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Preliminary Investigation Of Walking Motion Using A Combination Of Image And Signal Processing, Bradley Schneider, Tanvi Banerjee 2016 Wright State University - Main Campus

Preliminary Investigation Of Walking Motion Using A Combination Of Image And Signal Processing, Bradley Schneider, Tanvi Banerjee

Kno.e.sis Publications

We present the results of analyzing gait motion in first-person video taken from a commercially available wearable camera embedded in a pair of glasses. The video is analyzed with three different computer vision methods to extract motion vectors from different gait sequences from four individuals for comparison against a manually annotated ground truth dataset. Using a combination of signal processing and computer vision techniques, gait features are extracted to identify the walking pace of the individual wearing the camera as well as validated using the ground truth dataset. Our preliminary results indicate that the extraction of activity from the video ...


Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Raymond A. Enke 2016 enkera@jmu.edu

Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • analyzing qPCR standard curve data to determine primer efficiency
  • analyzing differential gene expression experimental qPCR data
  • applying KEGG pathway analysis of selected candidates genes


Fractal Analysis Of Dna Sequences, Christian G. Arias, Pedro Antonio Moreno Phd, Carlos Tellez 2016 Universidad del Valle - Colombia - Georgia Institute of Technology

Fractal Analysis Of Dna Sequences, Christian G. Arias, Pedro Antonio Moreno Phd, Carlos Tellez

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Strategies To Avoid Overfitting Of Mcmc Bayesian Learning In Some Biological Applications, Diego M. Garcia 2016 Universidad del Valle - Colombia

Strategies To Avoid Overfitting Of Mcmc Bayesian Learning In Some Biological Applications, Diego M. Garcia

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Using Citizen Science And Remote Sensing Data To Model Hummingbird Migration, Sarah R. Supp, Laura J. Graham, Frank A. La Sorte, Tina A. Cormier, Gil Bohrer, Donald Powers, Susan Wethington, Kevin Guay, Patrick Jantz, Scott Goetz, Catherine H. Graham 2016 University of Maine

Using Citizen Science And Remote Sensing Data To Model Hummingbird Migration, Sarah R. Supp, Laura J. Graham, Frank A. La Sorte, Tina A. Cormier, Gil Bohrer, Donald Powers, Susan Wethington, Kevin Guay, Patrick Jantz, Scott Goetz, Catherine H. Graham

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Modeling The Spread Of The Zika Virus At The 2016 Olympics, Triona S. Matheson, Brian Satterthwaite, Hannah L. Callender 2016 University of Portland

Modeling The Spread Of The Zika Virus At The 2016 Olympics, Triona S. Matheson, Brian Satterthwaite, Hannah L. Callender

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary 2016 University of Chicago

Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Modeling Of Human Circadian Clock: Per3 Provides Molecular Support For Behavioral Observations, Ha T. Vu 2016 Colgate University

Modeling Of Human Circadian Clock: Per3 Provides Molecular Support For Behavioral Observations, Ha T. Vu

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University 2016 Eastern Illinois University

Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University

Darwin Core Archive Download

ZIP file contains occurrences.csv, identivications.csv, and images.csv. The meta.xml document describes the content. Fields within the occurrences.csv file are defined by the Darwin Core exchange standard.


1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll 2016 Illinois Mathematics and Science Academy

1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll

Sequence Alignments

Pairwise Alignment: DNA

Pairwise Alignment: Protein

Multiple Sequence Alignment: DNA

Multiple Sequence Alignment: Protein


Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers 2016 The Graduate Center, City University of New York

Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Understanding the process of speciation is of central interest to evolutionary biologists. Speciation can be studied using a phylogeographic approach, by identifying regions that promote lineage divergence, addressing whether speciation has occurred with gene flow, and when extended to multiple taxa, addressing if the same patterns of speciation are shared across codistributed groups with different ecologies. Here I examine the comparative phylogeographic histories and population genomics of thirteen snake taxa that are widely distributed and co-occur across the arid southwest of North America. I first quantify the degree to which these species groups have a shared history of population divergence ...


Optimizing Gdna Purification And Qpcr Techniques For Specific Detection And Enumeration Of Probiotic Bacteria, Katelynn C. Lee, Jennifer VanderKelen, Christopher Kitts 2016 California Polytechnic State University, San Luis Obispo

Optimizing Gdna Purification And Qpcr Techniques For Specific Detection And Enumeration Of Probiotic Bacteria, Katelynn C. Lee, Jennifer Vanderkelen, Christopher Kitts

STAR (STEM Teacher and Researcher) Presentations

Probiotics are live microorganisms, like bacteria and yeast, which are thought to provide health benefits when ingested. Large manufacturers produce blends of probiotics for supplementing the diets of agriculturally important animals. Commercial probiotic products are labeled with the number of cells present at the time of manufacture. Our assignment was to develop an assay which can be used to quantify the number of specific lactic acid bacteria present in certain probiotic products, thus verifying the number reported on the product labels. This quantification process involves isolating genomic DNA (gDNA) from the given samples and then running the DNA through a ...


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager 2016 University of Wisconsin-La Crosse

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by ...


Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr. 2016 Washington University in St. Louis

Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.

Engineering and Applied Science Theses & Dissertations

In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess ...


Using Electronic Health Record Data To Identify Prostate Cancer Patients That May Qualify For Active Surveillance, Andrew J. Knighton, Tom Belnap, Kim Brunisholz, Kelly Huynh, Jay T. Bishoff 2016 Intermountain Healthcare

Using Electronic Health Record Data To Identify Prostate Cancer Patients That May Qualify For Active Surveillance, Andrew J. Knighton, Tom Belnap, Kim Brunisholz, Kelly Huynh, Jay T. Bishoff

eGEMs (Generating Evidence & Methods to improve patient outcomes)

Introduction: The introduction of the protein-specific antigen (PSA) test in care means that prostate cancer (PCa) is being detected earlier and more frequently. The result of increased screening using PSA, digital rectal examination and awareness of prostate was an increase in the number of men with low risk cancers. Active surveillance has become a viable alternative to immediate treatment with surgery, radiation and other forms of localized treatment. Evidence suggests that there is no significant difference in mortality rates between AS and surgery. In addition, patients may potentially delay other complications associated with surgery, radiation or deprivation therapy.

Methods: This ...


Computational Analyses Of Mrna Ribosome Loading In Arabidopsis Thaliana, Joseph Benjamin Ernest 2016 University of Tennessee, Knoxville

Computational Analyses Of Mrna Ribosome Loading In Arabidopsis Thaliana, Joseph Benjamin Ernest

Doctoral Dissertations

Translation of mRNA into protein is a critical step in gene expression, but the principles guiding its regulation at the genome level are not completely understood. Translation can be quantified at a genome scale by measuring the ribosome loading of mRNA—the extent to which mRNA is associated with ribosomes. In this dissertation, I present investigations into how genome-wide ribosome loading is controlled in Arabidopsis thaliana. In chapter 1, I give an overview of regulation of ribosome loading and translation. In chapter 2, I present research demonstrating for the first time that genome-wide ribosome loading in plants is partially controlled ...


Data Development And Analysis Pathways For Marine Mammals And Turtles: Creating A User Interface, Sarina Fernandez, Warren Asfazadour, Eric Archer, Lisa Komoroske 2016 California Polytechnic State University, San Luis Obispo

Data Development And Analysis Pathways For Marine Mammals And Turtles: Creating A User Interface, Sarina Fernandez, Warren Asfazadour, Eric Archer, Lisa Komoroske

STAR (STEM Teacher and Researcher) Presentations

A major obstacle in genetic research is developing streamlined methods for analyzing large amounts of data. The statistical computer programming language R provides users with the ability to develop packages containing specific functions in order to create more accessible data analysis pipelines. However, writing code in R can still be intimidating to those with little to no coding experience. Fortunately, the R package shiny provides a framework for developing web applications based on R functions. Using shiny, we developed a user-friendly web application containing functions of the R package strataG. The strataG package contains several functions for summarizing genetic data ...


Structure-Function Analysis And Characterization Of Metalloproteins., Sen Yao 2016 University of Louisville

Structure-Function Analysis And Characterization Of Metalloproteins., Sen Yao

Electronic Theses and Dissertations

Metalloproteins are proteins that can bind at least one metal ion as a cofactor. They utilize metal ions for a variety of biological purposes, and are essential for all domains of life. Due to the ubiquity of metalloprotein’s involvement across these processes across all domains of life, how proteins coordinate metal ions for different biochemical functions is of great relevance to understanding the implementation of these biological processes. One of the most important aspects of metal binding is its coordination geometry (CG), which often implies functional activities. Most of the current studies are based on the assumption of previously ...


Protein Residue-Residue Contact Prediction Using Stacked Denoising Autoencoders, Joseph Bailey Luttrell IV 2016 The University of Southern Mississippi

Protein Residue-Residue Contact Prediction Using Stacked Denoising Autoencoders, Joseph Bailey Luttrell Iv

Honors Theses

Protein residue-residue contact prediction is one of many areas of bioinformatics research that aims to assist researchers in the discovery of structural features of proteins. Predicting the existence of such structural features can provide a starting point for studying the tertiary structures of proteins. This has the potential to be useful in applications such as drug design where tertiary structure predictions may play an important role in approximating the interactions between drugs and their targets without expending the monetary resources necessary for preliminary experimentation. Here, four different methods involving deep learning, support vector machines (SVMs), and direct coupling analysis were ...


Metabolomics Approaches To Decipher The Antibacterial Mechanisms Of Yerba Mate (Ilex Paraguariensis) Against Staphylococcus Aureus And Salmonella Enterica Serovar Typhimurium, Caroline Sue Rempe 2016 University of Tennessee, Knoxville

Metabolomics Approaches To Decipher The Antibacterial Mechanisms Of Yerba Mate (Ilex Paraguariensis) Against Staphylococcus Aureus And Salmonella Enterica Serovar Typhimurium, Caroline Sue Rempe

Doctoral Dissertations

The increasing prevalence of drug-resistant pathogens is an urgent problem that requires novel methods of bacterial control. Plant extracts inhibit bacterial pathogens and could contain antibacterial compounds with novel mechanisms of action. Yerba mate, a common South American beverage made from Ilex paraguariensis, has antibiotic activity against a broad range of bacterial pathogens. In this work, an attempt was first made to characterize the antibacterial source of an aqueous yerba mate extract by generating a series of extract fractions, collecting GC-MS and antibacterial activity profiles, and then ranking the hundreds of compounds by their presence in fractions with high antibacterial ...


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