Scholarly Works, University Libraries

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Research articles, presentations, and other scholarship

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Environmental bodies of water as reservoirs for Salmonella: A Scoping Review
Chowdhury, Bhaswati; Ehsan, Rakib; Weller, Daniel; Kummer, Amber; Nguyen, Han; Comer, C. Cozette; Hoch, Jackson; Cheng, Rachel (2025-05)
Salmonella enterica is a leading cause of foodborne illness in the United States. Emerging evidence suggests that surface water may act as an environmental reservoir, contributing to its persistence and transmission. However, no comprehensive synthesis of the available literature exists to evaluate the strength of this evidence or to identify patterns in Salmonella occurrence in surface water sources from different regions in the United States. To address this gap, this protocol describes the methodology for conducting a scoping review, developed in accordance with PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines by trained reviewers in collaboration with evidence synthesis librarians, to assess the prevalence of Salmonella contamination in surface water in the US and evaluate its potential role in transmission, including links to agricultural runoff and wildlife activity. In brief, the descriptor terms for the pathogen of interest, i.e., “Salmonella” and surface water bodies (e.g., river, stream, wetland) were identified. These terms were then tailored to the syntax requirements of nine selected databases, based on scope and topical fit, and used to develop search strategies incorporating Boolean and proximity operators to enhance the retrieval of relevant records. Controlled vocabularies, such as MeSH and CAB Thesaurus terms, were also incorporated, and the search was restricted to studies conducted within the United States. Inclusion and exclusion criteria were defined a priori to guide the screening of retrieved records through title, abstract, and full-text review. Finally, data extraction items were identified to (i) synthesize evidence on risks associated with surface water used for irrigation in small and large produce operations and (ii) identify key knowledge gaps to inform future research on surface water as an environmental reservoir for Salmonella.
Holistic approaches to digital literacy: Perspectives from library partners
Dean, Kirsten; Feerrar, Julia; Griffin, Katlyn; Hammer, Kelsey (Wiley, 2024-12-01)
In this chapter, a team of academic librarians offers strategies to address four common challenges instructors face when incorporating digital literacy into their courses.
MetaArchive Across Its Life Cycle: Change and Resilience in the Digital Preservation Ecosystem
Meyerson, Jessica; Huang, Jackson; Becker, Snowden; Kinnaman, Alex; Vowell, Zach (2025-04-08)
This panel discusses how community-owned and -led digital infrastructure can – and should – incorporate contingencies for sunsetting into sustainability planning and how to embody core values and address diverse member needs throughout the sunset process. Through its twenty years of operation, MetaArchive, the first and longest-running Private LOCKSS Network (PLN) has been consistently defining what it entails to be a digital preservation network created and hosted by and for memory organizations. Now, as the first PLN to undergo a deliberative sunset, we have the opportunity to share lessons in how endings can be carried out with as much intention and care as beginnings. In a time of field- and nation-wide change and transition, investments in shared infrastructure and inter-institutional communities of practice are more valuable than ever to building a resilient information ecosystem – only collectively can we guarantee access to our cultural heritage in the long-term. https://www.cni.org/topics/digital-preservation/metaarchive-across-its-life-cycle-change-and-resilience-in-the-digital-preservation-ecosystem
Green Goes with Anything: Balancing Sustainability, Archives, and Outcomes
Kinnaman, Alex; Munshower, Alan (2025-04-09)
The authors were invited to participate in one of a six part panel series titled CLIR Climate Resiliency Action Series to discuss climate resiliency in digital libraries and digital preservation (https://climate-resiliency.clir.org/sessions/big-data-and-the-preservation-problem/). This presentation drew from the authors' paper "Green Goes with Anything: Decreasing Environmental Impact of Digital Libraries at Virginia Tech" at iPRES 2022. The presentation recording can be found at https://www.youtube.com/watch?v=0rY-crsOOII
Librarian Lobbyist? Front Lines of Virginia OER Legislative Advocacy
Walz, Anita R. (Association of College & Research Libraries, 2025-04-25)
Opportunities for librarian legislative involvement are somewhat inevitable. Those on the precipice can be propelled into policy and political engagement for personal and professional reasons. In the United States, employees of public institutions and corporations are typically bound by institutional policies regarding speech, policymaking, and communication with government entities on behalf of their respective institutions. This dual identity of government employee and private citizen can create complexity. Leadership approaches common to librarians emphasize human resources or cultural/symbolic framing rather than political framing (Bolman & Deal, 2017, p179). These can also create complexity. This peer-reviewed book chapter provides a case study of how one bill to encourage open educational resources at state institutions of higher education ("Virginia Bill to Encourage OER" HB454 2018) became Virginia law, though not as originally submitted. It offers insights for similiarly-situated public employees who wish to exercise their rights to engage with legislative processes as private citizens.
AI in Research Libraries: Supporting Research in the Age of AI
Pannabecker, Virginia (2025-04-08)
Group discussion with an opening presentation by AI in Research Operations member host Virginia Pannabecker. Did you know libraries are not just powerhouses for research but also for lately AI? They don’t just store books—they provide AI tools, training, and shape policies, facilitating access to AI solutions that help researchers work smarter and save time. Libraries are leading the way in AI adoption within higher education institutions. That is why this event is not just for librarians interested in AI—it is a must-attend event for everyone working in research, including: academics, researchers, research manager and administrator. What You Will Learn: - How AI is transforming research & how libraries are leading the way - Top AI approaches, applications, tools, and programs supporting research - How libraries help shape AI policies & research strategies - Real examples of libraries driving AI-powered research What We Will Discuss: - How do you currently interact with libraries in your work or institution? - What library-led AI or research support initiatives have been most valuable to research? - What would you like to see from libraries as AI continues to evolve?
JCDL 2024 Workshop: Generative AI for Resource Discovery in Libraries
Chen, Yinlin; Yang, Le; Xie, Zhiwu (ACM, 2024-12-16)
This workshop delves into the transformative role of Generative AI technologies in digital libraries, emphasizing advancements in resource discovery and user engagement. Participants will explore how cutting-edge large language models such as GPT-4 and Llama are leveraged to deliver highly personalized resource recommendations and improve the efficiency and precision of information retrieval processes. Through showcases of capstone projects developed as part of the AI Incubator Program, hands-on sessions, and collaborative discussions, attendees will gain practical insights into deploying AI-driven solutions that streamline library operations and elevate user experience.
Trust at Your Own Peril: A Mixed Methods Exploration of the Ability of Large Language Models to Generate Expert-Like Systems Engineering Artifacts and a Characterization of Failure Modes
Topcu, Taylan G.; Husain, Mohammed; Ofsa, Max; Wach, Paul (Wiley, 2025-02-21)
Multi-purpose large language models (LLMs), a subset of generative artificial intelligence (AI), have recently made significant progress. While expectations for LLMs to assist systems engineering (SE) tasks are paramount; the interdisciplinary and complex nature of systems, along with the need to synthesize deep-domain knowledge and operational context, raise questions regarding the efficacy of LLMs to generate SE artifacts, particularly given that they are trained using data that is broadly available on the internet. To that end, we present results from an empirical exploration, where a human expert-generated SE artifact was taken as a benchmark, parsed, and fed into various LLMs through prompt engineering to generate segments of typical SE artifacts. This procedure was applied without any fine-tuning or calibration to document baseline LLM performance. We then adopted a two-fold mixed-methods approach to compare AI generated artifacts against the benchmark. First, we quantitatively compare the artifacts using natural language processing algorithms and find that when prompted carefully, the state-of-the-art algorithms cannot differentiate AI-generated artifacts from the human-expert benchmark. Second, we conduct a qualitative deep dive to investigate how they differ in terms of quality. We document that while the two-material appear very similar, AI generated artifacts exhibit serious failure modes that could be difficult to detect. We characterize these as: premature requirements definition, unsubstantiated numerical estimates, and propensity to overspecify. We contend that this study tells a cautionary tale about why the SE community must be more cautious adopting AI suggested feedback, at least when generated by multi-purpose LLMs.
Evolution at Spike protein position 519 in SARS-CoV-2 facilitated adaptation to humans
Cereghino, C.; Michalak, K.; DiGiuseppe, S.; Yu, D.; Faraji, A.; Sharp, A.K.; Brown, Anne M.; Kang, L.; Weger-Lucarelli, James; Michalak, P. (Springer Nature, 2024)
As the COVID-19 pandemic enters its fourth year, the pursuit of identifying a progenitor virus to SARSCoV- 2 and understanding the mechanism of its emergence persists, albeit against the backdrop of intensified efforts to monitor the ongoing evolution of the virus and the influx of new mutations. Surprisingly, few residues hypothesized to be essential forSARS-CoV-2 emergence and adaptation to humans have been validated experimentally, despite the importance that these mutations could contribute to the development of effective antivirals. To remedy this,we searched for genomic regions in the SARS-CoV-2 genome that show evidence of past selection around residues unique to SARSCoV- 2 compared with closely related coronaviruses. In doing so, we identified a residue at position 519 in Spike within the receptor binding domain that holds a static histidine in human-derived SARSCoV- 2 sequences but an asparagine in SARS-related coronaviruses from bats and pangolins. In experimental validation, the SARS-CoV-2 Spike protein mutant carrying the putatively ancestral H519N substitution showed reduced replication in human lung cells, suggesting that the histidine residue contributes to viral fitness in the human host. Structural analyses revealed a potential role of Spike residue 519 in mediating conformational transitions necessary for Spike prior to binding with ACE2. Pseudotyped viruses bearing the putatively ancestral N519 also demonstrated significantly reduced infectivity in cells expressing the human ACE2 receptor compared to H519. ELISA data corroborated that H519 enhances Spike binding affinity to the human ACE2 receptor compared to the putatively ancestral N519. Collectively, these findings suggest that the evolutionary transition at position 519 of the Spike protein played a critical role inSARS-CoV-2 emergence and adaptation to the human host. Additionally, this residue presents as a potential drug target for designing small molecule inhibitors tailored to this site.
Curating Your Box of Chaos: Digitizing Collections of SWVA Community History
Kinnaman, Alex; Nehrt, Jennifer; Shortt, Ann-Margaret; Huffman, Sherri (2025-03-17)
Whether it’s your grandmother’s attic or the archival storage room of your favorite historical society, we’ve all encountered that “box of chaos” with documents, photos, and that one floppy disk no one can open. As time passes, though, the risk of losing material to degradation, obsolescence, and institutional memory increases. The Greater Southwest Virginia Digital Collective is a new community-owned, community-designed collaboration between regional cultural heritage organizations and Virginia Tech University Libraries to provide resources for organizing, digitizing, and preserving the SWVA historical record. Join our Roundtable to learn about GSDC, our resources, and ways to collaborate to preserve your box of chaos.
Research Tools for Graduate Students: Reflections on Eight Years of Graduate Student Workshops
Russell, Lisa Becksford (East Tennessee State University, Charles C. Sherrod Library, 2024-11-18)
This article will describe the author’s graduate student outreach efforts over the last eight years, including graduate student orientations, open houses, and workshops. The development of a long-running graduate student workshop series is described in detail, and the author shares lessons learned from her outreach experiences.
Identification of small molecule inhibitors of the Chloracidobacterium thermophilum type IV pilus protein PilB by ensemble virtual screening
McDonald-Ramos, Jay S.; Hicklin, Ian K.; Yang, Zhaomin; Brown, Anne M. (Elsevier, 2024-08-16)
Antivirulence strategy has been explored as an alternative to traditional antibiotic development. The bacterial type IV pilus is a virulence factor involved in host invasion and colonization in many antibiotic resistant pathogens. The PilB ATPase hydrolyzes ATP to drive the assembly of the pilus filament from pilin subunits. We evaluated Chloracidobacterium thermophilum PilB (CtPilB) as a model for structure-based virtual screening by molecular docking and molecular dynamics (MD) simulations. A hexameric structure of CtPilB was generated through homology modeling based on an existing crystal structure of a PilB from Geobacter metallireducens. Four representative structures were obtained from molecular dynamics simulations to examine the conformational plasticity of PilB and improve docking analyses by ensemble docking. Structural analyses after 1 μs of simulation revealed conformational changes in individual PilB subunits are dependent on ligand presence. Further, ensemble virtual screening of a library of 4234 compounds retrieved from the ZINC15 database identified five promising PilB inhibitors. Molecular docking and binding analyses using the four representative structures from MD simulations revealed that top-ranked compounds interact with multiple Walker A residues, one Asp-box residue, and one arginine finger, indicating these are key residues in inhibitor binding within the ATP binding pocket. The use of multiple conformations in molecular screening can provide greater insight into compound flexibility within receptor sites and better inform future drug development for therapeutics targeting the type IV pilus assembly ATPase.
CLIR Postdoctoral Fellowship in Community Data for the Rematriation Project: Summary Report
Yunes, Erin; Long, Kara (2024-08-19)
The CLIR Postdoctoral Fellowship in Community Data at the Virginia Tech University Libraries (VTUL) was a collaborative initiative designed to help bridge academic resources and community-led projects. The fellowship focused on supporting the Rematriation project through collaboration among scholars and staff from the VT University Libraries and Department of English and community members. A key directive was to work with an Inuit-led interdisciplinary team in creating a digital archive that centers Indigenous knowledges and perspectives. This report provides an overview of the fellowship's objectives, methodologies, key activities, and outcomes, emphasizing the collaborative efforts and innovative approaches that shaped this work.
Constructing Consistent Comprehensive Searches in Large Engineering Databases—Tips and Recommendations for Literature Reviews
Over, Sarah; Comer, C. Cozette (ASEE Conferences, 2024-06)
Engineering and STEM librarians and researchers regularly use a number of disciplinary databases for finding literature. For evidence synthesis (ES) research projects, knowing database capabilities and how to most effectively search each database is critical. The complex, often comprehensive search strategies necessary for ES reviews can require use of “advanced” search options and controlled vocabulary/index terms. However, the functionality of search interfaces used to access databases varies widely. Thus, searchers must expend more time and effort to translate searches consistently, as each database has different features and limitations. This article will cover major engineering databases used in comprehensive searches, including Engineering Village and more. Each database's search implementation will be explained using an example search on hearing disabilities in computing education, which was developed for a scoping review by the authors in collaboration with a faculty member and a graduate student from the Computer Science department at Virginia Tech. Aspects of advanced searching such as truncation, proximity searching, exact phrases, and controlled vocabulary/index terms will also be highlighted. Overall, these databases require more research into how to construct searches compared to some interdisciplinary databases, but still have their place in finding quality engineering research efficiently.
Structure Characterization of Zinc Finger Motif 1 and 2 of GLI1 DNA Binding Region
Wu, Mousheng; Jahan, Nusrat; Sharp, Amanda; Ullah, Anwar; Augelli-Szafran, Corinne E.; Zhang, Sixue; Boohaker, Rebecca J. (MDPI, 2024-12-13)
As a transcription factor, GLI1 plays an important role in cell cycle regulation, DNA replication, and DNA damage responses. The aberrant activation of GLI1 has been associated with cancers such as glioma, osteosarcoma, and rhabdomyosarcoma. The binding of GLI1 to a specific DNA sequence was achieved by five tandem zinc finger motifs (Zif motifs) on the N-terminal part of the molecule. Here, we reported a novel homodimeric crystal structure of Zif1-2. These two Zif motifs are linearized. Namely, Zif2 does not bend and interact with Zif1 of the same molecule. Instead, Zif1 from one molecule interacts with Zif2 from another molecule. The dimer interface of Zif1-2 is unique and different from the conformation of Zif1-2 from the GLI1-DNA co-crystal structure. The dimeric conformation of Zif motifs could represent the native conformation of apo form GLI1 Zif motifs in the cell. The molecular dynamics simulation result of the homodimer, the in silico mutagenesis, and the predicted protease stability of these mutants using a large language model are also presented.
Neuromodulating Alkaloids from Millipede Defensive Secretions
Menegatti, Carla; Wood, Jared S.; Banks, Paige; Knott, Kenneth; Briganti, Jonathan S.; Briganti, Anthony J.; McNally, Samuel V. G.; Marek, Paul E.; Brown, Anne M.; Jones, Tappey H.; Williamson, R. Thomas; Mevers, Emily (American Chemical Society, 2024)
Millipedes have long been known to produce structurally diverse chemical defenses, including hydrogen cyanide, terpenoid alkaloids, and oxidized aromatics. Although the hydrogen cyanide and oxidized aromatic producing millipedes have been well studied, less than 10% of the terpenoid alkaloid producers have been chemically investigated. Several previous studies have shown that alkaloids disorient predators, but their biochemical target is currently unknown. Herein, we investigated the defensive secretions of a colobognath millipede, Ischnocybe plicata, and elucidated the constitution, absolute configuration, and conformation of four new highly oxidized terpenoid alkaloids, termed ischnocybines, using a range of analytical techniques. The ischnocybines are actively secreted from the defensive glands and were shown to disorient ants, a likely common predator. Evaluation of the ischnocybines in a panel of neuroreceptors revealed that ischnocybine A possesses potent (Ki 13.6 nM) and selective (100-fold) binding affinity for sigma-1, an orphan neuroreceptor, over sigma-2. These molecules represent the most complex alkaloids to be discovered from millipedes and provide the first potential insights into a biochemical target responsible for their defensive properties.
Community-Owned-and-Operated: Amplifying Cultural Heritage through Inter-Institutional Collaboration
Kinnaman, Alex; Palazzo, Ashley (2024-11-15)
The Greater Southwest Virginia Digital Collective (GSDC) is a community-owned collective steered by a volunteer community advisory board composed of community members from the region and Virginia Tech University Library (VTUL) faculty members that reviews, approves, and champions community collections to be added to the Virginia Tech Digital Library. The challenge GSDC aims to address is the gap between well-resourced institutions and smaller cultural heritage organizations by providing community-tailored assistance in processing and describing collections, digitization and consultation, and depositing material into an access and preservation repository. This roundtable will consist of two GSDC members representing both a community organization and VTUL to discuss the relationship-building process, successes and challenges, and sharing the community-driven model of GSDC.
Dancing with Donors: Trust-Building Across Gaps of Curation Priorities
Munshower, Alan; Kinnaman, Alex (PubPub, 2024-09-16)
Virginia Tech University Libraries (VTUL) serves a range of cultural heritage, academic, and local communities aligned in the goal to “get stuff online and accessible.” Despite the same overarching goal, the specific requirements from each party to reach that goal do not always overlap. The initial dance of negotiation between library and donor collaborations sets the tone for the ongoing relationship between the two. Across the departments in VTUL that manage such relationships with donors and curate digital collections, there are common trends emerging in barriers and observations with building relationships, and also with the concessions, compromises, and adjustments made to meet the curation needs of both parties. There are noted gaps in priorities and knowledge of curation processes, expectations around the understanding of digital collections, communication and roles and responsibilities, and resource understandability and availability. This paper specifically addresses relationships with donors and that impact on the subsequent work resulting from agreement with both parties. Continuing the iPRES conversation around community archiving and successful collaborations, the authors of this paper look critically at their partnerships with donors of digital material. This paper aligns with the conference theme “Start 2 preserve” in that it both addresses the barriers to entering the digital preservation landscape for the non-librarian community, and the barriers of digital preservation practitioners in aligning collaborator needs with digital curation needs. The authors focus on spotlighting the learning curve present on both sides of the work of community archiving. In recognizing recurrent gaps in understanding, this paper aims to be a part of a larger conversation on how community partnerships can blossom with built trust and understanding, coupled with robust planning and technical capability.
Creation of an Incentivized Course for Managing Your Online Scholarly Identity
Miles, Rachel A.; Mazure, Emily S. (2024-11)
Librarians at a large research-intensive university in southwest Virginia in the United States developed an online asynchronous course on how researchers can manage their online scholarly identity. It explains the importance of understanding and efficiently using scholarly identifiers and profile systems and also guides participants through the process of creating and maintaining scholarly profiles and identifiers, with a goal to have participants complete specific activities. To encourage completion of those activities the course was designed with specific incentives; for example, credits earned from the course can be used by faculty to complete the university’s computer-refresh program, which enables them to acquire a new computer after a four-year period. The content was developed in the institutional professional development Canvas platform and was thus available internally to faculty and graduate students. Participants can self-select which modules to complete. Additionally, participants can submit proof and receive credit for completing specific tasks like registering for ORCID, linking IDs across profile systems (e.g., Scopus, Google Scholar Profile, Elements profile, etc.), completing profile details like education, academic positions, scholarly works, and so on. This course is intended as a pilot that we expect to expand upon. The future goals of the course will be to cover two additional strategies for boosting online scholarly visibility: increasing discoverability and openness of scholarship and promoting work through social media and other online channels.
Prompting Best Practices: How Are Libraries or Their Home Institutions Creating, Sharing, Applying, and Adapting GenAI Policies?
Pannabecker, Virginia (2024-06-11)
Join me for this 45-minute discussion-based review of institutional policies created by libraries or their larger institutions on the use of Gen AI in teaching, learning, and research. During the first 15 minutes, I will share a selection of policies from 5-10 institutions, highlighting examples of commonalities and key differences, including how each policy addresses ethical aspects of using AI in the institution's context. The second 15 minutes will be breakout small group discussions of the example policies, policies participants are aware of or use at their own institutions or at institutions they’re curious about; and each group will have an online space to jot down notes and add links to policies or resources they discuss. The last 15 minutes will include a 1-2 minute report back from each group about useful aspects they found in the example policies or other policies discussed in their group, questions or concerns about policies discussed, examples of applying such policies at their institutions, examples of how to stay up to date with changes in Gen AI usage and make nimble adjustments to policies, or recommendations and comments for Gen AI policies going forward. We’ll conclude with a wrap up and links to the shared discussion documents for reference.

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