Research and Informatics Division, University Libraries

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(Initial) Assessment of Research Data Services Through Client Interaction Records
Petters, Jonathan L. (Virginia Tech, 2022-04-12)
In this presentation we provide an internal assessment of consulting reach and effectiveness for our Data Services provided by the University Libraries at Virginia Tech and using client records from 2016 to 2020. Through this assessment, we explore how service growth and reach across Virginia Tech has evolved with time. We also look more closely at these aspects for one college and discuss how we will use this data to assess the impact of our services. Finally, through the lens of client outcomes, we examine the trends of client interactions over the term of the study.
A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation
Kang, Lin; He, Guijuan; Sharp, Amanda K.; Wang, Xiaofeng; Brown, Anne M.; Michalak, Pawel; Weger-Lucarelli, James (Virginia Tech, 2021-03-05)
While SARS-CoV-2 likely has animal origins, the viral genetic changes necessary to adapt this animal-derived ancestral virus to humans are largely unknown, mostly due to low levels of sequence polymorphism and the notorious difficulties in experimental manipulations of coronavirus genomes. We scanned more than 182,000 SARS-CoV-2 genomes for selective sweep signatures and found that a distinct footprint of positive selection is located around a non-synonymous change (A1114G; T372A) within the Receptor-Binding Domain of the Spike protein, which likely played a critical role in overcoming species barriers and accomplishing interspecies transmission from animals to humans. Structural analysis indicated that the substitution of threonine with an alanine in SARS-CoV-2 concomitantly removes a predicted glycosylation site at N370, resulting in more favorable binding predictions to human ACE2, the cellular receptor. Using a novel bacteria-free cloning system for manipulating RNA virus genomes, we experimentally validated that this SARS-CoV-2-unique substitution significantly increases replication in human cells relative to its putative ancestral variant. Notably, this mutation’s impact on virus replication in human cells was much greater than that of the Spike D614G mutant, which has been widely reported to have been selected for during human-to-human transmission.
Data Curation and Metadata Completeness - An Institutional Repository Perspective
Petters, Jonathan L. (2021-07-07)
Presentation on how Data Management and Curation Services in the Virginia Tech University Libraries works to improve the quality of published research datasets through its curation actions.
Introduction to Fair Use for Extension Master Gardeners
Haugen, Inga (Virginia Tech, 2021-02-24)
This presentation will discuss Fair Use. This was presented to Extension Master Gardeners but may be useful for others as well. The Fair Use LibGuide was used as well as the ala.org website
Introduction to Copyright for Extension Master Gardeners
Haugen, Inga (Virginia Tech, 2021-02-24)
This presentation will discuss Copyright. This was an introduction module made for Extension Master Gardeners but may be useful for others.
Introduction to Publicly Available Resources for Extension Master Gardeners
Haugen, Inga (Virginia Tech, 2021-02-24)
This presentation will discuss Publicly Available Resources. This was presented to Extension Master Gardeners but can be useful for others as well. This video will go through the Publicly Assessible Resources LibGuide and VTechWorks.
Introduction to Creative Commons for Extension Master Gardeners
Haugen, Inga (Virginia Tech, 2021-02-24)
This presentaion will discuss Creative Commons. This was a overview for the Extension Master Gardeners but may be useful for others.
Report: Public Access to Research Data at Virginia Tech
Ogier, Andrea; Petters, Jonathan L.; Pannabecker, Virginia; Public Access to Research Data Committee (University Libraries, Virginia Tech) (2019-11-07)
Recent reports and recommendations from AAU/APLU and National Academies of Science charge public universities, especially those with a land grant mission, to provide needed infrastructure and guidance that will enable researchers to more easily share the data supporting their research. In brief, the AAU/APLU Public Access Working Group states: “In light of governmental mandates and the scientific benefits of making data accessible to the public, universities will need to adopt new institutional policies, procedures, and approaches that actively support and promote research data sharing, while at the same time ensuring rigor in the research process and the veracity of its intellectual outputs.” Virginia Tech has resources to support public access to research data in the Office of Vice President of Research and Innovation, University Libraries, and Division of Information Technology; however, there are gaps in communication, policy, training, and implementation that make data sharing difficult and confusing for busy researchers. In response to a few of these identified gaps, the Public Access to Data Committee makes the following recommendations:

Policy 130015 should be revised to provide more pertinent information to researchers on how and where to obtain support for both restricting access to data and/or publicly sharing data,

The University Libraries should work with the Office of Sponsored Programs to create guidance for PIs who are working on grant applications and processes for ensuring that Data Management Plans are updated and followed over the lifetime of the grant,

The University Libraries, Division of IT, and Research Compliance Office should work together to create guidance helping researchers know when they can and should publicly share their data, and when they can and should keep the data secure.
Ultimately, we recommend the creation of a standing Data Security and Sharing Committee reporting to the Commission on Research to consider, create, and maintain this guidance to better support researchers at Virginia Tech.
Image Copyright and Fair Use
Haugen, Inga (Virginia Tech, 2020-06-12)
Open Educational Resources for Faculty Senate at Virginia Tech
Walz, Anita R. (2019-09-29)
[Invited] presentation to Faculty Senate. The presentation introduced Faculty Senators and guests to open educational resources (including local examples), Creative Commons licenses, and a draft version of the Guidelines for Open Educational Resources.
Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications
Hilu, Khidir W.; Friend, Sheena A.; Vallanadu, Viruthika; Brown, Anne M.; Hollingsworth, Louis R. IV (PLOS, 2019-11-01)
Food allergies are severe immune responses to plant and animal products mediated by immunoglobulin E (IgE). Peanuts (Arachis hypogaea L.) are among the top 15 crops that feed the world. However, peanuts is among the “big eight food allergens”, and allergies induced by peanuts are a significant public health problem and a life-threatening concern. Targeted mutation studies in peanuts demonstrate that single residue alterations in these allergen proteins could result in substantial reduction in allergenicity. Knowledge of peanut allergen proteins is confined to the allotetraploid crop and its two progenitors. We explored frequencies and positions of natural mutations in the hyperallergenic homologues Ara h 2 and Ara h 6 in newly generated sequences for 24 Arachis wild species and the crop species, assessed potential mutational impact on allergenicity using immunoblots and structural modeling, and evaluated whether these mutations follow evolutionary trends. We uncovered a wealth of natural mutations, both substitutions and gaps, including the elimination of immunodominant epitopes in some species. These molecular alterations appear to be associated with substantial reductions in allergenicity. The study demonstrated that Ara h 2 and Ara h 6 follow contrasting modes of natural selection and opposing mutational patterns, particularly in epitope regions. Phylogenetic analysis revealed a progressive trend towards immunodominant epitope evolution in Ara h 2. The findings provide valuable insight into the interactions among mutations, protein structure and immune system response, thus presenting a valuable platform for future manipulation of allergens to minimize, treat or eliminate allergenicity. The study strongly encourages exploration of genepools of economically important plants in allergenicity research.
Auditing an Institutional Data Repository With Respect to the CoreTrustSeal Certification Requirements
Petters, Jonathan L.; Pisharoti, Naina (2019-10-25)
J. Petters presented how Curation Services in Virginia Tech University Libraries used the CoreTrustSeal repository certification requirements to conduct a self audit of their institutional data repository VTechData. This presentation highlighted some of the issues faced by galleries, libraries, archives, and museums (GLAMs) in undergoing certification.
DESIGN THINKING for Visualizing Acid-Base Chemistry - Documenting a user-centered approach for designing and developing an ADA compliant online tool for visualizing acid-base chemistry
Stamper, Michael J.; Briganti, Jonathan; Brown, Anne M.; Dietrich, Andrea M.; Godrej, Adil N.; Schreiber, Madeline E.; Walz, Anita R. (2019-07-17)
This project created an online tool, that we call “The pkAnalyzer”. It enables the exploration of acid-conjugate base distributions in an easy to use Web interface. This project is also an example of the disciplines of Arts and Design into the STEM sciences, i.e. STEM to STEAM, and University Libraries commitment to faculty, students, and staff throughout the Virginia Tech system, in the areas of data visualization and design services to aid in the research process and communication of results. Beyond the functionality of the tool, this project involved the planning and designing a custom, modifiable, and attractive user interface (UI) and visualization that are "user-friendly", and incorporate the World Wide Web Consortium’s Web Content Accessibility Guidelines (WCAG), and falls with the Federal Governement’s Section 508 guidelines pertaining to creating and maintaining information and communications technology (ICT) that is accessible to people with disabilities relating to vision. Using a "Design Thinking" approach, all aspects of the design of this tool – User Interface (UI), User Experience (UX), Interaction Design (IxD), Graphic – were taken into account, and developed to enhance the user's experience using the tool, and undertanding of a complex chemical concept that is widely used in the basic and applied sciences and engineering.
Geospatial Data Services in the University Libraries: Recommendations for Development
Coleman, R. Shane; Brooks, Edwin L.; Petters, Jonathan L. (2019-06)
For many years University Libraries Geospatial Services has provided support for researchers and instructors in finding and providing access to geospatial data. More recently University Libraries Geospatial Services has also provided other forms of research and instructional support, including geospatial application-centered support. This past fiscal year we in the University Libraries Geospatial Services worked to develop a plan for further development for the near future, including recommendations to the University Libraries for resource and staffing needs.
The Impact of Targeted Data Management Training for Field Research Projects - A Case Study
Petters, Jonathan L.; Brooks, George C.; Smith, Jennifer A.; Haas, Carola A. (2019-05-21)
We present a joint effort at Virginia Tech between a research group in the Department of Fish and Wildlife Conservation and Data Services in the University Libraries to improve data management for long-term ecological field research projects in the Florida Panhandle. Consultative research data management support from Data Services in the University Libraries played an integral role in development of the training curriculum. Emphasizing the importance of data quality to the field workers at the beginning of this training curriculum was a vital part of its success. Also critical for success was the research group’s investment of time and effort to work with field workers and improve data management systems. We compare this case study to three others in the literature to compare and contrast data management processes and procedures. This case study serves as one example of how targeted training and efforts in data and project management for a research project can lead to substantial improvements in research data quality.
Eglin AFB Field Projects Data Management Training Curriculum
Petters, Jonathan L.; Haas, Carola A.; Brooks, George C.; Smith, Jennifer (2017-09-15)
A one-and-a-half day customized data management training curriculum for wildlife conservation research. includes material to help motivate the importance of research data management, selected modules and parts of modules from the DataONE educational modules, and a proposed framework for more formal data management principles, roles and responsibilities within a research group.
An Assessment of VTechData with respect to the CoreTrustSeal Repository Certification Requirements
Pisharoti, Naina; Petters, Jonathan L. (2019-02)
This report provides a brief internal assessment as to how well the current status of VTechData (“The Repository) meets the CoreTrustSeal repository certification requirements. VTechData has seen substantial development and improvements from when the first dataset was published in May of 2016 to the present day. However, this internal assessment shows that VTechData does not yet meet the CoreTrustSeal certification requirements.
Welcome to Overleaf: A Brief Overview of Opportunities
Browder, Robert; Cross, Carrie (Virginia Tech, 2018-11-07)
This presentation is an introduction to Overleaf at Virginia Tech, including a brief history of the program, features and benefits, and a list of resources.
Developing Library Strategy for 3D and Virtual Reality Collection Development and Reuse: An IMLS National Digital Platform Project
Hall, Nathan; Hardesty, Juliet; Cook, Robert; McDonald, Robert H.; Lischer Katz, Zack; Wittenbert, Jaime; Carlisle, Tara; Johnson, Jennifer; Griffin, Julie; Xie, Zhiwu; Ogier, Andrea (2018)
These are the preliminary and full proposals for an IMLS grant to develop a white paper (to be added here in late 2018) to host three national forums of invited experts to support library adoption of 3D and virtual reality (VR) services. The forums were hosted by Virginia Tech University Libraries, Indiana University Libraries, and the University of Oklahoma Libraries. Each forum covered a different 3D and VR theme: content creation and publishing, visualization and analysis, and repository practice and standards. Lower costs and greater computational power have made 3D and VR technologies financially realistic for a broad variety of institutions. Many academic libraries have developed archives for other forms of research data, but there is an absence of standards and best practices for producing, managing, and preserving 3D and VR content. This gap is an information management problem suited to the strengths of libraries and can benefit librarians and researchers alike across institutions.
What Is Open Access?
Young, Philip (Virginia Tech. University Libraries, 2018-03-29)
This presentation is an introduction to open access, including a definition, the need for access, two ways to make research OA, advantages of OA and evidence of its increased impact. The presentation also covers online hosts where articles can be posted, and services to support OA offered by the VT Libraries. This recording was made during the graduate seminar series in Crop and Soil Environmental Sciences.

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