Ready, Set, Network! Research Speed Networking for Clinicians, Scientists and Engineers

Objectives: A 2013 Institute of Medicine report urged researchers to “engage in additional substantive and productive collaborations” to address important clinical/translational science questions. To encourage team science among our researchers, Tompkins-McCaw Library for the Health Sciences and Center for Clinical and Translational Research hosted a speed networking event, specifically targeting engineers, clinicians, and basic scientists; an analysis of the event is below. Methods: Invitations were distributed to clinicians, engineers, and basic scientists. To maximize interactions without increasing time spent at the event, researchers were divided into three groups. The event was planned such that each group would meet everyone from the other two groups; researchers were placed into appropriate groups according to their interests. Seated at tables of three, attendees introduced themselves and discussed their research interests for three minutes; then they rotated according to their group’s instructions. Lunch was provided afterwards to give attendees an opportunity to follow up with potential collaborators. Results: Twenty-one faculty researchers attended the speed networking event, which took about 30 minutes, excluding lunch. Using a 5-point Likert scale, all participants selected “strongly agree” or “agree” to respond to questions about whether the event was a valuable use of their time. Also, 53% of attendees “strongly” agreed with the statement “I met a potential collaborator” at the event. Discussion: Subjective evaluations show that researchers see speed networking as an effective way to meet potential collaborators. Objective data including sustained research partnerships and collaborative grant and publication submissions will be tracked

Higher rank numerical ranges of normal matrices

The higher rank numerical range is closely connected to the construction of quantum error correction code for a noisy quantum channel. It is known that if a normal matrix $A \in M_n$ has eigenvalues $a_1, \..., a_n$, then its higher rank numerical range $\Lambda_k(A)$ is the intersection of convex polygons with vertices $a_{j_1}, \..., a_{j_{n-k+1}}$, where $1 \le j_1 < \... < j_{n-k+1} \le n$. In this paper, it is shown that the higher rank numerical range of a normal matrix with $m$ distinct eigenvalues can be written as the intersection of no more than $\max\{m,4\}$ closed half planes. In addition, given a convex polygon ${\mathcal P}$ a construction is given for a normal matrix $A \in M_n$ with minimum $n$ such that $\Lambda_k(A) = {\mathcal P}$. In particular, if ${\mathcal P}$ has $p$ vertices, with $p \ge 3$, there is a normal matrix $A \in M_n$ with $n \le \max\left\{p+k-1, 2k+2 \right\}$ such that $\Lambda_k(A) = {\mathcal P}$.Comment: 12 pages, 9 figures, to appear in SIAM Journal on Matrix Analysis and Application

Short Courses: Flexible Learning Opportunities in Informatics

In today’s fast-paced, data-driven world, researchers need to have a good foundation in informatics to store, organize, process, and analyze growing amounts of data. However, not all degree programs offer such training. Obtaining training in informatics on your own can be a daunting task for both new and established researchers who have little informatics experience. Providing educational opportunities appropriate for various skill levels and that mesh with a full-time schedule can remove barriers and foster a collaborative, informatics-savvy community that is better equipped to push science forward. To enhance informatics education in bioinformatics, VCUs Wright Center for Clinical and Translational Research of- fers a complementary series of seminars and workshops. These short course offerings introduce attendees to bioinformatics concepts and applications, and provide hands-on experience using online Bioinformatics databases. Bioinformatics 101 (B101) is an 8-week long series of 1-hour seminars focused on introducing topics in bioinformatics related to Next Generation Sequencing (NGS). Lectures are application focused and include overviews of NGS technology, practical bioinformatics pipelines, and examples of how the technology can influence downstream bioinformatics analyses. Bioinformatics 102 (B102) is a 5-day, 2 hours per day workshop developed in collaboration with VCU Libraries that provides attendees with hands-on experience accessing and using public data repositories. Sessions include a brief lecture followed by hands-on exercises. A Certificate of Completion is awarded upon meeting certain criteria for either the 101 or 102 courses. Bioinformatics 101 has been offered 3 times with a combined total of 246 registrants, and Bioinformatics 102 has been offered twice with a total of 78 registrants (limited to 30 per session per day). From course surveys, 82% (n=108) and 95% (n=47) of respondents gave B101 and B102 a positive rating, respectively. In addition, 89% of B101 respondents indicated their knowledge was improved, with 100% of B102 respondents indicating the same. A total of 84 and 33 certificates have been awarded for B101 and B102, respectively. The Bioinformatics 101 and 102 courses have become highly anticipated across the university, and have gained the external attention of surrounding businesses and colleges. Registrants have diverse backgrounds including biological, clinical, computational, administrative, librarian, business, and others with a total of 77 departments across VCU and VCU Health represented. Due to this interest, Bioinformatics 101 began offering live online attendance to accommodate those who were unable to travel across campus, or who are attending from outside VCU. This past year, 50% of attendance was online indicating a growing need for flexible education opportunities in informatics. Increasing researcher knowledge of Bioinformatics along with awareness of university resources for informatics support fosters an informatics-savvy research community that is empowered to take advantage of existing and new data sources in the pursuit of new insights and scientific discoveries for the betterment of human health. Future work will include the development of a more comprehensive educational framework by creating new and flexible learning opportunities that will make informatics education easy and convenient for our dedicated researchers

Health Sciences Collection Development: An Overview of Fundamental Knowledge and Practices (2nd Edition)

This Open Access work from the Medical Library Association Collection Development Caucus provides an overview of the responsibilities and tasks involved in the development and management of health sciences collections. Readers can explore topics in greater detail through references at the end of each chapter. You can access the most up-to-date version of this work at https://doi.org/10.21974/1tsq-na6

Re-evaluation of the surface ruptures of the November 1951 earthquake series in eastern Taiwan, and its neotectonic implications

The earthquakes of November 1951 constitute the most destructive seismic episode in the recorded history of the Longitudinal Valley, eastern Taiwan. However, information about their source parameters is sparse. To understand the relationship between the 1951 ruptures and new interpretations of the regional neotectonic architecture of the Longitudinal Valley, we re-evaluated the November 1951 ruptures by analyzing old documents, reports and photographs, and by interviewing local residents who experienced the earthquake. As a result, we have revised significantly the rupture map previously published. We divide the surface ruptures from south to north into the Chihshang, Yuli, and Rueisuei sections. The first shock of the 1951 series probably resulted from the Chihshang rupture, and the second shock probably resulted from the Yuli and Rueisuei ruptures. The lengths of these ruptures indicate that the two shocks had similar magnitudes. The Chihshang and Rueisuei ruptures are along segments of the Longitudinal Valley fault, a left-lateral oblique fault along which the Coastal Range thrusts westward over the Longitudinal Valley. The Yuli rupture, on the other hand, appears to be part of a separate, left-lateral strike-slip Yuli fault, which traverses the middle of the Longitudinal Valley. The complex behavior of these structures and interaction between them are important in understanding the future seismic hazard of the area

Millennial slip rate of the Longitudinal Valley fault from river terraces: Implications for convergence across the active suture of eastern Taiwan

The Longitudinal Valley fault is a key element in the active tectonics of Taiwan. It is the principal structure accommodating convergence across one of the two active sutures of the Taiwan orogeny. To understand more precisely its role in the suturing process, we analyzed fluvial terraces along the Hsiukuluan River, which cuts across the Coastal Range in eastern Taiwan in the fault's hanging wall block. This allowed us to determine both its subsurface geometry and its long-term slip rate. The uplift pattern of the terraces is consistent with a fault-bend fold model. Our analysis yields a listric geometry, with dips decreasing downdip from about 50° to about 30° in the shallowest 2.5 km. The Holocene rate of dip slip of the fault is about 22.7 mm/yr. This rate is less than the 40 mm/yr rate of shortening across the Longitudinal Valley derived from GPS measurements. The discrepancy may reflect an actual difference in millennial and decadal rates of convergence. An alternative explanation is that the discrepancy is accommodated by a combination of slip on the Central Range fault and subsidence of the Longitudinal Valley floor. The shallow, listric geometry of the Longitudinal Valley fault at the Hsiukuluan River valley differs markedly from the deep listric geometry illuminated by earthquake hypocenters near Chihshang, 45 km to the south. We hypothesize that this fundamental along-strike difference in geometry of the fault is a manifestation of the northward maturation of the suturing of the Luzon volcanic arc to the Central Range continental sliver

Phenotypic indicators to identify methionine rich European grain legumes and the correlation of grain methionine contents with the sulphur supply

Home grown legumes are a valuable protein source for pure on-farm diets for livestock in organic farming. Whereas protein of Glycine max naturally has higher contents of methionine nand also lysine typical European grain legumes (Pisum sativum L., Vicia faba L., Lupinus angustifolius L.) used in organic farms as component of animal food are relatively low in those amino acids

Providing Hands-on Training with Bioinformatics Databases: A Collaboration Between VCU Libraries & Wright Center for Clinical and Translational Research

BackgroundWith the goal of increasing specialized services for researchers, Virginia Commonwealth University (VCU) Libraries sent its basic science librarians to an intensive training on bioinformatics databases, “A Librarian’s Guide to NCBI.” VCU’s Wright Center for Clinical and Translational Research (Wright CCTR) was expanding the educational component of its bioinformatics support around the same time. This year, the librarians partnered with the Wright CCTR to offer an introductory bioinformatics database workshop introducing researchers to genetic/genomic databases. MethodsFor one week in June, sessions were conducted introducing up to 30 faculty and staff to The Cancer Genome Atlas and NCBI’s Gene, BLAST, Variation Viewer and Gene Expression Omnibus. Librarians taught resources they learned in the NCBI training, and Wright CCTR staff taught resources they use often. Each day’s 1.5 hour session included presentations, demonstrations, and hands-on assignment time. Certificates were awarded to participants who completed 4 out of 5 assignments. ResultsRegistration for the workshop was full in under a week with a waiting list. All survey respondents (n=27) evaluated the overall quality of the workshop as good or excellent and indicated that they would recommend the workshop to a colleague or student. ConclusionsThis successful partnership between VCU Libraries and the Wright CCTR allowed for a broader range of bioinformatics topics to be covered, in addition to easing the planning and teaching workload for each group. The strong interest in this series across a variety of disciplines from both VCU and VCU Health indicates a need for staff and faculty-oriented bioinformatics training within the university

FUBP3 interacts with FGF9 3′ microsatellite and positively regulates FGF9 translation

A TG microsatellite in the 3′-untranslated region (UTR) of FGF9 mRNA has previously been shown to modulate FGF9 expression. In the present study, we investigate the possible interacting protein that binds to FGF9 3′-UTR UG-repeat and study the mechanism underlying this protein–RNA interaction. We first applied RNA pull-down assays and LC-MS analysis to identify proteins associated with this repetitive sequence. Among the identified proteins, FUBP3 specifically bound to the synthetic (UG)15 oligoribonucleotide as shown by supershift in RNA-EMSA experiments. The endogenous FGF9 protein was upregulated in response to transient overexpression and downregulated after knockdown of FUBP3 in HEK293 cells. As the relative levels of FGF9 mRNA were similar in these two conditions, and the depletion of FUBP3 had no effect on the turn-over rate of FGF9 mRNA, these data suggested that FUBP3 regulates FGF9 expression at the post-transcriptional level. Further examination using ribosome complex pull-down assay showed overexpression of FUBP3 promotes FGF9 expression. In contrast, polyribosome-associated FGF9 mRNA decreased significantly in FUBP3-knockdown HEK293 cells. Finally, reporter assay suggested a synergistic effect of the (UG)-motif with FUBP3 to fine-tune the expression of FGF9. Altogether, results from this study showed the novel RNA-binding property of FUBP3 and the interaction between FUBP3 and FGF9 3′-UTR UG-repeat promoting FGF9 mRNA translation