Raising the visibility of protected data: A pilot data catalog project

Sharing research data that is protected for legal, regulatory, or contractual reasons can be challenging and current mechanisms for doing so may act as barriers to researchers and discourage data sharing. Additionally, the infrastructure commonly used for open data repositories does not easily support responsible sharing of protected data. This chapter presents a case study of an academic university library’s work to configure the existing institutional data repository to function as a data catalog. By engaging in this project, university librarians strive to enhance visibility and access to protected datasets produced at the institution and cultivate a data sharing culture

Introducing First Year Medical Students to Personalized Medicine Concepts in a Small Group Activity

Presented as a Poster Presentation at 2020 IUSM Education Day.An individuals’ genetic profile is becomingly an increasingly important parameter in healthcare decisions. This small group activity was developed to introduce first year medical students in the Molecules to Cells and Tissues course to the concept and significance of Pharmacogenomics and personalized medicine. Additionally, this activity provided students with an opportunity to work with a large dataset and use the information to impact clinical decision making. This activity has two cases, takes student groups approximately 2 hours to complete, and requires internet access. Case materials are available through the learning management system Canvas, and include open-ended questions to guide students through the cases. In these cases students explore the functional significance of different alleles of a panel of cytochrome P450 genes. The group activity has the students examine a large data set of cytochrome P450 genes and cognate alleles to determine their prevalence in the local population and calculate the individuals’ gene scores. The students are then asked to explain the impact of the genotype (or gene score) on the resulting patient phenotype (i.e. the functional significance of the genotype). The first case involves a breast cancer survivor support group in which patients taking Taxol discuss lack of adequate pain relief from opioids and the potential impact of concomitant use of natural compounds/supplements on drug metabolism. The second case involves a patient presenting with recurrent stroke-like symptoms despite being on the anticoagulant medication clopidogrel. The patient is initially suspected to be non-compliant, but is later determined to be a poor metabolizer of the anticoagulant clopidogrelto its active form thus decreasing its efficacy. The expertise of the IUSM Medical Genetics research faculty was leveraged to provide a large data set of cytochrome P450 genes and cognate alleles. The selection of cytochrome P450 was based upon delivering content focused on the biochemistry of the enzyme system and provided an opportunity to highlight the drug interaction database available through IUSM Clinical Pharmacology (The FlockhartTable™ ; https://drug-interactions.medicine.iu.edu/). The addition of natural compounds was to draw students’ attention to the Natural Medicines database, which is the recommended source for evidence-based data on complementary and alternative medicine. Natural Medicines is available through the Ruth Lilly Medical Library and can be searched by substance or condition. It provides both a summary of the literature available on substances as well as the level of evidence or quality of studies done on the substance

Kick starting use of electronic lab notebooks at IU School of Medicine

Presented at 2020 Medical Library Association Virtual Conference

Using an Electronic Lab Notebook System to Promote Data Management Plans

Presented at the 2019 Medical Library Association Annual Conference.Background: At an academic medical center, the rollout of an electronic lab notebook (ELN) system includes tailored support to develop functional data management plans for participating research labs. The office of research is sponsoring the adoption of the ELN and, while administrative drivers include improving lab efficiency and reducing institutional liability, the pilot primarily focuses on the benefits of ELN use. In particular, improving the collection of and access to experimental information for research projects. The creation of data management plans, in conjunction with the ELN adoption, allows participants to engage more holistically with the research processes of their laboratories. Description: Nine research labs are identified as “early adopters” for the 4-month pilot of the selected electronic lab notebook system. As participants in the pilot, these labs are expected to a) attend training on the ELN system and b) evaluate their current information and data management practices. To ensure these expectations are met, the institution's ELN implementation team meets with each lab prior to conducting the ELN training to discuss how they manage (i.e., organize, store, and share) research data. These consults result in a draft data management plan that reflect the labs’ current research data management processes and provides suggestions for potential areas of improvement/streamlining. The training on the functionality of the ELN follows this to encourage participating labs to develop concrete strategies for integrating the ELN into the research data/information management processes of the lab overall. Conclusion: As of this submission, the authors have worked directly with four of the “early adopter” labs (each with 6-10 members) to review their information and data management practices while onboarding them to the ELN. These labs receive an individualized data management plan in addition to training on the ELN. A primary outcome is to complete this process with the remaining five “early adopter” labs while gathering feedback on the ELN system itself and monitoring the adoption success of the ELN in these labs. A secondary outcome is to “scale up” this program for full rollout to the institution in 2019

Pilot implementation of a leadership framework in the National Library of Medicine Associate Fellowship Program

The National Library of Medicine Associate Fellowship Program is a nearly fifty year-old fellowship program for recent library science graduates interested in developing a leadership role in health sciences libraries. The program has used a number of informal methods of leadership development including the use of behavioral assessments, mentoring, and meeting with senior leadership. In 2015, the Associate Fellowship Program Coordinator introduced the “Five Practices of Exemplary Leaders” leadership model developed by Kouzes and Posner (2007) and began a pilot program of a series of leadership exercises to formally reinforce the leadership development aspect of the program. The model was selected after reviewing a number of leadership models because of its clarity, and the presumed adaptability of the practices to professionals early in their careers. The model uses the practices: Model the Way, Inspire a Shared Vision, Challenge the Process, Enable Others to Act, and Encourage the Heart. The program used the participating cohort members to explore the effectiveness of the leadership exercises and to shape the program going forward. The leadership framework and exercises were successfully revised based on comments from the cohort

Increasing Visibility of Research in IUPUI ScholarWorks through NCBI LinkOut

Background : To increase the visibility and access to an academic university’s institutional repository content by participating in the National Center for Biotechnology Information (NCBI) “Institutional Repository LinkOut” program. Description : The authors used R, an open source programming language, and an R package called ‘rentrez’ to a) identify those articles in the university's repository that were in PubMed and b) determine of those, which ones did not already have full-text available via PubMed Central. Identifying articles in PubMed that are not in PubMed Central is required by NCBI in order to participate in the “Institutional Repository LinkOut” program. Using the R package, a set of 4,400 open access items from the repository were processed, 557 eligible records were identified, and were sent to NCBI. In June 2018, the R scripts were revised to further streamline the process--at the beginning of July 2018 a total of 2,129 repository items were processed and 434 eligible records were identified for inclusion in the LinkOut program. Conclusion : The university’s institutional repository experienced a significant increase in visibility due to its participation in the NCBI’s “Institutional Repository LinkOut” program. In its first implementation (July 2017), this automated solution was estimated to save over 30 hours of manual work on the part of the library staff. The LinkOut program has resulted in a 9% annual increase in web traffic to the repository and PubMed is now the third most frequent referral site to the repository. The R script and implementation process are publicly available, via GitHub, to help other institutions reduce the barriers for participating in the LinkOut program

Building a community of practice: Situating data management in the transition to electronic lab notebooks

This poster will describe an information management initiative sponsored by the School of Medicine Research Administration. The 4-month pilot involved the rollout of an electronic lab notebook (ELN) system alongside tailored support for developing operational data management plans. Administrative drivers included improving lab efficiency and reducing institutional liability. The pilot primarily focused on the benefits of ELN use and formalizing data management practices. A key goal was to improve the collection of and access to experimental information and improve information management workflows. Integrating data management plan support as part of the ELN pilot contextualizes how the ELN fits into, and can potentially improve, existing lab workflows and highlights the unique information management needs of each research lab

Comparing the Effects of Two Tillage Operations on Beneficial Epigeal Arthropod Communities and Their Associated Ecosystem Services in Sugar Beets

Beneficial arthropods provide important ecosystem services in terms of arthropod pest and weed management, but these services can be adversely affected by farming practices such as tillage. This study investigated the impact of two tillage operations (zone tillage and moldboard plow) on the activity density of several beneficial, epigeal arthropod taxa, and postdispersal weed seed and prey removal in sugar beet agroecosystems. In addition, four omnivorous ground beetle species were selected for a weed-seed choice feeding assay, whereas a single species was selected for a weed-seed age preference assay. Ground beetles were the most commonly collected taxon (via pitfall sampling), with only a few dominant species. Tillage operation did not affect ground beetle activity density; however, spider, centipede, and rove beetle activity densities were higher in the reduced-tillage treatment. Live prey consumption was similar between tillage practices, with more prey consumed during nocturnal hours. More weed seeds were consumed in the reduced-tillage treatment, whereas weed-seed preference differed between the four weed species tested [Setaria pumila (Poir.) Roem. & Schult., Echinochloa crus-galli (L.), Kochia scoparia (L.), and Chenopodium album (L.)]. In the weed-seed choice feeding assay, significantly more broad-leaf weed seeds (C. album and K. scoparia) were consumed compared with grassy weed seeds (E. crus-galli and S. pumila). No preference for seed age was detected for E. crus-galli, but Harpalus pensylvanicus (De Geer) preferred old C. album seeds over fresh seeds. Zone tillage is compatible with ecosystem services, providing critical habitat within agricultural ecosystems needed to conserve beneficial, edaphic arthropods

Comparing the Effects of Two Tillage Operations on Beneficial Epigeal Arthropod Communities and Their Associated Ecosystem Services in Sugar Beets

Published ArticleBeneficial arthropods provide important ecosystem services in terms of arthropod pest and weed management, but these services can be adversely affected by farming practices such as tillage. This study investigated the impact of two tillage operations (zone tillage and moldboard plow) on the activity density of several beneficial, epigeal arthropod taxa, and postdispersal weed seed and prey removal in sugar beet agroecosystems. In addition, four omnivorous ground beetle species were selected for a weed-seed choice feeding assay, whereas a single species was selected for a weed-seed age preference assay. Ground beetles were the most commonly collected taxon (via pitfall sampling), with only a few dominant species. Tillage operation did not affect ground beetle activity density; however, spider, centipede, and rove beetle activity densities were higher in the reduced-tillage treatment. Live prey consumption was similar between tillage practices, with more prey consumed during nocturnal hours. More weed seeds were consumed in the reduced-tillage treatment, whereas weed-seed preference differed between the four weed species tested [Setaria pumila (Poir.) Roem. & Schult., Echinochloa crus-galli (L.), Kochia scoparia (L.), and Chenopodium album (L.)]. In the weed-seed choice feeding assay, significantly more broad-leaf weed seeds (C. album and K. scoparia) were consumed compared with grassy weed seeds (E. crus-galli and S. pumila). No preference for seed age was detected for E. crus-galli, but Harpalus pensylvanicus (De Geer) preferred old C. album seeds over fresh seeds. Zone tillage is compatible with ecosystem services, providing critical habitat within agricultural ecosystems needed to conserve beneficial, edaphic arthropods

Comparison of Commercial and Self-Initiated Weight Loss Programs in People With Prediabetes: A Randomized Control Trial

To determine if a widely available weight-management program (Weight Watchers) could achieve sufficient weight loss in persons with prediabetes compared with a Diabetes Prevention Program-based individual counseling program supported by National Diabetes Education Program materials. METHODS: We conducted an individual, randomized intervention trial in Indianapolis, Indiana, in 2013 to 2014, in 225 persons with prediabetes. We compared the Weight Watchers weight-management program (n = 112) with Your Game Plan to Prevent Type 2 Diabetes, a program developed by the National Diabetes Education Program. Outcomes were weight and metabolic markers measured at baseline, 6 months, and 12 months. RESULTS: Intervention participants lost significantly more weight than controls at 6 months (5.5% vs 0.8%) and 12 months (5.5% vs 0.2%; both P < .001). The intervention group also had significantly greater improvements in hemoglobin A1c and high-density lipoprotein cholesterol level than did controls. CONCLUSIONS: A large weight-management program is effective for achieving lifestyle changes associated with diabetes prevention. Such programs could significantly increase the availability of diabetes prevention programs worldwide making an immediate and significant public health impact