Open Access Policy Deposits

This series is automatically populated with publications deposited by UCSF Library researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

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Informed Consent Practices for Publication of Patient Images in Dermatology Journals (Preprint)

(2025)

A Benchmarking Survey of Open Access Funds at the University of California

(2025)

Objective – The purpose of this study was to examine the status and viability of application-based open access funds (OAFs) across the University of California (UC) Libraries to assist with long-term planning for this type of funding at UC. Methods – In 2022, the authors surveyed the 10 UC campus libraries about both the outcome of an earlier UC-wide OAF pilot and the current status of application-based OAFs to support article processing charges (APCs), book processing charges (BPCs), and open educational resources (OERs). Five campuses reported having a current OAF. These five campuses responded to additional questions about their budgets and their sustainability, the number of publications funded, policies, and staffing resources for managing the OAF. Results – Five UC campuses had an active application-based OAF, with budgets or expenditures ranging from $20,000 - $271,000 annually. Only two campuses felt their budget was sustainable. One of the five campuses closed its fund after the survey. The number of staff resources per fund ranged from 1 to 6 with 3 to 32 hours of work weekly. Funding policies were similar to other institutional OAFs with some distinctions. All campuses had revised their criteria to disallow funding for journals covered by UC’s transformative open access agreements. Conclusion – Providing application-based funds for OA publishing at high-publishing academic institutions requires a substantial budget and workforce. Though these funds benefit some authors, the wider equity of APCs and BPCs needs to be considered.

54798 Informed Consent Practices for Publication of Patient Images in Dermatology Journals

(2024)

Cover page of 2023 Society for Academic Emergency Medicine Consensus Conference on Precision Emergency Medicine: Development of a policy-relevant, patient-centered research agenda.

2023 Society for Academic Emergency Medicine Consensus Conference on Precision Emergency Medicine: Development of a policy-relevant, patient-centered research agenda.

(2024)

OBJECTIVES: Precision medicine is data-driven health care tailored to individual patients based on their unique attributes, including biologic profiles, disease expressions, local environments, and socioeconomic conditions. Emergency medicine (EM) has been peripheral to the precision medicine discourse, lacking both a unified definition of precision medicine and a clear research agenda. We convened a national consensus conference to build a shared mental model and develop a research agenda for precision EM. METHODS: We held a conference to (1) define precision EM, (2) develop an evidence-based research agenda, and (3) identify educational gaps for current and future EM clinicians. Nine preconference workgroups (biomedical ethics, data science, health professions education, health care delivery and access, informatics, omics, population health, sex and gender, and technology and digital tools), comprising 84 individuals, garnered expert opinion, reviewed relevant literature, engaged with patients, and developed key research questions. During the conference, each workgroup shared how they defined precision EM within their domain, presented relevant conceptual frameworks, and engaged a broad set of stakeholders to refine precision EM research questions using a multistage consensus-building process. RESULTS: A total of 217 individuals participated in this initiative, of whom 115 were conference-day attendees. Consensus-building activities yielded a definition of precision EM and key research questions that comprised a new 10-year precision EM research agenda. The consensus process revealed three themes: (1) preeminence of data, (2) interconnectedness of research questions across domains, and (3) promises and pitfalls of advances in health technology and data science/artificial intelligence. The Health Professions Education Workgroup identified educational gaps in precision EM and discussed a training roadmap for the specialty. CONCLUSIONS: A research agenda for precision EM, developed with extensive stakeholder input, recognizes the potential and challenges of precision EM. Comprehensive clinician training in this field is essential to advance EM in this domain.

Peer-reviewed publications in orthopaedic surgery from lower income countries: A comparative analysis

(2024)

Introduction

Musculoskeletal (MSK) disease is a substantial global burden, especially in lower income countries. However, limited research has been published on MSK health by scholars from these countries. We aimed to study the distribution of authorships, including trends in peer-reviewed orthopaedic publications based on each author's affiliated institution's country income status.

Methods

Based on a bibliometric search, 119 orthopaedic-related journals were identified using the Journal Citation Reports database. Details of all scientific articles published in these journals between 2012 and 2021 were used to study trends and association between each of the author's affiliated institution's country income status, using the World Bank Classification.

Results

Of the 133,718 unique articles, 87.6% had at least one author affiliation from a high-income country (HIC), 7.0% from an upper-middle income country (UMIC), 5.2% from a lower-middle income country (LMIC), and 0.2% from a low-income country (LIC). Overall, these articles were cited 1,825,365 times, with 92.5% of citations from HIC-affiliated authors and < 0.1% from LIC-affiliated authors. Over the 10-year study period, HIC-affiliated articles demonstrated the largest increase in the number of publications (9107-14,619), compared to UMIC-affiliated (495-1214), LMIC-affiliated (406-874), and LIC-affiliated articles (4-28).

Conclusions

There are large and persistent disparities in orthopaedic research publications based on the country income status of the author's affiliated institution, especially in the higher impact orthopaedic journals. Efforts should be made to increase opportunities for scholars from LICs and LMICs to publish their research in high-impact orthopaedic journals.

The role of information science within the clinical translational science ecosystem

(2024)

Academic health sciences libraries ("libraries") offer services that span the entire research lifecycle, positioning them as natural partners in advancing clinical and translational science. Many libraries enjoy active and productive collaborations with Clinical and Translational Science Award (CTSA) Program hubs and other translational initiatives like the IDeA Clinical & Translational Research Network. This article explores areas of potential partnership between libraries and Translational Science Hubs (TSH), highlighting areas where libraries can support the CTSA Program's five functional areas outlined in the Notice of Funding Opportunity. It serves as a primer for TSH and libraries to explore potential collaborations, demonstrating how libraries can connect researchers to services and resources that support the information needs of TSH.

From Python to Raspberry Pi: Celebrating Pi Day with data science

(2023)

The University of California-San Francisco (UCSF) Library is a graduate-only health science university with four professional schools (medicine, pharmacy, nursing, and dentistry), a graduate division, and an academic medical center. For several years UCSF has been the number one public recipient of NIH funding, reflecting the school’s dedication to biomedical research. Around 2015, the UCSF Library began investigating new ways to serve the university’s research population. Seeing a need for more computational and entrepreneurship training the library piloted two new programs: the Data Science Initiative (DSI) and the Makers Lab.

Automated indexing using NLM's Medical Text Indexer (MTI) compared to human indexing in Medline: a pilot study

(2023)

Objective

In 2002, the National Library of Medicine (NLM) introduced semi-automated indexing of Medline using the Medical Text Indexer (MTI). In 2021, NLM announced that it would fully automate its indexing in Medline with an improved MTI by mid-2022. This pilot study examines indexing using a sample of records in Medline from 2000, and how an early, public version of MTI's outputs compares to records created by human indexers.

Methods

This pilot study examines twenty Medline records from 2000, a year before the MTI was introduced as a MeSH term recommender. We identified twenty higher- and lower-impact biomedical journals based on Journal Impact Factor (JIF) and examined the indexing of papers by feeding their PubMed records into the Interactive MTI tool.

Results

In the sample, we found key differences between automated and human-indexed Medline records: MTI assigned more terms and used them more accurately for citations in the higher JIF group, and MTI tended to rank the Male check tag more highly than the Female check tag and to omit Aged check tags. Sometimes MTI chose more specific terms than human indexers but was inconsistent in applying specificity principles.

Conclusion

NLM's transition to fully automated indexing of the biomedical literature could introduce or perpetuate inconsistencies and biases in Medline. Librarians and searchers should assess changes to index terms, and their impact on PubMed's mapping features for a range of topics. Future research should evaluate automated indexing as it pertains to finding clinical information effectively, and in performing systematic searches.

Cover page of Associations between self-reported obstetric complications and experience of care: a secondary analysis of survey data from Ghana, Kenya, and India.

Associations between self-reported obstetric complications and experience of care: a secondary analysis of survey data from Ghana, Kenya, and India.

(2023)

Background

Although several indicators have been proposed to measure women's experience of care in health facilities during the intrapartum period, it is unknown if these indicators perform differently in the context of obstetric emergencies. We examined the relationship between experience of care indicators from the Person-Centered Maternity Care (PCMC) scale and obstetric complications.

Methods

We used data from four cross-sectional surveys conducted in Kenya (rural: N = 873; urban: N = 531), Ghana (N = 531), and India (N = 2018) between August 2016 and October 2017. The pooled sample included 3953 women aged 15-49 years who gave birth within 9 weeks prior to the survey. Experience of care was measured using the PCMC scale. Univariate, bivariate, and multivariable analyses were conducted to examine the associations between the composite and 31 individual PCMC indicators with (1) obstetric complications; (2) severity of complications; and (3) delivery by cesarean section (c-section).

Results

16% (632) of women in the pooled sample reported obstetric complications; and 4% (132) reported having given birth via c-Sect. (10.5% among those with complications). The average standardized PCMC scores (range 0-100) were 63.5 (SD = 14.1) for the full scale, 43.2 (SD = 20.6) for communication and autonomy, 67.8 (SD = 14.1) for supportive care, and 80.1 (SD = 18.2) for dignity and respect sub-scales. Women with complications had higher communication and autonomy scores (45.6 [SD = 20.2]) on average compared to those without complications (42.7 [SD = 20.6]) (p < 0.001), but lower supportive care scores, and about the same scores for dignity and respect and for the overall PCMC. 18 out of 31 experience of care indicators showed statistically significant differences by complications, but the magnitudes of the differences were generally small, and the direction of the associations were inconsistent. In general, women who delivered by c-section reported better experiences.

Conclusions

There is insufficient evidence based on our analysis to suggest that women with obstetric complications report consistently better or worse experiences of care than women without. Women with complications appear to experience better care on some indicators and worse care on others. More studies are needed to understand the relationship between obstetric complications and women's experience of care and to explore why women who deliver by c-section may report better experience of care.

Tableau (version. 9.1)

Deardorff, Ariel

(2022)

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