13,846 research outputs found

    Inter-individual variation of the human epigenome & applications

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    UMSL Bulletin 2023-2024

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    The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp

    Location Reference Recognition from Texts: A Survey and Comparison

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    A vast amount of location information exists in unstructured texts, such as social media posts, news stories, scientific articles, web pages, travel blogs, and historical archives. Geoparsing refers to recognizing location references from texts and identifying their geospatial representations. While geoparsing can benefit many domains, a summary of its specific applications is still missing. Further, there is a lack of a comprehensive review and comparison of existing approaches for location reference recognition, which is the first and core step of geoparsing. To fill these research gaps, this review first summarizes seven typical application domains of geoparsing: geographic information retrieval, disaster management, disease surveillance, traffic management, spatial humanities, tourism management, and crime management. We then review existing approaches for location reference recognition by categorizing these approaches into four groups based on their underlying functional principle: rule-based, gazetteer matchingā€“based, statistical learning-ā€“based, and hybrid approaches. Next, we thoroughly evaluate the correctness and computational efficiency of the 27Ā most widely used approaches for location reference recognition based on 26 public datasets with different types of texts (e.g., social media posts and news stories) containing 39,736 location references worldwide. Results from this thorough evaluation can help inform future methodological developments and can help guide the selection of proper approaches based on application needs

    ā€˜Shinu Shika Naiā€™ ā€“ ā€˜There is Nothing to Do but to Dieā€™: Contextualising the Rising Young Female Suicide Rate in Japan

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    During the Covid-19 pandemic, the suicide rate for the 18-39 age cohort of Japanese women has been drastically subverting a long period of prior sustained decline. This work is an anthropological study of social conditions contributing to a social zeitgeist in which these young women are taking their own lives, as told in survivor and advocate testimonies. It seeks to question the ways ideas around what suicide means in the Japanese cultural context to stakeholders in the suicide process. It further elucidates how these ideas exist, and how they have evolved to be meaningful to young women in contemporary Japan

    R-Pyocin Regulation, Release, and Susceptibility in Pseudomonas aeruginosa

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    Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen and a major determinant of declining lung function in individuals with cystic fibrosis (CF). P. aeruginosa possesses many intrinsic antibiotic resistance mechanisms and isolates from chronic CF lung infections develop increasing resistance to multiple antibiotics over time. Chronic infection with P. aeruginosa remains one of the main causes of mortality and morbidity in CF patients, thus new therapeutic interventions are necessary. R-type pyocins are narrow spectrum, phage tail-like bacteriocins, specifically produced by P. aeruginosa to kill other strains of P. aeruginosa. Due to their specific anti-pseudomonal activity and similarity to bacteriophage, R-pyocins have potential as additional therapeutics for P. aeruginosa, either in isolation, in combination with antibiotics, or as an alternative to phage therapy. There are five subtypes of R-pyocin (types R1-R5), and it is thought that each P. aeruginosa strain uniquely produces only one of these, suggesting a degree of strain-specificity. P. aeruginosa from CF lung infections develop increasing resistance to antibiotics, making new treatment approaches essential. It is known P. aeruginosa populations in CF chronic lung infection become phenotypically and genotypically diverse over time, however, little is known of the efficacy of R-pyocins against heterogeneous populations. Even less is known regarding the timing and regulation of R-pyocins in CF lung infections, or if P. aeruginosa utilizes R-pyocin production during infection for competition or otherwise ā€“ which may influence pressure towards R-pyocin resistance. In this work, I evaluated R-pyocin type and susceptibility among P. aeruginosa isolates sourced from CF infections and found that (i) R1-pyocins are the most prevalent R-type among respiratory infection and CF strains; (ii) a large proportion of P. aeruginosa strains lack R-pyocin genes entirely; (iii) isolates from P. aeruginosa populations collected from the same patient at a single time point have the same R-pyocin type; (iv) there is heterogeneity in susceptibility to R-pyocins within P. aeruginosa populations and (v) susceptibility is likely driven by diversity of LPS phenotypes within clinical populations. These findings suggest that there is likely heterogeneity in response to other types of LPS-binding antimicrobials, including phage, which is important for consideration of antimicrobials as therapeutics. To investigate the prevalence of R2-pyocin susceptible strains in CF, I then utilized 110 isolates of P. aeruginosa collected from five individuals with CF to test for R2-pyocin susceptibility and identify LPS phenotypes. From our collection we i) estimated that approximately 83% of sputum samples contain heterogenous P. aeruginosa populations without R2-pyocin resistant isolates and all sputum samples contained susceptible isolates; ii) we found that there is no correlation between R2-pyocin susceptibility and LPS phenotypes, and iii) we estimate that approximately 76% of isolates sampled from sputum lack O-specific antigen, 42% lack common antigen, and 27% exhibit altered LPS cores. This finding highlights that perhaps LPS packing density may play a more influential role in mediating R-pyocin susceptibility in infection. Finding the majority of our sampled P. aeruginosa populations to be R2-pyocin susceptible further supports the potential of these narrow-spectrum antimicrobials despite facing heterogenous susceptibility among diverse populations. In order to evaluate how R-pyocins may influence strain competition and growth in CF lung infection, I assessed R-pyocin activity in an infection-relevant environment (Synthetic Cystic Fibrosis Sputum Medium; SCFM2) and found that (i) R-pyocins genes are transcribed more in the CF nutrient environment than in rich laboratory medium and (ii) in a structured, CF-like environment, R-pyocin induction is costly to producing strains in competition rather than beneficial. Our work suggests that R-pyocins may not be essential in CF lung infection and can be costly to producing cells in the presence of stress response-inducing stimuli, such as those commonly found in infection. In this thesis I have studied R-pyocin susceptibility, regulation and release utilizing a biobank of whole populations of P. aeruginosa collected from 11 individuals with CF, as well as the CF infection model (SCFM) to understand the mechanisms of R-pyocin activity in an infection-relevant context and the role R-pyocins play in shaping P. aeruginosa populations during infection. The findings of this work have illuminated the impact of P. aeruginosa heterogeneity on R-pyocin susceptibility, furthered our understanding of R-pyocins as potential therapeutics, and built upon our knowledge of bacteriocin-mediated interactions.Ph.D

    UMSL Bulletin 2022-2023

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    The 2022-2023 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1087/thumbnail.jp

    Relatedly: Scaffolding Literature Reviews with Existing Related Work Sections

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    Scholars who want to research a scientific topic must take time to read, extract meaning, and identify connections across many papers. As scientific literature grows, this becomes increasingly challenging. Meanwhile, authors summarize prior research in papers' related work sections, though this is scoped to support a single paper. A formative study found that while reading multiple related work paragraphs helps overview a topic, it is hard to navigate overlapping and diverging references and research foci. In this work, we design a system, Relatedly, that scaffolds exploring and reading multiple related work paragraphs on a topic, with features including dynamic re-ranking and highlighting to spotlight unexplored dissimilar information, auto-generated descriptive paragraph headings, and low-lighting of redundant information. From a within-subjects user study (n=15), we found that scholars generate more coherent, insightful, and comprehensive topic outlines using Relatedly compared to a baseline paper list

    Rapid-Motion-Track: Markerless Tracking of Fast Human Motion with Deeper Learning

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    Objective The coordination of human movement directly reflects function of the central nervous system. Small deficits in movement are often the first sign of an underlying neurological problem. The objective of this research is to develop a new end-to-end, deep learning-based system, Rapid-Motion-Track (RMT) that can track the fastest human movement accurately when webcams or laptop cameras are used. Materials and Methods We applied RMT to finger tapping, a well-validated test of motor control that is one of the most challenging human motions to track with computer vision due to the small keypoints of digits and the high velocities that are generated. We recorded 160 finger tapping assessments simultaneously with a standard 2D laptop camera (30 frames/sec) and a high-speed wearable sensor-based 3D motion tracking system (250 frames/sec). RMT and a range of DLC models were applied to the video data with tapping frequencies up to 8Hz to extract movement features. Results The movement features (e.g. speed, rhythm, variance) identified with the new RMT system exhibited very high concurrent validity with the gold-standard measurements (97.3\% of RMT measures were within +/-0.5Hz of the Optotrak measures), and outperformed DLC and other advanced computer vision tools (around 88.2\% of DLC measures were within +/-0.5Hz of the Optotrak measures). RMT also accurately tracked a range of other rapid human movements such as foot tapping, head turning and sit-to -stand movements. Conclusion: With the ubiquity of video technology in smart devices, the RMT method holds potential to transform access and accuracy of human movement assessment

    Genomic architecture of selection for adaptation to challenging environments in aquaculture

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    Aquaculture, including freshwater and marine farming, has been important for global fish production during the past few decades. However, climate change presents a major risk threatening both quality and quantity of aquaculture production. The environmental stressors in aquaculture resulting from climate change, are temperature rise, salinity changes, sea level rise, acidification and changes of other chemical properties and changes of oxygen levels. Although a reasonable genetic gain can be achieved by selective breeding, this genetic response may not be enough to adapt fish species to the effects of climate change. Marker assisted selection focusing on specific genes or alleles that allow fish to cope with these changes would allow more rapid adaptation of fish to these new environments. In this thesis, I focused on three essential environmental stressors - dissolved oxygen, salinity and temperature as primarily determined in aquaculture production. The main objective is to provide insight in the genomic architecture underlying the mechanism of adaptation to challenging environments of aquaculture species under farming conditions. First, I determined candidate QTL associated with phenotypic variation during adaptation to hypoxia or normoxia. I identified overrepresented pathways that could explain the genetic regulation of hypoxia on growth. To identify fish with better hypoxia tolerance and growth under a hypoxic environment, I quantified the genetic correlations between an indicator trait for hypoxia tolerance (critical swimming performance) and growth. Moreover, the genomic architecture associated with swimming performance was demonstrated, while the effect of significant QTLs on growth was estimated. Beyond applying genome-wide association studies, I used selection signatures to identify QTLs and genes contributing to salinity tolerance. In addition, I also compared the genome of the saline-tolerant and highly productive tilapia ā€œSukamandiā€, that was developed by the aquaculture research institute in Indonesia, to that of blue tilapia and Nile tilapia, to identify the QTLs contributing to salinity tolerance. Finally, I investigated QTLs associated with growth-related traits and organ weights at two distinct commercial Mediterranean product sites differing in temperature (farms in Spain and Greece). Overall, this thesis considerably adds to insight into how fish adapt to challenging environments, which will aid marker-assisted selection for improved resilience of aquaculture species under climate change
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