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3,685 full-text articles. Page 7 of 143.

Draft Genome Sequence Of Lactobacillus Jensenii Strain Umb7766, Isolated From The Female Bladder, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Lactobacillus Jensenii Strain Umb7766, Isolated From The Female Bladder, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Lactobacillus jensenii is a beneficial and prominent community member within both the vaginal and female urinary microbiota. As more genomes for L. jensenii strains are made publicly available, we gain more knowledge about this beneficial community member. Here, we present the draft genome sequence of L. jensenii UMB7766, which was isolated from a urine specimen from a catheterized female patient with recurrent urinary tract infections.


Draft Genome Sequence Of Lactobacillus Mulieris Umb9245, Isolated From The Female Bladder, Lidia Ramotowski, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Lactobacillus Mulieris Umb9245, Isolated From The Female Bladder, Lidia Ramotowski, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Lactobacillus jensenii is an anaerobic bacterium found in the urogenital tract that is known to prevent common vaginal infections. Recently, it was divided into two species, L. jensenii and L. mulieris. Here, we report the draft genome sequence of L. mulieris UMB9245, with a genome length of 1,723,383 bp assembled into 52 contigs.


Draft Genome Sequence Of Proteus Mirabilis Umb1310, Isolated From The Female Urinary Tract, Olivia Allen, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Proteus Mirabilis Umb1310, Isolated From The Female Urinary Tract, Olivia Allen, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Proteus mirabilis is a Gram-negative bacterium that is linked to common complications within the urinary tract. Here, we present the draft genome for P. mirabilis UMB1310, which was isolated from the urine of a woman with a urinary tract infection.


Draft Genome Sequence Of Streptococcus Anginosus Umb1296, Isolated From The Female Urinary Tract, Sara Temelkova, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Streptococcus Anginosus Umb1296, Isolated From The Female Urinary Tract, Sara Temelkova, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

We present the draft genome sequence of a Streptococcus anginosus strain isolated from the female urinary tract. The S. anginosus UMB1296 draft genome has a size of 1,924,009 bp assembled into 35 contigs with a GC content of 38.69%. Genome annotation revealed 1,775 protein-coding genes, including several known virulence factors.


Draft Genome Sequence Of Klebsiella Pneumoniae Umb7779, Isolated From The Female Urinary Tract, Pavan Bhimalli, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Klebsiella Pneumoniae Umb7779, Isolated From The Female Urinary Tract, Pavan Bhimalli, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Klebsiella pneumoniae is a pathogenic bacterium commonly responsible for urinary tract infections (UTIs). Here, we report the draft genome sequence of K. pneumoniae strain UMB7779, isolated from catheterized urine of a woman with a recurrent UTI.


Draft Genome Sequence Of Corynebacterium Coyleae Umb8490, Isolated From The Female Urinary Tract, Abbas Ali Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Corynebacterium Coyleae Umb8490, Isolated From The Female Urinary Tract, Abbas Ali Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Here, we present the draft genome sequence for Corynebacterium coyleae UMB8490, isolated from the catheterized urine of a female with overactive bladder symptoms. The size of the genome is 2,483,223 bp assembled in 62 contigs with an observed GC content of 61.42%.


Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath 2020 Children's Mercy Kansas City

Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath

Research Days

No abstract provided.


The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig 2020 University of Nebraska Medical Center

The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig

Theses & Dissertations

Aortic stenosis (AS) and regurgitation (AR) may be treated with surgical aortic valve replacement (SAVR), transcatheter AVR (TAVR), or medical therapy (MT). Data are lacking regarding usage and cost of SAVR, TAVR, and MT for patients hospitalized with aortic valve disease. From the Nationwide Readmissions Database, we determined utilization and cost trends for SAVR, TAVR, and MT in patients with aortic valve disease admitted 2012-2016 for valve replacement, heart failure, unstable angina, non-ST-elevation myocardial infarction, or syncope. From 2012 through 2016, there was a 48.1% increase in the number of patients hospitalized for aortic valve disease annually. Overall, 19 ...


The Role Of The Cxcr3 Signaling Axes In Pancreatic Ductal Adenocarcinoma, Andrew C. Cannon 2020 University of Nebraska Medical Center

The Role Of The Cxcr3 Signaling Axes In Pancreatic Ductal Adenocarcinoma, Andrew C. Cannon

Theses & Dissertations

Numerous cytokines promote pancreatic ductal adenocarcinoma (PDAC) progression and suppress anti-tumor immune response leading to poor prognosis in PDAC patients. Despite this, many cytokines, have not been investigated in PDAC. Bioinformatic analyses of PDAC microarray and RNA-Seq datasets were used to identify cytokines overexpressed in PDAC, confirm the expression of cognate receptors, determine the association of cytokines with patient survival and define key underlying molecular associations. Bioinformatic findings were validated using immunohistochemical (IHC) staining, comparative cytokine qPCR-array in KrasLSL-G12D:TP53LSL-R172H:Pdx1-Cre (KPC) and KrasLSL-G12D:Pdx1-Cre (KC) PDAC models and multicolor immunofluorescence staining. Tail-vein injections of PDAC cells ...


A Genomic Analysis Of Bobcat Populations In North America With A Comparison To The Canada Lynx: An Assessment Of Local Adaptation To Unique Ecoregions And Phylogeography, Jennifer C. Broderick 2020 Duquesne University

A Genomic Analysis Of Bobcat Populations In North America With A Comparison To The Canada Lynx: An Assessment Of Local Adaptation To Unique Ecoregions And Phylogeography, Jennifer C. Broderick

Electronic Theses and Dissertations

Bobcats (Lynx rufus) are an ecologically and genetically diverse species with a large contiguous range throughout North America. The species not only has a wide array of phenotypic variation compared to other mammals, but shows marked adaptability across ecozones with differing ecological influences. It is these various selective pressures in distinctive parts of the continent that have likely led to localized adaptations within the bobcat metapopulations. The species is also marked by its ability to maintain connectivity and populations in anthropogenically developed areas, an advantage it has over other felids, including its close relative the Canada lynx (Lynx canadensis). The ...


Draft Genome Sequence Of Aeromonas Caviae Ufmg-H8, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Aeromonas Caviae Ufmg-H8, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni

Bioinformatics Faculty Publications

Aeromonas caviae is an emerging pathogen in humans, causing intestinal infections. Here, we report Aeromonas caviae strain UFMG-H8, isolated from the urine of a healthy heifer (Gyr breed).


Draft Genome Sequence Of Citrobacter Freundii Ufmg-H9, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Citrobacter Freundii Ufmg-H9, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni

Bioinformatics Faculty Publications

Citrobacter freundii is a pathogen associated with antibiotic resistance and severe infections in humans. Here, we report the draft genome sequence of C. freundii strain UFMG-H9, an isolate from urine from a healthy Gyr heifer.


Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park 2020 University of Tennessee, Knoxville

Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

The study of the insulin-like peptides of Drosophila can provide insight of their similarities to mammalian insulin and their potential usage in treating human insulin-related diseases. In this study, we isolated and characterized cDNA encoding insulin-like peptide (ILP) 5 in D. virilis by using RNA purification, reverse transcription, and RACE protocols. Subsequently, various bioinformatic softwares were employed to predict peptide structure. The ILP5 gene (587 base pairs) codes for 121 amino acids that make up prepro-ILP5. After maturation, functional ILP5 is a peptide of two 25 amino acid chains, A- and B-chain, connected by two disulfide bonds. Sequencing genomic DNA ...


Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb 2020 University of Nebraska - Lincoln

Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb

Dissertations, Theses, & Student Research in Food Science and Technology

Novel foods and Genetically Engineered (GE) organisms are being developed for nutritional, industrial, and environmental applications. Dietary interventions have been used recently to mitigate methane emissions in ruminants. In this project, bioinformatics tools have been used to answer two main questions. The first question is the potential allergy risks for consumption of novel foods and GE organisms. The second question is the effects of dietary interventions on microbiome functionality related to methane production in ruminants.

To answer the first question, regulatory authorities in the United States and Europe now expect an evaluation of new proteins in novel foods or genetically ...


Modeling Hybrid Novel Traits: A Case Study In Complex Petal Pigment Patterning In Hybrid Mimulus, Xingyu Zheng 2020 William & Mary

Modeling Hybrid Novel Traits: A Case Study In Complex Petal Pigment Patterning In Hybrid Mimulus, Xingyu Zheng

Undergraduate Honors Theses

Hybridization between species, by introducing dramatic trait variation into the population and creating viable, transgressive offsprings with novel phenotypes, can have huge evolutionary implications. Some hybrid traits have been studied in the classical genetics or population genetics context, but most complex traits are determined by multiple causes, e.g. the number of loci involved, the rewiring of the genetic circuitries, and the changes in gene expression pattern. Using the hybrid monkeyflower petal pigment patterning as an example, we present a case study to investigate complex hybrid traits in a systematic manner that includes empirical data analysis and quantitative mathematical modeling ...


Understanding Intercellular Signaling During Lung Injury-Repair, Margo Patricia Cain 2020 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Understanding Intercellular Signaling During Lung Injury-Repair, Margo Patricia Cain

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

The mammalian lung is a complex system of specialized cell types with precise spatial organization designed to cooperate to perform gas exchange. These cell types together coordinate organ development, homeostasis, and repair after injury through signals either presented or secreted, known as ligands, to be received by receptors on the surface of another, or in some cases, the same cell. The alveolar region of the lung, the primary region of gas exchange, responds to various types of injuries with different lung repair mechanisms. In order to explore how the various cell types in the lung communicate to drive tissue repair ...


Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin 2020 University of Arkansas, Fayetteville

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Theses and Dissertations

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population ...


Table-To-Text: Generating Descriptive Text For Scientific Tables From Randomized Controlled Trials, Qiang Wei 2020 University of Texas Health Science Center at Houston

Table-To-Text: Generating Descriptive Text For Scientific Tables From Randomized Controlled Trials, Qiang Wei

UT SBMI Dissertations (Open Access)

Unprecedented amounts of data have been generated in the biomedical domain, and the bottleneck for biomedical research has shifted from data generation to data management, interpretation, and communication. Therefore, it is highly desirable to develop systems to assist in text generation from biomedical data, which will greatly improve the dissemination of scientific findings. However, very few studies have investigated issues of data-to-text generation in the biomedical domain. Here I present a systematic study for generating descriptive text from tables in randomized clinical trials (RCT) articles, which includes: (1) an information model for representing RCT tables; (2) annotated corpora containing pairs ...


A Big-Data Approach To Understanding Metabolic Rate And Response To Obesity In Laboratory Mice, June K. Corrigan, Deepti Ramachandran, Yuchen He, Colin J. Palmer, Michael J. Jurczak, Rui Chen, Bingshan Li, Randall H. Friedline, Jason K. Kim, Jon J. Ramsey, Louise Lantier, Owen P. McGuinness, Alexander S. Banks 2020 Harvard Medical School

A Big-Data Approach To Understanding Metabolic Rate And Response To Obesity In Laboratory Mice, June K. Corrigan, Deepti Ramachandran, Yuchen He, Colin J. Palmer, Michael J. Jurczak, Rui Chen, Bingshan Li, Randall H. Friedline, Jason K. Kim, Jon J. Ramsey, Louise Lantier, Owen P. Mcguinness, Alexander S. Banks

Open Access Publications by UMMS Authors

Maintaining a healthy body weight requires an exquisite balance between energy intake and energy expenditure. To understand the genetic and environmental factors that contribute to the regulation of body weight, an important first step is to establish the normal range of metabolic values and primary sources contributing to variability. Energy metabolism is measured by powerful and sensitive indirect calorimetry devices. Analysis of nearly 10,000 wild-type mice from two large-scale experiments revealed that the largest variation in energy expenditure is due to body composition, ambient temperature, and institutional site of experimentation. We also analyze variation in 2329 knockout strains and ...


Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola 2020 University of Nebraska at Omaha

Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola

Theses/Capstones/Creative Projects

This study presents a novel methodology for analyzing metabolic pathways. Utilizing KEGG REST API through a Biopython package and file parser, data about whether or not a bacteria has an enzyme or not was extracted. The results found that differences in metabolic pathway enrichment values follow along the lines of genera and pathway type. In particular, bacteria found in food spoilage and commercial nitrogen fixing products had high values of enrichment.


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