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Open Access Publications from the University of California

Scholarly Works (394 results)

  • Article
Frontiers of Biogeography, Volume 13, Issue 4 (2021)

Human activities are altering the structure of ecosystems, compromising the benefits they provide to nature and people. Effective conservation actions and management under ongoing global change rely on a better understanding of socio-ecological patterns and processes across broad spatiotemporal scales. Both macroecology and conservation science contribute to this improved understanding and, while they have different scopes, these disciplines have become increasingly interconnected over time. Here we describe examples of how macroecology has contributed to conservation science, and how conservation science can motivate further macroecological developments and applications. We identify challenges and untapped potential to further strengthen the links between these two disciplines. Major macroecological contributions include developing ecological theory, providing methodologies useful for biodiversity assessments and projections, making data more accessible and addressing knowledge gaps. These contributions have played a major role in the development of conservation science, and have supported outreach to policy makers, media, and the public. Nonetheless, a pure macroecological lens is limited to inform conservation decisions, particularly in local contexts, which frequently leads to the misuse of macroecological analyses for conservation applications, misunderstandings of research outputs, and skepticism among conservation practitioners and scientists. We propose possible solutions to overcome these challenges and strengthen links between macroecology and conservation science, including a stronger focus on ecological mechanisms and predictive approaches, and the creation of hybrid journals and meetings. Finally, we suggest new avenues for macroecological research that would further benefit conservation science.

    Cover page: The interface between Macroecology and Conservation: existing links and untapped opportunitiesCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    LBL Publications (2018)
    In the framework of the high-luminosity upgrade of the large hadron collider, the U.S. LARP collaboration and CERN are jointly developing a 150-mm aperture Nb3Sn quadrupole for the Large Hadron Collider (LHC) interaction regions. Due to the large beam size and orbit displacement in the final focusing triplet, MQXF has challenging targets for field quality at nominal operation conditions. Three short model magnets have been tested and around 30 coils have been built, allowing a first analysis of the reproducibility of the coil size and turns positioning. The impact of the coil shimming on field quality is evaluated, with special emphasis on the warm magnetic measurements and the correlation to field measurements at cold and nominal field. The variability of the field harmonics along the magnet axis is studied by means of a Monte-Carlo analysis and the effects of the corrective actions implemented to suppress the low-order unallowed multipoles are discussed.
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      • Peer Reviewed
      UC Davis Previously Published Works (2018)
      The dilute magnetic semiconductors have promise in spin-based electronics applications due to their potential for ferromagnetic order at room temperature, and various unique switching and spin-dependent conductivity properties. However, the precise mechanism by which the transition-metal doping produces ferromagnetism has been controversial. Here we have studied a dilute magnetic semiconductor (5% manganese-doped gallium arsenide) with Bragg-reflection standing-wave hard X-ray angle-resolved photoemission spectroscopy, and resolved its electronic structure into element- and momentum- resolved components. The measured valence band intensities have been projected into element-resolved components using analogous energy scans of Ga 3d, Mn 2p, and As 3d core levels, with results in excellent agreement with element-projected Bloch spectral functions and clarification of the electronic structure of this prototypical material. This technique should be broadly applicable to other multi-element materials.
        Cover page: Element- and momentum-resolved electronic structure of the dilute magnetic semiconductor manganese doped gallium arsenide
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2024)
        STUDY OBJECTIVES: Post hoc analysis to evaluate the effect of daridorexant on sleep architecture in people with insomnia, focusing on features associated with hyperarousal. METHODS: We studied sleep architecture in adults with chronic insomnia disorder from two randomized phase 3 clinical studies (Clinicaltrials.gov: NCT03545191 and NCT03575104) investigating 3 months of daridorexant treatment (placebo, daridorexant 25 mg, daridorexant 50 mg). We analyzed sleep-wake transition probabilities, EEG spectra, and sleep spindle properties including density, dispersion, and slow oscillation phase coupling. The wake EEG similarity index (WESI) was determined using a machine learning algorithm analyzing the spectral profile of the EEG. RESULTS: At month 3, daridorexant 50 mg decreased wake-to-wake transition probabilities (p < .05) and increased the probability of transitions from wake-to-N1 (p < .05), N2 (p < .05), and REM sleep (p < .05), as well as from N1-to-N2 (p < .05) compared to baseline and placebo. Daridorexant 50 mg decreased relative beta power during wake (p = .011) and N1 (p < .001) compared to baseline and placebo. During the wake, relative alpha power decreased (p < .001) and relative delta power increased (p < .001) compared to placebo. Daridorexant did not alter EEG spectra bands in N2, N3, and REM stages or in sleep spindle activity. Daridorexant decreased the WESI score during wake compared to baseline (p = .004). Effects with 50 mg were consistent between months 1 and 3 and less pronounced with 25 mg. CONCLUSIONS: Daridorexant reduced EEG features associated with hyperarousal as indicated by reduced wake-to-wake transition probabilities and enhanced spectral features associated with drowsiness and sleep during wake and N1. CLINICAL TRIALS: ClinicalTrials.gov NCT03545191: study to assess the efficacy and safety of ACT-541468 (daridorexant) in adult and elderly participants with insomnia disorder. URL: Study Details | study to assess the efficacy and safety of ACT-541468 (daridorexant) in adult and elderly participants with insomnia disorder | ClinicalTrials.gov ClinicalTrials.gov NCT03575104:study to assess the efficacy and safety of ACT-541468 (daridorexant) in adult and elderly participants who experience difficulties sleeping. URL: study details | study to assess the efficacy and safety of ACT-541468 (daridorexant) in adult and elderly participants who experience difficulties sleeping | ClinicalTrials.gov.
          Cover page: Effect of daridorexant on sleep architecture in patients with chronic insomnia disorder: a pooled post hoc analysis of two randomized phase 3 clinical studies.
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          UC San Diego Previously Published Works (2015)
          Deregulation of the miR-15a/16-1 cluster has a key role in the pathogenesis of chronic lymphocytic leukemia (CLL), a clinically heterogeneous disease with indolent and aggressive forms. The miR-15a/16-1 locus is located at 13q14, the most frequently deleted region in CLL. Starting from functional investigations of a rare SNP upstream the miR cluster, we identified a novel allele-specific mechanism that exploits a cryptic activator region to recruit the RNA polymerase III for miR-15a/16-1 transcription. This regulation of the miR-15a/16- locus is independent of the DLEU2 host gene, which is often transcribed monoallellically by RPII. We found that normally one allele of miR-15a/16-1 is transcribed by RNAPII, the other one by RNAPIII. In our subset of CLL patients harboring 13q14 deletions, exclusive RNA polymerase III (RPIII)-driven transcription of the miR-15a/16-1 was the consequence of loss of the RPII-regulated allele and correlated with high expression of the poor prognostic marker ZAP70 (P=0.019). Thus, our findings point to a novel biological process, characterized by double allele-specific transcriptional regulation of the miR-15a/16-1 locus by alternative mechanisms. Differential usage of these mechanisms may distinguish at onset aggressive from indolent forms of CLL. This provides a basis for the clinical heterogeneity of the CLL patients carrying 13q14 deletions.
            Cover page: Allele-specific loss and transcription of the miR-15a/16-1 cluster in chronic lymphocytic leukemia
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            • Peer Reviewed
            UC Santa Cruz Previously Published Works (2023)
            The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.
              Cover page: Targeting of intracellular oncoproteins with peptide-centric CARs.
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              • Peer Reviewed
              UC Irvine Previously Published Works (2010)
              In April-July 2008, intensive measurements were made of atmospheric composition and chemistry in Sabah, Malaysia, as part of the "Oxidant and particle photochemical processes above a South-East Asian tropical rainforest" (OP3) project. Fluxes and concentrations of trace gases and particles were made from and above the rainforest canopy at the Bukit Atur Global Atmosphere Watch station and at the nearby Sabahmas oil palm plantation, using both ground-based and airborne measurements. Here, the measurement and modelling strategies used, the characteristics of the sites and an overview of data obtained are described. Composition measurements show that the rainforest site was not significantly impacted by anthropogenic pollution, and this is confirmed by satellite retrievals of NO2 and HCHO. The dominant modulators of atmospheric chemistry at the rainforest site were therefore emissions of BVOCs and soil emissions of reactive nitrogen oxides. At the observed BVOC:NOx volume mixing ratio (∼100 pptv/pptv), current chemical models suggest that daytime maximum OH concentrations should be ca. 105 radicals cm-3, but observed OH concentrations were an order of magnitude greater than this. We confirm, therefore, previous measurements that suggest that an unexplained source of OH must exist above tropical rainforest and we continue to interrogate the data to find explanations for this.
                Cover page: Overview: oxidant and particle photochemical processes above a south-east Asian tropical rainforest (the OP3 project): introduction, rationale, location characteristics and toolsCreative Commons 'BY' version 4.0 license
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                • Peer Reviewed
                UC Irvine Previously Published Works (2010)
                  Cover page: Corrigendum to "Overview: oxidant and particle photochemical processes above a south-east Asian tropical rainforest (the OP3 project): introduction, rationale, location characteristics and tools" published in Atmos. Chem. Phys., 10, 169–199, 2010Creative Commons 'BY' version 4.0 license
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                  UC San Francisco Previously Published Works (2024)
                  Germinal matrix hemorrhage (GMH) is a devastating neurodevelopmental condition affecting preterm infants, but why blood vessels in this brain region are vulnerable to rupture remains unknown. Here we show that microglia in prenatal mouse and human brain interact with nascent vasculature in an age-dependent manner and that ablation of these cells in mice reduces angiogenesis in the ganglionic eminences, which correspond to the human germinal matrix. Consistent with these findings, single-cell transcriptomics and flow cytometry show that distinct subsets of CD45+ cells from control preterm infants employ diverse signaling mechanisms to promote vascular network formation. In contrast, CD45+ cells from infants with GMH harbor activated neutrophils and monocytes that produce proinflammatory factors, including azurocidin 1, elastase and CXCL16, to disrupt vascular integrity and cause hemorrhage in ganglionic eminences. These results underscore the brain's innate immune cells in region-specific angiogenesis and how aberrant activation of these immune cells promotes GMH in preterm infants.
                    Cover page: Proinflammatory immune cells disrupt angiogenesis and promote germinal matrix hemorrhage in prenatal human brain
                    • Article
                    Lawrence Berkeley National Laboratory (2008)

                    An array of Neutral-Current Detectors (NCDs) has been built in order to make a unique measurement of the total active ux of solar neutrinos in the Sudbury Neutrino Observatory (SNO). Data in the third phase of the SNO experiment were collected between November 2004 and November 2006, after the NCD array was added to improve the neutral-current sensitivity of the SNO detector. This array consisted of 36 strings of proportional counters lled with a mixture of 3He and CF4 gas capable of detecting the neutrons liberated by the neutrino-deuteron neutral current reaction in the D2O, and four strings lled with a mixture of 4He and CF4 gas for background measurements. The proportional counter diameter is 5 cm. The total deployed array length was 398 m. The SNO NCD array is the lowest-radioactivity large array of proportional counters ever produced. This article describes the design, construction, deployment, and characterization of the NCD array, discusses the electronics and data acquisition system, and considers event signatures and backgrounds.

                      Cover page: An array of low-background 3He proportional counters for the Sudbury Neutrino Observatory
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