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Environmental Toxicants And Human B Cells: Insights From Crispr Editing And Genomic Sequencing, Clayton Allex-Buckner
Environmental Toxicants And Human B Cells: Insights From Crispr Editing And Genomic Sequencing, Clayton Allex-Buckner
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The human immunoglobulin heavy chain gene locus (IGH) has two 3 prime regulatory regions (3’IGHRR), each containing three enhancers (hs3, hs1.2, hs4). In animal models, the 3’IghRR regulates IgH expression and class switch recombination (CSR) to different Ig isotypes. The 3’IGHRR hs1.2 enhancer in humans is polymorphic in that an invariant sequence (IS) can be repeated one to four times in tandem. The hs1.2 polymorphism is of interest due to its association with several human autoimmune disorders and its potential sensitivity to exogenous substances such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin). In mouse models, TCDD inhibits the hs1.2 enhancer and 3’IghRR …
Novel Natural Language Processing Models For Medical Terms And Symptoms Detection In Twitter, Farahnaz Golrooy Motlagh
Novel Natural Language Processing Models For Medical Terms And Symptoms Detection In Twitter, Farahnaz Golrooy Motlagh
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This dissertation focuses on disambiguation of language use on Twitter about drug use, consumption types of drugs, drug legalization, ontology-enhanced approaches, and prediction analysis of data-driven by developing novel NLP models. Three technical aims comprise this work: (a) leveraging pattern recognition techniques to improve the quality and quantity of crawled Twitter posts related to drug abuse; (b) using an expert-curated, domain-specific DsOn ontology model that improve knowledge extraction in the form of drug-to-symptom and drug-to-side effect relations; and (c) modeling the prediction of public perception of the drug’s legalization and the sentiment analysis of drug consumption on Twitter. We collected …
Augmenting Structure/Function Relationship Analysis With Deep Learning For The Classification Of Psychoactive Drug Activity At Class A G Protein-Coupled Receptors, Hannah Willow Shows
Augmenting Structure/Function Relationship Analysis With Deep Learning For The Classification Of Psychoactive Drug Activity At Class A G Protein-Coupled Receptors, Hannah Willow Shows
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G protein-coupled receptors (GPCRs) initiate intracellular signaling pathways via interaction with external stimuli. [1-5] Despite sharing similar structure and cellular mechanism, GPCRs participate in a uniquely broad range of physiological functions. [6] Due to the size and functional diversity of the GPCR family, these receptors are a major focus for pharmacological applications. [1,7] Current state-of-the-art pharmacology and toxicology research strategies rely on computational methods to efficiently design highly selective, low toxicity compounds. [9], [10] GPCR-targeting therapeutics are associated with low selectivity resulting in increased risk of adverse effects and toxicity. Psychoactive drugs that are active at Class A GPCRs used …
Augmenting Structure/Function Relationship Analysis With Deep Learning For The Classification Of Psychoactive Drug Activity At Class A G Protein-Coupled Receptors, Hannah Willow Shows
Augmenting Structure/Function Relationship Analysis With Deep Learning For The Classification Of Psychoactive Drug Activity At Class A G Protein-Coupled Receptors, Hannah Willow Shows
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G protein-coupled receptors (GPCRs) initiate intracellular signaling pathways via interaction with external stimuli. [1-5] Despite sharing similar structure and cellular mechanism, GPCRs participate in a uniquely broad range of physiological functions. [6] Due to the size and functional diversity of the GPCR family, these receptors are a major focus for pharmacological applications. [1,7] Current state-of-the-art pharmacology and toxicology research strategies rely on computational methods to efficiently design highly selective, low toxicity compounds. [9], [10] GPCR-targeting therapeutics are associated with low selectivity resulting in increased risk of adverse effects and toxicity. Psychoactive drugs that are active at Class A GPCRs used …
Vespucci: A Free, Cross-Platform Software Tool For Spectroscopic Data Analysis And Imaging, Daniel Patrick Foose
Vespucci: A Free, Cross-Platform Software Tool For Spectroscopic Data Analysis And Imaging, Daniel Patrick Foose
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Vespucci is a software application developed for imaging and analysis of hyperspectral datasets. Vespucci offers several advantages over other software packages, including a simple user interface, no cost, and less restrictive licensing. Vespucci incorporates several analysis techniques including univariate imaging, principal components analysis, partial-least-squares regression, vertex components analysis and k- means clustering. Additionally, Vespucci can perform a number of useful data-processing operations, including filtering, normalization, baseline correction, and background subtraction. Datasets that consist of spatial or temporal data with a corresponding digital signal, including spectroscopic images, mass spectrometric images, and X-ray diffraction data can be processed in this software. The …
Extension Of Multivariate Analyses To The Field Of Microbial Ecology, Vijay Shankar
Extension Of Multivariate Analyses To The Field Of Microbial Ecology, Vijay Shankar
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Ground-breaking advancements in molecular and analytical techniques in the past decade have enabled researchers to accumulate data at an extraordinary rate. Especially in the field of microbial ecology, the introduction of technologies such as high-throughput sequencing, quantitative microarrays, nuclear magnetic resonance and mass spectrometry has led to the interrogation of diverse and previously unexplored microbial communities at unparalleled depth. Analysis and interpretation of patterns within datasets acquired with such high-throughput methods require powerful statistical approaches. A class of such techniques called multivariate statistical analyses is an excellent choice for analysis of complex microbiota-related datasets. This field of statistics is constantly …
Improving Remote Homology Detection Using A Sequence Property Approach, Gina Marie Cooper
Improving Remote Homology Detection Using A Sequence Property Approach, Gina Marie Cooper
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Understanding the structure and function of proteins is a key part of understanding biological systems. Although proteins are complex biological macromolecules, they are made up of only 20 basic building blocks known as amino acids. The makeup of a protein can be described as a sequence of amino acids. One of the most important tools in modern bioinformatics is the ability to search for biological sequences (such as protein sequences) that are similar to a given query sequence. There are many tools for doing this (Altschul et al., 1990, Hobohm and Sander, 1995, Thomson et al., 1994, Karplus and Barrett, …
Algorithmic Techniques Employed In The Isolation Of Codon Usage Biases In Prokaryotic Genomes, Douglas W. Raiford Iii
Algorithmic Techniques Employed In The Isolation Of Codon Usage Biases In Prokaryotic Genomes, Douglas W. Raiford Iii
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While genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Isolation of translational efficiency bias can have important …
Computational Methods For The Objective Review Of Forensic Dna Testing Results, Jason R. Gilder
Computational Methods For The Objective Review Of Forensic Dna Testing Results, Jason R. Gilder
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Since the advent of criminal investigations, investigators have sought a "gold standard" for the evaluation of forensic evidence. Currently, deoxyribonucleic acid (DNA) technology is the most reliable method of identification. Short Tandem Repeat (STR) DNA genotyping has the potential for impressive match statistics, but the methodology not infallible. The condition of an evidentiary sample and potential issues with the handling and testing of a sample can lead to significant issues with the interpretation of DNA testing results. Forensic DNA interpretation standards are determined by laboratory validation studies that often involve small sample sizes. This dissertation presents novel methodologies to address …