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Browsing by Subject "human"

Now showing 1 - 6 of 6
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    Computational Methods for Sequencing and Interpreting Killer-cell Immunoglobulin-like Receptors (KIRs) at Multiple Resolutions
    (2021-01) Roe, David
    The era of personalized genetic medicine has arrived. It is now routine to sequence an individual’s DNA, either whole genome sequences (WGS) or targeted, as part of a patient’s medical plan. One of the exceptions is an ~200 kilobase region in chromosome 19 containing the killer-cell immunoglobulin-like receptors (KIR). These genes encode proteins that influence the actions of natural killer (NK) cells based on whether or not they bind with peptide-bound human leukocyte antigen receptors. This is evolutionary important to fight pathogens and mediate pregnancy. Modern medicine has correlated low-resolution KIR with many diseases and treatments, although the findings are often relatively vague and sometimes contradictory due to low resolution interpretation and/or small cohort sizes. Whether for personal medicine or population studies, the current best practices for KIR genotyping are to determine the presence/absence (PA) or copy number variation (CNV) of each gene using oligo- or primer-based polymerase chain reaction.The goal of our research is to advance DNA sequencing and interpretation of human KIR haplotypes. To that end, we have created algorithms and workflows to enhance interpretations of KIR at resolutions from PA genotyping via short-read WGS to full-haplotype assembly from long-read targeted or whole-genome sequences. First, we developed the first workflow to efficiently and accurately capture, sequence, assemble, and annotate full KIR haplotype sequences. As part of this workflow, we designed small sequences to capture the DNA fragments. Next, we use the alignment pattern of those short sequences across finished KIR haplotypes to define and annotate haplotype structures. The results show, for the first time, that the KIR region is composed of 9 genes in 14 loci. Next, we annotated all 68 reported human haplotypes, aligned them at the structural level, and then refined the alignment down the base level, providing the first KIR haplotype multiple sequence alignment. These efforts have led to this region being the best annotated and most diverse in the human genome reference. We next leveraged the MSA to discover PA markers and leveraged them in the first KIR WGS genotyping application. It was evaluated independently and reported to be at least 97% accurate. These discoveries and inventions are the culmination of several computational methods we have developed that interpret KIR under different typing resolutions. This multi-resolution aspect is crucial to overall understanding; it improves resolution at any given level by leveraging references and/or markers from other resolutions. From low-resolution genotyping from any kind of DNA sequence to the first efficient full-haplotype assembly method, these results advance interpretation of this important genetic region to the personal and population levels.
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    Effects of a robot-assisted sensorimotor training program with vibro-tactile feedback on proprioception and motor function in people with chronic stroke
    (2017-08) Yeh, I-Ling
    Proprioceptive deficits are exhibited in nearly 50% of all stroke survivors and is associated with poor upper limb motor function and impaired activities of daily living function. Improving proprioception enhances motor learning and improves motor performance in non-stroke populations. Thus, improving proprioception could serve as an additional route to enhance motor recovery after stroke. The aims of this study were to examine whether a robot-aided sensorimotor training regimen requiring active wrist movements administered without vision would improve the proprioceptive acuity, proprioception-related somatosensory evoked potential (SEP) measures and motor performance in adults with chronic stroke. METHODS: Twelve adults with chronic stroke were recruited (Median age: 63 years, 42 – 74 years; median time after stroke: 12 months; median Fugl-Meyer Assessment – UE: 65 points). Participants completed two training sessions in two consecutive days (total training time: 1 hour). Users grasped the robot handle and performed wrist adduction/abduction movements to tilt a virtual board on which a virtual ball rolled. Users were tasked to roll the ball to a target area on the board. Real-time, vibro-tactile feedback about ball position and speed was provided to the forearm. The task difficulty increased as the user continued training. Assessments were conducted before, immediately after, and two days after the intervention. Outcome measures were wrist proprioceptive acuity indicated by the just-noticeable-difference (JND) threshold, spatial errors of wrist tracing tasks, movement time and endpoint error of a wrist pointing task and short-latency SEPs induced by median nerve stimulation. RESULTS: The stroke group significantly reduced JND thresholds at posttest and retention in comparison to the pretest (Medians: pretest: 1.8°, posttest: 1.4°, retention: 1.3°; W = 10, p = 0.0042 for both comparisons). Higher reduction in the JND threshold was associated with a higher increase in the P27-N30 peak-to-peak SEP amplitude at retention compared to pretest. Changes in SEP measures and motor measures across visits did not reach statistical significance. DISCUSSION: This exploratory, proof-of-concept study documented that proprioceptive function of adults with chronic stroke improved after a brief active proprioceptive-motor training. If proven effective, such interventions or elements could be employed in clinical practice in addition to existing rehabilitation approaches.
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    Measurement of Antibiotics in Water and Sediment: Determining Minnesota's Antibiotic Footprint
    (2020-05-22) Frankson, Lara E; Arnold, William A; arnol032@umn.edu; Arnold, William A; University of Minnesota, Department of Civil, Environmental, and Geo- Engineering
    Antimicrobial resistance is considered to be one of the greatest global public health threats of the 21st century. The discharge of antibiotics into the environment may increase antimicrobial resistance as well as disrupt proper ecosystem functioning. Thus, evaluating the antibiotics present in the environment as well as the contributing factors to their presence in the environment will provide invaluable information for improving water quality and protecting human and ecosystem health. This dissertation investigates the presence of antibiotics in water and sediment in both wastewater treatment effluent and agricultural animal affected areas throughout Minnesota. This is to provide a fine scale as well as a broadscale approach with multiple samples at each site at sites across Minnesota. Additionally, a snapshot of the antibiotics present and long term trends of antibiotics in the environment are investigated through water and sediment samples, respectively.
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    Perceptions of Invasive Species and Their Control Among the MN Tourism Industry
    (University of Minnesota Tourism Center, 2014) Schneider, Ingrid E.; Qian, Xinyi
    This project sought baseline information on perceptions of invasive species and theie control among the Minnesota tourism industry. The majority of respondents agreed that both invasive plant & aquatic invasives were harmful to Minnesota’s environment, economy & society. Similarly, the majority of respondents indicated all 7 control methods presented in the questionnaire would be effective to control invasive species.
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    Supplements for HA Fink JBMR manuscript titled, "Performance of Fracture Risk Assessment Tools by Race and Ethnicity: A Systematic Review for the ASBMR Task Force on Clinical Algorithms for Fracture Risk"
    (2023-05-05) Fink, Howard A; howard.fink@va.gov; Fink, Howard A; Evidence-Based Practice Center, Division of Health Policy & Management, School of Public Health, University of Minnesota
    These data are supplemental materials for the Journal of Bone & Mineral Research (JBMR) manuscript by Howard A Fink and co-authors titled, "Performance of Fracture Risk Assessment Tools by Race and Ethnicity: A Systematic Review for the ASBMR Task Force on Clinical Algorithms for Fracture Risk." JBMR requires that the data that support the findings of the systematic literature review be openly available in a data repository. The manuscript is about to be submitted to JBMR and the journal requires that submitted manuscripts have an active link to the supplemental data in a data repository.
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    Video Diver Dataset (VDD-C) 100,000 annotated images of divers underwater
    (2021-04-19) de Langis, Karin; Fulton, Michael; Sattar, Junaed; fulto081@umn.edu; Fulton, Michael; Interactive Robotics and Vision Lab
    This dataset contains over 100,000 annotated images of divers underwater, gathered from videos of divers in pools and the Caribbean off the coast of Barbados. It is intended for the development and testing of diver detection algorithms for use in autonomous underwater vehicles (AUVs). Because the images are sourced from videos, they are largely sequential, meaning that temporally aware algorithms (video object detectors) can be trained and tested on this data. Training on this data improved our current diver detection algorithms significantly because we increased our training set size by 17 times compared to our previous best dataset. It is released for free for anyone who wants to use it.