Redefining our Territory: Reaching Pre-Matriculation Students With Case-Based, Online Instruction

Online educational tools have made it possible for our library to claim some educational territory that was previously unavailable to us, the pre-matriculation period. During the summer of 2015 we were able to add a two-part, case-based, online tutorial to our incoming medical students’ pre-matriculation materials. We created the story of Sarah Pilger, a hypothetical, obese, pregnant teenager whose pregnancy is complicated by a fetal toxoplasmosis. The case introduces the incoming students to almost all the resources they might want to use while enrolled at UNMC and also introduces students to the roles of the many healthcare professionals who are essential to the care of Sarah and her daughter Emily. Questions are posted throughout the Guide-on-the-Side tutorials and instant feedback is provided. Student response to the 2016 tutorial was overwhelmingly positive. We revised the tutorial for use during the summer of 2017, added pre- and post-tests, and will be able to present results of the tests at meeting time. Our dream is to one day have tutorials for each of UNMC’s colleges’ entering classes based on Sarah’s case, and to use these tutorials to foster inter-professional conversation and education. We have already worked with faculty in UNMC’s College of Allied Health Professions to create versions of the tutorial for clinical nutrition and ultrasonography students. The new tutorials are now used as the basis of an interprofessional learning experience in these programs’ obstetric units

The Prophage and Us - Shiga Toxin Phages revisited

The authors first met in 1998 at the University of Würzburg, Germany, at the Institute of Hygiene and Microbiology, in Helge Karch's lab, where Herbert Schmidt worked as a PostDoc and Maite Muniesa visited the lab for a postdoctoral research stay to work on phages encoding Shiga toxin 2e (Stx2e) [1]. Since that time, we have been more or less, as much as our university duties allow, connected by Stx-phage research. Initially described in the early 1980s, Shiga toxin-converting bacteriophages (Stx-phages) have been the subject of numerous publications [ 2,3 ]. The ability to produce Stx, the major pathogenicity factor of enterohemorrhagic E. coli (EHEC), seems to be essentially connected to the location of the Shiga toxin genes (stx) in the genome of lysogenic phages, found always in a similar location within the late transcribed region, and upstream of the lysis and capsid genes [4 - 11]. Stx-phages are double-stranded DNA tailed phages showing a lambdoid or a non-lambdoid genome structure. To the best of our knowledge, stx genes have never been found in other mobile genetic elements other than phages, such as plasmids or pathogenicity islands [12 - 16 ]. Although the genetics and function of Stx-phages have been described in many publications, some basic questions remain still open, for example, (1) why are Stx-phages so successful in terms of evolution and spread among E. coli strains? (2) why do Stx-phages occur mainly in enteropathogenic E. coli strains but not, or only accidentally, in others such as extraintestinal pathogenic E. coli (EXPEC), (3) which advantage do EHEC strains have from the lysogenic state carrying single or multiple Stx-phages

Elevating Librarian-Mediated Search Services: When 2nd Best Isn\u27t Good Enough

Objective: To optimize librarian-mediated search services, librarians must consider all aspects of their search service that affect service utilization and efficacy. The library literature provides little information concerning the format in which libraries are providing literature search results and even less on the effect of format on search service utilization.  At our academic health science library, the number of search requests received rose dramatically after we began providing results in RefShare format. RefShare is the collaboration tool available in ProQuest’s RefWorks®.  We wanted to know how other libraries were providing results and whether they had seen format affect search service utilization. Methods: A survey created using Springshare’s LibWizard® was distributed to the MEDLIB-L listserv, the expertsearching listserv, and through direct email to AAHSL reference and education librarians. The survey was sent out on March 31st, 2019 and closed on April 30th, 2019. We asked about the audience that the librarian/library served and requested basic information about the librarian-mediated search services offered -- with a special focus on formats used to send literature search results to the requester. Results and Conclusion: We have analyzed the survey results, and we share our findings here

Transformer-based end-to-end classification of variable-length volumetric data

The automatic classification of 3D medical data is memory-intensive. Also, variations in the number of slices between samples is common. Naive solutions such as subsampling can solve these problems, but at the cost of potentially eliminating relevant diagnosis information. Transformers have shown promising performance for sequential data analysis. However, their application for long-sequences is data, computationally, and memory demanding. In this paper, we propose an end-to-end Transformer-based framework that allows to classify volumetric data of variable length in an efficient fashion. Particularly, by randomizing the input slice-wise resolution during training, we enhance the capacity of the learnable positional embedding assigned to each volume slice. Consequently, the accumulated positional information in each positional embedding can be generalized to the neighbouring slices, even for high resolution volumes at the test time. By doing so, the model will be more robust to variable volume length and amenable to different computational budgets. We evaluated the proposed approach in retinal OCT volume classification and achieved 21.96% average improvement in balanced accuracy on a 9-class diagnostic task, compared to state-of-the-art video transformers. Our findings show that varying the slice-wise resolution of the input during training results in more informative volume representation as compared to training with fixed number of slices per volume. Our code is available at: https://github.com/marziehoghbaie/VLFAT

Gaps in affiliation indexing in Scopus and PubMed.

OBJECTIVE: The authors sought to determine whether unexpected gaps existed in Scopus\u27s author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. METHODS: First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. RESULTS: We found that Scopus\u27s records for approximately 7% of UNMC/NM authors\u27 publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals\u27 publishers were supplying incomplete author affiliation information to PubMed. CONCLUSIONS: Institutions relying on Scopus to track their impact should determine whether Scopus\u27s affiliation identifiers will, in fact, identify all articles published by their authors and investigators

Alpha Band Signatures of Social Synchrony

Previous research has reported changes in mu rhythm, the central rhythm of the alpha frequency band, in both intentional and spontaneous interpersonal coordination. The current study was designed to extend existing findings on social synchrony to the pendulum swinging task and simultaneously measured time unfolding behavioral synchrony and EEG estimation of mu activity during spontaneous, intentional in-phase and intentional anti-phase interpersonal coordination. As expected, the behavioral measures of synchrony demonstrated the expected pattern of weak synchronization for spontaneous coordination, moderate synchronization for intentional anti-phase coordination, and strong synchronization for in-phase coordination. With respect to the EEG measures, we found evidence for mu enhancement for spontaneous coordination in contrast to mu suppression for intentional coordination (both in phase and anti-phase), with higher levels of synchronization associated with higher levels of mu suppression in the right hemisphere. The implications of the research findings and methodology for understanding the underlying mechanisms contributing to social problems in psychological disorders, leader-follower relationships, and inter-brain dynamics are discussed

Spinal Cord Pathology in Alpha-Synuclein Transgenic Mice

Accumulation of α-synuclein is observed in neurodegenerative diseases like Parkinson's disease and Multiple System Atrophy. In previous studies with transgenic C57BL/6 mice overexpressing α-synuclein carrying the mutations A53T and A30P found in Parkinson's disease or with a parkin-null background, we reported severe mitochondrial impairments in neurons and to a larger extent in glial cells of the mesencephalon. Neuron death was not observed in the brain. Here we show that the mice show severe motor impairments in behavioral tests. In addition, these mice exhibit astrocytic cell death in the spinal cord, accompanied by extensive gliosis and microglial activation. This is shown by cell death staining and immunohistochemistry. Ultrastructural analyses revealed severe mitochondrial impairments not only in astrocytes, but also in oligodendrocytes and, to a small extent, in neurons. Thus, the transgenic mice show a profound pathology in glial cells of the spinal cord

Bacteriophages of Shiga toxin-producing Escherichia coli and their contribution to pathogenicity

Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity

Selection and validation of reference genes for quantitative gene expression studies in Erythroxylum coca

Real-time quantitative PCR is a powerful technique for the investigation of comparative gene expression, but its accuracy and reliability depend on the reference genes used as internal standards. Only genes that show a high level of expression stability are suitable for use as reference genes, and these must be identified on a case-by-case basis. Erythroxylum coca produces and accumulates high amounts of the pharmacologically active tropane alkaloid cocaine (especially in the leaves), and is an emerging model for the investigation of tropane alkaloid biosynthesis. The identification of stable internal reference genes for this species is important for its development as a model species, and would enable comparative analysis of candidate biosynthetic genes in the different tissues of the coca plant. In this study, we evaluated the expression stability of nine candidate reference genes in E. coca ( Ec6409, Ec10131, Ec11142, Actin, APT2, EF1α, TPB1, Pex4, Pp2aa3). The expression of these genes was measured in seven tissues (flowers, stems, roots and four developmental leaf stages) and the stability of expression was assessed using three algorithms (geNorm, NormFinder and BestKeeper). From our results we conclude that Ec10131 and TPB1 are the most appropriate internal reference genes in leaves (where the majority of cocaine is produced), while Ec10131 and Ec6409 are the most suitable internal reference genes across all of the tissues tested