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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


Movement Path Tortuosity In Free Ambulation: Relationships To Age And Brain Disease, William D. Kearns, James L. Fozard, Vilis O. Nams 2016

Movement Path Tortuosity In Free Ambulation: Relationships To Age And Brain Disease, William D. Kearns, James L. Fozard, Vilis O. Nams

William D. Kearns, PhD

Ambulation is defined by duration, distance traversed, number and size of directional changes and the interval separating successive movement episodes; more complex measures of ambulation can be created by aggregating these features. This review article of published findings defines random changes in direction during movement as “movement path tortuosity”, and relates tortuosity to the understanding of cognitive impairments of persons of all ages. Path tortuosity is quantified by subjecting tracking data to fractal analysis, specifically Fractal Dimension (Fractal D), which ranges from a value of 1 when the movement path is perfectly straight to a value of 2 when the ...


Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret 2016 University of Washington - Seattle Campus

Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret

UW Biostatistics Working Paper Series

We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the ...


Automated Assessment Of Disease Progression In Acute Myeloid Leukemia By Probabilistic Analysis Of Flow Cytometry Data, Bartek Rajwa, Paul K. Wallace, Elizabeth A. Griffiths, Murat Dundar 2016 Purdue University

Automated Assessment Of Disease Progression In Acute Myeloid Leukemia By Probabilistic Analysis Of Flow Cytometry Data, Bartek Rajwa, Paul K. Wallace, Elizabeth A. Griffiths, Murat Dundar

Bindley Publications

Objective: Flow cytometry (FC) is a widely acknowledged technology in diagnosis of acute myeloid leukemia (AML) and has been indispensable in determining progression of the disease. Although FC plays a key role as a post-therapy prognosticator and evaluator of therapeutic efficacy, the manual analysis of cytometry data is a barrier to optimization of reproducibility and objectivity. This study investigates the utility of our recently introduced non-parametric Bayesian framework in accurately predicting the direction of change in disease progression in AML patients using FC data. Methods: The highly flexible non-parametric Bayesian model based on the infinite mixture of infinite Gaussian mixtures ...


Mmb-Gui: A Fast Morphing Method Demonstrates A Possible Ribosomal Trna Translocation Trajectory, Alex Tek, Andrei A. Korostelev, Samuel Coulbourn Flores 2016 Uppsala University

Mmb-Gui: A Fast Morphing Method Demonstrates A Possible Ribosomal Trna Translocation Trajectory, Alex Tek, Andrei A. Korostelev, Samuel Coulbourn Flores

Open Access Articles

Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use ...


A Study Of Social Web Data On Buprenorphine Abuse Using Semantic Web Technology, Raminta Daniulaityte, Amit P. Sheth 2016 Wright State University - Main Campus

A Study Of Social Web Data On Buprenorphine Abuse Using Semantic Web Technology, Raminta Daniulaityte, Amit P. Sheth

Kno.e.sis Publications

The Specific Aims of this application are to use a paradigmatic approach that combines Semantic Web technology, Natural Language Processing and Machine Learning techniques to:

1) Describe drug users’ knowledge, attitudes, and behaviors related to the non-medical use of Suboxone and Subutex as discussed on Web-based forums.
2) Identify and describe temporal patterns of non-medical use of Suboxone and Subutex as discussed on Web-based forums.

The research was carried out by an interdisciplinary team of members of the Center for Interventions, Treatment and Addictions Research (CITAR) and the Ohio Center of Excellence in Knowledge- enabled Computing (Kno.e.sis) at ...


The Marriage Of Biology And Applied Mathematics, Maggie ONeil 2015 Loyola Marymount University and Loyola Law School

The Marriage Of Biology And Applied Mathematics, Maggie Oneil

Research & Exhibition

Cells are able to perform different functions in response to conditions in their environment through regulated gene expression. This gene expression is regulated byproteins called transcription factors which can turn genes “on” or “off” depending on fwhat the cell needs, and these proteins can either work together in networks or workon their own. These networks and interactions between proteins can be expressedusing math and computer science to form a network “graph.” My project will be toexpress the mathematical properties of the network in a way which can help usersbetter understand the relationships of these proteins. To do this, I will ...


Statistical Tools For Transgene Copy Number Estimation Based On Real-Time Pcr, Joshua Yuan, Jason N Burris, Nathan Stewart, Ayalew Mentewab, C. Stewart 2015 University of Tennessee - Knoxville

Statistical Tools For Transgene Copy Number Estimation Based On Real-Time Pcr, Joshua Yuan, Jason N Burris, Nathan Stewart, Ayalew Mentewab, C. Stewart

C. Neal Stewart Jr.

Background

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination.

Results

Three experimental designs and four data quality control integrated statistical models are ...


Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe 2015 University of Nebraska-Lincoln

Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe

Dissertations and Theses in Biological Sciences

Inland waters cover about 2.5 percent of our planet and harbor huge numbers of known and unknown microorganisms including viruses. Viruses likely play dynamic, albeit largely undocumented roles in regulating microbial communities and in recycling nutrients in the ecosystem. Phycodnaviruses are a genetically diverse, yet morphologically similar, group of large dsDNA-containing viruses (160- to 560-kb) that inhabit aquatic environments. Members of the genus Chlorovirus are common in freshwater. They replicate in eukaryotic, single-celled, chlorella-like green algae that normally exist as endosymbionts of protists in nature. Very little is known about the natural history of the chloroviruses and how they ...


Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University 2015 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.


The Conformation Of Yeast Chromosome Iii Is Mating Type Dependent And Controlled By The Recombination Enhancer, Jon-Matthew Belton, Bryan R. Lajoie, Sylvain Audibert, Sylvain Cantaloube, Imen Lassadi, Isabelle Goiffon, Davide Bau, Marc A. Marti-Renom, Kerstin Bystricky, Job Dekker 2015 University of Massachusetts Medical School

The Conformation Of Yeast Chromosome Iii Is Mating Type Dependent And Controlled By The Recombination Enhancer, Jon-Matthew Belton, Bryan R. Lajoie, Sylvain Audibert, Sylvain Cantaloube, Imen Lassadi, Isabelle Goiffon, Davide Bau, Marc A. Marti-Renom, Kerstin Bystricky, Job Dekker

Open Access Articles

Mating-type switching in yeast occurs through gene conversion between the MAT locus and one of two silent loci (HML or HMR) on opposite ends of the chromosome. MATa cells choose HML as template, whereas MATalpha cells use HMR. The recombination enhancer (RE) located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating-type-specific and possibly RE-dependent chromosome folding. Here, we use Hi-C, 5C, and live-cell imaging to characterize the conformation of chromosome III in both mating types. We discovered a mating-type-specific conformational difference in the left arm. Deletion of a 1-kb subregion within ...


Hic-Pro: An Optimized And Flexible Pipeline For Hi-C Data Processing, Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot 2015 Institut Curie

Hic-Pro: An Optimized And Flexible Pipeline For Hi-C Data Processing, Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot

Open Access Articles

HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant ...


Apply Data Clustering To Gene Expression Data, Abdullah Jameel Abualhamayl Mr. 2015 California State University, San Bernardino

Apply Data Clustering To Gene Expression Data, Abdullah Jameel Abualhamayl Mr.

Electronic Theses, Projects, and Dissertations

Data clustering plays an important role in effective analysis of gene expression. Although DNA microarray technology facilitates expression monitoring, several challenges arise when dealing with gene expression datasets. Some of these challenges are the enormous number of genes, the dimensionality of the data, and the change of data over time. The genetic groups which are biologically interlinked can be identified through clustering. This project aims to clarify the steps to apply clustering analysis of genes involved in a published dataset. The methodology for this project includes the selection of the dataset representation, the selection of gene datasets, Similarity Matrix Selection ...


A Survey Of The Common Loon (Gavia Immer) Genome Reveals Patterns Of Natural Selection, Zach G. Gayk 2015 Northern Michigan University

A Survey Of The Common Loon (Gavia Immer) Genome Reveals Patterns Of Natural Selection, Zach G. Gayk

All NMU Master's Theses

With rapid advances in Next-Generation Sequencing technology, comparative genomics has become a viable method for studying the adaptation of species to their environment at the genome level. I investigated this in common loons (Gavia immer)—for which molecular adaptation has not been characterized—by finding signatures of positive selection as evidence for genomic adaptation.

I used Illumina short read sequencing data from a single female common loon to produce a fragmented assembly of the common loon (Gavia immer) genome. The resulting assembly had a contig N50 of 814 bp, a total length of 767,326,331 bp, and 45.7 ...


Intent Classification Of Short-Text On Social Media, Hemant Purohit, Guozhu Dong, Valerie L. Shalin, Krishnaprasad Thirunarayan, Amit P. Sheth 2015 Wright State University - Main Campus

Intent Classification Of Short-Text On Social Media, Hemant Purohit, Guozhu Dong, Valerie L. Shalin, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Social media platforms facilitate the emergence of citizen communities that discuss real-world events. Their content reflects a variety of intent ranging from social good (e.g., volunteering to help) to commercial interest (e.g., criticizing product features). Hence, mining intent from social data can aid in filtering social media to support organizations, such as an emergency management unit for resource planning. However, effective intent mining is inherently challenging due to ambiguity in interpretation, and sparsity of relevant behaviors in social data. In this paper, we address the problem of multiclass classification of intent with a use-case of social data generated ...


Early Seed Development Responses In Cereals Under Environmental Stresses, Kevin Begcy 2015 University of Nebraska-Lincoln

Early Seed Development Responses In Cereals Under Environmental Stresses, Kevin Begcy

Kevin Begcy

Plants are influenced by a large number of environmental factors. The search for higher yields at lower costs requires detailed knowledge of physiology, biochemistry, molecular and genetic level of plants, in order to optimize the relationship between different factors of production for maximum performance. Reproductive development has been demonstrated to be especially highly sensitive to environmental stresses. Within environmental stresses, drought and heat stress are the major restrictors of food production worldwide. With decreasing supplies of freshwater, increase in average temperature and predictions for the increased frequency of extreme precipitation events, there is a critical need for developing crops that ...


Effectiveness Of Group Kickboxing As A Means To Improve Gait And Balance In Individuals With Ms, Kurt Jackson, Kimberly Bigelow, Christina Cooper, Harold Merriman 2015 University of Dayton

Effectiveness Of Group Kickboxing As A Means To Improve Gait And Balance In Individuals With Ms, Kurt Jackson, Kimberly Bigelow, Christina Cooper, Harold Merriman

Harold L. Merriman

In recent years, there has been a particular emphasis on identifying and delivering appropriate therapeutic interventions that address the significant balance and gait impairments that affect individuals with multiple sclerosis (MS). Group interventions implemented in community settings have been especially of interest, including tai chi classes. Recently, the authors conducted a preliminary study to examine whether group kick-boxing, which requires more vigorous movements, might be a feasible intervention. Initial findings showed promise and led the authors to pursue a more rigorous follow-up study, with the objective of determining whether a 5-week group kickboxing class improved clinical measures of balance and ...


Identifying Molecular Differences In Pigs With Extreme Phenotypes For Weight Gain And Viral Load In Response To Prrs, Martine Schroyen, Juan Steibel, Igseo Choi, James Koltes, Christopher Eisley, Eric Fritz-Waters, James Reecy, Jack Dekkers, Bob Rowland, Joan Lunney, Catherine Ernst, Christopher Tuggle 2015 Iowa State University

Identifying Molecular Differences In Pigs With Extreme Phenotypes For Weight Gain And Viral Load In Response To Prrs, Martine Schroyen, Juan Steibel, Igseo Choi, James Koltes, Christopher Eisley, Eric Fritz-Waters, James Reecy, Jack Dekkers, Bob Rowland, Joan Lunney, Catherine Ernst, Christopher Tuggle

James M Reecy

Blood transcriptome analyses in the early phase after infection with the Porcine Reproductive and Respiratory Syndrome virus (PRRSv) revealed differential gene expression patterns and regulatory networks between pigs with extreme phenotypes for weight gain and viral load. Understanding these differences could lead to identifying biomarkers that would predict which pigs would be more resistant to PRRS.


A Survey Of Big Data Research, Hua Fang, Zhaoyang Zhang, Chanpaul Wang, Mahmoud Daneshmand, Chonggang Wang, Honggang Wang 2015 University of Massachusetts Medical School

A Survey Of Big Data Research, Hua Fang, Zhaoyang Zhang, Chanpaul Wang, Mahmoud Daneshmand, Chonggang Wang, Honggang Wang

Hua Julia Fang

Big data create values for business and research, but pose significant challenges in terms of networking, storage, management, analytics, and ethics. Multidisciplinary collaborations from engineers, computer scientists, statisticians, and social scientists are needed to tackle, discover, and understand big data. This survey presents an overview of big data initiatives, technologies, and research in industries and academia, and discusses challenges and potential solutions.


Satpdb: A Database Of Structurally Annotated Therapeutic Peptides, Sandeep Singh 2015 Institute of Microbial Technology, IMTECH

Satpdb: A Database Of Structurally Annotated Therapeutic Peptides, Sandeep Singh

Sandeep Singh

SATPdb (http://crdd.osdd.net/raghava/satpdb/) is a database of structurally annotated therapeutic peptides, curated from 22 public domain peptide databases/datasets including 9 of our own. The current version holds 19192 unique experimentally validated therapeutic peptide sequences having length between 2 and 50 amino acids. It covers peptides having natural, non-natural and modified residues. These peptides were systematically grouped into 10 categories based on their major function or therapeutic property like 1099 anticancer, 10585 antimicrobial, 1642 drug delivery and 1698 antihypertensive peptides. We assigned or annotated structure of these therapeutic peptides using structural databases (Protein Data Bank) and ...


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