RSS 1.0eScholarship@UMassChan
Welcome to the new eScholarship@UMassChan! eScholarship@UMassChan is a freely available digital repository offering worldwide access to the research and scholarly work of the UMass Chan Medical School community. We welcome submissions from our faculty, researchers, staff, and students. eScholarship@UMassChan is a service of the Lamar Soutter Library, Worcester, MA, USA.
Questions? See the Help menu in the sidebar or contact escholarship@umassmed.edu.
Communities in eScholarship@UMassChan
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Recently Published
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Remediating Faculty Scholarship for Accessibility: An Approach with Microsoft Word Docs as Supplemental FilesThis presentation will cover our approach to accessibility for our institutional repository of faculty scholarship. Accessibility is a legal, moral, and ethical commitment for both our researchers and the readers of their research. Our IR includes Swarthmore-affiliated research by faculty and staff, including emeriti, with about one-third of the citations providing full text access to PDFs. These PDFs range from preprints to version of record, with some holding Creative Commons licenses and others scanned from print and posted with the written permission of publishers. This leaves us with a collection of widely varied documents with regards to scan quality and base accessibility. Our previous approach to accessibility involved remediating PDFs in Adobe Acrobat, which presented a variety of issues. It was difficult to ensure the accuracy of OCR processing, particularly for: documents in non-Roman languages; images and figures incorrectly processed as text; older scanned documents from archival sources; and scans of works from our collection with marginalia. Furthermore, if a document needed a correction after it was initially processed, we often needed to reprocess the entire document rather than being able to make a simple correction. Building on the work of our College’s Accessibility Working Group, we decided to take a new approach by creating accessible Word documents to live alongside our PDFs in our repository. Our presentation will cover how we display these accessible documents and cross-link them to our posted PDFs, as well as how this new workflow addresses the aforementioned issues that we weren’t able to remediate in our previous process. We will provide a range of examples from our work, including the documentation we created to address situations such as: what we do when we find typos in the original publications; navigating internal references to page numbers; and handling documents that use aesthetic formatting decisions rather than best practices for accessibility.
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Long Term Interdisciplinary Research Collections in Digital CommonsSalve Regina University and McKillop library maintain an instance of Digital Commons as an Institutional Repository. Historically this repository has been used for housing student work such as theses and dissertations as well as Special Collections and Archives. Formats vary from pure text to images and sound. Recently the library was approached by faculty seeking to create an interdisciplinary collection focused on the Islands of Narraganset Bay. This is part of an ongoing multiyear project that involves students in Biology, Education and History researching these islands. The results will be housed in the Institutional Repository. The creation of this collection posed some challenges in organization since: the contributors would come from a variety of disciplines rather than being organized by class or department; the data would be in a variety of formats from text to audio visual; the metadata would be entered in by students rather than library staff. Discussion will focus on some of the challenges and opportunities of presenting findings in a variety of formats including audiovisual, data centric and images. Dr. Chace will focus on recruiting and training students from a variety of disciplines while Director Emsellem will discuss some of the challenges of integrating this ongoing project into our library including commitments of time and resources as well as organizational challenges. Finally Edward Iglesias will discuss the technical challenges involved with organization and display of such a collection including the use of Digital Commons Exhibits as a way of combining resources from disparate disciplines in a variety of formats.
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Red Hawks Soar!: Showcasing our Unique Collections to Engage the University Community and BeyondThe purpose of our presentation is to share our experiences in building relationships in order to create several unique and socially relevant collections in the Montclair State University Digital Commons. We will discuss issues related to community engagement, outreach and librarian liaison work undertaken to form new partnerships. During this process we learned how to adapt to change and how to find new ways to innovate, create and collaborate in order to demonstrate the value of the library, while promoting faculty research and our students scholarly activities, in support of the Strategic Plan of the University. In our presentation, we will discuss how we created Personas from the results of our research study to identify faculty members to use as a guide when evaluating services and outreach. We will address the process of promoting the repository to the campus community at large, and everything in between from the planning stages to the continued growth and sustainability of the repository. As this evolving culture of research is embraced throughout the University, the need for a vibrant, adaptable, and creative use of the repository becomes just as crucial as an IR’s archival capabilities, especially when impacting the University’s strategic vision and mission.
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JavaScript as Your Assistant: How to Populate Batch Spreadsheets FAST using CrossRef APIHave you ever felt that Excel spreadsheets and OpenRefine are not helpful anymore? Your metadata cleaning project is so messy, so complicated, and there isn’t a single tool out there to help you? Maybe what you really need is not a better tool, but something that is programmed to act like you? My presentation shares instructions and insights about how to program with Google Apps Script, CrossRef API, and OpenAlex API, so that Google Spreadsheets fills out on its own, if you provide DOIs. You don’t need programming knowledge, but access to Google Spreadsheet is necessary in order to use the source code I will share. At Denison, we archive faculty papers in Denison Digital Commons. To populate this collection, we use Google Spreadsheet with Google Apps Script that fetches metadata from CrossRef API. The custom source code in Google Apps Script finds a faculty paper if the paper has a DOI number. Then it fills out the spreadsheet. Here’s a quick demonstration that shows how the spreadsheet works: https://www.loom.com/share/71e4556f265145d0b3ac77337f2f38c1. CrossRef API and Open Alex API do similar things, but the data they offer and the way they offer are slightly different. We will also look at the differences and similarities, pros and cons between them.
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Adulting Shorts: The "TEA" on IEPs Part 3This info-comic is for high school students to help them understand what an Individualized Educational Plan or IEP is, what transition planning is, and the importance of the student being involved in them. Part 3 focuses on Mateo creating a career goal and steps to reach it. Parts 1 and 2 can be found on our website: https://www.umassmed.edu/TransitionsACR/publication/comic/
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Chinese American Librarians Association and the CALASYS: An Institutional Repository Celebrating CALA 50th AnniversaryAs the Chinese American Librarians Association (CALA)’s Institutional Repository, CALASYS hosts scholarly works and educational materials from its members and library professionals in the Library and Information Science field, and it also archives CALA’s official documents, conference materials, and Chinese cultural heritage collections. Currently, over 600 items have been added to CALASYS’ open and private collections. In celebration of the CALA’s 50th Anniversary, the CALA 50th Celebration Taskforce and the CALASYS Committee created a collection grant which aimed to preserve the history of CALA, Chinese American librarians, and the Chinese American community, encourage CALA members’ participation in CALASYS and enrich its collections. Three proposed collections have been awarded or recognized including CALA: A Path to the Future Library Leaders, CALA/YALSA Chinese American Reading List and Ming Qing Women's Poetry Collection. Open trainings have been designed and delivered to the grant participants and efforts have been made to collect data and build data models for deposit of these collections. This presentation will address the Omeka-based CALASYS system, its scope and collection policy, content and collections especially the awarded collections, the self-contribution and mediated contribution workflows and share some metadata and record examples. By opening CALASYS to all, the CALA President and officers hope that each contributing individual, committee, and chapter will be able to deposit works and documents and become the manager of their own collections after going through additional training. CALASYS will thus continue to grow at a faster pace and in a more inclusive direction in promoting diverse scholarships and research as well as association history.
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The creation of an institutional repository migration checklistColorado School of Mines recently migrated from a consortial DSpace repository which was managed by a member library, to a commercial hosted DSpace repository, now called the Mines Repository. The presenters received administrative privileges in the new repository, and this added to the migration learning curve. The new repository host provided documentation and several communication channels concerning the migration. However, the library was not given an easy-to-read and follow checklist of action items as the migration moved forward. After searching the literature, not many articles were found to include a desired migration checklist related to repositories. As the presenters learned more about administering the new repository, they created a basic checklist to keep track of the moving parts of the migration process. For example, they wanted to be sure that digitized items and associated metadata migrated correctly. They also worked to ensure that hyperlinks, search features, specific administrative actions (e.g. editing records, creating collections), and integrations (e.g. SSO, DOIs) were progressing and working as expected. This checklist served as a visual reminder, showing what had been accomplished as well as items and processes that still required attention. The checklist was intended to be a living document; members of the Mines Repository Working Group were encouraged to add items to the list and to participate in testing. It is meant to be platform agnostic, and this could be adapted by other organizations considering a repository migration. We plan to show the major components of the checklist, and to request feedback from conference attendees.
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U.S. Repository Network: Moving from Vision to ActionThe U.S. Repository Network is an initiative of SPARC with support from the Confederation of Open Access Repositories (COAR). In its “Modernizing the Global Repository Network Initiative,” COAR identified the need for assistance in breaking down institutional silos and developing a more cohesive approach and greater collaboration around repositories in the U.S. Through a Visiting Program Officer, SPARC engaged an expert group of library/repository professionals as well as the broader U.S. repository community to develop a strategic vision for U.S. repositories. The strategic vision is “an interoperable network of repositories is an essential component of our national research infrastructure, offering rapid and open access to research, and plays a crucial role in collective efforts to transform global research communications, leading to a more open, inclusive, and equitable system.” This strategic vision and its complimentary foundational characteristics guide the U.S. Repository Network (USRN) Action Plan, which is structured to advance the vision and to ensure the ongoing engagement and sustainability of the network. The presenter will briefly describe the vision development process, review the strategic vision itself, and discuss the current status of the action plan. The USRN is intended to be inclusive of all U.S. repositories, and the presenter will also discuss potential avenues for future engagement.
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It gets worse before it gets better: The promises and pitfalls of automating IR workflowsWhat are the pros and cons of automating IR workflows? In the past few years, we have increasingly used batch processes and automation to manage IR content. On the positive side, these changes have saved time and increased accuracy. There have been opportunities to gain new skills and forge new partnerships. On the other hand, we learned that when you’re doing batch processes, the stakes are higher for getting it right! I will discuss three examples of where this transition involved growing pains and sometimes visible missteps, but paid off in the long run: transferring ETD's from ProQuest to the IR; registering new DOI's in Crossref and adding them to the IR; and, harvesting faculty article metadata from Scopus to the IR for our Open Access Policy. I will also briefly share the workflows themselves, touching on using OpenRefine and collaborating with IT.
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Zotero: Low-budget, high-power middleware for electronic theses and dissertation (ETD) repository workflowsZotero is powerful, free, and open source software that can be used to manage bibliographic collections. Traditionally, users leverage Zotero to manage their personal research collections, or use group libraries to share resources with their collaborators. As a part of its openness, Zotero supports import and export of metadata in no fewer than 15 formats. This flexibility, as well as paid features that allow for multiple users to contribute to shared Group Libraries of large or even unlimited sizes, make it well-suited for collaboratively preparing bulk deposits for repositories. Using a Zotero Lab License, Digital Scholarship staff at the Columbia University Libraries (CUL) have designed a novel workflow that allows partners across campus to submit batches of thesis and/or dissertation metadata and PDFs for deposit in Academic Commons, our institutional repository. This process is structured, but moderately complex, and relies on knowledge of Google Sheets, csv, RIS, python, OpenRefine, and, of course, Zotero. We have piloted this workflow with one partner, and plan to use it to manage additional ETD deposit workflows, including a trial with the Columbia University Graduate School of Arts and Sciences for all doctoral dissertations. In this lightning talk we plan to outline the workflow we developed, give a brief report of partner feedback thus far, and speak to our opinions about the long-term viability of this solution.
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IR Management: Handling the Hard CasesAdministering an institutional repository (IR) can be challenging. Aside from common but nuanced tasks such as explaining the difference between a publisher's PDF and a post-print or establishing ingest workflows for different kinds of content, IR administrators sometimes encounter situations that push at IR policy, call into question fundamental assumptions about the benefits of Open Access, or complicate the relationship among searchability, access, and an item's authenticity. When these situations arise, it is tempting to seek guidance from trusted sources; however, privacy concerns and other details specific to these requests can make it difficult or even impossible to discuss them with other IR administrators and colleagues or to find adequate help in the literature. These situations can leave one feeling professionally isolated and uncertain. In an effort to help provide some relief and bring awareness to the ubiquity of challenging IR requests and the kinds of careful consideration that they require, I will share some of the hard cases that I have encountered as an IR administrator, how I have handled them, and lessons learned.
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MBLWHOI Library’s Institutional Repository – WHOAS: DSpace 7.2 migrationThe MBLWHOI Library’s Institutional Repository (IR) is a DSpace repository. We are migrating from version 5.6 to 7.2. This presentation will demonstrate new DSpace 7 features in our repository, while discussing our story and our takeaways from our migration.
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Climate Justice and Racial and Gender Equity: Creating and Promoting Featured CollectionsPDXScholar, the repository for Portland State University, showcases three main collections that are automatically curated based on filters – tags that collect and display the content: Climate Justice, Racial and Gender Equity, and COVID-19. In this presentation, I will give an overview of our featured collections, their development and promotion, including the criteria for inclusion, technical aspects, and impact. The Digital Commons automated collection tool and system configuration will be briefly explained.
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A tale of two migrations: a medical library case reportLaunched in 2006, the eScholarship@UMassChan institutional repository has been an important digital platform at UMass Chan Medical School, hosting faculty research, student research, and unique original publications and scholarship. In June 2021, UMass Chan’s Lamar Soutter Library decided to migrate eScholarship@UMassChan from the bepress Digital Commons platform to two separate hosted platforms. Most content – over 25,000 items representing faculty and staff publications, theses and dissertations, conference proceedings, and departmental and project collections – moved to Open Repository, a DSpace repository platform hosted by Atmire. The Janeway publishing platform became the new home for the open access, peer-reviewed journals and ebook chapters actively published through eScholarship@UMassChan. Both migrations were completed in September 2022. This lightning talk will briefly cover the migration process, challenges encountered and lessons learned.
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Introduction to Pelvic UltrasoundThis presentation is part of the PEER Liberia Radiology Lecture Series. It provides an overview for clinicians of basic ultrasound techniques and imaging of the female pelvis, including normal anatomy and sonographic appearance of common adnexal and uterine pathologies.
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3 Tips to Improve Communication with Your Youth & Young AdultsThis tip sheet provides parents and allies of youth and young adults with lived experience of a mental health condition tips be able to improve their connection with them. This tip sheet was developed as a collaboration between the family member and young adult advisory boards that work with the Transitions to Adulthood Center for Research. The tips are based on advisory board members’ real experiences.
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Negative regulation of innate immunity by novel nuclear receptor NHR-42/NR1D1 with implications in infection survival, metabolism, and fitnessDetection of pathogenic signals leads to extensive changes in cellular transcriptional programs mediated by transcription factors. Positive and negative regulators of this host defense response work together to maintain immune homeostasis. Over the past two decades, several evolutionary conserved positive regulators of innate immunity have been identified in C. elegans. However, negative regulators remain unknown, and repression of the host defense response poorly understood. We previously discovered that HLH-30/TFEB is a positive regulator of immunity in C. elegans and murine macrophages after S. aureus infection, respectively. In this study, I identify nhr-42 as a negative regulator of immunity functioning downstream of HLH-30, with major implications for host survival, metabolism, and fitness. In nhr-42 mutants, several host defense genes, such as antimicrobial peptides, C-type lectins, and lysozymes, are upregulated constitutively. This enables nhr-42 mutants to have enhanced survival and lower pathogen burden after infection compared to wild type animals. I show that nhr-42 expression is induced in the pharynx and pharyngeal-intestinal valve after infection. Furthermore, I find that antimicrobial peptides abf-2 and cnc-2 are required for enhanced survival and lower pathogen burden in nhr-42 mutants. Moreover, induction of nhr-42 after infection leads to upregulation of lipid catabolism genes involved in beta-oxidation, driving lipid mobilization. These data show that nhr-42 functions to limit the host defense response to maintain immune homeostasis and reallocate energy resources through lipid mobilization towards other cellular processes. Additionally, I identify Nr1d1 (Rev-Erbα) as a functional homolog of nhr-42. I show that Nr1d1 functions downstream of TFEB to negatively regulate pro-inflammatory cytokines Il-6 and Il1b in macrophages, after S. aureus infection. These data open up new research avenues into mammalian nuclear receptor mediated regulation of immunity.
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Prescribed Medications and Healthcare Resource Utilization in Reproductive-Age Women and Men with Rheumatic DiseaseBackground: Axial spondyloarthritis (axSpA), rheumatoid arthritis (RA), and psoriatic arthritis (PsA) are the most prevalent forms of chronic immune-mediated inflammatory arthritis, affecting approximately 0.3-1.4% of adults in the US. These rheumatic diseases (RD) have an early age of onset and may have a significant impact on women and men of reproductive ages, particularly during pregnancy and the postpartum period. Methods: Using the IBM® MarketScan® Commercial Claims and Encounters Database (2013-2018), this dissertation first described sex differences in time to non-steroidal anti-inflammatory drugs (NSAIDs) or biologic disease modifying antirheumatic drugs (bDMARDs) initiation among patients with axSpA. We then evaluated co-management with rheumatology and bDMARD prescriptions filled during pregnancy among pregnant women with axSpA, RA, and PsA. Finally, we evaluated postpartum depression (PPD) rates among reproductive-age women with axSpA, RA or PsA compared to those without RD. Results: Overall, women experienced a delay in biologic treatment initiation compared with men. Dispensations for bDMARDs during pregnancy were low in the RA/PsA subgroup, and extremely uncommon among those with axSpA, and did not align with recommendations from clinical practice guidelines. While the receipt of rheumatologic care during and after pregnancy among RD patients was low, the prevalence of PPD in women with RD was higher compared to those without any RD. Conclusions: Findings from this dissertation emphasize the need for additional research to improve and prioritize care for reproductive-age women with rheumatic disease, particularly before, during, and after pregnancy. This could be accomplished through patient education, counseling, increased access, screening, and timely referrals to rheumatologists and mental health care specialists through enhanced care coordination of providers.
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Introns Safeguard mRNA Expression in the C. elegans Germline against Multiple Surveillance MechanismsOrganisms employ sophisticated systems for genome defense against foreign and potentially harmful elements, while leaving room for gene adaptation. In animals, conserved PIWI Argonautes use genomically encoded small RNA guides (called piRNAs) to detect and silence foreign nucleotide sequences, such as transposons. In Caenorhabditis elegans, the detection of foreign transcripts by PIWI triggers the production of a second class of antisense small RNAs (called 22G-RNAs), which guide worm-specific Argonautes (WAGOs) to direct transcriptional and posttranscriptional silencing. PIWI-piRNA complexes recognize targets via imperfect base-pairing, which could threaten the expression of endogenous host genes. Nevertheless, worms use yet a third small RNA pathway involving the Argonaute CSR-1 to license endogenous germline gene expression and prevent inappropriate silencing by the PIWI pathway. How and why certain genes are licensed remains unknown. Here I show that introns and, by inference, mRNA splicing protect messenger RNAs from germline silencing. Intronless reporters encounter 22G-RNA-dependent and -independent silencing mechanisms, which we collectively termed “intronless silencing.” Genetic studies revealed that primary Argonautes, e.g., PIWI, are not required for the 22G-RNA-dependent intronless silencing mechanism, suggesting that intronless reporters are silenced by default. Nuclear and cytoplasmic WAGOs enabled the transmission of silencing from an intronless allele to a homologous intron-containing allele. The 22G-RNA-independent mechanism not only reduced intronless reporter mRNA levels, compared to the homologous intron-containing genes, but also prevented polyadenylation and nuclear export. Cis-acting elements that promote export from the nucleus nevertheless failed to fully activate expression of intronless reporters, suggesting additional layers of regulation in the small RNA-independent mechanism of intronless silencing. These findings suggest that multiple germline surveillance systems monitor transcript splicing, reveal a protective role of splicing in transcript licensing, and provide evidence for a splicing-dependent, sequence-independent mode of Argonaute programming.
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Dual Inhibitors of Main Protease (M) and Cathepsin L as Potent Antivirals against SARS-CoV2Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.
