UCSF Library

Objectives: To synthesize and map literature on automated indexing of the biomedical literature, with a focus on the Medical Text Indexer (MTI) at the National Library of Medicine (NLM). We review the drivers, benefits, and challenges of automated indexing, evolution of the MTI from 2000-2025, and impacts on information retrieval in MEDLINE. Methods: We conducted a scoping review following the JBI Manual for Evidence Synthesis and reported findings using PRISMA-ScR and PRISMA-S. We searched several bibliographic databases, key journals, conference proceedings, and grey literature sources, with no restrictions on language or study design. Eligible publications were published 2000-2025 and focused on MTI development. Screening, data charting, and thematic analysis were conducted by multiple reviewers. Results: We included 64 publications, with most originating from the United States (n=53, 83%) and five from Canada (8%). Study methods included evaluation or comparative studies (65%), qualitative descriptions (25%), and mixed methods (11%). MTI evolved from a rules-based recommendation tool in 2002 to the neural network-based MTIX in 2024. Despite numerous enhancements to the MTI, human curation remains necessary for approximately one-third of records to correct inaccuracies, capture missed concepts, and address errors arising from figurative language or algorithmic biases. Conclusions: This review synthesizes twenty-five years of MTI research (2000-2025). Despite reduced indexing times and a markedly improved algorithm, the MTIX has not yet achieved full equivalence to human indexing. Our findings suggest searchers should watch for algorithmic ambiguities in their MEDLINE searching and adapt accordingly. Health sciences librarians should work with stakeholders, including authors, to shape future algorithmic indexing methods, outputs, evaluation and research.

[This corrects the article DOI: 10.2196/60795.].

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.

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.

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.

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.

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.

BACKGROUND: Rural U.S. communities are at risk from COVID-19 due to advanced age and limited access to acute care. Recognizing this, the Vashon Medical Reserve Corps (VMRC) in King County, Washington, implemented an all-volunteer, community-based COVID-19 response program. This program integrated public engagement, SARS-CoV-2 testing, contact tracing, vaccination, and material community support, and was associated with the lowest cumulative COVID-19 case rate in King County. This study aimed to investigate the contributions of demographics, geography and public health interventions to Vashon's low COVID-19 rates. METHODS: This observational cross-sectional study compares cumulative COVID-19 rates and success of public health interventions from February 2020 through November 2021 for Vashon Island with King County (including metropolitan Seattle) and Whidbey Island, located ~50 km north of Vashon. To evaluate the role of demography, we developed multiple linear regression models of COVID-19 rates using metrics of age, race/ethnicity, wealth and educational attainment across 77 King County zip codes. To investigate the role of remote geography we expanded the regression models to include North, Central and South Whidbey, similarly remote island communities with varying demographic features. To evaluate the effectiveness of VMRC's community-based public health measures, we directly compared Vashon's success of vaccination and contact tracing with that of King County and South Whidbey, the Whidbey community most similar to Vashon. RESULTS: Vashon's cumulative COVID-19 case rate was 29% that of King County overall (22.2 vs 76.8 cases/K). A multiple linear regression model based on King County demographics found educational attainment to be a major correlate of COVID-19 rates, and Vashon's cumulative case rate was just 38% of predicted (p < .05), so demographics alone do not explain Vashon's low COVID-19 case rate. Inclusion of Whidbey communities in the model identified a major effect of remote geography (-49 cases/K, p < .001), such that observed COVID-19 rates for all remote communities fell within the model's 95% prediction interval. VMRC's vaccination effort was highly effective, reaching a vaccination rate of 1500 doses/K four months before South Whidbey and King County and maintaining a cumulative vaccination rate 200 doses/K higher throughout the latter half of 2021 (p < .001). Including vaccination rates in the model reduced the effect of remote geography to -41 cases/K (p < .001). VMRC case investigation was also highly effective, interviewing 96% of referred cases in an average of 1.7 days compared with 69% in 3.7 days for Washington Department of Health investigating South Whidbey cases and 80% in 3.4 days for Public Health-Seattle & King County (both p<0.001). VMRC's public health interventions were associated with a 30% lower case rate (p<0.001) and 55% lower hospitalization rate (p = 0.056) than South Whidbey. CONCLUSIONS: While the overall magnitude of the pre-Omicron COVID-19 pandemic in rural and urban U.S. communities was similar, we show that island communities in the Puget Sound region were substantially protected from COVID-19 by their geography. We further show that a volunteer community-based COVID-19 response program was highly effective in the Vashon community, augmenting the protective effect of geography. We suggest that Medical Reserve Corps should be an important element of future pandemic planning.