Digital Commons Network^™

Dna Analysis Using Grammatical Inference, Cory Cook

Master's Projects

An accurate language definition capable of distinguishing between coding and non-coding DNA has important applications and analytical significance to the field of computational biology. The method proposed here uses positive sample grammatical inference and statistical information to infer languages for coding DNA.

An algorithm is proposed for the searching of an optimal subset of input sequences for the inference of regular grammars by optimizing a relevant accuracy metric. The algorithm does not guarantee the finding of the optimal subset; however, testing shows improvement in accuracy and performance over the basis algorithm.

Testing shows that the accuracy of inferred languages for …

Unpacking Social And Structural Roadblocks To Accessibility In Southern Illinois University Carbondale, Abimbola Olamide Iyun

Research Papers

This research paper alongside an audio documentary, Living In Our Space, explores from the perspective of four students with physical disabilities at Southern Illinois University (SIU) consistent issues of inaccessibility and its effects on students with disabilities at SIU. It explores what inaccessibility means for participants in this study and how it affects their lives. Data was gathered through the use of semi structured interviews and autobiographical accounts and analysed with thematic analysis and Invivo coding.

Intronic Cleavage And Polyadenylation Regulates Gene Expression During Dna Damage Response Through U1 Snrna, Emral Devany, Ji Yeon Park, Michael R. Murphy, George Zakusilo, Jorge Baquero, Xiaokan Zhang, Mainul Hoque, Bin Tian, Frida E. Kleiman

Publications and Research

The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage …

Electrical Double Layer Potential Distribution In Nanoporous Electrodes From Molecular Modeling And Classical Electrodynamics Analysis, Evan Marshall Ney

Theses

When a solid surface is immersed in a solution, the surface can become charged in a variety of ways including crystal lattice defects, dissociation of atoms or molecules, ionization of surface groups, and adsorption of external ions or, in the case of an electrode, via the application of an external potential. The excess charge at the surface results in an accumulation of mobile ions in the solution near the surface. Relative to the charge on the surface, ions of opposite charge (counterions) build up near the surface to neutralize the surface charge, and ions of like charge (coions) are depleted …

Observed Shifts In The Contact Zone Between Two Forms Of The Diving Beetle Hydroporus Memnonius Are Consistent With Predictions From Sexual Conflict., David T. Bilton, Garth N. Foster

School of Biological and Marine Sciences

Sexual conflict drives both inter- and intrasexual dimorphisms in many diving beetles, where male persistence and female resistance traits co-evolve in an antagonistic manner. To date most studies have focussed on species where rough and smooth females and their associated males typically co-occur within populations, where phenotype matching between morphs may maintain forms as stable polymorphisms. The Palaearctic diving beetle Hydroporus memnonius is characterised by having dimorphic (rough var. castaneus and smooth, shining) females and associated males which differ in persistence traits; the two forms being largely distributed parapatrically. In this species, instead of mating trade-offs between morphs, males associated …

Stemming On Stem: A Stem Education Framework For Students With Disabilities, Jiwon Hwang, Jonte C. Taylor

Journal of Science Education for Students with Disabilities

There has been increased attention paid to science, technology, engineering, and mathematics also known as STEM. The focus on STEM has been both educational and occupational. Unfortunately, students with disabilities perform below their peers without disabilities in math and science. The authors discuss issues related to STEM and students with disabilities. These issues include (1) traditional views of STEM education, (2) the importance of STEM education, and (3) students with disabilities performance in STEM. The authors posit a framework for STEM education for students with disabilities and promote the incorporation of the arts to increase students’ STEM knowledge and achievement.

Developing A Sustainable Water Supply In The American West: The Case Of Rio Rancho, New Mexico, Hubert B. Stroud, Mary K. Kilmer

Suburban Sustainability

Suburban and urban communities in the American West are challenged by rapid population growth combined with limited natural resources. Supporting sustainable development is of great concern in this region and in similar regions throughout the world. This research examines the sustainability of the water supply within a rapidly growing suburban city in the American West. The city, Rio Rancho, New Mexico, began as an interstate land sales operation and rapidly became a “boom” town, in part because of its location near metropolitan Albuquerque.

Because of a very limited water supply and an increasing demand for water associated with population growth, …

Escherichia Coli O157:H7 Strains Isolated From High-Event Period Beef Contamination Have Strong Biofilm-Forming Ability And Low Sanitizer Susceptibility, Which Are Associated With High Po157 Plasmid Copy Number, Rong Wang, Brandon E. Luedtke

Roman L. Hruska U.S. Meat Animal Research Center: Reports

In the meat industry, a high-event period (HEP) is defined as a time period when beef processing establishments experience an increased occurrence of product contamination by Escherichia coli O157:H7. Our previous studies suggested that bacterial biofilm formation and sanitizer resistance might contribute to HEPs. We conducted the present study to further characterize E. coli O157:H7 strains isolated during HEPs for their potential to cause contamination and to investigate the genetic basis for their strong biofilm-forming ability and high sanitizer resistance. Our results show that, compared with the E. coli O157:H7 diversity control panel strains, the HEP strains had a significantly …

The Ticker, June 13, 2016

The Ticker

The Ticker is the student newspaper of Baruch College. It has been published continuously since 1932, when the Baruch College campus was the School of Business and Civic Administration of the City College of New York.

Nx∙∙Y Halogen Bonds. Comparison With Nh∙∙Y H-Bonds And Cx∙∙Y Halogen Bonds, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations examine how the NH∙∙Y H-bond compares to the equivalent NX∙∙Y halogen bond, as well as to comparable CH/CX donors. Succinimide and saccharin, and their corresponding halogen-substituted derivatives, are chosen as the prototype NH/NX donors, paired with a wide range of electron donor molecules. The NH∙∙Y H-bond is weakened if the bridging H is replaced by Cl, and strengthened by I; a Br halogen bond is roughly comparable to a H-bond. The lone pairs of the partner molecule are stronger electron donors than are π-systems. Whereas Coulombic forces represent the largest fraction of the attractive force in the H-bonds, …

Expanded Parameters In The Self-Organized Critical Forest Fire Model, Riley Self

Senior Theses

The forest fire model has been used to test the theory of Self-Organized Criticality as a model of complexity. The goal is to search for scale invariance in randomly generated forest fires using a computer simulation. In a previous model by B. Drossel and F. Schwabl,¹ power-law behavior was seen when the nearest neighbors to a tree on fire catch on fire, and it has been assumed that if further trees also catch fire, then it will still exhibit self-organized criticality, showing scale invariance. Testing this assumption aids to the exploration of the applicability of self-organized criticality because the …

Environmental Impact Report Draft, Uc Hastings College Of The Law

Long Range Campus Planning Archive

No abstract provided.

Plant Biology Alum Headed Food Safety At Pepsico Gets International Award, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

Michael Jaramillo Positional Covariance In Multi-Wavelength Astronomy, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

Hexavalent Chromium Induces Malignant Transformation Of Human Lung Bronchial Epithelial Cells Via Ros-Dependent Activation Of Mir-21-Pdcd4 Signaling, Poyil Pratheeshkumar, Young-Ok Son, Sasidharan Padmaja Divya, Lilia Turcios, Ram Vinod Roy, John Andrew Hitron, Lei Wang, Donghern Kim, Jin Dai, Padmaja Asha, Zhuo Zhang, Xianglin Shi

Center for Research on Environmental Disease Faculty Publications

Hexavalent chromium [Cr(VI)] is a well-known human carcinogen associated with an increased risk of lung cancer. However, the mechanisms underlying Cr(VI)-induced carcinogenesis remain unclear. MicroRNA-21 (miR-21) is a key regulator of oncogenic processes. Studies have shown that miR-21 exerts its oncogenic activity by targeting the tumor suppressor gene programmed cell death 4 (PDCD4). The present study examined the role of miR-21-PDCD4 signaling in Cr(VI)-induced cell transformation and tumorigenesis. Results showed that Cr(VI) induces ROS generation in human bronchial epithelial (BEAS-2B) cells. Chronic exposure to Cr(VI) is able to cause malignant transformation in BEAS-2B cells. Cr(VI) caused a significant increase of …

Combining Doe With An Empirical Approach To Improve Vaccine Formulation Development, Jill Livengood, Tim Powell, Melissa Bushey

Vaccine Technology VI

Vaccine development and formulation is based upon understanding of the candidate’s target product profile, and leverages knowledge and experience in pharmaceutical products. Developing an optimal formulation takes into account factors such as ensuring route of administration, product stability, and identifying Quality Target Product Profiles that are suitable for the product’s intended use. Based upon such knowledge and experience, multiple excipient formulations may be first identified for initial screening. Achieving the QTPP is a measure of results, and can be achieved with screening formulations by aggressive accelerated stability study conditions to enable the final formulation components to be down-selected. This presentation …

(Mis)Representation By Bravo: Maintaining/Countering Stereotypes Of Black Women On Reality Television, Michelle Mayfield

Honors Theses

This honors thesis investigates the use of stereotypes used to portray Black women on reality television.  Focusing on Bravo’s Blood Sweat and Heels, this project utilizes an Afrosemiotic framework, which is a combination of Afrocentricity and Semiotics.  Afrocentricity focuses on the agency and consciousness of Africans and African Americans.  Semiotics focuses on the study of signs and the explicit and implicit markers of these signs.  The first season’s narrative focuses on the positive lives of single, successful Black women but shifts to mainly negative portrayals inspired by Bravo’s Real Housewives franchise.  This project focuses on stereotypes associated with Black …

Expression Of A Constitutively Active Nitrate Reductase Variant In Tobacco Reduces Tobacco-Specific Nitrosamine Accumulation In Cured Leaves And Cigarette Smoke, Jianli Lu, Leichen Zhang, Ramsey S. Lewis, Lucien Bovet, Simon Goepfert, Anne M. Jack, James D. Crutchfield, Huihua Ji, Ralph E. Dewey

Kentucky Tobacco Research and Development Center Faculty Publications

Burley tobaccos (Nicotiana tabacum) display a nitrogen-use-deficiency phenotype that is associated with the accumulation of high levels of nitrate within the leaf, a trait correlated with production of a class of compounds referred to as tobacco-specific nitrosamines (TSNAs). Two TSNA species, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N-nitrosonornicotine (NNN), have been shown to be strong carcinogens in numerous animal studies. We investigated the potential of molecular genetic strategies to lower nitrate levels in burley tobaccos by overexpressing genes encoding key enzymes of the nitrogen-assimilation pathway. Of the various constructs tested, only the expression of a constitutively active nitrate reductase (NR) …

The Restrictive Deterrent Effect Of Warning Banners In A Compromised Computer System, Christian Jordan-Michael Howell

USF Tampa Graduate Theses and Dissertations

System trespassing, which refers to the unauthorized access of computer systems, has rapidly become a worldwide phenomenon. Despite growing concern, criminological literature has paid system trespassing little attention. The current study utilizes data gathered from a Chinese computer network to examine system trespasser behavior after exposure to one of three warning messages: an altruistic message used for moral persuasion (warning 1), a legal sanction threat (warning 2), and an ambiguous threat (warning 3). More specifically, the current study examines the temporal order of various keystroke commands to determine if some keystroke commands are used as a tactical skill to avoid …

Cellulose Structural Polymorphism In Plant Primary Cell Walls Investigated By High-Field 2d Solid-State Nmr Spectroscopy And Density Functional Theory Calculations, Tuo Wang, Hui Yang, James D. Kubicki, Mei Hong

Faculty Publications

© 2016 American Chemical Society. The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) …

Il-4 Sensitivity Shapes The Peripheral Cd8+ T Cell Pool And Response To Infection, Kristin R. Renkema, June-Yong Lee, You Jeong Lee, Sara E. Hamilton, Kristin A. Hogquist, Stephen C. Jameson

Peer Reviewed Articles

Previous studies have revealed that a population of innate memory CD8⁺ T cells is generated in response to IL-4, first appearing in the thymus and bearing high expression levels of Eomesodermin (Eomes) but not T-bet. However, the antigen specificity and functional properties of these cells is poorly defined. In this study, we show that IL-4 regulates not only the frequency and function of innate memory CD8⁺ T cells, but also regulates Eomes expression levels and functional reactivity of naive CD8⁺ T cells. Lack of IL-4 responsiveness attenuates the capacity of CD8⁺ T cells to mount a …

Female Chromosome X Mosaicism Is Age-Related And Preferentially Affects The Inactivated X Chromosome, Mitchell J. Machiela, Weiyin Zhou, Eric Karlins, Joshua N. Sampson, Neal D. Freedman, Qi Yang, Belynda Hicks, Casey Dagnall, Christopher Hautman, Kevin B. Jacobs, Christian C. Abnet, Melinda C. Aldrich, Christopher Amos, Laufey T. Amundadottir, Alan A. Arslan, Laura E. Beane-Freeman, Sonja I. Berndt, Amanda Black, William J. Blot, Cathryn H. Bock, Paige M. Bracci, Louise A. Brinton, H Bas Bueno-De-Mesquita, Laurie Burdett, Julie E. Buring, Mary A. Butler, Federico Canzian, Tania Carreon, Kari G. Chaffee, I-Shou Chang, Nilanjan Chatterjee, Chu Chen, Constance Chen, Kexin Chen, Charles C. Chung, Linda S. Cook, Marta Crous Bou, Michael Cullen, Faith G. Davis, Immaculata De Vivo, Ti Ding, Jennifer Doherty

Dartmouth Scholarship

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events 4 2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses …

Psychological Factors That Underlie Hazing Perceptions: A Mixed Methods Study, Jenna Strawhun

College of Education and Human Sciences: Dissertations, Theses, and Student Research

The quantitative phase of this mixed-methods study examined psychological predictors, including previous bullying involvement, moral disengagement, the need to belong, and their influence on students’ perceptions of hypothetical hazing behaviors. The following qualitative phase was used to explain and contextualize Phase I results through an understanding of the psychological processes related to participants’ constructed meanings of their experiences as perpetrators, witnesses, and/or victims of bullying and hazing. Study participants for Phase I and Phase II included undergraduate students enrolled in psychology courses who participated in the study for research credit. Phase II participants also received a $25.00 gift card as …

Global Attractors And Random Attractors Of Reaction-Diffusion Systems, Junyi Tu

USF Tampa Graduate Theses and Dissertations

The dissertation studies about the existence of three different types of attractors of three multi-component reaction-diffusion systems. These reaction-diffusion systems play important role in both chemical kinetics and biological pattern formation in the fast-growing area of mathematical biology.

In Chapter 2, we prove the existence of a global attractor and an exponential attractor for the solution semiflow of a reaction-diffusion system called Boissonade equations in the L² phase space. We show that the global attractor is an (H, E) global attractor with the L^∞ and H² regularity and that the Hausdorff dimension and the …

Credit Availability For Tanzania's Small Businesses: A Gender Perspective, Josephat Lotto

Business Management Review

The purpose of this study was to examine whether firm and owners ' characteristics are driven by gender and whether gender is attributable to credit accessibility in small and locally-owned firms in Tanzania. The study uses data collected from 400 small businesses through questionnaires and interviews and analyses it using univariate and multivariate statistical tools The findings show that female owners are less educated, have less work experiences and their firms are relatively smaller and younger than in the case for males. Moreover, female-owned firms were more likely to be organised as sole proprietorship or partnerships. Also the findings indicate …

The Bet Inhibitor Jq1 Selectively Impairs Tumour Response To Hypoxia And Downregulates Ca9 And Angiogenesis In Triple Negative Breast Cancer, Ll Da Motta, I Ledaki, K Purshouse, S Haider, Et Al

Peninsula Medical School

The availability of bromodomain and extra-terminal inhibitors (BETi) has enabled translational epigenetic studies in cancer. BET proteins regulate transcription by selectively recognizing acetylated lysine residues on chromatin. BETi compete with this process leading to both downregulation and upregulation of gene expression. Hypoxia enables progression of triple negative breast cancer (TNBC), the most aggressive form of breast cancer, partly by driving metabolic adaptation, angiogenesis and metastasis through upregulation of hypoxia-regulated genes (for example, carbonic anhydrase 9 (CA9) and vascular endothelial growth factor A (VEGF-A). Responses to hypoxia can be mediated epigenetically, thus we investigated whether BETi JQ1 could impair the TNBC …

Local Muscle Metabolic Demand Induced By Neuromuscular Electrical Stimulation And Voluntary Contractions At Different Force Levels: A Nirs Study, Makii Muthalib, Graham Kerr, Kazunori Nosaka, Stephane Perrey

Research outputs 2014 to 2021

Functional Muscle metabolic demand during contractions evoked by neuromuscular electrical stimulation (NMES) has been consistently documented to be greater than voluntary contractions (VOL) at the same force level (10-50% maximal voluntary contraction-MVC). However, we have shown using a near-infrared spectroscopy (NIRS) technique that local muscle metabolic demand is similar between NMES and VOL performed at MVC levels, thus controversy exists. This study therefore compared biceps brachii muscle metabolic demand (tissue oxygenation index-TOI and total hemoglobin volume-tHb) during a 10s isometric contraction of the elbow flexors between NMES (stimulation frequency of 30Hz and current level to evoke 30% MVC) and VOL …

Conference Program (Vaccine Technology Vi), Laura A. Palomares, Tarit Mukhopadhyay, Manon Cox, Nathalie Garçon

Vaccine Technology VI

No abstract provided.

Nucleotide Interdependency In Transcription Factor Binding Sites In The Drosophila Genome, Jacqueline M. Dresch, Rowan G. Zellers, Daniel K. Bork, Robert A. Drewell

Biology

A long-standing objective in modern biology is to characterize the molecular components that drive the development of an organism. At the heart of eukaryotic development lies gene regulation. On the molecular level, much of the research in this field has focused on the binding of transcription factors (TFs) to regulatory regions in the genome known as cis-regulatory modules (CRMs). However, relatively little is known about the sequence-specific binding preferences of many TFs, especially with respect to the possible interdependencies between the nucleotides that make up binding sites. A particular limitation of many existing algorithms that aim to predict binding site …

Lack Of An Association Or An Inverse Association Between Low-Density-Lipoprotein Cholesterol And Mortality In The Elderly: A Systematic Review, Uffe Ravnskov, Rokura Hama, Tomohito Hamazaki, Paul J. Rosch, Tore Schersten, Ralf Sundberg

NYMC Faculty Publications

OBJECTIVE: It is well known that total cholesterol becomes less of a risk factor or not at all for all-cause and cardiovascular (CV) mortality with increasing age, but as little is known as to whether low-density lipoprotein cholesterol (LDL-C), one component of total cholesterol, is associated with mortality in the elderly, we decided to investigate this issue.

SETTING, PARTICIPANTS AND OUTCOME MEASURES: We sought PubMed for cohort studies, where LDL-C had been investigated as a risk factor for all-cause and/or CV mortality in individuals ≥60 years from the general population.

RESULTS: We identified 19 cohort studies including 30 cohorts with …