivity reductions on the frequency of high ozone days in California's San Joaquin Valley. We use sixteen years of observations of ozone, nitrogen oxides, and temperature at sites upwind, within, and downwind of three cities to assess the probability of exceeding the California 8-h average ozone standard of 70.4 ppb at each location. The comprehensive data records in the region and the steep decreases in emissions over the last decade are sufficient to constrain the relative import of NOx and organic reactivity reductions on the frequency of violations. We show that high ozone has a large component that is due to local production, as the probability of exceeding the state standard is lowest for each city at the upwind site, increases in the city center, is highest at downwind locations, and then decreases at the receptor city to the south. We see that reductions in organic reactivity have been very effective in the central and northern regions of the San Joaquin but less so in the southern portion of the Valley. We find evidence for two distinct categories of reactivity sources: one source that has decreased and dominates at moderate temperatures, and a second source that dominates at high temperatures, particularly in the southern San Joaquin, and has not changed over the last twelve years. We show that NOx reductions are already effective or are poised to become so in the southern and central Valley, where violations are most frequent, as conditions in these regions have or are transitioning to NOx-limited chemistry when temperatures are hottest and high ozone most probable.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/43k5z7t2articleAtmospheric Chemistry and Physicsvol 12, iss 18, 8323-83391680-7324oai:escholarship.org:ark:/13030/qt7wr650p62016-12-22T17:53:36Zqt7wr650p6Fungal Diversity Associated with Hawaiian Drosophila Host PlantsOrt, Brian SBantay, Roxanne MPantoja, Norma AO'Grady, Patrick M2012-07-20Hawaiian Drosophila depend primarily, sometimes exclusively, on specific host plants for oviposition and larval development, and most specialize further on a particular decomposing part of that plant. Differences in fungal community between host plants and substrate types may establish the basis for host specificity in Hawaiian Drosophila. Fungi mediate decomposition, releasing plant micronutrients and volatiles that can indicate high quality substrates and serve as cues to stimulate oviposition. This study addresses major gaps in our knowledge by providing the first culture-free, DNA-based survey of fungal diversity associated with four ecologically important tree genera in the Hawaiian Islands. Three genera, Cheirodendron, Clermontia, and Pisonia, are important host plants for Drosophila. The fourth, Acacia, is not an important drosophilid host but is a dominant forest tree. We sampled fresh and rotting leaves from all four taxa, plus rotting stems from Clermontia and Pisonia. Based on sequences from the D1/D2 domain of the 26S rDNA gene, we identified by BLAST search representatives from 113 genera in 13 fungal classes. A total of 160 operational taxonomic units, defined on the basis of ≥97% genetic similarity, were identified in these samples, but sampling curves show this is an underestimate of the total fungal diversity present on these substrates. Shannon diversity indices ranged from 2.0 to 3.5 among the Hawaiian samples, a slight reduction compared to continental surveys. We detected very little sharing of fungal taxa among the substrates, and tests of community composition confirmed that the structure of the fungal community differed significantly among the substrates and host plants. Based on these results, we hypothesize that fungal community structure plays a central role in the establishment of host preference in the Hawaiian Drosophila radiation.BRII recipient: OrtpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7wr650p6articlePLoS ONEvol 7, iss 7, e405501932-6203oai:escholarship.org:ark:/13030/qt3022692p2016-12-22T17:19:42Zqt3022692pClimate change and disruptions to global fire activityMoritz, Max AParisien, Marc-AndreBatllori, EnricKrawchuk, Meg AVan Dorn, JeffGanz, David JHayhoe, Katharine2012-06-01Future disruptions to fire activity will threaten ecosystems and human well-being throughout the world, yet there are few fire projections at global scales and almost none from a broad range of global climate models (GCMs). Here we integrate global fire datasets and environmental covariates to build spatial statistical models of fire probability at a 0.5° resolution and examine environmental controls on fire activity. Fire models are driven by climate norms from 16 GCMs (A2 emissions scenario) to assess the magnitude and direction of change over two time periods, 2010–2039 and 2070–2099. From the ensemble results, we identify areas of consensus for increases or decreases in fire activity, as well as areas where GCMs disagree. Although certain biomes are sensitive to constraints on biomass productivity and others to atmospheric conditions promoting combustion, substantial and rapid shifts are projected for future fire activity across vast portions of the globe. In the near term, the most consistent increases in fire activity occur in biomes with already somewhat warm climates; decreases are less pronounced and concentrated primarily in a few tropical and subtropical biomes. However, models do not agree on the direction of near-term changes across more than 50% of terrestrial lands, highlighting major uncertainties in the next few decades. By the end of the century, the magnitude and the agreement in direction of change are projected to increase substantially. Most far-term model agreement on increasing fire probabilities (∼62%) occurs at mid- to high-latitudes, while agreement on decreasing probabilities (∼20%) is mainly in the tropics. Although our global models demonstrate that long-term environmental norms are very successful at capturing chronic fire probability patterns, future work is necessary to assess how much more explanatory power would be added through interannual variation in climate variables. This study provides a first examination of global disruptions to fire activity using an empirically based statistical framework and a multi-model ensemble of GCM projections, an important step toward assessing fire-related vulnerabilities to humans and the ecosystems upon which they depend.BRII recipient: MoritzpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3022692particleEcospherevol 3, iss 6, art492150-8925oai:escholarship.org:ark:/13030/qt2826h6412016-12-22T17:17:53Zqt2826h641Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edgeMorelli, T. LSmith, A. BKastely, C. RMastroserio, I.Moritz, C.Beissinger, S. R2012-08-15We conducted detailed resurveys of a montane mammal, Urocitellus beldingi, to examine the effects of climate change on persistence along the trailing edge of its range. Of 74 California sites where U. beldingi were historically recorded (1902–1966), 42 per cent were extirpated, with no evidence for colonization of previously unoccupied sites. Increases in both precipitation and temperature predicted site extirpations, potentially owing to snowcover loss. Surprisingly, human land-use change buffered climate change impacts, leading to increased persistence and abundance. Excluding human-modified sites, U. beldingi has shown an upslope range retraction of 255 m. Generalized additive models of past distribution were predictive of modern range contractions (AUC = 0.76) and projected extreme reductions (52% and 99%, respectively) of U. beldingi's southwestern range to 2080 climates (Hadley and CCCMA A2). Our study suggests the strong impacts of climate change on montane species at their trailing edge and how anthropogenic refugia may mitigate these effects.BRII recipient: Beissinger (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2826h641articleProceedings of the Royal Society B: Biological Sciencesvol 279, iss 1745, 4279-42860962-8452 1471-2954oai:escholarship.org:ark:/13030/qt0f29w31t2016-12-22T17:16:52Zqt0f29w31tObservations of atmosphere-biosphere exchange of total and speciated peroxynitrates: nitrogen fluxes and biogenic sources of peroxynitratesMin, K.-E.Pusede, S. EBrowne, E. CLaFranchi, B. WWooldridge, P. JWolfe, G. MHarrold, S. AThornton, J. ACohen, R. C2012-10-29Peroxynitrates are responsible for global scale transport of reactive nitrogen. Recent laboratory observations suggest that they may also play an important role in delivery of nutrients to plant canopies. We measured eddy covariance fluxes of total peroxynitrates (ΣPNs) and three individual peroxynitrates (APNs ≡ PAN + PPN + MPAN) over a ponderosa pine forest during the Biosphere Effects on AeRosols and Photochemistry EXperiment 2009 (BEARPEX 2009). Concentrations of these species were also measured at multiple heights above and within the canopy. While the above-canopy daytime concentrations are nearly identical for ΣPNs and APNs, we observed the downward flux of ΣPNs to be 30–60% slower than the flux of APNs. The vertical concentration gradients of ΣPNs and APNs vary with time of day and exhibit different temperature dependencies. These differences can be explained by the production of peroxynitrates other than PAN, PPN, and MPAN within the canopy (presumably as a consequence of biogenic VOC emissions) and upward fluxes of these PN species. The impact of this implied peroxynitrate flux on the interpretation of NOx fluxes and ecosystem N exchange is discussed.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0f29w31tarticleAtmospheric Chemistry and Physicsvol 12, iss 20, 9763-97731680-7324oai:escholarship.org:ark:/13030/qt2qc5x9r32016-12-22T17:15:54Zqt2qc5x9r3The Social Brain: Transcriptome Assembly and Characterization of the Hippocampus from a Social Subterranean Rodent, the Colonial Tuco-Tuco (Ctenomys sociabilis)MacManes, Matthew DLacey, Eileen A2012-09-25Elucidating the genetic mechanisms that underlie complex adaptive phenotypes is a central problem in evolutionary biology. For behavioral biologists, the ability to link variation in gene expression to the occurrence of specific behavioral traits has long been a largely unobtainable goal. Social interactions with conspecifics represent a fundamental component of the behavior of most animal species. Although several studies of mammals have attempted to uncover the genetic bases for social relationships using a candidate gene approach, none have attempted more comprehensive, transcriptome-based analyses using high throughout sequencing. As a first step toward improved understanding of the genetic underpinnings of mammalian sociality, we generated a reference transcriptome for the colonial tuco-tuco (Ctenomys sociabilis), a social species of subterranean rodent that is endemic to southwestern Argentina. Specifically, we analyzed over 500 million Illumina sequencing reads derived from the hippocampi of 10 colonial tuco-tucos housed in captivity under a variety of social conditions. The resulting reference transcriptome provides a critical tool for future studies aimed at exploring relationships between social environment and gene expression in this non-model species of social mammal.BRII recipient: MacManespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2qc5x9r3articlePLoS ONEvol 7, iss 9, e455241932-6203oai:escholarship.org:ark:/13030/qt554881kc2016-12-22T17:14:53Zqt554881kcIs Promiscuity Associated with Enhanced Selection on MHC-DQα in Mice (genus Peromyscus)?MacManes, Matthew DLacey, Eileen A2012-05-23Reproductive behavior may play an important role in shaping selection on Major Histocompatibility Complex (MHC) genes. For example, the number of sexual partners that an individual has may affect exposure to sexually transmitted pathogens, with more partners leading to greater exposure and, hence, potentially greater selection for variation at MHC loci. To explore this hypothesis, we examined the strength of selection on exon 2 of the MHC-DQα locus in two species of Peromyscus. While the California mouse (P. californicus) is characterized by lifetime social and genetic monogamy, the deer mouse (P. maniculatus) is socially and genetically promiscuous; consistent with these differences in mating behavior, the diversity of bacteria present within the reproductive tracts of females is significantly greater for P. maniculatus. To test the prediction that more reproductive partners and exposure to a greater range of sexually transmitted pathogens are associated with enhanced diversifying selection on genes responsible for immune function, we compared patterns and levels of diversity at the Class II MHC-DQα locus in sympatric populations of P. maniculatus and P. californicus. Using likelihood based analyses, we show that selection is enhanced in the promiscuous P. maniculatus. This study is the first to compare the strength of selection in wild sympatric rodents with known differences in pathogen milieu.BRII recipient: MacManespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/554881kcarticlePLoS ONEvol 7, iss 5, e375621932-6203oai:escholarship.org:ark:/13030/qt7pq208hb2016-12-22T17:13:44Zqt7pq208hbContribution of organic carbon to wood smoke particulate matter absorption of solar radiationKirchstetter, T. WThatcher, T. L2012-07-16A spectroscopic analysis of 115 wintertime particulate matter samples collected in rural California shows that wood smoke absorbs solar radiation with a strong spectral selectivity. This is consistent with prior work that has demonstrated that organic carbon (OC), in addition to black carbon (BC), appreciably absorbs solar radiation in the visible and ultraviolet spectral regions. We apportion light absorption to OC and BC and find that the absorption Ångström exponent of the light-absorbing OC in these samples ranges from 3.0 to 7.4 and averages 5.0. Further, we calculate that OC would account for 14% and BC would account for 86% of solar radiation absorbed by the wood smoke in the atmosphere (integrated over the solar spectrum from 300 to 2500 nm). OC would contribute 49% of the wood smoke particulate matter absorption of ultraviolet solar radiation at wavelengths below 400 nm and, therefore, may affect tropospheric photochemistry. These results illustrate that BC is the dominant light-absorbing particulate matter species in atmospheres burdened with residential wood smoke and OC absorption is secondary but not insignificant. Further, these results add to the growing body of evidence that light-absorbing OC is ubiquitous in atmospheres influenced by biomass burning and may be important to include when considering particulate matter effects on climate.BRII recipient: KirchstetterpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7pq208hbarticleAtmospheric Chemistry and Physicsvol 12, iss 14, 6067-60721680-7324oai:escholarship.org:ark:/13030/qt2x5150gz2016-12-22T17:08:05Zqt2x5150gzSoil-Aggregate-Scale Heterogeneity in Microbial Selenium ReductionKausch, MatteoNg, PeterHa, JuyoungPallud, Celine2012-01-01Given the role of Se as both an environmental contaminant and a micronutrient, the microbial reduction and subsequent sequestration of bioavailable Se in soils are of great ecological interest. Primary particles in surface soils are typically bound into loosely packed, microporous aggregates, which may be critical spatial units in determining the fate of Se in soils. Surrounded by macropores where preferential flow rapidly advects dissolved compounds, soil aggregates are domains of slow diffusive transport where spatial variations in chemical concentrations and biogeochemical reactions can prevail. We conducted a series of controlled flow-through experiments utilizing three-dimensional, artificial soil aggregates (2.5-cm i.d.) surrounded by a macropore. Aggregates were composed of either quartz sand or ferrihydrite-coated sand inoculated with one of two Se-reducing bacteria (Thauera selenatis or Enterobacter cloacae SLD1a-1). Selenite export rates varied between 0.02 ± 0.01 and 3.4 ± 0.2 nmol h−1 g−1 as a function of aeration condition and input solution composition (higher SeO4
2− or C-source concentrations led to higher SeO3
2− export). Oxic input conditions significantly decreased Se reduction; however, the detection of SeO3
2− in effluent samples indicates the occurrence of anoxic microzones within aggregates. Furthermore, we found that solid-phase concentrations of reduced Se increased toward the core of aggregates and are estimated to at least double within the first millimeter into the aggregate under all conditions investigated. This indicates that concentrations of reduced Se may generally be expected to increase with distance from the advection boundary (macropore) inside aggregates, which would imply that soils with larger aggregates retain more Se.BRII recipient: Pallud (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2x5150gzarticleVadose Zone Journalvol 11, iss 2, 01539-1663oai:escholarship.org:ark:/13030/qt0x92p3632016-12-22T17:07:00Zqt0x92p363Implications of the Cressie-Read Family of Additive Divergences for Information RecoveryJudge, GeorgeMittelhammer, Ron2012-12-03To address the unknown nature of probability-sampling models, in this paper we use information theoretic concepts and the Cressie-Read (CR) family of information divergence measures to produce a flexible family of probability distributions, likelihood functions, estimators, and inference procedures. The usual case in statistical modeling is that the noisy indirect data are observed and known and the sampling model-error distribution-probability space, consistent with the data, is unknown. To address the unknown sampling process underlying the data, we consider a convex combination of two or more estimators derived from members of the flexible CR family of divergence measures and optimize that combination to select an estimator that minimizes expected quadratic loss. Sampling experiments are used to illustrate the finite sample properties of the resulting estimator and the nature of the recovered sampling distribution.BRII recipient: JudgepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0x92p363articleEntropyvol 14, iss 12, 2427-24381099-4300oai:escholarship.org:ark:/13030/qt3sf0d15w2016-12-22T17:05:21Zqt3sf0d15wGlobal Gradients in Vertebrate Diversity Predicted by Historical Area-Productivity Dynamics and Contemporary EnvironmentJetz, WalterFine, Paul V. A2012-03-27Broad-scale geographic gradients in species richness have now been extensively documented, but their historical underpinning is still not well understood. While the importance of productivity, temperature, and a scale dependence of the determinants of diversity is broadly acknowledged, we argue here that limitation to a single analysis scale and data pseudo-replication have impeded an integrated evolutionary and ecological understanding of diversity gradients. We develop and apply a hierarchical analysis framework for global diversity gradients that incorporates an explicit accounting of past environmental variation and provides an appropriate measurement of richness. Due to environmental niche conservatism, organisms generally reside in climatically defined bioregions, or “evolutionary arenas,” characterized by in situ speciation and extinction. These bioregions differ in age and their total productivity and have varied over time in area and energy available for diversification. We show that, consistently across the four major terrestrial vertebrate groups, current-day species richness of the world's main 32 bioregions is best explained by a model that integrates area and productivity over geological time together with temperature. Adding finer scale variation in energy availability as an ecological predictor of within-bioregional patterns of richness explains much of the remaining global variation in richness at the 110 km grain. These results highlight the separate evolutionary and ecological effects of energy availability and provide a first conceptual and empirical integration of the key drivers of broad-scale richness gradients. Avoiding the pseudo-replication that hampers the evolutionary interpretation of non-hierarchical macroecological analyses, our findings integrate evolutionary and ecological mechanisms at their most relevant scales and offer a new synthesis regarding global diversity gradients.BRII recipient: FinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3sf0d15warticlePLoS Biologyvol 10, iss 3, e10012921545-7885oai:escholarship.org:ark:/13030/qt5k78x05c2016-12-22T17:04:02Zqt5k78x05cDirect comparison of small RNA and transcription factor signalingHussein, R.Lim, H. N2012-05-22Small RNAs (sRNAs) and proteins acting as transcription factors (TFs) are the principal components of gene networks. These two classes of signaling molecules have distinct mechanisms of action; sRNAs control mRNA translation, whereas TFs control mRNA transcription. Here, we directly compare the properties of sRNA and TF signaling using mathematical models and synthetic gene circuits in Escherichia coli. We show the abilities of sRNAs to act on existing target mRNAs (as opposed to TFs, which alter the production of future target mRNAs) and, without needing to be first translated, have surprisingly little impact on the dynamics. Instead, the dynamics are primarily determined by the clearance rates, steady-state concentrations and response curves of the sRNAs and TFs; these factors determine the time delay before a target gene’s expression can maximally respond to changes in sRNA and TF transcription. The findings are broadly applicable to the analysis of signaling in gene networks, and we demonstrate that they can be used to rationally reprogram the dynamics of synthetic circuits.BRII recipient: LimpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5k78x05carticleNucleic Acids Researchvol 40, iss 15, 7269-72790305-1048 1362-4962oai:escholarship.org:ark:/13030/qt6kb1s6gs2016-12-22T17:02:53Zqt6kb1s6gsSteps towards a mechanistic model of global soil nitric oxide emissions: implementation and space based-constraintsHudman, R. CMoore, N. EMebust, A. KMartin, R. VRussell, A. RValin, L. CCohen, R. C2012-08-30Soils have been identified as a major source (~15%) of global nitrogen oxide (NOx) emissions. Parameterizations of soil NOx emissions (SNOx
) commonly used in the current generation of chemical transport models were designed to capture mean seasonal behaviour. These parameterizations do not, however, respond quantitatively to the meteorological triggers that are observed to result in pulsed SNOx
. Here we present a new parameterization of SNOx
implemented within a global chemical transport model (GEOS-Chem). The parameterization represents available nitrogen (N) in soils using biome specific emission factors, online wet- and dry-deposition of N, and fertilizer and manure N derived from a spatially explicit dataset, distributed using seasonality derived from data obtained by the Moderate Resolution Imaging Spectrometer. Moreover, it represents the functional form of emissions derived from point measurements and ecosystem scale experiments including pulsing following soil wetting by rain or irrigation, and emissions that are a smooth function of soil moisture as well as temperature between 0 and 30 °C. This parameterization yields global above-soil SNOx
of 10.7 Tg N yr−1, including 1.8 Tg N yr−1 from fertilizer N input (1.5% of applied N) and 0.5 Tg N yr−1 from atmospheric N deposition. Over the United States (US) Great Plains region, SNOx
are predicted to comprise 15–40% of the tropospheric NO2 column and increase column variability by a factor of 2–4 during the summer months due to chemical fertilizer application and warm temperatures. SNOx
enhancements of 50–80% of the simulated NO2 column are predicted over the African Sahel during the monsoon onset (April–June). In this region the day-to-day variability of column NO2 is increased by a factor of 5 due to pulsed-N emissions. We evaluate the model by comparison with observations of NO2 column density from the Ozone Monitoring Instrument (OMI). We find that the model is able to reproduce the observed interannual variability of NO2 (induced by pulsed-N emissions) over the US Great Plains. We also show that the OMI mean (median) NO2 observed during the overpass following first rainfall over the Sahel is 49% (23%) higher than in the five days preceding. The measured NO2 on the day after rainfall is still 23% (5%) higher, providing a direct measure of the pulse's decay time of 1–2 days. This is consistent with the pulsing representation used in our parameterization and much shorter than 5–14 day pulse decay length used in current models.BRII recipient: CohenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6kb1s6gsarticleAtmospheric Chemistry and Physicsvol 12, iss 16, 7779-77951680-7324oai:escholarship.org:ark:/13030/qt7kh527nm2016-12-22T17:01:44Zqt7kh527nmA genetic bistable switch utilizing nonlinear protein degradationHuang, DanielHoltz, William JMaharbiz, Michel M2012-01-01Bistability is a fundamental property in engineered and natural systems, conferring the ability to switch and retain states. Synthetic bistable switches in prokaryotes have mainly utilized transcriptional components in their construction. Using both transcriptional and enzymatic components, creating a hybrid system, allows for wider bistable parameter ranges in a circuit.ResultsIn this paper, we demonstrate a tunable family of hybrid bistable switches in E. coli using both transcriptional components and an enzymatic component. The design contains two linked positive feedback loops. The first loop utilizes the lambda repressor, CI, and the second positive feedback loop incorporates the Lon protease found in Mesoplasma florum (mf-Lon). We experimentally tested for bistable behavior in exponential growth phase, and found that our hybrid bistable switch was able to retain its state in the absence of an input signal throughout 40 cycles of cell division. We also tested the transient behavior of our switch and found that switching speeds can be tuned by changing the expression rate of mf-Lon.Conclusions:To our knowledge, this work demonstrates the first use of dynamic expression of an orthogonal and heterologous protease to tune a nonlinear protein degradation circuit. The hybrid switch is potentially a more robust and tunable topology for use in prokaryotic systems.BRII recipient: MaharbizpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7kh527nmarticleJournal of Biological Engineeringvol 6, iss 1, 91754-1611oai:escholarship.org:ark:/13030/qt3h0441zw2016-12-21T23:39:12Zqt3h0441zwChromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ HybridizationHsu, JoanneZeng, HuiLemke, KalistynPolyzos, ArisWeier, JinglyWang, MeiLawin-O'Brien, AnnaWeier, Heinz-UlrichO'Brien, Benjamin2012-12-20Chromosome enumeration in interphase and metaphase cells using fluorescence in situ hybridization (FISH) is an established procedure for the rapid and accurate cytogenetic analysis of cell nuclei and polar bodies, the unambiguous gender determination, as well as the definition of tumor-specific signatures. Present bottlenecks in the procedure are a limited number of commercial, non-isotopically labeled probes that can be combined in multiplex FISH assays and the relatively high price and effort to develop additional probes. We describe a streamlined approach for rapid probe definition, synthesis and validation, which is based on the analysis of publicly available DNA sequence information, also known as “database mining”. Examples of probe preparation for the human gonosomes and chromosome 16 as a selected autosome outline the probe selection strategy, define a timeline for expedited probe production and compare this novel selection strategy to more conventional probe cloning protocols.BRII recipient: HsupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3h0441zwarticleInternational Journal of Molecular Sciencesvol 14, iss 1, 57-711422-0067oai:escholarship.org:ark:/13030/qt3gt9n03c2016-12-21T23:37:21Zqt3gt9n03cA Feedback Quenched Oscillator Produces Turing Patterning with One DiffuserHsia, JustinHoltz, William JHuang, Daniel CArcak, MuratMaharbiz, Michel M2012-01-26Efforts to engineer synthetic gene networks that spontaneously produce patterning in multicellular ensembles have focused on Turing's original model and the “activator-inhibitor” models of Meinhardt and Gierer. Systems based on this model are notoriously difficult to engineer. We present the first demonstration that Turing pattern formation can arise in a new family of oscillator-driven gene network topologies, specifically when a second feedback loop is introduced which quenches oscillations and incorporates a diffusible molecule. We provide an analysis of the system that predicts the range of kinetic parameters over which patterning should emerge and demonstrate the system's viability using stochastic simulations of a field of cells using realistic parameters. The primary goal of this paper is to provide a circuit architecture which can be implemented with relative ease by practitioners and which could serve as a model system for pattern generation in synthetic multicellular systems. Given the wide range of oscillatory circuits in natural systems, our system supports the tantalizing possibility that Turing pattern formation in natural multicellular systems can arise from oscillator-driven mechanisms.BRII recipient: HsiapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3gt9n03carticlePLoS Computational Biologyvol 8, iss 1, e10023311553-7358oai:escholarship.org:ark:/13030/qt37n0k6dw2016-12-21T23:32:29Zqt37n0k6dwWhen Wet Gets Wetter: Decoupling of Moisture, Redox Biogeochemistry, and Greenhouse Gas Fluxes in a Humid Tropical Forest SoilHall, Steven JMcDowell, William HSilver, Whendee L2012-12-22Upland humid tropical forest soils are often characterized by fluctuating redox dynamics that vary temporally and spatially across the landscape. An increase in the frequency and intensity of rainfall events with climate change is likely to affect soil redox reactions that control the production and emissions of greenhouse gases. We used a 24-day rainfall manipulation experiment to evaluate temporal and spatial trends of surface soil (0–20 cm) redox-active chemical species and greenhouse gas fluxes in the Luquillo Experimental Forest, Puerto Rico. Treatments consisted of a high rainfall simulation (60 mm day−1), a fluctuating rainfall regime, and a control. Water addition generated high temporal and spatial variation in soil moisture (0.3–0.6 m3 m−3), but had no significant effect on soil oxygen (O2) concentrations. Extractable nitrate (NO3
−) concentrations decreased with daily water additions and reduced iron (Fe(II)) concentrations increased towards the end of the experiment. Overall, redox indicators displayed a weak, non-deterministic, nonlinear relationship with soil moisture. High concentrations of Fe(II) and manganese (Mn) were present even where moisture was relatively low, and net Mn reduction occurred in all plots including controls. Mean CO2 fluxes were best explained by soil C concentrations and a composite redox indicator, and not water addition. Several plots were CH4 sources irrespective of water addition, whereas other plots oscillated between weak CH4 sources and sinks. Fluxes of N2O were highest in control plots and were consistently low in water-addition plots. Together, these data suggest (1) a relative decoupling between soil moisture and redox processes at our spatial and temporal scales of measurement, (2) the co-occurrence of aerobic and anaerobic biogeochemical processes in well-drained surface soils, and (3) an absence of threshold effects from sustained precipitation on redox reactions over the scale of weeks. Our data suggest a need to re-evaluate representations of moisture in biogeochemical models.BRII recipient: Hall (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/37n0k6dwarticleEcosystemsvol 16, iss 4, 576-5891432-9840 1435-0629oai:escholarship.org:ark:/13030/qt3s23v00k2016-12-21T23:31:28Zqt3s23v00kEvolution of patterns on Conus shellsGong, Z.Matzke, N. JErmentrout, B.Song, D.Vendetti, J. ESlatkin, M.Oster, G.2012-01-04The pigmentation patterns of shells in the genus Conus can be generated by a neural-network model of the mantle. We fit model parameters to the shell pigmentation patterns of 19 living Conus species for which a well resolved phylogeny is available. We infer the evolutionary history of these parameters and use these results to infer the pigmentation patterns of ancestral species. The methods we use allow us to characterize the evolutionary history of a neural network, an organ that cannot be preserved in the fossil record. These results are also notable because the inferred patterns of ancestral species sometimes lie outside the range of patterns of their living descendants, and illustrate how development imposes constraints on the evolution of complex phenotypes.BRII recipient: Oster (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3s23v00karticleProceedings of the National Academy of Sciencesvol 109, iss 5, E234-E2410027-8424 1091-6490oai:escholarship.org:ark:/13030/qt76w9z2dr2016-12-21T23:30:26Zqt76w9z2drContingent Kernel Density EstimationFortmann-Roe, ScottStarfield, RichardGetz, Wayne M2012-02-24Kernel density estimation is a widely used method for estimating a distribution based on a sample of points drawn from that distribution. Generally, in practice some form of error contaminates the sample of observed points. Such error can be the result of imprecise measurements or observation bias. Often this error is negligible and may be disregarded in analysis. In cases where the error is non-negligible, estimation methods should be adjusted to reduce resulting bias. Several modifications of kernel density estimation have been developed to address specific forms of errors. One form of error that has not yet been addressed is the case where observations are nominally placed at the centers of areas from which the points are assumed to have been drawn, where these areas are of varying sizes. In this scenario, the bias arises because the size of the error can vary among points and some subset of points can be known to have smaller error than another subset or the form of the error may change among points. This paper proposes a “contingent kernel density estimation” technique to address this form of error. This new technique adjusts the standard kernel on a point-by-point basis in an adaptive response to changing structure and magnitude of error. In this paper, equations for our contingent kernel technique are derived, the technique is validated using numerical simulations, and an example using the geographic locations of social networking users is worked to demonstrate the utility of the method.BRII recipient: Fortmann-RoepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/76w9z2drarticlePLoS ONEvol 7, iss 2, e305491932-6203oai:escholarship.org:ark:/13030/qt97n5b0qd2016-12-21T23:29:23Zqt97n5b0qdDoes neighborhood environment influence girls' pubertal onset? findings from a cohort studyDeardorff, JuliannaFyfe, MollyEkwaru, J PaulKushi, Lawrence HGreenspan, Louise CYen, Irene H2012-01-01Pubertal onset occurs earlier than in the past among U.S. girls. Early onset is associated with numerous deleterious outcomes across the life course, including overweight, breast cancer and cardiovascular health. Increases in childhood overweight have been implicated as a key reason for this secular trend. Scarce research, however, has examined how neighborhood environment may influence overweight and, in turn, pubertal timing. The current study prospectively examined associations between neighborhood environment and timing of pubertal onset in a multi-ethnic cohort of girls. Body mass index (BMI) was examined as a mediator of these associations.Methods:Participants were 213 girls, 6-8 years old at baseline, in an on-going longitudinal study. The current report is based on 5 time points (baseline and 4 annual follow-up visits). Neighborhood environment, assessed at baseline, used direct observation. Tanner stage and anthropometry were assessed annually in clinic. Survival analysis was utilized to investigate the influence of neighborhood factors on breast and pubic hair onset, with BMI as a mediator. We also examined the modifying role of girls' ethnicity.Results:When adjusting for income, one neighborhood factor (Recreation) predicted delayed onset of breast and pubic hair development, but only for African American girls. BMI did not mediate the association between Recreation and pubertal onset; however, these associations persisted when BMI was included in the models.Conclusions:For African American girls, but not girls from other ethnic groups, neighborhood availability of recreational outlets was associated with onset of breast and pubic hair. Given the documented risk for early puberty among African American girls, these findings have important potential implications for public health interventions related to timing of puberty and related health outcomes in adolescence and adulthood.BRII recipient: DeardorffpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/97n5b0qdarticleBMC Pediatricsvol 12, iss 1, 271471-2431oai:escholarship.org:ark:/13030/qt8kc898852016-12-21T23:20:28Zqt8kc89885Windows to the soul: vision science as a tool for studying biological mechanisms of information processing deficits in schizophreniaYoon, Jong HSheremata, Summer LRokem, ArielSilver, Michael A2013-01-01Cognitive and information processing deficits are core features and important sources of disability in schizophrenia. Our understanding of the neural substrates of these deficits remains incomplete, in large part because the complexity of impairments in schizophrenia makes the identification of specific deficits very challenging. Vision science presents unique opportunities in this regard: many years of basic research have led to detailed characterization of relationships between structure and function in the early visual system and have produced sophisticated methods to quantify visual perception and characterize its neural substrates. We present a selective review of research that illustrates the opportunities for discovery provided by visual studies in schizophrenia. We highlight work that has been particularly effective in applying vision science methods to identify specific neural abnormalities underlying information processing deficits in schizophrenia. In addition, we describe studies that have utilized psychophysical experimental designs that mitigate generalized deficit confounds, thereby revealing specific visual impairments in schizophrenia. These studies contribute to accumulating evidence that early visual cortex is a useful experimental system for the study of local cortical circuit abnormalities in schizophrenia. The high degree of similarity across neocortical areas of neuronal subtypes and their patterns of connectivity suggests that insights obtained from the study of early visual cortex may be applicable to other brain regions. We conclude with a discussion of future studies that combine vision science and neuroimaging methods. These studies have the potential to address pressing questions in schizophrenia, including the dissociation of local circuit deficits vs. impairments in feedback modulation by cognitive processes such as spatial attention and working memory, and the relative contributions of glutamatergic and GABAergic deficits.BRII recipient: SherematapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8kc89885articleFrontiers in Psychologyvol 41664-1078oai:escholarship.org:ark:/13030/qt2486d3rc2016-12-21T22:48:20Zqt2486d3rcRegulatory consequences of gene translocation in bacteriaBlock, D. H. SHussein, R.Liang, L. WLim, H. N2012-07-24Gene translocations play an important role in the plasticity and evolution of bacterial genomes. In this study, we investigated the impact on gene regulation of three genome organizational features that can be altered by translocations: (i) chromosome position; (ii) gene orientation; and (iii) the distance between a target gene and its transcription factor gene (‘target-TF distance’). Specifically, we quantified the effect of these features on constitutive expression, transcription factor binding and/or gene expression noise using a synthetic network in Escherichia coli composed of a transcription factor (LacI repressor) and its target gene (yfp). Here we show that gene regulation is generally robust to changes in chromosome position, gene orientation and target-TF distance. The only demonstrable effect was that chromosome position alters constitutive expression, due to changes in gene copy number and local sequence effects, and that this determines maximum and minimum expression levels. The results were incorporated into a mathematical model which was used to quantitatively predict the responses of a simple gene network to gene translocations; the predictions were confirmed experimentally. In summary, gene translocation can modulate constitutive gene expression levels due to changes in chromosome position but it has minimal impact on other facets of gene regulation.BRII recipient: LimpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2486d3rcarticleNucleic Acids Researchvol 40, iss 18, 8979-89920305-1048 1362-4962oai:escholarship.org:ark:/13030/qt26m9416r2016-12-21T22:46:54Zqt26m9416rTranscriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scalesBi, KeVanderpool, DanSinghal, SonalLinderoth, TylerMoritz, CraigGood, Jeffrey M2012-01-01To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. We developed a novel strategy for designing array-based exon capture in chipmunks (Tamias) based on de novo transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species.ResultsWe selectively targeted 11,975 exons (~4 Mb) on custom capture arrays, and enriched over 99% of the targets in all libraries. The percentage of aligned reads was highly consistent (24.4-29.1%) across all specimens, including in multiplexing up to 20 barcoded individuals on a single array. Base coverage among specimens and within targets in each species library was uniform, and the performance of targets among independent exon captures was highly reproducible. There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions. We did observe a decline in capture performance of a subset of targets designed from a much more divergent ground squirrel genome (30 My), however, over 90% of the targets were also recovered. Final assemblies yielded over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified.ConclusionsOur study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life.BRII recipient: BipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/26m9416rarticleBMC Genomicsvol 13, iss 1, 4031471-2164oai:escholarship.org:ark:/13030/qt6ft202q82016-12-21T22:45:38Zqt6ft202q8Environmental justice implications of arsenic contamination in California's San Joaquin Valley: a cross-sectional, cluster-design examining exposure and compliance in community drinking water systemsBalazs, Carolina LMorello-Frosch, RachelHubbard, Alan ERay, Isha2012-01-01Few studies of environmental justice examine inequities in drinking water contamination. Those studies that have done so usually analyze either disparities in exposure/harm or inequitable implementation of environmental policies. The US EPA’s 2001 Revised Arsenic Rule, which tightened the drinking water standard for arsenic from 50 μg/L to 10 μg/L, offers an opportunity to analyze both aspects of environmental justice.MethodsWe hypothesized that Community Water Systems (CWSs) serving a higher proportion of minority residents or residents of lower socioeconomic status (SES) have higher drinking water arsenic levels and higher odds of non-compliance with the revised standard. Using water quality sampling data for arsenic and maximum contaminant level (MCL) violation data for 464 CWSs actively operating from 2005–2007 in California’s San Joaquin Valley we ran bivariate tests and linear regression models.ResultsHigher home ownership rate was associated with lower arsenic levels (ß-coefficient= −0.27 μg As/L, 95% (CI), -0.5, -0.05). This relationship was stronger in smaller systems (ß-coefficient= −0.43, CI, -0.84, -0.03). CWSs with higher rates of homeownership had lower odds of receiving an MCL violation (OR, 0.33; 95% CI, 0.16, 0.67); those serving higher percentages of minorities had higher odds (OR, 2.6; 95% CI, 1.2, 5.4) of an MCL violation.ConclusionsWe found that higher arsenic levels and higher odds of receiving an MCL violation were most common in CWSs serving predominantly socio-economically disadvantaged communities. Our findings suggest that communities with greater proportions of low SES residents not only face disproportionate arsenic exposures, but unequal MCL compliance challenges.BRII recipient: Morello-FroschpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6ft202q8articleEnvironmental Healthvol 11, iss 1, 841476-069Xoai:escholarship.org:ark:/13030/qt4pc8w0t92016-12-21T22:44:32Zqt4pc8w0t9Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial matArmitage, David W.Gallagher, Kimberley L.Youngblut, Nicholas D.Buckley, Daniel H.Zinder, Stephen H.2012-08-10Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.BRII recipient: ArmitagepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4pc8w0t9articleFrontiers in Microbiologyvol 31664302Xoai:escholarship.org:ark:/13030/qt65h3k72x2016-12-21T22:41:10Zqt65h3k72xAllostatic load amplifies the effect of blood lead levels on elevated blood pressure among middle-aged U.S. adults: a cross-sectional studyZota, Ami RShenassa, Edmond DMorello-Frosch, Rachel2013-01-01Scientists and regulators have sought to understand whether and how physiologic dysregulation due to chronic stress exposure may enhance vulnerability to the adverse health effects of toxicant exposures. We conducted a cross-sectional study to determine whether allostatic load (AL), a composite measure of physiologic response to chronic exposure to stress, amplifies the effect of lead exposure on blood pressure among middle-aged adults.Methods:We analyzed associations between blood lead levels and blood pressure in a nationally representative sample of 8,194 U.S. adults (aged 40-65 years) participating in the National Health and Nutritional Examination Survey, 1999--2008. Outcomes were elevated systolic (≥ 140 mm Hg) and diastolic (≥ 90 mm Hg) blood pressure. AL was defined as the aggregate score of seven components, reflecting dysregulation of the cardiovascular, inflammatory, and endocrine systems.Results:Logistic regression models showed a linear dose-response relationship for quintiles of blood lead and elevated systolic blood pressure in the high AL group (p = 0.03) but not the low AL group (p = 0.24). Similarly, the relationship between lead exposure and elevated diastolic blood pressure was stronger among the high AL group than the low AL group. Within the high AL group, the fourth and fifth quintiles had significantly elevated odds of elevated blood pressure compared to lowest quintile [OR = 1.92, (95% CI, 1.07, 3.47) and OR =2.28 (95% CI, 1.33, 3.91), respectively]. In the low AL group, none of the quintile effects were significantly different than the referent group although there was evidence of a linear trend (p =0.03). The lead by AL interaction term was not statistically significant for either systolic or diastolic blood pressure models.Conclusions:Results suggest that higher AL may amplify the adverse effects of lead on blood pressure. Future research should assess the implications of cumulative exposures to environmental and social stressors for regulatory decision-making.BRII recipient: Morello-FroschpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/65h3k72xarticleEnvironmental Healthvol 12, iss 1, 641476-069Xoai:escholarship.org:ark:/13030/qt3rz5g0d22016-12-21T22:37:37Zqt3rz5g0d2Physics of Three-Dimensional Bosonic Topological Insulators: Surface-Deconfined Criticality and Quantized Magnetoelectric EffectVishwanath, AshvinSenthil, T.2013-02-28We discuss physical properties of “integer” topological phases of bosons in D=3+1 dimensions, protected by internal symmetries like time reversal and/or charge conservation. These phases invoke interactions in a fundamental way but do not possess topological order; they are bosonic analogs of free-fermion topological insulators and superconductors. While a formal cohomology-based classification of such states was recently discovered, their physical properties remain mysterious. Here, we develop a field-theoretic description of several of these states and show that they possess unusual surface states, which, if gapped, must either break the underlying symmetry or develop topological order. In the latter case, symmetries are implemented in a way that is forbidden in a strictly two-dimensional theory. While these phases are the usual fate of the surface states, exotic gapless states can also be realized. For example, tuning parameters can naturally lead to a deconfined quantum critical point or, in other situations, to a fully symmetric vortex metal phase. We discuss cases where the topological phases are characterized by a quantized magnetoelectric response θ, which, somewhat surprisingly, is an odd multiple of 2π. Two different surface theories are shown to capture these phenomena: The first is a nonlinear sigma model with a topological term. The second invokes vortices on the surface that transform under a projective representation of the symmetry group. We identify a bulk-field theory consistent with these properties, which is a multicomponent background-field theory supplemented, crucially, with a topological term. We also provide bulk sigma-model field theories of these phases and discuss a possible topological phase characterized by the thermal analog of the magnetoelectric effect.BRII recipient: VishwanathpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3rz5g0d2articlePhysical Review Xvol 3, iss 12160-3308oai:escholarship.org:ark:/13030/qt82f7m32n2016-12-21T22:36:38Zqt82f7m32nAn Information Theoretic Approach to Understanding the Micro Foundations of Macro ProcessesVillas-Boas, Sofia B.Judge, George2013-01-01In the context of a simple equilibrium macro process we suggest a probability basis for recovering information regarding the unknown and unobservable micro process, and solving the resulting inverse problem.BRII: Villas-BoaspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/82f7m32narticleTheoretical Economics Lettersvol 03, iss 01, 48-512162-2078 2162-2086oai:escholarship.org:ark:/13030/qt2qq838242016-12-21T22:35:01Zqt2qq83824Body Size and Extinction Risk in Terrestrial Mammals Above the Species LevelTomiya, Susumu2013-12-01AbstractMammalian body mass strongly correlates with life history and population properties at the scale of mouse to elephant. Large body size is thus often associated with elevated extinction risk. I examined the North American fossil record (28–1 million years ago) of 276 terrestrial genera to uncover the relationship between body size and extinction probability above the species level. Phylogenetic comparative analysis revealed no correlation between sampling-adjusted durations and body masses ranging 7 orders of magnitude, an observation that was corroborated by survival analysis. Most of the ecological and temporal groups within the data set showed the same lack of relationship. Size-biased generic extinctions do not constitute a general feature of the Holarctic mammalian faunas in the Neogene. Rather, accelerated loss of large mammals occurred during intervals that experienced combinations of regional aridification and increased biomic heterogeneity within continents. The latter phenomenon is consistent with the macroecological prediction that large geographic ranges are critical to the survival of large mammals in evolutionary time. The frequent lack of size selectivity in generic extinctions can be reconciled with size-biased species loss if extinctions of large and small mammals at the species level are often driven by ecological perturbations of different spatial and temporal scales, while those at the genus level are more synchronized in time as a result of fundamental, multiscale environmental shifts.BRII recipient: Tomiya (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2qq83824articleThe American Naturalistvol 182, iss 6, E196-E2140003-0147 1537-5323oai:escholarship.org:ark:/13030/qt1jz3s3gm2016-12-21T22:33:13Zqt1jz3s3gmThis Examined Life: The Upside of Self-Knowledge for Interpersonal RelationshipsTenney, Elizabeth RVazire, SimineMehl, Matthias R2013-07-31Although self-knowledge is an unquestioned good in many philosophical traditions, testing this assumption scientifically has posed a challenge because of the difficulty of measuring individual differences in self-knowledge. In this study, we used a novel, naturalistic, and objective criterion to determine individuals’ degree of self-knowledge. Specifically, self-knowledge was measured as the congruence between people’s beliefs about how they typically behave and their actual behavior as measured with unobtrusive audio recordings from daily life. We found that this measure of self-knowledge was positively correlated with informants’ perceptions of relationship quality. These results suggest that self-knowledge is interpersonally advantageous. Given the importance of relationships for our social species, self-knowledge could have great social value that has heretofore been overlooked.BRII recipient: TenneypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1jz3s3gmarticlePLoS ONEvol 8, iss 7, e696051932-6203oai:escholarship.org:ark:/13030/qt6sj1q95k2016-12-21T22:31:54Zqt6sj1q95kOpposing selection and environmental variation modify optimal timing of breedingTarwater, C. EBeissinger, S. R2013-09-03Studies of evolution in wild populations often find that the heritable phenotypic traits of individuals producing the most offspring do not increase proportionally in the population. This paradox may arise when phenotypic traits influence both fecundity and viability and when there is a tradeoff between these fitness components, leading to opposing selection. Such tradeoffs are the foundation of life history theory, but they are rarely investigated in selection studies. Timing of breeding is a classic example of a heritable trait under directional selection that does not result in an evolutionary response. Using a 22-y study of a tropical parrot, we show that opposing viability and fecundity selection on the timing of breeding is common and affects optimal breeding date, defined by maximization of fitness. After accounting for sampling error, the directions of viability (positive) and fecundity (negative) selection were consistent, but the magnitude of selection fluctuated among years. Environmental conditions (rainfall and breeding density) primarily and breeding experience secondarily modified selection, shifting optimal timing among individuals and years. In contrast to other studies, viability selection was as strong as fecundity selection, late-born juveniles had greater survival than early-born juveniles, and breeding later in the year increased fitness under opposing selection. Our findings provide support for life history tradeoffs influencing selection on phenotypic traits, highlight the need to unify selection and life history theory, and illustrate the importance of monitoring survival as well as reproduction for understanding phenological responses to climate change.BRII recipient: BeissingerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6sj1q95karticleProceedings of the National Academy of Sciencesvol 110, iss 38, 15365-153700027-8424 1091-6490oai:escholarship.org:ark:/13030/qt07s272wj2016-12-21T22:30:48Zqt07s272wjInflated Applicants: Attribution Errors in Performance Evaluation by ProfessionalsSwift, Samuel AMoore, Don ASharek, Zachariah SGino, Francesca2013-07-24When explaining others' behaviors, achievements, and failures, it is common for people to attribute too much influence to disposition and too little influence to structural and situational factors. We examine whether this tendency leads even experienced professionals to make systematic mistakes in their selection decisions, favoring alumni from academic institutions with high grade distributions and employees from forgiving business environments. We find that candidates benefiting from favorable situations are more likely to be admitted and promoted than their equivalently skilled peers. The results suggest that decision-makers take high nominal performance as evidence of high ability and do not discount it by the ease with which it was achieved. These results clarify our understanding of the correspondence bias using evidence from both archival studies and experiments with experienced professionals. We discuss implications for both admissions and personnel selection practices.BRII recipient: SwiftpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/07s272wjarticlePLoS ONEvol 8, iss 7, e692581932-6203oai:escholarship.org:ark:/13030/qt9606k8dt2016-12-21T22:29:46Zqt9606k8dtSauron: embedded single-camera sensing of printed physical user interfacesSavage, ValkyrieChang, ColinHartmann, Bjoern2013-10-083D printers enable designers and makers to rapidly produce physical models of future products. Today these physical prototypes are mostly passive. Our research goal is to enable users to turn models produced on commodity 3D printers into interactive objects with a minimum of required assembly or instrumentation. We present Sauron, an embedded machine vision-based system for sensing human input on physical controls like buttons, sliders, and joysticks. With Sauron, designers attach a single camera with integrated ring light to a printed prototype. This camera observes the interior portions of input components to determine their state. In many prototypes, input components may be occluded or outside the viewing frustum of a single camera. We introduce algorithms that generate internal geometry and calculate mirror placements to redirect input motion into the visible camera area. To investigate the space of designs that can be built with Sauron along with its limitations, we built prototype devices, evaluated the suitability of existing models for vision sensing, and performed an informal study with three CAD users. While our approach imposes some constraints on device design, results suggest that it is expressive and accessible enough to enable constructing a useful variety of devices.BRII recipient: Hartmann (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9606k8dtpublicationoai:escholarship.org:ark:/13030/qt7mq7s0z52016-12-21T22:28:38Zqt7mq7s0z5Content-based tools for editing audio storiesRubin, SteveBerthouzoz, FloraineMysore, Gautham JLi, WilmotAgrawala, Maneesh2013-09-08Audio stories are an engaging form of communication that combine speech and music into compelling narratives. Existing audio editing tools force story producers to manipulate speech and music tracks via tedious, low-level waveform editing. In contrast, we present a set of tools that analyze the audio content of the speech and music and thereby allow producers to work at much higher level. Our tools address several challenges in creating audio stories, including (1) navigating and editing speech, (2) selecting appropriate music for the score, and (3) editing the music to complement the speech. Key features include a transcript-based speech editing tool that automatically propagates edits in the transcript text to the corresponding speech track; a music browser that supports searching based on emotion, tempo, key, or timbral similarity to other songs; and music retargeting tools that make it easy to combine sections of music with the speech. We have used our tools to create audio stories from a variety of raw speech sources, including scripted narratives, interviews and political speeches. Informal feedback from first-time users suggests that our tools are easy to learn and greatly facilitate the process of editing raw footage into a final story.BRII recipient: Agrawala (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7mq7s0z5publicationoai:escholarship.org:ark:/13030/qt3s42g5mh2016-12-21T22:26:34Zqt3s42g5mhBis (2,2'-bipyridine-2N,N') (4-methylbenzoato-2O,O')copper(II) iodide hemihydrateKazhdan, DanielHu, Yung-JinKokai, AkosLevi, ZerubbaRozenel, Sergio2008-08-06In the title compound, [Sr(C10H15)2(C10H8N2)], the Sr-N distances are 2.624 (3) and 2.676 (3) Å, the SrCp ring centroid distances are 2.571 and 2.561 Å and the N-C-C-N torsion angle in the bipyridine ligand is -2.2 (4)°. Interestingly, the bipyridine ligand is tilted. The angle between the plane defined by the Sr atom and the two bipyridyl N atoms and the plane defined by the 12 atoms of the bipyridine ligand is 10.7 (1)°.BRII recipient: KazhdanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3s42g5mharticleActa Crystallographica Section E Structure Reports Onlinevol 64, iss 9, m1134-m11341600-5368oai:escholarship.org:ark:/13030/qt9fv5c7x82016-12-21T22:23:44Zqt9fv5c7x85,6-Dimethyl-1,10-phenanthrolineRozenel, Sergio S2013-09-18In the title compound, C14H12N2, the N⋯N distance is 2.719 (1) Å. The N—C—C—N torsion angle [0.9 (1)°] is close to the ideal value of 0° as expected. Bond lengths and angles are consistent with those observed for [1,10]phenanthroline and coordinated 5,6 dimethyl[1,10]phenanthroline. In the crystal, C—H⋯N hydrogen bonds link the molecules into C(4) chains running parallel to the b axis. Weak π–π interactions between benzene and pyridine rings [centroid–centroid distance = 3.5337 (7) Å] and between benzene rings [centroid–centroid distances = 3.6627 (7) and 3.8391 (7)Å] also occur.BRII recipient: RozenelpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9fv5c7x8articleActa Crystallographica Section E Structure Reports Onlinevol 69, iss 10, o1560-o15601600-5368oai:escholarship.org:ark:/13030/qt5vq6d4wt2016-12-21T22:22:21Zqt5vq6d4wtComplex history of the amphibian-killing chytrid fungus revealed with genome resequencing dataRosenblum, Erica BreeJames, Timothy YZamudio, Kelly RPoorten, Thomas JIlut, DanRodriguez, DavidEastman, Jonathan MRichards-Hrdlicka, KatyJoneson, SuzanneJenkinson, Thomas SLongcore, Joyce EParra Olea, GabrielaToledo, LuÃs FelipeArellano, Maria LuzMedina, Edgar MRestrepo, SilviaFlechas, Sandra VictoriaBerger, LeeBriggs, Cheryl JStajich, Jason E2013-06-04Understanding the evolutionary history of microbial pathogens is critical for mitigating the impacts of emerging infectious diseases on economically and ecologically important host species. We used a genome resequencing approach to resolve the evolutionary history of an important microbial pathogen, the chytrid Batrachochytrium dendrobatidis (Bd), which has been implicated in amphibian declines worldwide. We sequenced the genomes of 29 isolates of Bd from around the world, with an emphasis on North, Central, and South America because of the devastating effect that Bd has had on amphibian populations in the New World. We found a substantial amount of evolutionary complexity in Bd with deep phylogenetic diversity that predates observed global amphibian declines. By investigating the entire genome, we found that even the most recently evolved Bd clade (termed the global panzootic lineage) contained more genetic variation than previously reported. We also found dramatic differences among isolates and among genomic regions in chromosomal copy number and patterns of heterozygosity, suggesting complex and heterogeneous genome dynamics. Finally, we report evidence for selection acting on the Bd genome, supporting the hypothesis that protease genes are important in evolutionary transitions in this group. Bd is considered an emerging pathogen because of its recent effects on amphibians, but our data indicate that it has a complex evolutionary history that predates recent disease outbreaks. Therefore, it is important to consider the contemporary effects of Bd in a broader evolutionary context and identify specific mechanisms that may have led to shifts in virulence in this system.BRII recipient: Rosenblum (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5vq6d4wtarticleProceedings of the National Academy of Sciencesvol 110, iss 23, 9385-93900027-8424 1091-6490oai:escholarship.org:ark:/13030/qt6x94v6f82016-12-21T22:20:07Zqt6x94v6f8Obesity in the United States -- Dysbiosis from Exposure to Low-Dose Antibiotics?Riley, Lee WRaphael, EvaFaerstein, Eduardo2013-01-01The rapid increase in obesity prevalence in the United States in the last 20 years is unprecedented and not well explained. Here, we explore a hypothesis that the obesity epidemic may be driven by population-wide chronic exposures to low-residue antibiotics that have increasingly entered the American food chain over the same time period. We propose this hypothesis based on two recent bodies of published reports – (1) those that provide evidence for the spread of antibiotics into the American food chain, and (2) those that examine the relationship between the gut microbiota and body physiology. The livestock use of antimicrobial agents has sharply increased in the US over the same 20-year period of the obesity epidemic, especially with the expansion of intensified livestock production, such as the concentrated animal feeding operations. Observational and experimental studies support the idea that changes in the intestinal microbiota exert a profound effect on body physiology. We propose that chronic exposures to low-residue antimicrobial drugs in food could disrupt the equilibrium state of intestinal microbiota and cause dysbiosis that can contribute to changes in body physiology. The obesity epidemic in the United States may be partly driven by the mass exposure of Americans to food containing low-residue antimicrobial agents. While this hypothesis cannot discount the impact of diet and other factors associated with obesity, we believe studies are warranted to consider this possible driver of the epidemic.BRII recipient: RileypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6x94v6f8publicationoai:escholarship.org:ark:/13030/qt42p816dg2016-12-21T22:19:08Zqt42p816dgGenetic Diversity of Black Salamanders (Aneides flavipunctatus) across Watersheds in the Klamath MountainsReilly, SeanMulks, MitchellReilly, JasonJennings, W.Wake, David2013-08-29Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prior ecological results, which suggest that Black Salamanders avoid high elevations such as the ridges that separate watersheds. Our mitochondrial results revealed two major lineages, one in the Sacramento River watershed, and another containing the Klamath, Smith, and Rogue River watersheds. Clustering analyses of our thirteen nuclear loci show the Sacramento watershed population to be genetically distinctive. Populations in the Klamath, Smith, and Rogue watersheds are also distinctive but not as differentiated and their boundaries do not correspond to watersheds. Our historical demographic analyses suggest that the Sacramento population has been isolated from the Klamath populations since the mid-Pleistocene, with negligible subsequent gene flow (2 Nm ≤ 0.1). The Smith and Rogue River watershed populations show genetic signals of recent population expansion. These results suggest that the Sacramento River and Klamath River watersheds served as Pleistocene refugia, and that the Rogue and Smith River watersheds were colonized more recently by northward range expansion from the Klamath.BRII recipient: ReillypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/42p816dgarticleDiversityvol 5, iss 3, 657-6791424-2818oai:escholarship.org:ark:/13030/qt1b38w79h2016-12-21T22:17:35Zqt1b38w79hRelative Susceptibility of Vitis vinifera Cultivars to Vector-Borne Xylella fastidiosa through TimeRashed, ArashKwan, JoyceBaraff, BreannaLing, DianeDaugherty, Matthew PKilliny, NabilAlmeida, Rodrigo P. P2013-02-12Understanding the interactions between pathogen, crop and vector are necessary for the development of disease control practices of vector-borne pathogens. For instance, resistant plant genotypes can help constrain disease symptoms due to infections and limit pathogen spread by vectors. On the other hand, genotypes susceptible to infection may increase pathogen spread owing to their greater pathogen quantity, regardless of their symptom status. In this study, we evaluated under greenhouse conditions the relative levels of resistance (i.e. relatively lower pathogen quantity) versus tolerance (i.e. less symptom severity) of 10 commercial grapevine (Vitis vinifera) cultivars to Pierce’s disease etiological agent, the bacterium Xylella fastidiosa. Overall, no correlation was detected between pathogen quantity and disease severity, indicating the existence of among-cultivar variation in plant response to infection. Thompson Seedless and Barbera were the two most susceptible among 10 evaluated cultivars. Rubired showed the least severe disease symptoms and was categorized as one of the most resistant genotypes in this study. However, within each cultivar the degree of resistance/tolerance was not consistent across sampling dates. These cultivar and temporal differences in susceptibility to infection may have important consequences for disease epidemiology and the effectiveness of management protocols.BRII recipient: AlmeidapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1b38w79harticlePLoS ONEvol 8, iss 2, e553261932-6203oai:escholarship.org:ark:/13030/qt4fn5q9fv2016-12-21T21:44:00Zqt4fn5q9fvFood webs in Mediterranean riversPower, Mary EHolomuzki, Joseph RLowe, Rex L2013-05-28River food webs are subject to two regimes of longitudinally varying ecological control: productivity and disturbance. Light-limited productivity increases as channels widen downstream. Time windows for growth, however, shrink as discharge increases, substrate particle size decreases, and the frequency of flood-driven bed mobilization increases downstream. Mediterranean rivers are periodically reset by hydrologic events with somewhat predictable timing. Typically, a rainy winter with high river discharge is followed by summer drought with little or no rainfall and slowly declining river flow. The magnitude and timing of winter floods and severity of subsequent summer drought can vary considerably from year to year, however. Episodic scouring floods or prolonged periods of drought are experienced as disturbances, stressors, or opportunities by river biota. The timing, duration, and intensity of these hydrologic controls affect performances of individuals, distribution and abundances of populations, and outcomes and consequences of species interactions. These interactions in turn determine how river food webs will assemble, develop, and reconfigure after disturbance. We discuss how spatial variation in solar radiation and spatial and temporal variations in disturbance affects river food webs under Mediterranean climate seasonality, focusing primarily on long-term observations in the Eel River of northwestern California, USA.BRII recipient: Power (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4fn5q9fvarticleHydrobiologiavol 719, iss 1, 119-1360018-8158 1573-5117oai:escholarship.org:ark:/13030/qt2g76b31r2016-12-21T21:42:44Zqt2g76b31rDoes land abandonment decrease species richness and abundance of plants and animals in Mediterranean pastures, arable lands and permanent croplands?Plieninger, TobiasGaertner, MirijamHui, CangHuntsinger, Lynn2013-01-01Obscured by the more prevalent discussion of intensification and expansion of agricultural land, the impacts of the abandonment of many grasslands and croplands of the world in recent decades have received limited attention in the literature. Land abandonment is a common phenomenon in the Mediterranean Basin, a global biodiversity hotspot, but little is known about the impacts of this process on biodiversity. To upscale existing case-study insight to a Pan-Mediterranean level, we plan to perform a systematic review of the effects of land abandonment on plant and animal richness and abundance in pastures, arable lands and permanent crops of the Mediterranean Basin. In particular, we ask (1) which taxonomic groups are most affected by land abandonment; (2) whether different spatial and temporal scales of studies influence species richness and abundance outcomes; (3) whether previous land use and current anthropogenic impacts on abandoned lands determine differences in the number and abundance of species; and (4) whether landscape context modifies the impacts.Methods:Our review will be based on searching scientific databases as well as the internet for empirical studies on the effects of land abandonment on biodiversity in the Mediterranean Basin. Study selection follows a three-stage process and includes study quality assessment. Extracted data will be synthesized through meta-analysis. Results will be presented in the form of a quantitative (e.g. figures indicating effect sizes, tables summarizing heterogeneity statistics) and narrative synthesis. Additional aspects will be addressed through meta-regression and sub-group analyses.BRII recipient: HuntsingerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2g76b31rarticleEnvironmental Evidencevol 2, iss 1, 32047-2382oai:escholarship.org:ark:/13030/qt8g4234q92016-12-21T21:40:37Zqt8g4234q9FUEGO — Fire Urgency Estimator in Geosynchronous Orbit — A Proposed Early-Warning Fire Detection SystemPennypacker, CarltonJakubowski, MarekKelly, MaggiLampton, MichaelSchmidt, ChristopherStephens, ScottTripp, Robert2013-10-17Current and planned wildfire detection systems are impressive but lack both sensitivity and rapid response times. A small telescope with modern detectors and significant computing capacity in geosynchronous orbit can detect small (12 m2) fires on the surface of the earth, cover most of the western United States (under conditions of moderately clear skies) every few minutes or so, and attain very good signal-to-noise ratio against Poisson fluctuations in a second. Hence, these favorable statistical significances have initiated a study of how such a satellite could operate and reject the large number of expected systematic false alarms from a number of sources. Here we present both studies of the backgrounds in Geostationary Operational Environmental Satellites (GOES) 15 data and studies that probe the sensitivity of a fire detection satellite in geosynchronous orbit. We suggest a number of algorithms that can help reduce false alarms, and show efficacy on a few. Early detection and response would be of true value in the United States and other nations, as wildland fires continue to severely stress resource managers, policy makers, and the public, particularly in the western US. Here, we propose the framework for a geosynchronous satellite with modern imaging detectors, software, and algorithms able to detect heat from early and small fires, and yield minute-scale detection timesBRII recipient: KellypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8g4234q9articleRemote Sensingvol 5, iss 10, 5173-51922072-4292oai:escholarship.org:ark:/13030/qt62c785th2016-12-21T21:39:39Zqt62c785thDetecting Evolutionary Strata on the Human X Chromosome in the Absence of Gametologous Y-Linked SequencesPandey, R. SWilson Sayres, M. AAzad, R. K2013-09-13Mammalian sex chromosomes arose from a pair of homologous autosomes that differentiated into the X and Y chromosomes following a series of recombination suppression events between the X and Y. The stepwise recombination suppressions from the distal long arm to the distal short arm of the chromosomes are reflected as regions with distinct X-Y divergence, referred to as evolutionary strata on the X. All current methods for stratum detection depend on X-Y comparisons but are severely limited by the paucity of X-Y gametologs. We have developed an integrative method that combines a top-down, recursive segmentation algorithm with a bottom-up, agglomerative clustering algorithm to decipher compositionally distinct regions on the X, which reflect regions of unique X-Y divergence. In application to human X chromosome, our method correctly classified a concatenated set of 35 previously assayed X-linked gene sequences by evolutionary strata. We then extended our analysis, applying this method to the entire sequence of the human X chromosome, in an effort to define stratum boundaries. The boundaries of more recently formed strata on X-added region, namely the fourth and fifth strata, have been defined by previous studies and are recapitulated with our method. The older strata, from the first up to the third stratum, have remained poorly resolved due to paucity of X-Y gametologs. By analyzing the entire X sequence, our method identified seven evolutionary strata in these ancient regions, where only three could previously be assayed, thus demonstrating the robustness of our method in detecting the evolutionary strata.BRII recipient: Wilson SayrespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/62c785tharticleGenome Biology and Evolutionvol 5, iss 10, 1863-18711759-6653oai:escholarship.org:ark:/13030/qt0nx352qh2016-12-21T21:38:35Zqt0nx352qhFinancial performance measures in credit scoringOliver, Robert M2013-10-22In this paper, we suggest that financial performance of loans and loan portfolios, rather than statistical performance of scores, should be the critical focus for lenders and lending institutions using credit scoring to fund and acquire new borrowers. We propose two measures for measuring relative financial performance of loan accounts when portfolio acquisition decisions are based on risk assessments. These compare with numerous statistical performance measures for response and risk scores that assess borrower response to offers, default, bankruptcy, late payment and fraud. Popular statistical measures often used in scorecard development and validation testing include the K-S statistic, Gini coefficient, AUROC, ROC curves, divergence, and others. The measures that we suggest focus on relative return on equity (ROE) and market share; in our opinion, such financial performance measures are more meaningful to lenders and businesses than statistical measures of scorecard performance.BRII recipient: Oliver (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/0nx352qharticleEURO Journal on Decision Processesvol 1, iss 3-4, 169-1852193-9438 2193-9446oai:escholarship.org:ark:/13030/qt69s8908n2016-12-21T21:37:38Zqt69s8908nGenome-Wide Functional and Stress Response Profiling Reveals Toxic Mechanism and Genes Required for Tolerance to Benzo[a]pyrene in S. cerevisiaeO'Connor, Sean Timothy FrancisLan, JiaqiNorth, MatthewLoguinov, AlexandreZhang, LuopingSmith, Martyn TGu, April ZVulpe, Chris2013-01-01Benzo[a]pyrene (BaP) is a ubiquitous, potent, and complete carcinogen resulting from incomplete organic combustion. BaP can form DNA adducts but other mechanisms may play a role in toxicity. We used a functional toxicology approach in S. cerevisiae to assess the genetic requirements for cellular resistance to BaP. In addition, we examined translational activities of key genes involved in various stress response pathways. We identified multiple genes and processes involved in modulating BaP toxicity in yeast which support DNA damage as a primary mechanism of toxicity, but also identify other potential toxicity pathways. Gene ontology enrichment analysis indicated that DNA damage and repair as well as redox homeostasis and oxidative stress are key processes in cellular response to BaP suggesting a similar mode of action of BaP in yeast and mammals. Interestingly, toxicant export is also implicated as a potential novel modulator of cellular susceptibility. In particular, we identified several transporters with human orthologs (solute carrier family 22) which may play a role in mammalian systems.BRII recipient: VulpepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/69s8908npublicationoai:escholarship.org:ark:/13030/qt6gp9m1gw2016-12-21T21:36:02Zqt6gp9m1gwAvailability and Readability of Emergency Preparedness Materials for Deaf and Hard-of-Hearing and Older Adult Populations: Issues and AssessmentsNeuhauser, LindaIvey, Susan LHuang, DebbieEngelman, AlinaTseng, WinstonDahrouge, DonnaGurung, SidhantaKealey, Melissa2013-02-25A major public health challenge is to communicate effectively with vulnerable populations about preparing for disasters and other health emergencies. People who are Deaf or Hard of Hearing (Deaf/HH) and older adults are particularly vulnerable during health emergencies and require communications that are accessible and understandable. Although health literacy studies indicate that the readability of health communication materials often exceeds people’s literacy levels, we could find no research about the readability of emergency preparedness materials (EPM) intended for Deaf/HH and older adult populations. The objective of this study was to explore issues related to EPM for Deaf/HH and older adult populations, to assess the availability and readability of materials for these populations, and to recommend improvements. In two California counties, we interviewed staff at 14 community-based organizations (CBOs) serving Deaf/HH clients and 20 CBOs serving older adults selected from a stratified, random sample of 227 CBOs. We collected 40 EPM from 10 CBOs and 2 public health departments and 40 EPM from 14 local and national websites with EPM for the public. We used computerized assessments to test the U.S. grade reading levels of the 16 eligible CBO and health department EPM, and the 18 eligible website materials. Results showed that less than half of CBOs had EPM for their clients. All EPM intended for clients of Deaf/HH-serving CBOs tested above the recommended 4th grade reading level, and 91% of the materials intended for clients of older adult-serving CBOs scored above the recommended 6th grade level. EPM for these populations should be widely available through CBOs and public health departments, adhere to health literacy principles, and be accessible in alternative formats including American Sign Language. Developers should engage the intended users of EPM as co-designers and testers. This study adds to the limited literature about EPM for these populations.BRII recipient: NeuhauserpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6gp9m1gwarticlePLoS ONEvol 8, iss 2, e556141932-6203oai:escholarship.org:ark:/13030/qt7ch9m8db2016-12-21T21:34:30Zqt7ch9m8dbMolecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: Recurrence of tyrosine aminotransferase activity in the Iα subfamilyMuratore, Kathryn EEngelhardt, Barbara ESrouji, John RJordan, Michael IBrenner, Steven EKirsch, Jack F2013-09-01The subfamily Iα aminotransferases are typically categorized as having narrow specificity toward carboxylic amino acids (AATases), or broad specificity that includes aromatic amino acid substrates (TATases). Because of their general role in central metabolism and, more specifically, their association with liver-related diseases in humans, this subfamily is biologically interesting. The substrate specificities for only a few members of this subfamily have been reported, and the reliable prediction of substrate specificity from protein sequence has remained elusive. In this study, a diverse set of aminotransferases was chosen for characterization based on a scoring system that measures the sequence divergence of the active site. The enzymes that were experimentally characterized include both narrow-specificity AATases and broad-specificity TATases, as well as AATases with broader-specificity and TATases with narrower-specificity than the previously known family members. Molecular function and phylogenetic analyses underscored the complexity of this family's evolution as the TATase function does not follow a single evolutionary thread, but rather appears independently multiple times during the evolution of the subfamily. The additional functional characterizations described in this article, alongside a detailed sequence and phylogenetic analysis, provide some novel clues to understanding the evolutionary mechanisms at work in this family.BRII recipient: Kirsch (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7ch9m8dbarticleProteins: Structure, Function, and Bioinformaticsvol 81, iss 9, 1593-160908873585oai:escholarship.org:ark:/13030/qt8vj7111f2016-12-21T21:33:23Zqt8vj7111fScleral Micro-RNA Signatures in Adult and Fetal EyesMetlapally, RavikanthGonzalez, PedroHawthorne, Felicia ATran-Viet, Khanh-NhatWildsoet, Christine FYoung, Terri L2013-10-21In human eyes, ocular enlargement/growth reflects active extracellular matrix remodeling of the outer scleral shell. Micro-RNAs are small non-coding RNAs that regulate gene expression by base pairing with target sequences. They serve as nodes of signaling networks. We hypothesized that the sclera, like most tissues, expresses micro-RNAs, some of which modulate genes regulating ocular growth. In this study, the scleral micro-RNA expression profile of rapidly growing human fetal eyes was compared with that of stable adult donor eyes using high-throughput microarray and quantitative PCR analyses. Methods: Scleral samples from normal human fetal (24 wk) and normal adult donor eyes were obtained (n=4 to 6, each group), and RNA extracted. Genome-wide micro-RNA profiling was performed using the Agilent micro-RNA microarray platform. Micro-RNA target predictions were obtained using Microcosm, TargetScan and PicTar algorithms. TaqMan® micro-RNA assays targeting micro-RNAs showing either highest significance, detection, or fold differences, and collagen specificity, were applied to scleral samples from posterior and peripheral ocular regions (n=7, each group). Microarray data were analyzed using R, and quantitative PCR data with 2^-deltaCt methods.Results :Human sclera was found to express micro-RNAs, and comparison of microarray results for adult and fetal samples revealed many to be differentially expressed (p<0.01, min p= 6.5x1011). Specifically, fetal sclera showed increased expression of mir-214, let-7c, let-7e, mir-103, mir-107, and mir-98 (1.5 to 4 fold changes, p<0.01). However, no significant regionally specific differences .i.e., posterior vs. peripheral sclera, were observed for either adult or fetal samples. Conclusion: For the first time, micro-RNA expression has been catalogued in human sclera. Some micro-RNAs show age-related differential regulation, higher in the sclera of rapidly growing fetal eyes, consistent with a role in ocular growth regulation. Thus micro-RNAs represent potential targets for ocular growth manipulation, related to myopia and/or other disorders such as scleral ectasia.BRII recipient: MetlapallypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8vj7111farticlePLoS ONEvol 8, iss 10, e789841932-6203oai:escholarship.org:ark:/13030/qt1ff3j79h2016-12-21T21:30:39Zqt1ff3j79hAxis-aligned filtering for interactive physically-based diffuse indirect lightingMehta, Soham UdayWang, BrandonRamamoorthi, RaviDurand, Fredo2013-07-01We introduce an algorithm for interactive rendering of physically-based global illumination, based on a novel frequency analysis of indirect lighting. Our method combines adaptive sampling by Monte Carlo ray or path tracing, using a standard GPU-accelerated raytracer, with real-time reconstruction of the resulting noisy images. Our theoretical analysis assumes diffuse indirect lighting, with general Lambertian and specular receivers. In practice, we demonstrate accurate interactive global illumination with diffuse and moderately glossy objects, at 1-3 fps. We show mathematically that indirect illumination is a structured signal in the Fourier domain, with inherent band-limiting due to the BRDF and geometry terms. We extend previous work on sheared and axis-aligned filtering for motion blur and shadows, to develop an image-space filtering method for interreflections. Our method enables 5--8X reduced sampling rates and wall clock times, and converges to ground truth as more samples are added. To develop our theory, we overcome important technical challenges---unlike previous work, there is no light source to serve as a band-limit in indirect lighting, and we also consider non-parallel geometry of receiver and reflecting surfaces, without first-order approximations.BRII recipient: RamamoorthipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1ff3j79harticleACM Transactions on Graphicsvol 32, iss 4, 107300301oai:escholarship.org:ark:/13030/qt9m37d9n02016-12-21T21:27:32Zqt9m37d9n0Home range plus: a space-time characterization of movement over real landscapesLyons, Andrew JTurner, Wendy CGetz, Wayne M2013-01-01Advances in GPS technology have created both opportunities in ecology as well as a need for analytical tools that can deal with the growing volume of data and ancillary variables associated with each location.Results: We present T-LoCoH, a home range construction algorithm that incorporates time into the construction and aggregation of local kernels. Time is integrated with Euclidean space using an adaptive scaling of the individual's characteristic velocity, enabling the construction of utilization distributions that capture temporal partitions of space as well as contours that differentiate internal space based on movement phase and time-use metrics. We test T-LoCoH against a simulated dataset and provide illustrative examples from a GPS dataset from springbok in Namibia.Conclusions: The incorporation of time into home range construction expands the concept of utilization distributions beyond the traditional density gradient to spatial models of movement and time, opening the door to new applications in movement ecology.BRII recipient: GetzpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9m37d9n0articleMovement Ecologyvol 1, iss 1, 22051-3933oai:escholarship.org:ark:/13030/qt2530k6x12016-12-21T21:26:11Zqt2530k6x1An inconvenient dataset: bias and inappropriate inference with the multilevel modelLucas, Samuel R2013-06-06The multilevel model has become a staple of social research. I textually and formally explicate sample design features that, I contend, are required for unbiased estimation of macro-level multilevel model parameters and the use of tools for statistical inference, such as standard errors. After detailing the limited and conflicting guidance on sample design in the multilevel model didactic literature, illustrative nationally-representative datasets and published examples that violate the posited requirements are identified. Because the didactic literature is either silent on sample design requirements or in disagreement with the constraints posited here, two Monte Carlo simulations are conducted to clarify the issues. The results indicate that bias follows use of samples that fail to satisfy the requirements outlined; notably, the bias is poorly-behaved, such that estimates provide neither upper nor lower bounds for the population parameter. Further, hypothesis tests are unjustified. Thus, published multilevel model analyses using many workhorse datasets, including NELS, AdHealth, NLSY, GSS, PSID, and SIPP, often unwittingly convey substantive results and theoretical conclusions that lack foundation. Future research using the multilevel model should be limited to cases that satisfy the sample requirements described.BRII recipient: Lucas (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2530k6x1articleQuality & Quantityvol 48, iss 3, 1619-16490033-5177 1573-7845oai:escholarship.org:ark:/13030/qt7t44s0082016-12-21T21:21:40Zqt7t44s008Characterization of the Transient Oxaphosphetane BChE Inhibitor Formed from Spontaneously Activated EthephonLantz, Stephen RCasida, John E2013-09-16The major plant growth regulator ethephon degrades to ethylene and phosphate in aqueous solutions and plants and is spontaneously activated to a butyrylcholinesterase (BChE) inhibitor in alkaline solutions and animal tissues. In the present 31P NMR kinetic study of the reactions of ethephon in pH 7.4 carbonate buffer, we observed a transient peak at 28.11 ppm. The time course for the appearance and disappearance of this peak matches the activation/degradation kinetic profile of the BChE inhibitor, and the chemical shift supports the proposed 2-oxo-2-hydroxy-1,2-oxaphosphetane structure.BRII recipient: Casida (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7t44s008articleChemical Research in Toxicologyvol 26, iss 9, 1320-13220893-228X 1520-5010oai:escholarship.org:ark:/13030/qt8r2081m42016-12-21T21:20:28Zqt8r2081m4Pan-neuronal maturation but not neuronal subtype differentiation of adult neural stem cells is mechanosensitiveKeung, Albert JDong, MeimeiSchaffer, David VKumar, Sanjay2013-05-10Most past studies of the biophysical regulation of stem cell differentiation have focused on initial lineage commitment or proximal differentiation events. It would be valuable to understand whether biophysical inputs also influence distal endpoints more closely associated with physiological function, such as subtype specification in neuronal differentiation. To explore this question, we cultured adult neural stem cells (NSCs) on variable stiffness ECMs under conditions that promote neuronal fate commitment for extended time periods to allow neuronal subtype differentiation. We find that ECM stiffness does not modulate the expression of NeuroD1 and TrkA/B/C or the percentages of pan-neuronal, GABAergic, or glutamatergic neuronal subtypes. Interestingly, however, an ECM stiffness of 700 Pa maximizes expression of pan-neuronal markers. These results suggest that a wide range of stiffnesses fully permit pan-neuronal NSC differentiation, that an intermediate stiffness optimizes expression of pan-neuronal genes, and that stiffness does not impact commitment to particular neuronal subtypes.BRII recipient: KumarpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8r2081m4articleScientific Reportsvol 32045-2322oai:escholarship.org:ark:/13030/qt73z3b79m2016-12-21T17:45:32Zqt73z3b79mScience, Policy, and Management of Irrigation-Induced Selenium Contamination in CaliforniaKausch, Matteo FPallud, Celine E2013-01-01Selenium was recognized as an important aquatic contaminant following the identification of widespread deformities in waterfowl at the agricultural drainage evaporation ponds of the Kesterson Reservoir (California) in 1983. Since then, California has been the focal point for global research and management of Se contamination. We analyzed the history and current developments in science, policy, and management of irrigation-induced Se contamination in California. In terms of management, we evaluated the effects of improvements in the design of local attenuation methods (drainage reuse and evaporation ponds) in conjunction with the development of programs for Se load reductions at the regional scale (namely the Grassland Bypass Project). In terms of policy, the USEPA is currently working on site-specific water quality criteria for the San Francisco Bay Delta that may be a landmark for future legislation on Se in natural water bodies. We provide a critical analysis of this approach and discuss challenges and opportunities in expanding it to other locations such as the Salton Sea. Management lessons learned in California and the novel policy approach may help prevent future events of Se contamination.BRII recipient: Pallud (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/73z3b79marticleJournal of Environment Qualityvol 42, iss 6, 16050047-2425oai:escholarship.org:ark:/13030/qt0h56z7202016-12-21T17:44:21Zqt0h56z720Modeling the impact of soil aggregate size on selenium immobilizationKausch, M. FPallud, C. E2013-03-01Soil aggregates are mm- to cm-sized microporous structures separated by macropores. Whereas fast advective transport prevails in macropores, advection is inhibited by the low permeability of intra-aggregate micropores. This can lead to mass transfer limitations and the formation of aggregate scale concentration gradients affecting the distribution and transport of redox sensitive elements. Selenium (Se) mobilized through irrigation of seleniferous soils has emerged as a major aquatic contaminant. In the absence of oxygen, the bioavailable oxyanions selenate, Se(VI), and selenite, Se(IV), can be microbially reduced to solid, elemental Se, Se(0), and anoxic microzones within soil aggregates are thought to promote this process in otherwise well-aerated soils. To evaluate the impact of soil aggregate size on selenium retention, we developed a dynamic 2-D reactive transport model of selenium cycling in a single idealized aggregate surrounded by a macropore. The model was developed based on flow-through-reactor experiments involving artificial soil aggregates (diameter: 2.5 cm) made of sand and containing Enterobacter cloacae SLD1a-1 that reduces Se(VI) via Se(IV) to Se(0). Aggregates were surrounded by a constant flow providing Se(VI) and pyruvate under oxic or anoxic conditions. In the model, reactions were implemented with double-Monod rate equations coupled to the transport of pyruvate, O2, and Se species. The spatial and temporal dynamics of the model were validated with data from experiments, and predictive simulations were performed covering aggregate sizes 1–2.5 cm in diameter. Simulations predict that selenium retention scales with aggregate size. Depending on O2, Se(VI), and pyruvate concentrations, selenium retention was 4–23 times higher in 2.5 cm aggregates compared to 1 cm aggregates. Under oxic conditions, aggregate size and pyruvate concentrations were found to have a positive synergistic effect on selenium retention. Promoting soil aggregation on seleniferous agricultural soils, through organic matter amendments and conservation tillage, may thus help decrease the impacts of selenium contaminated drainage water on downstream aquatic ecosystems.BRII recipient: PalludpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0h56z720articleBiogeosciencesvol 10, iss 3, 1323-13361726-4189oai:escholarship.org:ark:/13030/qt84f8z8mm2016-12-21T17:42:20Zqt84f8z8mmReducing the numerical effort of finite-temperature density matrix renormalization group calculationsKarrasch, CBardarson, J HMoore, J E2013-08-13Finite-temperature transport properties of one-dimensional systems can be studied using the time dependent density matrix renormalization group via the introduction of auxiliary degrees of freedom which purify the thermal statistical operator. We demonstrate how the numerical effort of such calculations is reduced when the physical time evolution is augmented by an additional time evolution within the auxiliary Hilbert space. Specifically, we explore a variety of integrable and non-integrable, gapless and gapped models at temperatures ranging from T = ∞ down to T/bandwidth = 0.05 and study both (i) linear response where (heat and charge) transport coefficients are determined by the current–current correlation function and (ii) non-equilibrium driven by arbitrary large temperature gradients. The modified density matrix renormalization algorithm removes an 'artificial' build-up of entanglement between the auxiliary and physical degrees of freedom. Thus, longer time scales can be reached.BRII recipient: KarraschpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/84f8z8mmarticleNew Journal of Physicsvol 15, iss 8, 0830311367-2630oai:escholarship.org:ark:/13030/qt9sq1j0212016-12-21T17:40:40Zqt9sq1j021Early life growth trajectories and future risk for overweightJones-Smith, J CNeufeld, L MLaraia, BRamakrishnan, UGarcia-Guerra, AFernald, L C H2013-02-01Objective: Standard approaches have found that rapid growth during the first 2 years of life is a risk factor for overweight in later childhood. Our objective was to test whether growth velocity, independent of concurrent size, was associated with overweight using a nonlinear random-effects model that allows for enhanced specifications and estimations.Methods: Longitudinal data from a birth cohort in Mexico (n=586) were used to estimate growth trajectories over 0–24 months for body mass index (BMI), length and weight using the SuperImposition by Translation and Rotation (SITAR) models. The SITAR models use a nonlinear random-effects model to estimate an average growth curve for BMI, length and weight and each participant’s deviation from this curve on three dimensions—size, velocity and timing of peak velocity. We used logistic regression to estimate the association between overweight status at 7–9 years and size, velocity and timing of BMI, length and weight trajectories during 0–24 months. We tested whether any association between velocity and overweight varied by relative size during 0–24 months or birth weight.Results: SITAR models explained the majority of the variance in BMI (73%), height (86%) and weight (85%) between 0–24 months. When analyzed individually, relative BMI/length/weight (size) and BMI/length/weight velocity during 0–24 months were each associated with increased odds of overweight in late childhood. Associations for timing of peak velocity varied by anthropometric measure. However, in the mutually adjusted models, only relative BMI/length/weight (size) remained statistically significant. We found no evidence that any association between velocity and overweight varied by size during 0–24 months or birth weight.Conclusions: After mutual adjustment, size during 0–24 months of life (as opposed to birth size), but not velocity or timing of peak velocity, was most consistently associated with overweight in later childhood.BRII recipient: FernaldpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9sq1j021articleNutrition and Diabetesvol 3, iss 2, e602044-4052oai:escholarship.org:ark:/13030/qt4xj7q7122016-12-21T17:38:44Zqt4xj7q712Delineating Individual Trees from Lidar Data: A Comparison of Vector- and Raster-based Segmentation ApproachesJakubowski, MarekLi, WenkaiGuo, QinghuaKelly, Maggi2013-08-26Light detection and ranging (lidar) data is increasingly being used for ecosystem monitoring across geographic scales. This work concentrates on delineating individual trees in topographically-complex, mixed conifer forest across the California’s Sierra Nevada. We delineated individual trees using vector data and a 3D lidar point cloud segmentation algorithm, and using raster data with an object-based image analysis (OBIA) of a canopy height model (CHM). The two approaches are compared to each other and to ground reference data. We used high density (9 pulses/m2), discreet lidar data and WorldView-2 imagery to delineate individual trees, and to classify them by species or species types. We also identified a new method to correct artifacts in a high-resolution CHM. Our main focus was to determine the difference between the two types of approaches and to identify the one that produces more realistic results. We compared the delineations via tree detection, tree heights, and the shape of the generated polygons. The tree height agreement was high between the two approaches and the ground data (r2: 0.93–0.96). Tree detection rates increased for more dominant trees (8–100 percent). The two approaches delineated tree boundaries that differed in shape: the lidar-approach produced fewer, more complex, and larger polygons that more closely resembled real forest structure.BRII recipient: KellypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4xj7q712articleRemote Sensingvol 5, iss 9, 4163-41862072-4292oai:escholarship.org:ark:/13030/qt0vc6138j2016-12-21T17:37:07Zqt0vc6138jPseudomonas aeruginosa Utilizes the Type III Secreted Toxin ExoS to Avoid Acidified Compartments within Epithelial CellsHeimer, Susan REvans, David JStern, Michael EBarbieri, Joseph TYahr, TimothyFleiszig, Suzanne M. J2013-09-18Invasive Pseudomonas aeruginosa (PA) can enter epithelial cells wherein they mediate formation of plasma membrane bleb-niches for intracellular compartmentalization. This phenotype, and capacity for intracellular replication, requires the ADP-ribosyltransferase (ADPr) activity of ExoS, a PA type III secretion system (T3SS) effector protein. Thus, PA T3SS mutants lack these capacities and instead traffic to perinuclear vacuoles. Here, we tested the hypothesis that the T3SS, via the ADPr activity of ExoS, allows PA to evade acidic vacuoles that otherwise suppress its intracellular viability. The acidification state of bacteria-occupied vacuoles within infected corneal epithelial cells was studied using LysoTracker to visualize acidic, lysosomal vacuoles. Steady state analysis showed that within cells wild-type PAO1 localized to both membrane bleb-niches and vacuoles, while both exsA (transcriptional activator) and popB (effector translocation) T3SS mutants were only found in vacuoles. The acidification state of occupied vacuoles suggested a relationship with ExoS expression, i.e. vacuoles occupied by the exsA mutant (unable to express ExoS) were more often acidified than either popB mutant or wild-type PAO1 occupied vacuoles (p < 0.001). An exoS-gfp reporter construct pJNE05 confirmed that high exoS transcriptional output coincided with low occupation of acidified vacuoles, and vice versa, for both popB mutants and wild-type bacteria. Complementation of a triple effector null mutant of PAO1 with exoS (pUCPexoS) reduced the number of acidified bacteria-occupied vacuoles per cell; pUCPexoSE381D which lacks ADPr activity did not. The H+-ATPase inhibitor bafilomycin rescued intracellular replication to wild-type levels for exsA mutants, showing its viability is suppressed by vacuolar acidification. Taken together, the data show that the mechanism by which ExoS ADPr activity allows intracellular replication by PA involves suppression of vacuolar acidification. They also show that variability in ExoS expression by wild-type PA inside cells can differentially influence the fate of individual intracellular bacteria, even within the same cell.BRII recipient: FleiszigpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0vc6138jarticlePLoS ONEvol 8, iss 9, e731111932-6203oai:escholarship.org:ark:/13030/qt9dk1h7vg2016-12-21T17:36:03Zqt9dk1h7vgWorking Memory and Decision Processes in Visual Area V4Hayden, Benjamin YGallant, Jack L2013-01-01Recognizing and responding to a remembered stimulus requires the coordination of perception, working memory, and decision-making. To investigate the role of visual cortex in these processes, we recorded responses of single V4 neurons during performance of a delayed match-to-sample task that incorporates rapid serial visual presentation of natural images. We found that neuronal activity during the delay period after the cue but before the images depends on the identity of the remembered image and that this change persists while distractors appear. This persistent response modulation has been identified as a diagnostic criterion for putative working memory signals; our data thus suggest that working memory may involve reactivation of sensory neurons. When the remembered image reappears in the neuron’s receptive field, visually evoked responses are enhanced; this match enhancement is a diagnostic criterion for decision. One model that predicts these data is the matched filter hypothesis, which holds that during search V4 neurons change their tuning so as to match the remembered cue, and thus become detectors for that image. More generally, these results suggest that V4 neurons participate in the perceptual, working memory, and decision processes that are needed to perform memory-guided decision-making.BRII recipient: GallantpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9dk1h7vgarticleFrontiers in Neurosciencevol 71662-4548oai:escholarship.org:ark:/13030/qt20p2r2w92016-12-21T17:34:52Zqt20p2r2w9A Stepped Wedge, Cluster-Randomized Trial of a Household UV-Disinfection and Safe Storage Drinking Water Intervention in Rural Baja California Sur, MexicoGruber, J. SReygadas, F.Arnold, B. FRay, I.Nelson, K.Colford, J. M2013-06-03In collaboration with a local non-profit organization, this study evaluated the expansion of a program that promoted and installed Mesita Azul, an ultraviolet-disinfection system designed to treat household drinking water in rural Mexico. We conducted a 15-month, cluster-randomized stepped wedge trial by randomizing the order in which 24 communities (444 households) received the intervention. We measured primary outcomes (water contamination and diarrhea) during seven household visits. The intervention increased the percentage of households with access to treated and safely stored drinking water (23–62%), and reduced the percentage of households with Escherichia coli contaminated drinking water (risk difference (RD): −19% [95% CI: −27%, −14%]). No significant reduction in diarrhea was observed (RD: −0.1% [95% CI: −1.1%, 0.9%]). We conclude that household water quality improvements measured in this study justify future promotion of the Mesita Azul, and that future studies to measure its health impact would be valuable if conducted in populations with higher diarrhea prevalence.BRII recipient: Colford (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/20p2r2w9articleAmerican Journal of Tropical Medicine and Hygienevol 89, iss 2, 238-2450002-9637oai:escholarship.org:ark:/13030/qt0kq697522016-12-21T17:33:47Zqt0kq69752Accessibility of Myofilament Cysteines and Effects on ATPase Depend on the Activation State during Exposure to OxidantsGross, Sean MLehman, Steven L2013-07-19Signaling by reactive oxygen species has emerged as a major physiological process. Due to its high metabolic rate, striated muscle is especially subject to oxidative stress, and there are multiple examples in cardiac and skeletal muscle where oxidative stress modulates contractile function. Here we assessed the potential of cysteine oxidation as a mechanism for modulating contractile function in skeletal and cardiac muscle. Analyzing the cysteine content of the myofilament proteins in striated muscle, we found that cysteine residues are relatively rare, but are very similar between different muscle types and different vertebrate species. To refine this list of cysteines to those that may modulate function, we estimated the accessibility of oxidants to cysteine residues using protein crystal structures, and then sharpened these estimates using fluorescent labeling of cysteines in cardiac and skeletal myofibrils. We demonstrate that cysteine accessibility to oxidants and ATPase rates depend on the contractile state in which preparations are exposed. Oxidant exposure of skeletal and cardiac myofibrils in relaxing solution exposes myosin cysteines not accessible in rigor solution, and these modifications correspond to a decrease in maximum ATPase. Oxidant exposure under rigor conditions produces modifications that increase basal ATPase and calcium sensitivity in ventricular myofibrils, but these effects were muted in fast twitch muscle. These experiments reveal how structural and sequence variations can lead to divergent effects from oxidants in different muscle types.BRII recipient LehmanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0kq69752articlePLoS ONEvol 8, iss 71932-6203oai:escholarship.org:ark:/13030/qt883977h12016-12-21T17:32:01Zqt883977h1Molecular Phylogeny and Biogeography of the Hawaiian Craneflies Dicranomyia (Diptera: Limoniidae)Goodman, Kari RoeschO'Grady, Patrick2013-09-13The Hawaiian Diptera offer an opportunity to compare patterns of diversification across large and small endemic radiations with varying species richness and levels of single island endemism. The craneflies (Limoniidae: Dicranomyia) represent a small radiation of 13 described species that have diversified within the Hawaiian Islands. We used Bayesian and maximum likelihood approaches to generate a molecular phylogeny of the Hawaiian Dicranomyia using a combination of nuclear and mitochondrial loci, estimated divergence times and reconstructed ancestral ranges. Divergence time estimation and ancestral range reconstruction suggest that the colonization that led to most of the diversity within the craneflies arrived prior to the formation of Kauai and demonstrates that the two major clades within that radiation contrast sharply in their patterns of diversification.BRII recipient: GoodmanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/883977h1articlePLoS ONEvol 8, iss 9, e730191932-6203oai:escholarship.org:ark:/13030/qt9861q47q2016-12-21T17:30:16Zqt9861q47qNew Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species "Leptospirillum Group IV UBA BS"Goltsman, D. S. ADasari, M.Thomas, B. CShah, M. BVerBerkmoes, N. CHettich, R. LBanfield, J. F2013-05-03Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and “Leptospirillum rubarum” (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species “Leptospirillum group IV UBA BS.” These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.BRII recipient: Goltsman (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9861q47qarticleApplied and Environmental Microbiologyvol 79, iss 17, 5384-53930099-2240oai:escholarship.org:ark:/13030/qt2cg6v4wq2016-12-21T17:26:36Zqt2cg6v4wqAuthoring multi-stage code examples with editable code historiesGinosar, ShiryDe Pombo, Luis FernandoAgrawala, ManeeshHartmann, Bjoern2013-10-08Multi-stage code examples present multiple versions of a program where each stage increases the overall complexity of the code. In order to acquire strategies of program construction using a new language or API, programmers consult multi-stage code examples in books, tutorials and online videos. Authoring multi-stage code examples is currently a tedious process, as it involves keeping several stages of code synchronized in the face of edits and error corrections. We document these difficulties with a formative study examining how programmers author multi-stage code examples. We then present an IDE extension that helps authors create multi-stage code examples by propagating changes (insertions, deletions and modifications) to multiple saved versions of their code. Our system adapts revision control algorithms to the specific task of evolving example code. An informal evaluation finds that taking snapshots of a program as it is being developed and editing these snapshots in hindsight help users in creating multi-stage code examples.BRII recipient: Hartmann (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2cg6v4wqpublicationoai:escholarship.org:ark:/13030/qt2b1555g02016-12-21T17:24:23Zqt2b1555g0Measuring Unsafe Abortion-Related Mortality: A Systematic Review of the Existing MethodsGerdts, CaitlinVohra, DivyaAhern, Jennifer2013-01-14The WHO estimates that 13% of maternal mortality is due to unsafe abortion, but challenges with measurement and data quality persist. To our knowledge, no systematic assessment of the validity of studies reporting estimates of abortion-related mortality exists. Study Design: To be included in this study, articles had to meet the following criteria: (1) published between September 1st, 2000-December 1st, 2011; (2) utilized data from a country where abortion is “considered unsafe”; (3) specified and enumerated causes of maternal death including “abortion”; (4) enumerated ≥100 maternal deaths; (5) a quantitative research study; (6) published in a peer-reviewed journal.Results :7,438 articles were initially identified. Thirty-six studies were ultimately included. Overall, studies rated “Very Good” found the highest estimates of abortion related mortality (median 16%, range 1–27.4%). Studies rated “Very Poor” found the lowest overall proportion of abortion related deaths (median: 2%, range 1.3–9.4%). Conclusions: Improvements in the quality of data collection would facilitate better understanding global abortion-related mortality. Until improved data exist, better reporting of study procedures and standardization of the definition of abortion and abortion-related mortality should be encouragedBRII recipient: AhernpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2b1555g0articlePLoS ONEvol 8, iss 1oai:escholarship.org:ark:/13030/qt4xs413342016-12-21T17:22:57Zqt4xs41334Functional Profiling Discovers the Dieldrin Organochlorinated Pesticide Affects Leucine Availability in YeastGaytan, B. DLoguinov, A. VLantz, S. RLerot, J.-M.Denslow, N. DVulpe, C. D2013-01-28Exposure to organochlorinated pesticides such as dieldrin has been linked to Parkinson’s and Alzheimer’s diseases, endocrine disruption, and cancer, but the cellular and molecular mechanisms of toxicity behind these effects remain largely unknown. Here we demonstrate, using a functional genomics approach in the model eukaryote Saccharomyces cerevisiae, that dieldrin alters leucine availability. This model is supported by multiple lines of congruent evidence: (1) mutants defective in amino acid signaling or transport are sensitive to dieldrin, which is reversed by the addition of exogenous leucine; (2) dieldrin sensitivity of wild-type or mutant strains is dependent upon leucine concentration in the media; (3) overexpression of proteins that increase intracellular leucine confer resistance to dieldrin; (4) leucine uptake is inhibited in the presence of dieldrin; and (5) dieldrin induces the amino acid starvation response. Additionally, we demonstrate that appropriate negative regulation of the Ras/protein kinase A pathway, along with an intact pyruvate dehydrogenase complex, is required for dieldrin tolerance. Many yeast genes described in this study have human orthologs that may modulate dieldrin toxicity in humans.BRII recipient: Gaytan (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4xs41334articleToxicological Sciencesvol 132, iss 2, 347-3581096-6080 1096-0929oai:escholarship.org:ark:/13030/qt6620x4b82016-12-20T22:02:11Zqt6620x4b8Interhemispheric Temperature Asymmetry over the Twentieth Century and in Future ProjectionsFriedman, Andrew RHwang, Yen-TingChiang, John C. HFrierson, Dargan M. W2013-08-01The temperature contrast between the Northern and Southern Hemispheres—the interhemispheric temperature asymmetry (ITA)—is an emerging indicator of global climate change, potentially relevant to the Hadley circulation and tropical rainfall. The authors examine the ITA in historical observations and in phases 3 and 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5) simulations. The observed annual-mean ITA (north minus south) has varied within a 0.8°C range and features a significant positive trend since 1980. The CMIP multimodel ensembles simulate this trend, with a stronger and more realistic signal in CMIP5. Both ensembles project a continued increase in the ITA over the twenty-first century, well outside the twentieth-century range. The authors mainly attribute this increase to the uneven spatial impacts of greenhouse forcing, which result in amplified warming in the Arctic and northern landmasses. The CMIP5 specific-forcing simulations indicate that, before 1980, the greenhouse-forced ITA trend was primarily countered by anthropogenic aerosols. The authors also identify an abrupt decrease in the observed ITA in the late 1960s, which is generally not present in the CMIP simulations; it suggests that the observed drop was caused by internal variability. The difference in the strengths of the northern and southern Hadley cells covaries with the ITA in the CMIP5 simulations, in accordance with previous findings; the authors also find an association with the hemispheric asymmetry in tropical rainfall. These relationships imply a northward shift in tropical rainfall with increasing ITA in the twenty-first century, though this result is difficult to separate from the response to global-mean temperature change.BRII recipient: Friedman (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6620x4b8articleJournal of Climatevol 26, iss 15, 5419-54330894-8755 1520-0442oai:escholarship.org:ark:/13030/qt2c16n2932016-12-20T22:00:45Zqt2c16n293Unraveling the Anxious Mind: Anxiety, Worry, and Frontal Engagement in Sustained Attention Versus Off-Task ProcessingForster, S.Nunez Elizalde, A. OCastle, E.Bishop, S. J2013-09-22Much remains unknown regarding the relationship between anxiety, worry, sustained attention, and frontal function. Here, we addressed this using a sustained attention task adapted for functional magnetic resonance imaging. Participants responded to presentation of simple stimuli, withholding responses to an infrequent “No Go” stimulus. Dorsolateral prefrontal cortex (DLPFC) activity to “Go” trials, and dorsal anterior cingulate (dACC) activity to “No Go” trials were associated with faster error-free performance; consistent with DLPFC and dACC facilitating proactive and reactive control, respectively. Trait anxiety was linked to reduced recruitment of these regions, slower error-free performance, and decreased frontal-thalamo-striatal connectivity. This indicates an association between trait anxiety and impoverished frontal control of attention, even when external distractors are absent. In task blocks where commission errors were made, greater DLPFC-precuneus and DLPFC-posterior cingulate connectivity were associated with both trait anxiety and worry, indicative of increased off-task thought. Notably, unlike trait anxiety, worry was not linked to reduced frontal-striatal-thalamo connectivity, impoverished frontal recruitment, or slowed responding during blocks without commission errors, contrary to accounts proposing a direct causal link between worry and impoverished attentional control. This leads us to propose a new model of the relationship between anxiety, worry and frontal engagement in attentional control versus off-task thought.BRII recipient: Bishop (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2c16n293articleCerebral Cortexvol 25, iss 3, 609-6181047-3211 1460-2199oai:escholarship.org:ark:/13030/qt67d834v32016-12-20T21:59:25Zqt67d834v3The epidemiology and surveillance response to pandemic influenza A (H1N1) among local health departments in the San Francisco Bay AreaEnanoria, Wayne TCrawley, Adam WTseng, WinstonFurnish, JasmineBalido, JeannieAragon, Tomas J2013-01-01Public health surveillance and epidemiologic investigations are critical public health functions for identifying threats to the health of a community. Very little is known about how these functions are conducted at the local level. The purpose of the Epidemiology Networks in Action (EpiNet) Study was to describe the epidemiology and surveillance response to the 2009 pandemic influenza A (H1N1) by city and county health departments in the San Francisco Bay Area in California. The study also documented lessons learned from the response in order to strengthen future public health preparedness and response planning efforts in the region.Methods:In order to characterize the epidemiology and surveillance response, we conducted key informant interviews with public health professionals from twelve local health departments in the San Francisco Bay Area. In order to contextualize aspects of organizational response and performance, we recruited two types of key informants: public health professionals who were involved with the epidemiology and surveillance response for each jurisdiction, as well as the health officer or his/her designee responsible for H1N1 response activities. Information about the organization, data sources for situation awareness, decision-making, and issues related to surge capacity, continuity of operations, and sustainability were collected during the key informant interviews. Content and interpretive analyses were conducted using ATLAS.ti software.Results:The study found that disease investigations were important in the first months of the pandemic, often requiring additional staff support and sometimes forcing other public health activities to be put on hold. We also found that while the Incident Command System (ICS) was used by all participating agencies to manage the response, the manner in which it was implemented and utilized varied. Each local health department (LHD) in the study collected epidemiologic data from a variety of sources, but only case reports (including hospitalized and fatal cases) and laboratory testing data were used by all organizations. While almost every LHD attempted to collect school absenteeism data, many respondents reported problems in collecting and analyzing these data. Laboratory capacity to test influenza specimens often aided an LHD’s ability to conduct disease investigations and implement control measures, but the ability to test specimens varied across the region and even well-equipped laboratories exceeded their capacity. As a whole, the health jurisdictions in the region communicated regularly about key decision-making (continued on next page) (continued from previous page) related to the response, and prior regional collaboration on pandemic influenza planning helped to prepare the region for the novel H1N1 influenza pandemic. The study did find, however, that many respondents (including the majority of epidemiologists interviewed) desired an increase in regional communication about epidemiology and surveillance issues.Conclusion:The study collected information about the epidemiology and surveillance response among LHDs in the San Francisco Bay Area that has implications for public health preparedness and emergency response training, public health best practices, regional public health collaboration, and a perceived need for information sharing.BRII recipient: EnanoriapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/67d834v3articleBMC Public Healthvol 13, iss 1, 2761471-2458oai:escholarship.org:ark:/13030/qt00q385612016-12-20T21:58:00Zqt00q38561De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genesCroucher, Peter JBrewer, Michael SWinchell, Christopher JOxford, Geoff SGillespie, Rosemary G2013-01-01A number of spider species within the family Theridiidae exhibit a dramatic abdominal (opisthosomal) color polymorphism. The polymorphism is inherited in a broadly Mendelian fashion and in some species consists of dozens of discrete morphs that are convergent across taxa and populations. Few genomic resources exist for spiders. Here, as a first necessary step towards identifying the genetic basis for this trait we present the near complete transcriptomes of two species: the Hawaiian happy-face spider Theridion grallator and Theridion californicum. We mined the gene complement for pigment-pathway genes and examined differential expression (DE) between morphs that are unpatterned (plain yellow) and patterned (yellow with superimposed patches of red, white or very dark brown).Results:By deep sequencing both RNA-seq and normalized cDNA libraries from pooled specimens of each species we were able to assemble a comprehensive gene set for both species that we estimate to be 98-99% complete. It is likely that these species express more than 20,000 protein-coding genes, perhaps 4.5% (ca. 870) of which might be unique to spiders. Mining for pigment-associated Drosophila melanogaster genes indicated the presence of all ommochrome pathway genes and most pteridine pathway genes and DE analyses further indicate a possible role for the pteridine pathway in theridiid color patterning.Conclusions:Based upon our estimates, T. grallator and T. californicum express a large inventory of protein-coding genes. Our comprehensive assembly illustrates the continuing value of sequencing normalized cDNA libraries in addition to RNA-seq in order to generate a reference transcriptome for non-model species. The identification of pteridine-related genes and their possible involvement in color patterning is a novel finding in spiders and one that suggests a biochemical link between guanine deposits and the pigments exhibited by these species.BRII recipient: GillespiepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/00q38561articleBMC Genomicsvol 14, iss 1, 8621471-2164oai:escholarship.org:ark:/13030/qt02f4314p2016-12-20T21:56:13Zqt02f4314pHeterogeneous global crop yield response to biochar: a meta-regression analysisCrane-Droesch, AndrewAbiven, SamuelJeffery, SimonTorn, Margaret S2013-12-01Biochar may contribute to climate change mitigation at negative cost by sequestering photosynthetically fixed carbon in soil while increasing crop yields. The magnitude of biochar's potential in this regard will depend on crop yield benefits, which have not been well-characterized across different soils and biochars. Using data from 84 studies, we employ meta-analytical, missing data, and semiparametric statistical methods to explain heterogeneity in crop yield responses across different soils, biochars, and agricultural management factors, and then estimate potential changes in yield across different soil environments globally. We find that soil cation exchange capacity and organic carbon were strong predictors of yield response, with low cation exchange and low carbon associated with positive response. We also find that yield response increases over time since initial application, compared to non-biochar controls. High reported soil clay content and low soil pH were weaker predictors of higher yield response. No biochar parameters in our dataset—biochar pH, percentage carbon content, or temperature of pyrolysis—were significant predictors of yield impacts. Projecting our fitted model onto a global soil database, we find the largest potential increases in areas with highly weathered soils, such as those characterizing much of the humid tropics. Richer soils characterizing much of the world's important agricultural areas appear to be less likely to benefit from biochar.BRII recipient: Crane-DroeschpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/02f4314particleEnvironmental Research Lettersvol 8, iss 4, 0440491748-9326oai:escholarship.org:ark:/13030/qt3vg2k7ww2016-12-20T21:55:03Zqt3vg2k7wwDemoCut: generating concise instructional videos for physical demonstrationsChi, Pei-YuLiu, JoyceLinder, JasonDontcheva, MiraLi, WilmotHartmann, Bjoern2013-10-08Amateur instructional videos often show a single uninterrupted take of a recorded demonstration without any edits. While easy to produce, such videos are often too long as they include unnecessary or repetitive actions as well as mistakes. We introduce DemoCut, a semi-automatic video editing system that improves the quality of amateur instructional videos for physical tasks. DemoCut asks users to mark key moments in a recorded demonstration using a set of marker types derived from our formative study. Based on these markers, the system uses audio and video analysis to automatically organize the video into meaningful segments and apply appropriate video editing effects. To understand the effectiveness of DemoCut, we report a technical evaluation of seven video tutorials created with DemoCut. In a separate user evaluation, all eight participants successfully created a complete tutorial with a variety of video editing effects using our system.BRII recipient: Hartmann (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3vg2k7wwpublicationoai:escholarship.org:ark:/13030/qt1jv0w8032016-12-20T21:53:47Zqt1jv0w803Infrastructure and automobile shifts: positioning transit to reduce life-cycle environmental impacts for urban sustainability goalsChester, MikhailPincetl, StephanieElizabeth, ZoeEisenstein, WilliamMatute, Juan2013-03-01Public transportation systems are often part of strategies to reduce urban environmental impacts from passenger transportation, yet comprehensive energy and environmental life-cycle measures, including upfront infrastructure effects and indirect and supply chain processes, are rarely considered. Using the new bus rapid transit and light rail lines in Los Angeles, near-term and long-term life-cycle impact assessments are developed, including consideration of reduced automobile travel. Energy consumption and emissions of greenhouse gases and criteria pollutants are assessed, as well the potential for smog and respiratory impacts. Results show that life-cycle infrastructure, vehicle, and energy production components significantly increase the footprint of each mode (by 48–100% for energy and greenhouse gases, and up to 6200% for environmental impacts), and emerging technologies and renewable electricity standards will significantly reduce impacts. Life-cycle results are identified as either local (in Los Angeles) or remote, and show how the decision to build and operate a transit system in a city produces environmental impacts far outside of geopolitical boundaries. Ensuring shifts of between 20–30% of transit riders from automobiles will result in passenger transportation greenhouse gas reductions for the city, and the larger the shift, the quicker the payback, which should be considered for time-specific environmental goals.BRII recipient: EisensteinpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1jv0w803articleEnvironmental Research Lettersvol 8, iss 1, 0150411748-9326oai:escholarship.org:ark:/13030/qt4pc0p20w2016-12-20T21:52:19Zqt4pc0p20wPax6 Downregulation Mediates Abnormal Lineage Commitment of the Ocular Surface Epithelium in Aqueous-Deficient Dry Eye DiseaseChen, Ying TingChen, Feeling Y. TVijmasi, TrinkaStephens, Denise NGallup, MarianneMcNamara, Nancy A2013-10-15Keratinizing squamous metaplasia (SQM) of the ocular surface is a blinding consequence of systemic autoimmune disease and there is no cure. Ocular SQM is traditionally viewed as an adaptive tissue response during chronic keratoconjunctivitis sicca (KCS) that provokes pathological keratinization of the corneal epithelium and fibrosis of the corneal stroma. Recently, we established the autoimmune regulator-knockout (Aire KO) mouse as a model of autoimmune KCS and identified an essential role for autoreactive CD4+ T cells in SQM pathogenesis. In subsequent studies, we noted the down-regulation of paired box gene 6 (Pax6) in both human patients with chronic KCS associated with Sjögren’s syndrome and Aire KO mice. Pax6 encodes a pleiotropic transcription factor guiding eye morphogenesis during development. While the postnatal function of Pax6 is largely unknown, we hypothesized that its role in maintaining ocular surface homeostasis was disrupted in the inflamed eye and that loss of Pax6 played a functional role in the initiation and progression of SQM. Adoptive transfer of autoreactive T cells from Aire KO mice to immunodeficient recipients confirmed CD4+ T cells as the principal downstream effectors promoting Pax6 downregulation in Aire KO mice. CD4+ T cells required local signaling via Interleukin-1 receptor (IL-1R1) to provoke Pax6 loss, which prompted a switch from corneal-specific cytokeratin, CK12, to epidermal-specific CK10. The functional role of Pax6 loss in SQM pathogenesis was indicated by the reversal of SQM and restoration of ocular surface homeostasis following forced expression of Pax6 in corneal epithelial cells using adenovirus. Thus, tissue-restricted restoration of Pax6 prevented aberrant epidermal-lineage commitment suggesting adjuvant Pax6 gene therapy may represent a novel therapeutic approach to prevent SQM in patients with chronic inflammatory diseases of the ocular surface.BRII recipient: McNamarapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4pc0p20warticlePLoS ONEvol 8, iss 10, e772861932-6203oai:escholarship.org:ark:/13030/qt3hz0w2zp2016-12-20T21:50:13Zqt3hz0w2zpDevelopment and Assessment of Traditional and Innovative Media to Reduce Individual HIV/AIDS-Related Stigma Attitudes and Beliefs in IndiaCatalani, CariciaCastaneda, DiegoSpielberg, Freya2013-01-01Although stigma is considered a major barrier to effective response to the HIV/AIDS epidemic, there is a lack of evidence on effective interventions. This media intervention took place among key HIV-vulnerable communities in Southern India. Two HIV stigma videos were created using techniques from traditional film production and new media digital storytelling. A series of 16 focus group discussions were held in 4 rural and 4 urban sites in South India, with specific groups for sex workers, men who have sex with men, young married women, and others. Focus groups with viewers of the traditional film (8 focus groups, 80 participants) and viewers of the new media production (8 focus groups, 69 participants) revealed the mechanisms through which storyline, characters, and esthetics influence viewers’ attitudes and beliefs about stigma. A comparative pre-/post-survey showed that audiences of both videos significantly improved their stigma scores. We found that a simple illustrated video, produced on a limited budget by amateurs, and a feature film, produced with an ample budget by professionals, elicited similar responses from audiences and similar positive short-term outcomes on stigma.BRII recipient: CatalanipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3hz0w2zparticleFrontiers in Public Healthvol 12296-2565oai:escholarship.org:ark:/13030/qt0671r44v2016-12-20T21:48:22Zqt0671r44vAAV-Mediated, Optogenetic Ablation of Muller Glia Leads to Structural and Functional Changes in the Mouse RetinaByrne, Leah CKhalid, FakhraLee, TrevorZin, Emilia AGreenberg, Kenneth PVisel, MeikeSchaffer, David VFlannery, John G2013-09-27Müller glia, the primary glial cell in the retina, provide structural and metabolic support for neurons and are essential for retinal integrity. Müller cells are closely involved in many retinal degenerative diseases, including macular telangiectasia type 2, in which impairment of central vision may be linked to a primary defect in Müller glia. Here, we used an engineered, Müller-specific variant of AAV, called ShH10, to deliver a photo-inducibly toxic protein, KillerRed, to Müller cells in the mouse retina. We characterized the results of specific ablation of these cells on visual function and retinal structure. ShH10-KillerRed expression was obtained following intravitreal injection and eyes were then irradiated with green light to induce toxicity. Induction of KillerRed led to loss of Müller cells and a concomitant decrease of Müller cell markers glutamine synthetase and cellular retinaldehyde-binding protein, reduction of rhodopsin and cone opsin, and upregulation of glial fibrillary acidic protein. Loss of Müller cells also resulted in retinal disorganization, including thinning of the outer nuclear layer and the photoreceptor inner and outer segments. High resolution imaging of thin sections revealed displacement of photoreceptors from the ONL, formation of rosette-like structures and the presence of phagocytic cells. Furthermore, Müller cell ablation resulted in increased area and volume of retinal blood vessels, as well as the formation of tortuous blood vessels and vascular leakage. Electrophysiologic measures demonstrated reduced retinal function, evident in decreased photopic and scotopic electroretinogram amplitudes. These results show that loss of Müller cells can cause progressive retinal degenerative disease, and suggest that AAV delivery of an inducibly toxic protein in Müller cells may be useful to create large animal models of retinal dystrophies.BRII recipient: ByrnepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0671r44varticlePLoS ONEvol 8, iss 9, e760751932-6203oai:escholarship.org:ark:/13030/qt9n91s2852016-12-20T21:46:34Zqt9n91s285Redeeming qualities: exploring factors that affect women's use of reproductive health vouchers in CambodiaBrody, Carinne DFreccero, JulieBrindis, Claire DBellows, Ben2013-01-01One approach to delivering healthcare in developing countries is through voucher programs, where vouchers are distributed to a specific population for free or subsidized health care. Recent evaluations suggest that vouchers have the potential to extend coverage of priority health services to the poor in developing countries. In Cambodia, a reproductive health voucher program was implemented in January 2011. This study aims to explore women’s early experiences accessing health services with their vouchers at accredited clinics.MethodsThis qualitative exploratory study used focus group methodology to gather information from five groups of older (>25 years) and four groups of younger (18–25 years) women who were eligible for the voucher program in three rural provinces. Focus groups were digitally recorded, transcribed and translated from Khmer into English. Data analysis was an iterative process, which comprised of open coding to find commonalities that reflected categories or themes and axial coding to relate initial themes to each other. Next, a basic framework for analysis was formed by integrating the themes into the framework.ResultsTwo overarching themes were identified in the data: 1) factors that facilitate voucher use and 2) factors that inhibit voucher use. Within each of these themes, three subthemes were identified: 1) pre-existing factors, 2) distribution factors, and 3) redemption factors. Overall, women expressed positive feelings towards the voucher program, while several areas for program improvement were identified including the importance of addressing pre-existing demand-side barriers to using reproductive health services, the need for more comprehensive counselling during voucher distribution, and the persistent cost of unofficial payments expected by midwives after delivery irrespective of voucher use.ConclusionsEarly information from program beneficiaries can lead to timely and responsive changes that can help to maximize program success. This study highlights the importance of tailoring voucher programs to specific community needs, a strategy that can lead to better program uptake.BRII recipient: BrodypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9n91s285articleBMC International Health and Human Rightsvol 13, iss 1, 131472-698Xoai:escholarship.org:ark:/13030/qt7vf6m6zn2016-12-20T21:45:38Zqt7vf6m6znCommunity Health Workers and Mobile Technology: A Systematic Review of the LiteratureBraun, RebeccaCatalani, CariciaWimbush, JulianIsraelski, Dennis2013-06-12In low-resource settings, community health workers are frontline providers who shoulder the health service delivery burden. Increasingly, mobile technologies are developed, tested, and deployed with community health workers to facilitate tasks and improve outcomes. We reviewed the evidence for the use of mobile technology by community health workers to identify opportunities and challenges for strengthening health systems in resource-constrained settings.Methods We conducted a systematic review of peer-reviewed literature from health, medical, social science, and engineering databases, using PRISMA guidelines. We identified a total of 25 unique full-text research articles on community health workers and their use of mobile technology for the delivery of health services.Results Community health workers have used mobile tools to advance a broad range of health aims throughout the globe, particularly maternal and child health, HIV/AIDS, and sexual and reproductive health. Most commonly, community health workers use mobile technology to collect field-based health data, receive alerts and reminders, facilitate health education sessions, and conduct person-to-person communication. Programmatic efforts to strengthen health service delivery focus on improving adherence to standards and guidelines, community education and training, and programmatic leadership and management practices. Those studies that evaluated program outcomes provided some evidence that mobile tools help community health workers to improve the quality of care provided, efficiency of services, and capacity for program monitoring.Discussion Evidence suggests mobile technology presents promising opportunities to improve the range and quality of services provided by community health workers. Small-scale efforts, pilot projects, and preliminary descriptive studies are increasing, and there is a trend toward using feasible and acceptable interventions that lead to positive program outcomes through operational improvements and rigorous study designs. Programmatic and scientific gaps will need to be addressed by global leaders as they advance the use and assessment of mobile technology tools for community health workers.BRII recipient: BraunpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7vf6m6znarticlePLoS ONEvol 8, iss 6, e657721932-6203oai:escholarship.org:ark:/13030/qt9rh2m5s12016-12-20T21:44:20Zqt9rh2m5s1Fungi at a Small Scale: Spatial Zonation of Fungal Assemblages around Single TreesBranco, SaraBruns, Thomas DSingleton, Ian2013-10-16Biological communities are often structured by environmental factors even at small spatial scales. Fungi are no exception, though the patterns and mechanisms underlying their community structure are usually unknown. Previous work documented zonation in fungi under tree canopies primarily through their fruiting patterns. Here we investigate the existence of zonation patterns in fungal communities around isolated Pinus muricata trees of different ages in northern coastal California. Using a combination of ingrowth bags and pyrosequencing to target underground mycelium we found highly diverse soil fungal communities associated with single trees. Both ectomycorrhizal and non-ectomycorrhizal fungi were present in all samples, but the latter were more species rich, dominated the samples by sequence read abundance, and showed partitioning by canopy-defined zones and tree age. Soil chemistry was correlated with fungal zonation, but host root density was not. Our results indicate different guilds of fungi partition space differently and are driven by distinct environmental parameters.BRII recipient: BrancopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9rh2m5s1articlePLoS ONEvol 8, iss 10, e782951932-6203oai:escholarship.org:ark:/13030/qt0w02f0022016-12-20T21:43:23Zqt0w02f002What can ecological science tell us about opportunities for carbon sequestration on arid rangelands in the United States?Booker, KayjeHuntsinger, LynnBartolome, James WSayre, Nathan FStewart, William2013-02-01Scientific interest in carbon sequestration on rangelands is largely driven by their extent, while the interest of ranchers in the United States centers on opportunities to enhance revenue streams. Rangelands cover approximately 30% of the earth's ice-free land surface and hold an equivalent amount of the world's terrestrial carbon. Rangelands are grasslands, shrublands, and savannas and cover 312 million hectares in the United States. On the arid and semi-arid sites typical of rangelands annual fluxes are small and unpredictable over time and space, varying primarily with precipitation, but also with soils and vegetation. There is broad scientific consensus that non-equilibrium ecological models better explain the dynamics of such rangelands than equilibrium models, yet current and proposed carbon sequestration policies and associated grazing management recommendations in the United States often do not incorporate this developing scientific understanding of rangeland dynamics. Carbon uptake on arid and semi-arid rangelands is most often controlled by abiotic factors not easily changed by management of grazing or vegetation. Additionality may be impossible to achieve consistently through management on rangelands near the more xeric end of a rangeland climatic gradient. This point is illustrated by a preliminary examination of efforts to develop voluntary cap and trade markets for carbon credits in the United States, and options including payment for ecosystem services or avoided conversion, and carbon taxation. A preliminary analysis focusing on cap and trade and payment for avoided conversion or ecosystem services illustrates the misalignment between policies targeting vegetation management for enhanced carbon uptake and non-equilibrium carbon dynamics on arid United States rangelands. It is possible that current proposed carbon policy as exemplified by carbon credit exchange or offsets will result in a net increase in emissions, as well as investment in failed management. Rather than focusing on annual fluxes, policy and management initiatives should seek long-term protection of rangelands and rangeland soils to conserve carbon, and a broader range of environmental and social benefits.BRIi recipient: Huntsinger (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/0w02f002articleGlobal Environmental Changevol 23, iss 1, 240-25109593780oai:escholarship.org:ark:/13030/qt572654h02016-12-20T21:42:26Zqt572654h0Cluster-randomised controlled trials of individual and combined water, sanitation, hygiene and nutritional interventions in rural Bangladesh and Kenya: the WASH Benefits study design and rationaleArnold, B. FNull, C.Luby, S. PUnicomb, L.Stewart, C. PDewey, K. GAhmed, T.Ashraf, S.Christensen, G.Clasen, T.Dentz, H. NFernald, L. C. HHaque, R.Hubbard, A. EKariger, P.Leontsini, E.Lin, A.Njenga, S. MPickering, A. JRam, P. KTofail, F.Winch, P. JColford, J. M2013-08-30Introduction Enteric infections are common during the first years of life in low-income countries and contribute to growth faltering with long-term impairment of health and development. Water quality, sanitation, handwashing and nutritional interventions can independently reduce enteric infections and growth faltering. There is little evidence that directly compares the effects of these individual and combined interventions on diarrhoea and growth when delivered to infants and young children. The objective of the WASH Benefits study is to help fill this knowledge gap.Methods and analysis WASH Benefits includes two cluster-randomised trials to assess improvements in water quality, sanitation, handwashing and child nutrition—alone and in combination—to rural households with pregnant women in Kenya and Bangladesh. Geographically matched clusters (groups of household compounds in Bangladesh and villages in Kenya) will be randomised to one of six intervention arms or control. Intervention arms include water quality, sanitation, handwashing, nutrition, combined water+sanitation+handwashing (WSH) and WSH+nutrition. The studies will enrol newborn children (N=5760 in Bangladesh and N=8000 in Kenya) and measure outcomes at 12 and 24 months after intervention delivery. Primary outcomes include child length-for-age Z-scores and caregiver-reported diarrhoea. Secondary outcomes include stunting prevalence, markers of environmental enteropathy and child development scores (verbal, motor and personal/social). We will estimate unadjusted and adjusted intention-to-treat effects using semiparametric estimators and permutation tests.Ethics and dissemination Study protocols have been reviewed and approved by human subjects review boards at the University of California, Berkeley, Stanford University, the International Centre for Diarrheal Disease Research, Bangladesh, the Kenya Medical Research Institute, and Innovations for Poverty Action. Independent data safety monitoring boards in each country oversee the trials. This study is funded by a grant from the Bill & Melinda Gates Foundation to the University of California, Berkeley.Registration Trial registration identifiers (http://www.clinicaltrials.gov): NCT01590095 (Bangladesh), NCT01704105 (Kenya).BRII recipient: ArnoldpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/572654h0articleBMJ Openvol 3, iss 8, e003476-e0034762044-6055oai:escholarship.org:ark:/13030/qt5gt819mk2016-12-20T19:25:25Zqt5gt819mkDescription and first application of a new technique to measure the gravitational mass of antihydrogenAmole, C.Ashkezari, M. DBaquero-Ruiz, M.Bertsche, W.Butler, E.Capra, A.Cesar, C. LCharlton, M.Eriksson, S.Fajans, J.Friesen, T.Fujiwara, M. CGill, D. RGutierrez, A.Hangst, J. SHardy, W. NHayden, M. EIsaac, C. AJonsell, S.Kurchaninov, L.Little, A.Madsen, N.McKenna, J. T. KMenary, S.Napoli, S. CNolan, P.Olin, A.Pusa, P.Rasmussen, C. ØRobicheaux, F.Sarid, E.Silveira, D. MSo, C.Thompson, R. Ivan der Werf, D. PWurtele, J. SZhmoginov, A. ICharman, A. E2013-04-30Physicists have long wondered whether the gravitational interactions between matter and antimatter might be different from those between matter and itself. Although there are many indirect indications that no such differences exist and that the weak equivalence principle holds, there have been no direct, free-fall style, experimental tests of gravity on antimatter. Here we describe a novel direct test methodology; we search for a propensity for antihydrogen atoms to fall downward when released from the ALPHA antihydrogen trap. In the absence of systematic errors, we can reject ratios of the gravitational to inertial mass of antihydrogen >75 at a statistical significance level of 5%; worst-case systematic errors increase the minimum rejection ratio to 110. A similar search places somewhat tighter bounds on a negative gravitational mass, that is, on antigravity. This methodology, coupled with ongoing experimental improvements, should allow us to bound the ratio within the more interesting near equivalence regime.BRII recipient: FajanspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5gt819mkarticleNature Communicationsvol 4, 17852041-1723oai:escholarship.org:ark:/13030/qt3vd3s7dr2016-12-20T19:24:15Zqt3vd3s7drThe PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classificationAfrasiabi, C.Samad, B.Dineen, D.Meacham, C.Sjolander, K.2013-05-18The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.BRII recipient: SjolanderpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3vd3s7drarticleNucleic Acids Researchvol 41, iss W1, W242-W2480305-1048 1362-4962oai:escholarship.org:ark:/13030/qt19b9c37m2016-12-20T19:22:22Zqt19b9c37mFacilitating recognition of crowded faces with presaccadic attentionWolfe, Benjamin AWhitney, David2014-01-01In daily life, we make several saccades per second to objects we cannot normally recognize in the periphery due to visual crowding. While we are aware of the presence of these objects, we cannot identify them and may, at best, only know that an object is present at a particular location. The process of planning a saccade involves a presaccadic attentional component known to be critical for saccadic accuracy, but whether this or other presaccadic processes facilitate object identification as opposed to object detection—especially with high level natural objects like faces—is less clear. In the following experiments, we show that presaccadic information about a crowded face reduces the deleterious effect of crowding, facilitating discrimination of two emotional faces, even when the target face is never foveated. While accurate identification of crowded objects is possible in the absence of a saccade, accurate identification of a crowded object is considerably facilitated by presaccadic attention. Our results provide converging evidence for a selective increase in available information about high level objects, such as faces, at a presaccadic stage.BRII recipient: WolfepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/19b9c37marticleFrontiers in Human Neurosciencevol 81662-5161oai:escholarship.org:ark:/13030/qt94r908ts2016-12-20T19:21:20Zqt94r908tsTo move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in 'Terebinthaceae'� (Anacardiaceae and Burseraceae)Weeks, AndreaZapata, FelipePell, Susan KDaly, Douglas CMitchell, John DFine, Paul V. A2014-11-28Many angiosperm families are distributed pantropically, yet for any given continent little is known about which lineages are ancient residents or recent arrivals. Here we use a comprehensive sampling of the pantropical sister pair Anacardiaceae and Burseraceae to assess the relative importance of continental vicariance, long-distance dispersal and niche-conservatism in generating its distinctive pattern of diversity over time. Each family has approximately the same number of species and identical stem age, yet Anacardiaceae display a broader range of fruit morphologies and dispersal strategies and include species that can withstand freezing temperatures, whereas Burseraceae do not. We found that nuclear and chloroplast data yielded a highly supported phylogenetic reconstruction that supports current taxonomic concepts and time-calibrated biogeographic reconstructions that are broadly congruent with the fossil record. We conclude that the most recent common ancestor of these families was widespread and likely distributed in the Northern Hemisphere during the Cretaceous and that vicariance between Eastern and Western Hemispheres coincided with the initial divergence of the families. The tempo of diversification of the families is strikingly different. Anacardiaceae steadily accumulated lineages starting in the Late Cretaceous–Paleocene while the majority of Burseraceae diversification occurred in the Miocene. Multiple dispersal- and vicariance-based intercontinental colonization events are inferred for both families throughout the past 100 million years. However, Anacardiaceae have shifted climatic niches frequently during this time, while Burseraceae have experienced very few shifts between dry and wet climates and only in the tropics. Thus, we conclude that both Anacardiaceae and Burseraceae move easily but that Anacardiaceae have adapted more often, either due to more varied selective pressures or greater intrinsic lability.BRII recipient: FinepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/94r908tsarticleFrontiers in Geneticsvol 51664-8021oai:escholarship.org:ark:/13030/qt1s81s8pk2016-12-20T19:19:24Zqt1s81s8pkComparing the implementation of team approaches for improving diabetes care in community health centersVan der Wees, Philip JFriedberg, Mark WGuzman, ElenaAyanian, John ZRodriguez, Hector P2014-01-01BackgroundPatient panel management and community-based care management may be viable strategies for community health centers to improve the quality of diabetes care for vulnerable patient populations. The objective of our study was to clarify implementation processes and experiences of integrating office-based medical assistant (MA) panel management and community health worker (CHW) community-based management into routine care for diabetic patients.MethodsMixed methods study with interviews and surveys of clinicians and staff participating in a study comparing the effectiveness of MA and CHW health coaching for improving diabetes care. Participants included 24 key informants in five role categories and 249 clinicians and staff survey respondents from 14 participating practices. We conducted thematic analyses of key informant interview transcripts to clarify implementation processes and describe barriers to integrating the new roles into practice. We surveyed clinicians and staff to assess differences in practice culture among intervention and control groups. We triangulated findings to identify concordant and disparate results across data sources.ResultsImplementation processes and experiences varied considerably among the practices implementing CHW and MA team-based approaches, resulting in differences in the organization of health coaching and self-management support activities. Importantly, CHW and MA responsibilities converged over time to focus on health coaching of diabetic patients. MA health coaches experienced difficulty in allocating dedicated time due to other MA responsibilities that often crowded out time for diabetic patient health coaching. Time constraints also limited the personal introduction of patients to health coaches by clinicians. Participants highlighted the importance of a supportive team climate and proactive leadership as important enablers for MAs and CHWs to implement their health coaching responsibilities and also promoted professional growth.ConclusionImplementation of team-based strategies to improve diabetes care for vulnerable populations was diverse, however all practices converged in their foci on health coaching roles of CHWs and MAs. Our study suggests that a flexible approach to implementing health coaching is more important than fidelity to rigid models that do not allow for variable allocation of responsibilities across team members. Clinicians play an instrumental role in supporting health coaches to grow into their new patient care responsibilities.BRII recipient: RodriguezpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1s81s8pkarticleBMC Health Services Researchvol 14, iss 1, 6081472-6963oai:escholarship.org:ark:/13030/qt6tm4c54r2016-12-20T19:18:02Zqt6tm4c54rGlobal assessment of urban and peri-urban agriculture: irrigated and rainfed croplandsThebo, A LDrechsel, PLambin, E F2014-11-01The role of urban agriculture in global food security is a topic of increasing discussion. Existing research on urban and peri-urban agriculture consists largely of case studies that frequently use disparate definitions of urban and peri-urban agriculture depending on the local context and study objectives. This lack of consistency makes quantification of the extent of this practice at the global scale difficult. This study instead integrates global data on croplands and urban extents using spatial overlay analysis to estimate the global area of urban and peri-urban irrigated and rainfed croplands. The global area of urban irrigated croplands was estimated at about 24 Mha (11.0 percent of all irrigated croplands) with a cropping intensity of 1.48. The global area of urban rainfed croplands found was approximately 44 Mha (4.7 percent of all rainfed croplands) with a cropping intensity of 1.03. These values were derived from the MIRCA2000 Maximum Monthly Cropped Area Grids for irrigated and rainfed crops and therefore their sum does not necessarily represent the total urban cropland area when the maximum extent of irrigated and rainfed croplands occurs in different months. Further analysis of croplands within 20 km of urban extents show that 60 and 35 percent of, respectively, all irrigated and rainfed croplands fall within this distance range.BRII recipient: ThebopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6tm4c54rarticleEnvironmental Research Lettersvol 9, iss 11, 1140021748-9326oai:escholarship.org:ark:/13030/qt7120k2sq2016-12-20T19:04:01Zqt7120k2sqTopREML: a topological restricted maximum likelihood approach to regionalize trended runoff signatures in stream networksMüller, M. FThompson, S. E2015-01-29We introduce topological restricted maximum likelihood (TopREML) as a method to predict runoff signatures in ungauged basins. The approach is based on the use of linear mixed models with spatially correlated random effects. The nested nature of streamflow networks is taken into account by using water balance considerations to constrain the covariance structure of runoff and to account for the stronger spatial correlation between flow-connected basins. The restricted maximum likelihood (REML) framework generates the best linear unbiased predictor (BLUP) of both the predicted variable and the associated prediction uncertainty, even when incorporating observable covariates into the model. The method was successfully tested in cross-validation analyses on mean streamflow and runoff frequency in Nepal (sparsely gauged) and Austria (densely gauged), where it matched the performance of comparable methods in the prediction of the considered runoff signature, while significantly outperforming them in the prediction of the associated modeling uncertainty. The ability of TopREML to combine deterministic and stochastic information to generate BLUPs of the prediction variable and its uncertainty makes it a particularly versatile method that can readily be applied in both densely gauged basins, where it takes advantage of spatial covariance information, and data-scarce regions, where it can rely on covariates, which are increasingly observable via remote-sensing technology.BRII recipient: MüllerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7120k2sqarticleHydrology and Earth System Sciences Discussionsvol 12, iss 1, 1355-13961812-2116oai:escholarship.org:ark:/13030/qt4716f29j2016-12-20T18:52:13Zqt4716f29jThe role of chemical policy in improving supply chain knowledge and product safetyScruggs, Caroline EOrtolano, LeonardSchwarzman, Megan RWilson, Michael P2014-01-12Although the US government has made important improvements in chemical management since the 1970s, these advances have not kept pace with scientific knowledge about chemical hazards. While US federal chemical policy reform is being debated for the first time since 1976, some US businesses have voluntarily sought to improve their knowledge of chemical hazards in their supply chains, and several US states, the European Union, China, and other countries have moved forward with chemical policy reforms. Until policy reforms occur in the USA, the US chemical market will continue to experience problems associated with poor information on hazardous chemicals in supply chains. These market conditions make it difficult for consumer product companies to identify hazards and create safer products. Results from interviews with consumer product company representatives demonstrate that challenges in obtaining chemical-related information exist across sectors, and information on chemical hazards and uses can be conflicting, protected by trade secrets, lost in supply chains, or nonexistent. Interview results illustrate how some consumer product companies are exceeding regulatory requirements by voluntarily restricting from their products chemicals that could harm human health or the environment. Understanding the motivations behind—and barriers to—these actions could inform efforts to modernize US chemicals policies in ways that promote effective chemical management in supply chains. Using examples from the European Union and some US states, we introduce policy suggestions that would increase knowledge, market transparency, and information flows regarding hazardous chemicals and their uses; these would support the efforts of companies to develop and market safer products.BRII recipient: Schwarzman (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4716f29jarticleJournal of Environmental Studies and Sciencesvol 4, iss 2, 132-1412190-6483 2190-6491oai:escholarship.org:ark:/13030/qt2dm3t0sk2016-12-20T18:51:12Zqt2dm3t0skMonocyte Recruitment to the Dermis and Differentiation to Dendritic Cells Increases the Targets for Dengue Virus ReplicationSchmid, Michael AHarris, Eva2014-12-04Dengue virus (DENV) causes the most prevalent arthropod-borne viral disease in humans. Although Aedes mosquitoes transmit DENV when probing for blood in the skin, no information exists on DENV infection and immune response in the dermis, where the blood vessels are found. DENV suppresses the interferon response, replicates, and causes disease in humans but not wild-type mice. Here, we used mice lacking the interferon-α/β receptor (Ifnar
–/–), which had normal cell populations in the skin and were susceptible to intradermal DENV infection, to investigate the dynamics of early DENV infection of immune cells in the skin. CD103+ classical dendritic cells (cDCs), Ly6C– CD11b+ cDCs, and macrophages in the steady-state dermis were initial targets of DENV infection 12-24 hours post-inoculation but then decreased in frequency. We demonstrated recruitment of adoptively-transferred Ly6Chigh monocytes from wild-type and Ifnar
–/– origin to the DENV-infected dermis and differentiation to Ly6C+ CD11b+ monocyte-derived DCs (moDCs), which became DENV-infected after 48 hours, and were then the major targets for virus replication. Ly6Chigh monocytes that entered the DENV-infected dermis expressed chemokine receptor CCR2, likely mediating recruitment. Further, we show that ∼100-fold more hematopoietic cells in the dermis were DENV-infected compared to Langerhans cells in the epidermis. Overall, these results identify the dermis as the main site of early DENV replication and show that DENV infection in the skin occurs in two waves: initial infection of resident cDCs and macrophages, followed by infection of monocytes and moDCs that are recruited to the dermis. Our study reveals a novel viral strategy of exploiting monocyte recruitment to increase the number of targets for infection at the site of invasion in the skin and highlights the skin as a potential site for therapeutic action or intradermal vaccination.BRII recipient: HarrispubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2dm3t0skarticlePLoS Pathogensvol 10, iss 12, e10045411553-7374oai:escholarship.org:ark:/13030/qt9561d69j2016-12-16T23:17:07Zqt9561d69jModeling Tidal Marsh Distribution with Sea-Level Rise: Evaluating the Role of Vegetation, Sediment, and Upland Habitat in Marsh ResiliencySchile, Lisa MCallaway, John CMorris, James TStralberg, DianaParker, V. ThomasKelly, Maggi2014-02-13Tidal marshes maintain elevation relative to sea level through accumulation of mineral and organic matter, yet this dynamic accumulation feedback mechanism has not been modeled widely in the context of accelerated sea-level rise. Uncertainties exist about tidal marsh resiliency to accelerated sea-level rise, reduced sediment supply, reduced plant productivity under increased inundation, and limited upland habitat for marsh migration. We examined marsh resiliency under these uncertainties using the Marsh Equilibrium Model, a mechanistic, elevation-based soil cohort model, using a rich data set of plant productivity and physical properties from sites across the estuarine salinity gradient. Four tidal marshes were chosen along this gradient: two islands and two with adjacent uplands. Varying century sea-level rise (52, 100, 165, 180 cm) and suspended sediment concentrations (100%, 50%, and 25% of current concentrations), we simulated marsh accretion across vegetated elevations for 100 years, applying the results to high spatial resolution digital elevation models to quantify potential changes in marsh distributions. At low rates of sea-level rise and mid-high sediment concentrations, all marshes maintained vegetated elevations indicative of mid/high marsh habitat. With century sea-level rise at 100 and 165 cm, marshes shifted to low marsh elevations; mid/high marsh elevations were found only in former uplands. At the highest century sea-level rise and lowest sediment concentrations, the island marshes became dominated by mudflat elevations. Under the same sediment concentrations, low salinity brackish marshes containing highly productive vegetation had slower elevation loss compared to more saline sites with lower productivity. A similar trend was documented when comparing against a marsh accretion model that did not model vegetation feedbacks. Elevation predictions using the Marsh Equilibrium Model highlight the importance of including vegetation responses to sea-level rise. These results also emphasize the importance of adjacent uplands for long-term marsh survival and incorporating such areas in conservation planning efforts.BRII recipient: KellypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9561d69jarticlePLoS ONEvol 9, iss 2, e887601932-6203oai:escholarship.org:ark:/13030/qt16g8v82q2016-12-16T23:15:49Zqt16g8v82qDiversification of the Alpine Chipmunk, Tamias alpinus, an alpine endemic of the Sierra Nevada, CaliforniaRubidge, Emily MPatton, James LMoritz, Craig2014-01-01BackgroundThe glaciation cycles that occurred throughout the Pleistocene in western North America caused frequent shifts in species’ ranges with important implications for models of species divergence. For example, long periods of allopatry during species’ range contractions allowed for the accumulation of differences between separated populations promoting lineage divergence. In contrast, range expansions during interglacial periods may have had homogenizing effects via increased gene flow following secondary contact. These range dynamics are particularly pronounced in the Sierra Nevada, California, given the complex topography and climatic history of the area, thus providing a natural laboratory to examine evolutionary processes that have led to the diversity patterns observed today.ResultsHere we examined the role of late Pleistocene climate fluctuations on the divergence of the Sierra Nevada endemic Alpine Chipmunk (Tamias alpinus) from its sister taxon, western populations of the Least Chipmunk (T. minimus) from the Great Basin. We used one mitochondrial gene (cytochrome b) and 14 microsatellite loci to examine the evolutionary relationship between these species. Mitochondrial sequence data revealed that T. alpinus and T. minimus populations share mitochondrial haplotypes with no overall geneaological separation, and that diversity at this locus is better explained by geography than by species’ boundaries. In contrast, the microsatellite analysis showed that populations of the same species are more similar to each other than they are to members of the other species. Similarly, a morphological analysis of voucher specimens confirmed known differences in morphological characters between species providing no evidence of recent hybridization. Coalescent analysis of the divergence history indicated a late Pleistocene splitting time (~450 ka) and subsequent, though limited, gene flow between the two lineages.ConclusionsOur results suggest that the two species are distinct and there is no contemporary introgression along their geographic boundary. The divergence of T. alpinus during this time period provides additional evidence that Pleistocene glacial cycles played an important role in diversification of species in Sierra Nevada and North America in general.BRII recipient: PattonpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/16g8v82qarticleBMC Evolutionary Biologyvol 14, iss 1, 341471-2148oai:escholarship.org:ark:/13030/qt3ss414jw2016-12-16T23:13:47Zqt3ss414jwFarmer Strategies for Dealing with Climatic Variability: A Case Study from the Mixteca Alta Region of Oaxaca, MexicoRoge, PaulFriedman, Andrew RonaldAstier, MartaAltieri, Miguel A2014-06-19This study describes an interdisciplinary methodology for helping small farmers prepare for climatic variability. We facilitated workshops in the Mixteca Alta region of Oaxaca, Mexico, in which groups of small farmers described how they had adapted to and prepared for past climate challenges. Farmers reported that their cropping systems were changing for multiple reasons: more drought, later rainfall onset, decreased rural labor, and introduced labor-saving technologies. Examination of climate data found that farmers’ climate narratives were largely consistent with the observational record. There have been increases in temperature and rainfall intensity, and an increase in rainfall seasonality that may be perceived as later rainfall onset. Farmers also identified 14 indicators that they subsequently used to evaluate the condition of their agroecosystems. Farmers ranked landscape-scale indicators as more marginal than farmer management or soil quality indicators. From this analysis, farmers proposed strategies to improve the ability of their agroecosystems to cope with climatic variability. Notably, they recognized that social organizing and education are required for landscape-scale indicators to be improved. This outcome suggests that climate change adaptation by small farmers involves much more than just a set of farming practices, but also community action to tackle collective problems.BRII recipient: Roge (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3ss414jwarticleAgroecology and Sustainable Food Systemsvol 38, iss 7, 786-8112168-3565 2168-3573oai:escholarship.org:ark:/13030/qt9254j2kb2016-12-16T23:12:35Zqt9254j2kbThe GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the InternetRobertson, TimDoring, MarkusGuralnick, RobertBloom, DavidWieczorek, JohnBraak, KyleOtegui, JavierRussell, LauraDesmet, Peter2014-08-06The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT) is a software package developed to support biodiversity dataset publication in a common format. The IPT’s two primary functions are to 1) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.BRII recipient: BloompubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9254j2kbarticlePLoS ONEvol 9, iss 8, e1026231932-6203oai:escholarship.org:ark:/13030/qt6qc4p3mw2016-12-16T23:11:28Zqt6qc4p3mwHighly-cited estimates of the cumulative incidence and recurrence of vulvovaginal candidiasis are inadequately documentedRathod, Sujit DBuffler, Patricia A2014-01-01BackgroundAvailable literature concerning the epidemiologic or clinical features of vulvovaginal candidiasis commonly reports that: 75% of women will experience an episode of vulvovaginal candidiasis in their lifetimes, 50% of whom will experience at least a second episode, and 5-10% of all women will experience recurrent vulvovaginal candidiasis (≥4 episodes/1 year). In this debate we traced the three commonly cited statistics to their presumed origins.DiscussionIt is apparent that these figures were inadequately documented and lacked supporting epidemiologic evidence. Population-based studies are needed to make reliable estimates of the lifetime risk of vulvovaginal candidiasis and the proportion of women who experience recurrent candidiasis.SummaryThe extent to which vulvovaginal candidiasis is a source of population-level morbidity remains uncertain.BRII recipient: RathodpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6qc4p3mwarticleBMC Women's Healthvol 14, iss 1, 431472-6874oai:escholarship.org:ark:/13030/qt1r05847c2016-12-16T23:10:02Zqt1r05847cModulation of Ras signaling alters the toxicity of hydroquinone, a benzene metabolite and component of cigarette smokeNorth, MatthewShuga, JoeFromowitz, MicheleLoguinov, AlexandreShannon, KevinZhang, LuopingSmith, Martyn TVulpe, Chris D2014-01-01BackgroundBenzene is an established human leukemogen, with a ubiquitous environmental presence leading to significant population exposure. In a genome-wide functional screen in the yeast Saccharomyces cerevisiae, inactivation of IRA2, a yeast ortholog of the human tumor suppressor gene NF1 (Neurofibromin), enhanced sensitivity to hydroquinone, an important benzene metabolite. Increased Ras signaling is implicated as a causal factor in the increased pre-disposition to leukemia of individuals with mutations in NF1.MethodsGrowth inhibition of yeast by hydroquinone was assessed in mutant strains exhibiting varying levels of Ras activity. Subsequently, effects of hydroquinone on both genotoxicity (measured by micronucleus formation) and proliferation of WT and Nf1 null murine hematopoietic precursors were assessed.ResultsHere we show that the Ras status of both yeast and mammalian cells modulates hydroquinone toxicity, indicating potential synergy between Ras signaling and benzene toxicity. Specifically, enhanced Ras signaling increases both hydroquinone-mediated growth inhibition in yeast and genotoxicity in mammalian hematopoetic precursors as measured by an in vitro erythroid micronucleus assay. Hydroquinone also increases proliferation of CFU-GM progenitor cells in mice with Nf1 null bone marrow relative to WT, the same cell type associated with benzene-associated leukemia.ConclusionsTogether our findings show that hydroquinone toxicity is modulated by Ras signaling. Individuals with abnormal Ras signaling could be more vulnerable to developing myeloid diseases after exposure to benzene. We note that hydroquinone is used cosmetically as a skin-bleaching agent, including by individuals with cafe-au-lait spots (which may be present in individuals with neurofibromatosis who have a mutation in NF1), which could be unadvisable given our findings.BRII recipient: VulpepubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1r05847carticleBMC Cancervol 14, iss 1, 61471-2407oai:escholarship.org:ark:/13030/qt8gd1q4dj2016-12-16T23:08:43Zqt8gd1q4djProductive disciplinary engagement as a recursive process: Initial engagement in a scientific investigation as a resource for deeper engagement in the scientific disciplineMeyer, Xenia2014-01-01Engle and Conant (2002) show how productive disciplinary engagement (PDE) for students can be attained through learning environments structured to support problematizing subject matter, give students authority to address content problems, hold students accountable to others and disciplinary norms, and provide students with resources. This paper considers how one classroom's involvement in a scientific investigation embodied and extended the PDE framework. In this U.S. based classroom, 5th grade non-native and English language learning students engaged in scientific inquiry and contributed their findings to a greater scientific community. This paper proposes that these students experienced PDE at both initial and deeper levels, where students’ initial PDE in scientific activities served as a resource for PDE at a more discipline-specific level.BRII recipient: Meyer (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/8gd1q4djarticleInternational Journal of Educational Researchvol 64, 184-19808830355oai:escholarship.org:ark:/13030/qt2vw3212z2016-12-16T23:07:32Zqt2vw3212zThe evolution of morphogenetic fitness landscapes: conceptualising the interplay between the developmental and ecological drivers of morphological innovationMarshall, Charles R2014-01-01Here I show how fitness landscapes can be used to understand the relative importance of developmental and ecological change in initiating morphological innovation. Key is the use of morphogenetic ‘rules’ as the axes of the landscape, which enables explicit incorporation of the contribution that specific morphologies make to fitness. Four modes of fitness landscape evolution are identified: (1) change in the density of peaks on the landscape, driven by an increase in the number of selective pressures encountered; (2) change in the dimensionality of the landscape through the addition of morphogenetic rules; (3) change in the size of one or more dimensions of the landscape through elaboration of already existing morphogenetic rules; and, (4) shifting the position of peaks in the landscape. Morphological innovation is initiated by ecological change in Mode (1), for example the Cambrian explosion of animals, and Mode (4), for example, when taxa such as sticklebacks make a shift in environment, or during coevolutionary escalation. Morphological change is initiated by developmental innovation for Mode (2), typified by some macroevolutionary innovations, such as the emergence of jaws, and in Mode (3), for example, in the differentiation of flower morphology facilitated by gene duplication of the B-class developmental genes.BRII recipient: Marshall (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/2vw3212zarticleAustralian Journal of Zoologyvol 62, iss 1, 30004-959Xoai:escholarship.org:ark:/13030/qt8w7410392016-12-16T23:06:16Zqt8w741039An Assessment of Health Risks and Mortality from Exposure to Secondhand Smoke in Chinese Restaurants and BarsLiu, RuilingJiang, YuanLi, QiangHammond, S. Katharine2014-01-08Introduction Smoking is generally not regulated in restaurants or bars in China, or the restrictions are not fully implemented if there are any, while the related hazard health effects are not recognized by the majority of the Chinese population.Objectives This study aims to assess the excess health risks and mortality attributed to secondhand smoke (SHS) exposure in restaurants and bars for both servers and patrons to provide necessary evidence for advancing tobacco control in this microenvironment.Methods Two approaches were used for the assessment. One is a continuous approach based on existing field measurements and Repace and Lowrey’s dose-response model, and the other is a categorical approach based on exposure or not and epidemiological studies.Results Based on the continuous approach, servers were estimated to have a lifetime excess risk (LER) of lung cancer death (LCD) of 730 to 1,831×10−6 for working five days a week for 45 years in smoking restaurants and 1,862 to 8,136×10−6 in smoking bars, and patrons could have a LER of LCD of 47 to 117×10−6 due to visiting smoking restaurants for an average of 13 minutes a day for 60 years, and 119 to 522×10−6 due to visiting smoking bars. The categorical approach estimated that SHS exposure in restaurants and bars alone caused 84 LCD and 57 ischemic heart disease (IHD) deaths among nonsmoking servers and 1,2419 LCDs and 1,689 IHD deaths among the nonsmoking patron population.Conclusions SHS exposure in restaurants and bars alone can impose high lifetime excess risks of lung cancer death and ischemic heart disease deaths to both servers and patrons, and can cause a significant number of deaths each year in China. These health risks and deaths can be prevented by banning smoking in restaurants and bars and effectively implementing these smoking bans.BRII recipient: LiupubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8w741039articlePLoS ONEvol 9, iss 1, e848111932-6203oai:escholarship.org:ark:/13030/qt3tb7c6c42016-12-16T21:40:07Zqt3tb7c6c4Technology as
Pharmakon
: The Promise and Perils of the Internet for Foreign Language EducationKern, Richard2014-03-01Globalization and networking technologies have transformed the contexts, means, and uses of foreign language learning. The Internet offers a vast array of texts, films, music, news, information, pedagogical resources, sounds, and images from around the world as well as unprecedented opportunities for direct communication with native speakers in real time. However, the very technology that delivers these materials and interactions can produce subtle mediational effects that can influence how learners evaluate and interpret them. Focusing first on technological mediation broadly, and then on the specific context of desktop videoconferencing in a telecollaboration project, this article outlines the benefits and the potential pitfalls that computer mediation presents for the learning of languages and cultures. Specific attention is given to the question of what it means to mediate the foreign culture through interfaces that are familiar from one's home culture. The principal argument is that the dynamics of online language learning call for a relational pedagogy that focuses on how medium and context interact with language use. The goal of such an approach is to expose students to a broader scope of symbolic inquiry, to connect present text-making practices with those of the past, and to foster a critical perspective that will prepare young people to understand and shape future language and literacy practices.BRII recipient: Kern (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3tb7c6c4articleThe Modern Language Journalvol 98, iss 1, 340-35700267902oai:escholarship.org:ark:/13030/qt45n2z9p12016-12-16T21:39:00Zqt45n2z9p1Navigation outside of the box: what the lab can learn from the field and what the field can learn from the labJacobs, Lucia FMenzel, Randolf2014-01-01Space is continuous. But the communities of researchers that study the cognitive map in non-humans are strangely divided, with debate over its existence found among behaviorists but not neuroscientists. To reconcile this and other debates within the field of navigation, we return to the concept of the parallel map theory, derived from data on hippocampal function in laboratory rodents. Here the cognitive map is redefined as the integrated map, which is a construction of dual mechanisms, one based on directional cues (bearing map) and the other on positional cues (sketch map). We propose that the dual navigational mechanisms of pigeons, the navigational map and the familiar area map, could be homologous to these mammalian parallel maps; this has implications for both research paradigms. Moreover, this has implications for the lab. To create a bearing map (and hence integrated map) from extended cues requires self-movement over a large enough space to sample and model these cues at a high resolution. Thus a navigator must be able to move freely to map extended cues; only then should the weighted hierarchy of available navigation mechanisms shift in favor of the integrated map. Because of the paucity of extended cues in the lab, the flexible solutions allowed by the integrated map should be rare, despite abundant neurophysiological evidence for the existence of the machinery needed to encode and map extended cues through voluntary movement. Not only do animals need to map extended cues but they must also have sufficient information processing capacity. This may require a specific ontogeny, in which the navigator’s nervous system is exposed to naturally complex spatial contingencies, a circumstance that occurs rarely, if ever, in the lab. For example, free-ranging, flying animals must process more extended cues than walking animals and for this reason alone, the integrated map strategy may be found more reliably in some species. By taking concepts from ethology and the parallel map theory, we propose a path to directly integrating the three great experimental paradigms of navigation: the honeybee, the homing pigeon and the laboratory rodent, towards the goal of a robust, unified theory of animal navigation.BRII recipient: JacobspubliceScholarship, University of Californiahttps://escholarship.org/uc/item/45n2z9p1articleMovement Ecologyvol 2, iss 1, 32051-3933oai:escholarship.org:ark:/13030/qt9p07w3m72016-12-16T21:34:55Zqt9p07w3m7Analytical method for the determination of organic acids in dilute acid pretreated biomass hydrolysate by liquid chromatography-time-of-flight mass spectrometryIbanez, Ana BBauer, Stefan2014-01-01BackgroundFor the development of lignocellulosic biofuels a common strategy to release hemicellulosic sugars and enhance the enzymatic digestibility of cellulose is the heat pretreatment of biomass with dilute acid. During this process, fermentation inhibitors such as 5-hydroxymethylfurfural, furfural, phenolics, and organic acids are formed and released into the so-called hydrolysate. The phenolic inhibitors have been studied fairly extensively, but fewer studies have focused on the analysis of the organic acids profile. For this purpose, a simple and fast liquid chromatography/mass spectrometry (LC/MS) method for the analysis of organic acids in the hydrolysate has been developed using an ion exchange column based on a polystyrene-divinylbenzene polymer frequently used in biofuel research. The application of the LC/MS method to a hydrolysate from Miscanthus has been evaluated.ResultsThe presented LC/MS method involving only simple sample preparation (filtration and dilution) and external calibration for the analysis of 24 organic acids present in dilute acid pretreated biomass hydrolysate is fast (12 min) and reasonably sensitive despite the small injection volume of 2 μL used. The lower limit of quantification ranged from 0.2 μg/mL to 2.9 μg/mL and the limit of detection from 0.03 μg/mL to 0.7 μg/mL. Analyte recoveries obtained from a spiked hydrolysate were in the range of 70 to 130% of the theoretical yield, except for glyoxylic acid, malic acid, and malonic acid, which showed a higher response due to signal enhancement. Relative standard deviations for the organic acids ranged from 0.4 to 9.2% (average 3.6%) for the intra-day experiment and from 2.1 to 22.8% (average 8.9%) for the inter-day (three-day) experiment.ConclusionWe have shown that the analysis of the profile of 24 organic acids present in biomass hydrolysate can be achieved by a simple LC/MS method applying external calibration and minimal sample preparation. The organic acids eluted within only 12 min by isocratic elution, enabling high sample throughput. Repeatability (precision and accuracy) and recovery were sufficiently accurate for most of the organic acids tested, making the method suitable for their fast determination in hydrolysate. We envision that this method can be further expanded to a larger number of organic acids, including phenolic acids such as p-coumaric acid and ferulic acid and other molecules depending on the researchers’ needs.BRII recipient: BauerpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9p07w3m7articleBiotechnology for Biofuelsvol 7, iss 1, 1451754-6834oai:escholarship.org:ark:/13030/qt5mh0c5w22016-12-16T21:32:46Zqt5mh0c5w2Development and evaluation of a food environment survey in three urban environments of Kunming, ChinaHua, JennaSeto, EdmundLi, YanWang, May C2014-01-01BackgroundGiven the rapid pace of urbanization and Westernization and the increasing prevalence of obesity, there is a need for research to better understand the influence of the built environment on overweight and obesity in world’s developing regions. Culturally-specific food environment survey instruments are important tools for studying changing food availability and pricing. Here, we present findings from an effort to develop and evaluate food environment survey instruments for use in a rapidly developing city in southwest China.MethodsWe developed two survey instruments (for stores and restaurants), each designed to be completed within 10 minutes. Two pairs of researchers surveyed a pre-selected 1-km stretch of street in each of three socio-demographically different neighborhoods to assess inter-rater reliability. Construct validity was assessed by comparing the food environments of the neighborhoods to cross-sectional height and weight data obtained on 575 adolescents in the corresponding regions of the city.Results273 food establishments (163 restaurants and 110 stores) were surveyed. Sit-down, take-out, and fast food restaurants accounted for 40%, 21% and 19% of all restaurants surveyed. Tobacco and alcohol shops, convenience stores and supermarkets accounted for 25%, 12% and 11%, respectively, of all stores surveyed. We found a high percentage of agreement between teams (>75%) for all categorical variables with moderate kappa scores (0.4-0.6), and no statistically significant differences between teams for any of the continuous variables. More developed inner city neighborhoods had a higher number of fast food restaurants and convenience stores than surrounding neighborhoods. Adolescents who lived in the more developed inner neighborhoods also had a higher percentage of overweight, indicating well-founded construct validity. Depending on the cutoff used, 19% to 36% of male and 10% to 22% of female 16-year old adolescents were found to be overweight.ConclusionsThe prevalence of overweight Chinese adolescents, and the food environments they are exposed to, deserve immediate attention. To our knowledge, these are the first food environment surveys developed specifically to assess changing food availability, accessibility, and pricing in China. These instruments may be useful in future systematic longitudinal assessments of the changing food environment and its health impact in China.BRII recipient: HuapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5mh0c5w2articleBMC Public Healthvol 14, iss 1, 2351471-2458oai:escholarship.org:ark:/13030/qt0335128m2016-12-16T21:31:08Zqt0335128mRealistic and verifiable coherent control of excitonic states in a light-harvesting complexHoyer, StephanCaruso, FilippoMontangero, SimoneSarovar, MohanCalarco, TommasoPlenio, Martin BWhaley, K Birgitta2014-04-08We explore the feasibility of the coherent control of excitonic dynamics in light-harvesting complexes, analyzing the limits imposed by the open nature of these quantum systems. We establish feasible targets for phase and phase/amplitude control of the electronically excited state populations in the Fenna–Mathews–Olson (FMO) complex and analyze the robustness of this control with respect to orientational and energetic disorder, as well as the decoherence arising from coupling to the protein environment. We further present two possible routes to verification of the control target, with simulations for the FMO complex showing that steering of the excited state is experimentally verifiable either by extending excitonic coherence or by producing novel states in a pump–probe setup. Our results provide a first step toward coherent control of these complex biological quantum systems in an ultrafast spectroscopy setup.BRII recipient: WhaleypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0335128marticleNew Journal of Physicsvol 16, iss 4, 0450071367-2630oai:escholarship.org:ark:/13030/qt4p6443j72016-12-16T21:29:33Zqt4p6443j7Effects of Woodsmoke Exposure on Airway Inflammation in Rural Guatemalan WomenGuarnieri, Michael JDiaz, Janet VBasu, ChandreyiDiaz, AnaitePope, DanielSmith, Kirk RSmith-Sivertsen, ToneBruce, NigelSolomon, ColinMcCracken, JohnBalmes, John R2014-03-13Background: More than two-fifths of the world’s population uses solid fuels, mostly biomass, for cooking. The resulting biomass smoke exposure is a major cause of chronic obstructive pulmonary disease (COPD) among women in developing countries.Objective: To assess whether lower woodsmoke exposure from use of a stove with a chimney, compared to open fires, is associated with lower markers of airway inflammation in young women.Design: We carried out a cross-sectional analysis on a sub-cohort of participants enrolled in a randomized controlled trial in rural Guatemala, RESPIRE.Participants: We recruited 45 indigenous women at the end of the 18-month trial; 19 women who had been using the chimney stove for 18–24 months and 26 women still using open fires.Measurements: We obtained spirometry and induced sputum for cell counts, gene expression of IL-8, TNF-α, MMP-9 and 12, and protein concentrations of IL-8, myeloperoxidase and fibronectin. Exhaled carbon monoxide (CO) and 48-hr personal CO tubes were measured to assess smoke exposure.Results: MMP-9 gene expression was significantly lower in women using chimney stoves. Higher exhaled CO concentrations were significantly associated with higher gene expression of IL-8, TNF-α, and MMP-9. Higher 48-hr personal CO concentrations were associated with higher gene expression of IL-8, TNF- α, MMP-9 and MMP-12; reaching statistical significance for MMP-9 and MMP-12.Conclusions: Compared to using an open wood fire for cooking, use of a chimney stove was associated with lower gene expression of MMP-9, a potential mediator of airway remodeling. Among all participants, indoor biomass smoke exposure was associated with higher gene expression of multiple mediators of airway inflammation and remodeling; these mechanisms may explain some of the observed association between prolonged biomass smoke exposure and COPD.BRII recipient: BalmespubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4p6443j7articlePLoS ONEvol 9, iss 3, e884551932-6203oai:escholarship.org:ark:/13030/qt2rh033ps2016-12-16T21:26:53Zqt2rh033psColiform Bacteria as Indicators of Diarrheal Risk in Household Drinking Water: Systematic Review and Meta-AnalysisGruber, Joshua SErcumen, AyseColford, John M2014-09-24Background: Current guidelines recommend the use of Escherichia coli (EC) or thermotolerant (“fecal”) coliforms (FC) as indicators of fecal contamination in drinking water. Despite their broad use as measures of water quality, there remains limited evidence for an association between EC or FC and diarrheal illness: a previous review found no evidence for a link between diarrhea and these indicators in household drinking water.Objectives: We conducted a systematic review and meta-analysis to update the results of the previous review with newly available evidence, to explore differences between EC and FC indicators, and to assess the quality of available evidence.Methods: We searched major databases using broad terms for household water quality and diarrhea. We extracted study characteristics and relative risks (RR) from relevant studies. We pooled RRs using random effects models with inverse variance weighting, and used standard methods to evaluate heterogeneity and publication bias.Results: We identified 20 relevant studies; 14 studies provided extractable results for meta-analysis. When combining all studies, we found no association between EC or FC and diarrhea (RR 1.26 [95% CI: 0.98, 1.63]). When analyzing EC and FC separately, we found evidence for an association between diarrhea and EC (RR: 1.54 [95% CI: 1.37, 1.74]) but not FC (RR: 1.07 [95% CI: 0.79, 1.45]). Across all studies, we identified several elements of study design and reporting (e.g., timing of outcome and exposure measurement, accounting for correlated outcomes) that could be improved upon in future studies that evaluate the association between drinking water contamination and health.Conclusions: Our findings, based on a review of the published literature, suggest that these two coliform groups have different associations with diarrhea in household drinking water. Our results support the use of EC as a fecal indicator in household drinking water.BRII recipient: GruberpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2rh033psarticlePLoS ONEvol 9, iss 9, e1074291932-6203oai:escholarship.org:ark:/13030/qt9s7986rb2016-12-16T21:23:49Zqt9s7986rbEfficiency and large deviations in time-asymmetric stochastic heat enginesGingrich, Todd RRotskoff, Grant MVaikuntanathan, SuriyanarayananGeissler, Phillip L2014-10-23In a stochastic heat engine driven by a cyclic non-equilibrium protocol, fluctuations in work and heat give rise to a fluctuating efficiency. Using computer simulations and tools from large deviation theory, we have examined these fluctuations in detail for a model two-state engine. We find in general that the form of efficiency probability distributions is similar to those described by Verley et al (2014 Nat. Commun. 5 4721), in particular featuring a local minimum in the long-time limit. In contrast to the time-symmetric engine protocols studied previously, however, this minimum need not occur at the value characteristic of a reversible Carnot engine. Furthermore, while the local minimum may reside at the global minimum of a large deviation rate function, it does not generally correspond to the least likely efficiency measured over finite time. We introduce a general approximation for the finite-time efficiency distribution, , based on large deviation statistics of work and heat, that remains very accurate even when deviates significantly from its large deviation form.BRII recipient: GingrichpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9s7986rbarticleNew Journal of Physicsvol 16, iss 10, 1020031367-2630oai:escholarship.org:ark:/13030/qt1tm4g6082016-12-16T19:50:18Zqt1tm4g608Contrasting Spatial Patterns in Active-Fire and Fire-Suppressed Mediterranean Climate Old-Growth Mixed Conifer ForestsFry, Danny LStephens, Scott LCollins, Brandon MNorth, Malcolm PFranco-Vizcaino, ErnestoGill, Samantha J2014-02-20In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference forest sites can help management efforts to restore forests conditions that may be more resilient to future changes in disturbance regimes and climate. In this study, we characterize tree spatial patterns using four-ha stem maps from four old-growth, Jeffrey pine-mixed conifer forests, two with active-fire regimes in northwestern Mexico and two that experienced fire exclusion in the southern Sierra Nevada. Most of the trees were in patches, averaging six to 11 trees per patch at 0.007 to 0.014 ha−1, and occupied 27–46% of the study areas. Average canopy gap sizes (0.04 ha) covering 11–20% of the area were not significantly different among sites. The putative main effects of fire exclusion were higher densities of single trees in smaller size classes, larger proportion of trees (≥56%) in large patches (≥10 trees), and decreases in spatial complexity. While a homogenization of forest structure has been a typical result from fire exclusion, some similarities in patch, single tree, and gap attributes were maintained at these sites. These within-stand descriptions provide spatially relevant benchmarks from which to manage for structural heterogeneity in frequent-fire forest types.BRII recipient: FrypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1tm4g608articlePLoS ONEvol 9, iss 2, e889851932-6203oai:escholarship.org:ark:/13030/qt47h225fm2016-12-16T19:48:25Zqt47h225fmInsight Maker: A general-purpose tool for web-based modeling & simulationFortmann-Roe, Scott2014-09-01A web-based, general-purpose simulation and modeling tool is presented in this paper. The tool, Insight Maker, has been designed to make modeling and simulation accessible to a wider audience of users. Insight Maker integrates three general modeling approaches – System Dynamics, Agent-Based Modeling, and imperative programming – in a unified modeling framework. The environment provides a graphical model construction interface that is implemented purely in client-side code that runs on users’ machines. Advanced features, such as model scripting and an optimization tool, are also described. Insight Maker, under development for several years, has gained significant adoption with currently more than 20,000 registered users. In addition to detailing the tool and its guiding philosophy, this first paper on Insight Maker describes lessons learned from the development of a complex web-based simulation and modeling tool.BRII recipient: Fortmann-Roe (hybrid)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/47h225fmarticleSimulation Modelling Practice and Theoryvol 47, 28-451569190Xoai:escholarship.org:ark:/13030/qt5b0330pc2016-12-16T19:47:30Zqt5b0330pcFox Squirrels Match Food Assessment and Cache Effort to Value and ScarcityDelgado, Mikel MNicholas, MollyPetrie, Daniel JJacobs, Lucia F2014-03-26Scatter hoarders must allocate time to assess items for caching, and to carry and bury each cache. Such decisions should be driven by economic variables, such as the value of the individual food items, the scarcity of these items, competition for food items and risk of pilferage by conspecifics. The fox squirrel, an obligate scatter-hoarder, assesses cacheable food items using two overt movements, head flicks and paw manipulations. These behaviors allow an examination of squirrel decision processes when storing food for winter survival. We measured wild squirrels' time allocations and frequencies of assessment and investment behaviors during periods of food scarcity (summer) and abundance (fall), giving the squirrels a series of 15 items (alternating five hazelnuts and five peanuts). Assessment and investment per cache increased when resource value was higher (hazelnuts) or resources were scarcer (summer), but decreased as scarcity declined (end of sessions). This is the first study to show that assessment behaviors change in response to factors that indicate daily and seasonal resource abundance, and that these factors may interact in complex ways to affect food storing decisions. Food-storing tree squirrels may be a useful and important model species to understand the complex economic decisions made under natural conditions.BRII recipient: DelgadopubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5b0330pcarticlePLoS ONEvol 9, iss 3, e928921932-6203oai:escholarship.org:ark:/13030/qt9rp710zk2016-12-16T19:46:10Zqt9rp710zkCharacterization of particulate matter emissions from on-road gasoline and diesel vehicles using a soot particle aerosol mass spectrometerDallmann, T. ROnasch, T. BKirchstetter, T. WWorton, D. RFortner, E. CHerndon, S. CWood, E. CFranklin, J. PWorsnop, D. RGoldstein, A. HHarley, R. A2014-07-29Particulate matter (PM) emissions were measured in July 2010 from on-road motor vehicles driving through a highway tunnel in the San Francisco Bay area. A soot particle aerosol mass spectrometer (SP-AMS) was used to measure the chemical composition of PM emitted by gasoline and diesel vehicles at high time resolution. Organic aerosol (OA) and black carbon (BC) concentrations were measured during various time periods that had different levels of diesel influence, as well as directly in the exhaust plumes of individual heavy-duty (HD) diesel trucks. BC emission factor distributions for HD trucks were more skewed than OA distributions (N = 293), with the highest 10% of trucks accounting for 56 and 42% of total measured BC and OA emissions, respectively. OA mass spectra measured for HD truck exhaust plumes show cycloalkanes are predominate in exhaust OA emissions relative to saturated alkanes (i.e., normal and iso-paraffins), suggesting that lubricating oil rather than fuel is the dominant source of primary organic aerosol (POA) emissions in diesel vehicle exhaust. This finding is supported by the detection of trace elements such as zinc and phosphorus in the exhaust plumes of individual trucks. Trace elements were emitted relative to total OA at levels that are consistent with typical weight fractions of commonly used additives present in lubricating oil. A comparison of measured OA and BC mass spectra across various sampling periods revealed a high degree of similarity in OA and BC emitted by gasoline and diesel engines. This finding indicates a large fraction of OA in gasoline exhaust is lubricant-derived as well. The similarity in OA and BC mass spectra for gasoline and diesel engine exhaust is likely to confound ambient source apportionment efforts to determine contributions to air pollution from these two important sources.BRII recipient: HarleypubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9rp710zkarticleAtmospheric Chemistry and Physicsvol 14, iss 14, 7585-75991680-7324oai:escholarship.org:ark:/13030/qt5hp497rv2016-12-16T19:43:18Zqt5hp497rvConsumption of Clarified Grapefruit Juice Ameliorates High-Fat Diet Induced Insulin Resistance and Weight Gain in MiceChudnovskiy, RostislavThompson, AirliaTharp, KevinHellerstein, MarcNapoli, Joseph LStahl, Andreas2014-10-08To determine the metabolic effects of grapefruit juice consumption we established a model in which C57Bl/6 mice drank 25–50% sweetened GFJ, clarified of larger insoluble particles by centrifugation (cGFJ), ad libitum as their sole source of liquid or isocaloric and sweetened water. cGFJ and control groups consumed similar amounts of liquids and calories. Mice fed a high-fat diet and cGFJ experienced a 18.4% decrease in weight, a 13–17% decrease in fasting blood glucose, a three-fold decrease in fasting serum insulin, and a 38% decrease in liver triacylglycerol values, compared to controls. Mice fed a low-fat diet that drank cGFJ experienced a two-fold decrease in fasting insulin, but not the other outcomes observed with the high-fat diet. cGFJ consumption decreased blood glucose to a similar extent as the commonly used anti-diabetic drug metformin. Introduction of cGFJ after onset of diet-induced obesity also reduced weight and blood glucose. A bioactive compound in cGFJ, naringin, reduced blood glucose and improved insulin tolerance, but did not ameliorate weight gain. These data from a well-controlled animal study indicate that GFJ contains more than one health-promoting neutraceutical, and warrant further studies of GFJ effects in the context of obesity and/or the western diet.BRII recipient: StahlpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5hp497rvarticlePLoS ONEvol 9, iss 10, e1084081932-6203oai:escholarship.org:ark:/13030/qt8w45051h2016-12-16T19:39:42Zqt8w45051hImproved control of exogenous attention in action video game playersCain, Matthew SPrinzmetal, WilliamShimamura, Arthur PLandau, Ayelet N2014-01-01Action video game players (VGPs) have demonstrated a number of attentional advantages over non-players. Here, we propose that many of those benefits might be underpinned by improved control over exogenous (i.e., stimulus-driven) attention. To test this we used an anti-cueing task, in which a sudden-onset cue indicated that the target would likely appear in a separate location on the opposite side of the fixation point. When the time between the cue onset and the target onset was short (40 ms), non-players (nVGPs) showed a typical exogenous attention effect. Their response times were faster to targets presented at the cued (but less probable) location compared with the opposite (more probable) location. VGPs, however, were less likely to have their attention drawn to the location of the cue. When the onset asynchrony was long (600 ms), VGPs and nVGPs were equally able to endogenously shift their attention to the likely (opposite) target location. In order to rule out processing-speed differences as an explanation for this result, we also tested VGPs and nVGPs on an attentional blink (AB) task. In a version of the AB task that minimized demands on task switching and iconic memory, VGPs and nVGPs did not differ in second target identification performance (i.e., VGPs had the same magnitude of AB as nVGPs), suggesting that the anti-cueing results were due to flexible control over exogenous attention rather than to more general speed-of-processing differences.BRII recipient: ShimamurapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8w45051harticleFrontiers in Psychologyvol 51664-1078oai:escholarship.org:ark:/13030/qt30t124cz2016-12-16T19:38:22Zqt30t124czSpatial variability and mechanisms underlying El Nino-induced droughts in MexicoBhattacharya, TriptiChiang, John C. H2014-03-16The El Niño Southern Oscillation plays a key role in modulating interannual rainfall variability in Mexico. While El Niño events are linked to drought in Mexico, uncertainty exists about the spatial pattern and causal mechanisms behind El Niño-induced drought. We use lead/lag correlation analysis of rainfall station data to identify the spatial pattern of drought associated with the summer before, and the spring following, the peak of warm SST anomalies in the eastern equatorial Pacific. We also use atmospheric fields from the North American Regional Reanalysis to calculate the anomalous moisture budget and diagnose the mechanisms associated with El Niño-induced drought in Mexico. We find that reduced rainfall occurs in Mexico in both the summer before and the spring after a peak El Niño event, especially in regions of climatologically strong convection. The teleconnection in the developing phase of El Niño is primarily driven by changes in subsidence resulting from anomalous convection in the equatorial Pacific. The causes of drought during the decaying phase of El Niño events are varied: in some years, descent anomalies dominate other moisture budget terms, while in other years, drying of the boundary layer on the Mexican plateau is important. We suggest that the latter may result from the interaction of weakened southeasterly winds in the Intra-Americas Sea with high topography along the Atlantic coast of Mexico. Weakened winds are likely driven by a reduced sea level pressure gradient between the Atlantic and the Pacific. Changes in easterly wave activity may contribute to drought in the developing phase of El Niño, but may be less important in the decaying phase of El Niño.BRII recipient: Bhattacharya (hybrid journal)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/30t124czarticleClimate Dynamicsvol 43, iss 12, 3309-33260930-7575 1432-0894oai:escholarship.org:ark:/13030/qt68z446902016-12-16T19:37:08Zqt68z44690iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina librariesAndersen, Jeremy CMills, Nicholas J2014-01-01Background: Illumina sequencing with its high number of reads and low per base pair cost is an attractive technology for development of molecular resources for non-model organisms. While many software packages have been developed to identify short tandem repeats (STRs) from next-generation sequencing data, these methods do not inform the investigator as to whether or not candidate loci are polymorphic in their target populations.Results: We provide a python program iMSAT that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs. Using this approach, we identified 9,119 candidate polymorphic STRs for use with the parasitoid wasp Trioxys pallidus and 2,378 candidate polymorphic STRs for use with the aphid Chromaphis juglandicola. For both organisms we selected 20 candidate tri-nucleotide STRs for validation. Using fluorescent-labeled oligonucleotide primers, we genotyped 91 female T. pallidus collected in nine localities and 46 female C. juglandicola collected in 4 localities and found 15 of the examined markers to be polymorphic for T. pallidus and 12 of the examined markers to be polymorphic for C. juglandicola.Conclusions: We present a novel approach that uses standard Illumina barcoding primers and a single Illumina HiSeq run to target polymorphic STR fragments to develop and test STR markers. We validate this approach using the parasitoid wasp T. pallidus and its aphid host C. juglandicola. This approach, which would also be compatible with 454 Sequencing, allowed us to quickly identify markers with known variability. Accordingly, our method constitutes a significant improvement over existing STR identification software packages.BRII recipient: AndersenpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/68z44690articleBMC Genomicsvol 15, iss 1, 8581471-2164oai:escholarship.org:ark:/13030/qt7133f8rm2016-12-16T19:35:28Zqt7133f8rmQualitative Feedback From a Text Messaging Intervention for Depression: Benefits, Drawbacks, and Cultural DifferencesAguilera, AdrianBerridge, Clara2014-11-05Background: Mobile health interventions are often standardized and assumed to work the same for all users; however, we may be missing cultural differences in the experiences of interventions that may impact how and if an intervention is effective.Objective: The objective of the study was to assess qualitative feedback from participants to determine if there were differences between Spanish speakers and English speakers. Daily text messages were sent to patients as an adjunct to group Cognitive Behavioral Therapy (CBT) for depression.Methods: Messages inquired about mood and about specific themes (thoughts, activities, social interactions) of a manualized group CBT intervention. There were thirty-nine patients who participated in the text messaging pilot study. The average age of the participants was 53 years (SD 10.4; range of 23-72).Results: Qualitative feedback from Spanish speakers highlighted feelings of social support, whereas English speakers noted increased introspection and self-awareness of their mood state.Conclusions: These cultural differences should be explored further, as they may impact the effect of supportive mobile health interventions.Trial Registration: Trial Registration: Clinicaltrials.gov NCT01083628; http://clinicaltrials.gov/ct2/show/study/NCT01083628BRII recipient: AguilerapubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7133f8rmarticleJMIR mHealth and uHealthvol 2, iss 4, e462291-5222oai:escholarship.org:ark:/13030/qt5gx6x7kc2016-12-16T19:33:09Zqt5gx6x7kcCoherent all-optical control of ultracold atoms arrays in permanent magnetic trapsAbdelrahman, AhmedMukai, TetsuyaHaffner, HartmutByrnes, Tim2014-02-06We propose a hybrid architecture for quantum information processing based on magnetically trapped ultracold atoms coupled via optical fields. The ultracold atoms, which can be either Bose-Einstein condensates or ensembles, are trapped in permanent magnetic traps and are placed in microcavities, connected by silica based waveguides on an atom chip structure. At each trapping center, the ultracold atoms form spin coherent states, serving as a quantum memory. An all-optical scheme is used to initialize, measure and perform a universal set of quantum gates on the single and two spin-coherent states where entanglement can be generated addressably between spatially separated trapped ultracold atoms. This allows for universal quantum operations on the spin coherent state quantum memories. We give detailed derivations of the composite cavity system mediated by a silica waveguide as well as the control scheme. Estimates for the necessary experimental conditions for a working hybrid device are given.BRII recipient: AbdelrahmanpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5gx6x7kcarticleOptics Expressvol 22, iss 3, 35011094-4087oai:escholarship.org:ark:/13030/qt1tt348xw2016-12-16T19:32:03Zqt1tt348xwNHE8 Is Essential for RPE Cell Polarity and Photoreceptor SurvivalXia, Chun-hongLiu, HaiquanCheung, DebraTang, FeliciaChang, BoLi, MeiGong, Xiaohua2015-03-20A new N-ethyl-N-nitrosourea (ENU)-induced mouse recessive mutation, identified by fundus examination of the eye, develops depigmented patches, indicating retinal disorder. Histology data show aberrant retinal pigment epithelium (RPE) and late-onset photoreceptor cell loss in the mutant retina. Chromosomal mapping and DNA sequencing reveal a point mutation (T to A) of the Slc9a8 gene, resulting in mutant sodium/proton exchanger 8 (NHE8)-M120K protein. The lysine substitution decreases the probability of forming the 3rd transmembrane helix, which impairs the pore structure of the Na+/H+ exchanger. Various RPE defects, including mislocalization of the apical marker ezrin, and disrupted apical microvilli and basal infoldings are observed in mutant mice. We have further generated NHE8 knockout mice and confirmed similar phenotypes, including abnormal RPE cells and late-onset photoreceptor cell loss. Both in vivo and in vitro data indicate that NHE8 co-localizes with ER, Golgi and intracellular vesicles in RPE cells. Thus, NHE8 function is necessary for the survival of photoreceptor cells and NHE8 is important for RPE cell polarity and function. Dysfunctional RPE may ultimately lead to photoreceptor cell death in the NHE8 mutants. Further studies will be needed to elucidate whether or not NHE8 regulates pH homeostasis in the protein secretory pathways of RPE.BRII recipient: GongpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1tt348xwarticleScientific Reportsvol 5, 93582045-2322oai:escholarship.org:ark:/13030/qt0hn4p8z32016-12-15T19:29:04Zqt0hn4p8z3Niche divergence builds the case for ecological speciation in skinks of the
Plestiodon skiltonianus
species complexWogan, Guinevere O. URichmond, Jonathan Q2015-10-01Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.BRII recipient: WoganpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0hn4p8z3articleEcology and Evolutionvol 5, iss 20, 4683-469520457758oai:escholarship.org:ark:/13030/qt8b02v1r02016-12-15T18:41:43Zqt8b02v1r0Using mHealth to Improve Usage of Antenatal Care, Postnatal Care, and Immunization: A Systematic Review of the LiteratureWatterson, Jessica LWalsh, JuliaMadeka, Isheeta2015-01-01Mobile health (mHealth) technologies have been implemented in many low- and middle-income countries to address challenges in maternal and child health. Many of these technologies attempt to influence patients’, caretakers’, or health workers’ behavior. The purpose of this study was to conduct a systematic review of the literature to determine what evidence exists for the effectiveness of mHealth tools to increase the coverage and use of antenatal care (ANC), postnatal care (PNC), and childhood immunizations through behavior change in low- and middle-income countries. The full text of 53 articles was reviewed and 10 articles were identified that met all inclusion criteria. The majority of studies used text or voice message reminders to influence patient behavior change (80%, ) and most were conducted in African countries (80%, ). All studies showed at least some evidence of effectiveness at changing behavior to improve antenatal care attendance, postnatal care attendance, or childhood immunization rates. However, many of the studies were observational and further rigorous evaluation of mHealth programs is needed in a broader variety of settings.BRII recipient: WalshpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8b02v1r0articleBioMed Research Internationalvol 2015, 1-92314-6133 2314-6141oai:escholarship.org:ark:/13030/qt8551f9w52016-12-15T18:40:25Zqt8551f9w5Mechanisms of recovery of visual function in adult amblyopia through a tailored action video gameVedamurthy, InduNahum, MorBavelier, DaphneLevi, Dennis M2015-02-26Amblyopia is a deficit in vision that arises from abnormal visual experience early in life. It was long thought to develop into a permanent deficit, unless properly treated before the end of the sensitive period for visual recovery. However, a number of studies now suggest that adults with long-standing amblyopia may at least partially recover visual acuity and stereopsis following perceptual training. Eliminating or reducing interocular suppression has been hypothesized to be at the root of these changes. Here we show that playing a novel dichoptic video game indeed results in reduced suppression, improved visual acuity and, in some cases, improved stereopsis. Our relatively large cohort of adults with amblyopia, allowed us, for the first time, to assess the link between visual function recovery and reduction in suppression. Surprisingly, no significant correlation was found between decreased suppression and improved visual function. This finding challenges the prevailing view and suggests that while dichoptic training improves visual acuity and stereopsis in adult amblyopia, reduced suppression is unlikely to be at the root of visual recovery. These results are discussed in the context of their implication on recovery of amblyopia in adults.BRII recipient: LevipubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8551f9w5articleScientific Reportsvol 5, 84822045-2322oclc_dc:berkeleylibrary:500:652:eyJmaXJzdCI6NTAwLCJpbmNsdWRlIjpbIlBVQkxJU0hFRCIsIkVNQkFSR09FRCJdLCJvcmRlciI6IlVQREFURURfREVTQyIsImxhc3RJRCI6InF0ODU1MWY5dzUiLCJsYXN0RGF0ZSI6IjIwMTYtMTItMTVUMTA6NDA6MjUtMDg6MDAifQ