Digital Commons Network^™

Evaluation Of The Metabolic Response, Blood Chemistry Profile, And Cardiac Morphology Of Beef Heifers Supplemented With Zilpaterol Hydrochloride Followed By An Endocrine Induced Stress Challenge, Joe O. Buntyn

Department of Animal Science: Dissertations, Theses, and Student Research

The objective of this study was to determine the metabolic, stress, hematology, organ weights, histology and cardiac anatomical features of beef heifers supplemented with zilpaterol hydrochloride (ZH) when exposed to a corticotropin-releasing hormone (CRH) and arginine vasopressin (VP) challenge. Crossbred heifers (n = 20; 556 ± 7 kg BW) were randomized into two treatment groups: 1) Control (CON): no ZH, and 2) Zilpaterol (ZIL): supplemented with ZH at 8.33 mg / kg (DM basis). The ZIL group was supplemented ZH for 20 d, with a 3-d withdrawal period. On d 24, heifers received an intravenous bolus of CRH (0.3 µg …

Evaluating The Impacts Of Sleep Disruptions In Women Through Automated Analysis (Sjsl Framework), Shalini Gupta

Industrial, Manufacturing, and Systems Engineering Dissertations - Archive

The proposed research suggests a solution for female sleep disruption by using automated analytics and attempts to improve our understanding of sleep disruption physiology. Although, sleep disruption monitoring is gaining attention with the use of sleep monitoring devices that track sleep disruptions. Automated technology can capture repeated measurements, evaluate sleep patterns, and make suggestions. However, facts revealed by clinical research suggest that it can measure sleep – disruption records, and sleep disorders. Moreover, this research can be useful for prescribing individual treatment, and hence improve individual healthcare optimization. In fact, some of the health tracking electronic devices assist individuals in …

Effects Of Salt And Nitrite Concentration On The Shelf Life Of Deli-Style Ham, Regan Elise Stanley

Department of Animal Science: Dissertations, Theses, and Student Research

Deli-style hams were manufactured to measure the effects of salt and nitrite concentration on shelf life and physicochemical characteristics. Three replications of deli-style ham treatments were manufactured in a 3 x 4 factorial arrangement of salt concentration (0.7%, 1.4%, or 2.1%, meat block basis) and nitrite concentration and source (0 ppm, 100 ppm or 200 ppm sodium nitrite, SN, or 100 ppm sodium nitrite equivalent from pre-converted celery juice powder, CP; Veg Stable 506, Florida Food Products). Salt concentration, water activity, cook yield, and texture profile analysis (TPA) were measured on w 0. Color, pH, residual nitrite, and aerobic and …

Development Of Terminal And Maternal Economic Selection Indices In Beefmaster Cattle, Kathleen Pearl Ochsner

Department of Animal Science: Dissertations, Theses, and Student Research

In the design of economic selection indices, the relative importance of traits in the breeding objective is reflected by their relative economic weighting. The objective of this study was to develop two economic selection indices for Beefmaster cattle: one for a terminal production system and one for a maternal production system. The terminal index was developed assuming bulls are mated to mature cows with all resulting progeny harvested. The maternal index was developed assuming bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning.

National average prices from 2010 …

Β1 Integrin- And Jnk-Dependent Tumor Growth Upon Hypofractionated Radiation., Aejaz Sayeed, Huimin Lu, Qin Liu, David Deming, Alexander Duffy, Peter Mccue, Adam P. Dicker, Roger J. Davis, Dmitry Gabrilovich, Ulrich Rodeck, Dario C. Altieri, Lucia R. Languino

Department of Cancer Biology Faculty Papers

Radiation therapy is an effective cancer treatment modality although tumors invariably become resistant. Using the transgenic adenocarcinoma of mouse prostate (TRAMP) model system, we report that a hypofractionated radiation schedule (10 Gy/day for 5 consecutive days) effectively blocks prostate tumor growth in wild type (β1wt /TRAMP) mice as well as in mice carrying a conditional ablation of β1 integrins in the prostatic epithelium (β1pc-/- /TRAMP). Since JNK is known to be suppressed by β1 integrins and mediates radiation-induced apoptosis, we tested the effect of SP600125, an inhibitor of c-Jun amino-terminal kinase (JNK) in the TRAMP model system. Our results show …

Cutr Connections [August 2016], Cutr

CUTR Newsletters

No abstract provided.

General Catalog 2016-2017, Utah State University

University Catalogs

This catalog contains information on the Academic Departments and Programs as well as Course Descriptions for the above school year at Utah State University. To avoid large file downloads, the Academic Departments and Programs information is located in this file. The Course Description information is located in the secondary file.

Three Siblings With Familial Non-Medullary Thyroid Carcinoma: A Case Series, Owais Rashid, Naeemul Haque, Saad Farooq, Zareen Kiran,, Sabeeh Siddique, Shahid Pervez

Department of Biological & Biomedical Sciences

Abstract

BACKGROUND:

In 2015, thyroid carcinoma affected approximately 63,000 people in the USA, yet it remains one of the most treatable cancers. It is mainly classified into medullary and non-medullary types. Conventionally, medullary carcinoma was associated with heritability but increasing reports have now begun to associate non-medullary thyroid carcinoma with a genetic predisposition as well. It is important to identify a possible familial association in patients diagnosed with non-medullary thyroid carcinoma because these cancers behave more destructively than would otherwise be expected. Therefore, it is important to aggressively manage such patients and screening of close relatives might be justified. Our …

Nonparametric Tests For The Interaction In Two-Way Factorial Designs Using R, Jos Feys

The R Journal

An increasing number of R packages include nonparametric tests for the interaction in two-way factorial designs. This paper briefly describes the different methods of testing and reports the resulting p-values of such tests on datasets for four types of designs: between, within, mixed, and pretest-posttest designs. Potential users are advised only to apply tests they are quite familiar with and not be guided by p-values for selecting packages and tests.

Using Decipher V2.0 To Analyze Big Biological Sequence Data In R, Erik S. Wright

The R Journal

In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity. It is now common to collect or have access to many gigabytes of biological sequences. This has created an urgent need for approaches that analyze sequences in subsets without requiring all of the sequences to be loaded into memory at one time. It has also opened opportunities to improve the organization and accessibility of information acquired in sequencing projects. The DECIPHER package offers solutions to these problems by assisting in the curation of large sets of biological sequences stored in …

Swmpr: An R Package For Retrieving, Organizing, And Analyzing Environmental Data For Estuaries, Marcus W. Beck

The R Journal

The System-Wide Monitoring Program (SWMP)was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, and analysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to …

Variable Clustering In High-Dimensional Linear Regression: The R Package Clere, Loïc Yengo, Julien Jacques, Christophe Biernacki, Mickael Canouil

The R Journal

Dimension reduction is one of the biggest challenges in high-dimensional regression models. We recently introduced a new methodology based on variable clustering as a means to reduce dimensionality. We present here the R package clere that implements some refinements of this methodology. An overview of the package functionalities as well as examples to run an analysis are described. Numerical experiments on real data were performed to illustrate the good predictive performance of our parsimonious method compared to standard dimension reduction approaches.

Editorial, Michael Lawrence

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 8, Issue 1 of the R Journal. This issue contains 27 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). It thus provides a small but current cross-section of the burgeoning R ecosystem.

Metaplus: An R Package For The Analysis Of Robust Meta-Analysis And Meta-Regression, Ken J. Beath

The R Journal

The metaplus package is described with examples of its use for fitting meta-analysis and meta-regression. For either meta-analysis or meta-regression it is possible to fit one of three models: standard normal random effect, t-distribution random effect or mixture of normal random effects. The latter two models allow for robustness by allowing for a random effect distribution with heavier tails than the normal distribution, and for both robust models the presence of outliers may be tested using the parametric bootstrap. For the mixture of normal random effects model the outlier studies may be identified through their posterior probability of membership in …

Progenyclust: An R Package For Progeny Clustering, Chenyue W. Hu, Amina A. Qutub

The R Journal

Identifying the optimal number of clusters is a common problem faced by data scientists in various research fields and industry applications. Though many clustering evaluation techniques have been developed to solve this problem, the recently developed algorithm Progeny Clustering is a much faster alternative and one that is relevant to biomedical applications. In this paper, we introduce an R package progenyClust that implements and extends the original Progeny Clustering algorithm for evaluating clustering stability and identifying the optimal cluster number. We illustrate its applicability using two examples: a simulated test dataset for proof-of-concept, and a cell imaging dataset for demonstrating …

Statmod: Probability Calculations For The Inverse Gaussian Distribution, Göknur Giner, Gordon K. Smyth

The R Journal

The inverse Gaussian distribution (IGD) is a well known and often used probability distribution for which fully reliable numerical algorithms have not been available. We develop fast, reliable basic probability functions (dinvgauss, pinvgauss, qinvgauss and rinvgauss) for the IGD that work for all possible parameter values and which achieve close to full machine accuracy. The most challenging task is to compute quantiles for given cumulative probabilities and we develop a simple but elegant mathematical solution to this problem. We show that Newton’s method for finding the quantiles of a IGD always converges monotonically when started from the mode of the …

Sbtools: A Package Connecting R To Cloud-Based Data For Collaborative Online Research, Luke A. Winslow, Scott Chamberlain, Alison P. Appling, Jordan S. Read

The R Journal

The adoption of high-quality tools for collaboration and reproducibile research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A number of scientific data repositories are coming online and are often focused on dataset archival and publication. To handle collaborative workflows using large scientific datasets, there is increasing need to connect cloud-based online data storage to R. In this article, we describe how the new R package sbtools enables direct …

Fwdselect: An R Package For Variable Selection In Regression Models, Marta Sestelo, Nora M. Villanueva, Luis Meira-Machado, Javier Roca-Pardiñas

The R Journal

In multiple regression models, when there are a large number (p) of explanatory variables which may o rmay not be relevant for predicting the response, it is useful to be able to reduce the model. To this end, it is necessary to determine the best subset of q (q p) predictors which will establish the model with the best prediction capacity. FWDselect package introduces a new forward stepwise based selection procedure to select the best model in different regression frameworks (parametric or nonparametric). The developed methodology, which can be equally applied to linear models, generalized linear models or generalized additive …

The R Journal (August 2016) 8(1): Complete Issue, The R Foundation

The R Journal

Editorial, Michael Lawrence

Contributed Research Articles

metaplus: An R Package for the Analysis of Robust Meta-Analysis and Meta-Regression, Ken J. Beath

Gender Prediction Methods Based on First Names with genderizeR, Kamil Wais

Conditional Fractional Gaussian Fields with the Package FieldSim, Alexandre Brouste, Jacques Istas, and Sophie Lambert-Lacroix

rTableICC: An R Package for Random Generation of 22K and RC Contingency Tables, Haydar Demirhan

Maps, Coordinate Reference Systems and Visualising Geographic Data with mapmisc, Patrick E. Brown

Variable Clustering in High-Dimensional Linear Regression: The R Package clere, Loïc Yengo, Julien Jacques, Christophe Biernacki, and Mickael Canouil

Stylometry with R: A Package for …

Cheers To Haptic Sensations And Alcohol Consumption: How Glassware Weight Impacts Perceived Intoxication And Positive Emotions, Courtney Szocs, Dipayan Biswas, Adilson Borges

Business Faculty Publications and Presentations

People often consume alcohol as a means of emotional control. More specifically, people frequently consume alcohol to enhance positive feelings (e.g., happiness) and reduce negative feelings (e.g., stress, tension). The results of two field studies and one laboratory study showed that holding the volume of alcohol consumed constant and varying the haptic (i.e., weight) sensations individuals experience during consumption can influence these emotional responses and also perceived intoxication. Specifically, we manipulated haptic weight sensations by varying the weight of the cup/container (e.g., champagne flute) alcohol was consumed from and showed that consuming champagne from lighter (vs. heavier) flutes leads to …

The History Of Algorithmic Complexity, Audrey A. Nasar

The Mathematics Enthusiast

This paper provides a historical account of the development of algorithmic complexity in a form that is suitable to instructors of mathematics at the high school or undergraduate level. The study of algorithmic complexity, despite being deeply rooted in mathematics, is usually restricted to the computer science curriculum. By providing a historical account of algorithmic complexity through a mathematical lens, this paper aims to equip mathematics educators with the necessary background and framework for incorporating the analysis of algorithmic complexity into mathematics courses as early on as algebra or pre-calculus.

A Two-Strain Tb Model With Multiple Latent Stages, Azizeh Jabbari, Carlos Castillo-Chavez, Fereshteh Nazari, Baojun Song, Hossein Kheiri

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

A two-strain tuberculosis (TB) transmission model incorporating antibiotic-generated TB resistant strains and long and variable waiting periods within the latently infected class is introduced. The mathematical analysis is carried out when the waiting periods are modeled via parametrically friendly gamma distributions, a reasonable alternative to the use of exponential distributed waiting periods or to integral equations involving "arbitrary" distributions. The model supports a globally-asymptotically stable disease-free equilibrium when the reproduction number is less than one and an endemic equilibriums, shown to be locally asymptotically stable, or l.a.s., whenever the basic reproduction number is greater than one. Conditions for the existence …

Neurobiological Correlates Of Stress And The Pathophysiology Of Depression: Associations Among Social Victimization, Il-6, Crp, And Bdnf Val66met, Allyson Antoinette Arana

Psychology Dissertations - Archive

Peer victimization, a common psychosocial stressor in adolescence, is linked to adverse health outcomes ranging from depression to changes in biological functioning. Social victimization is particularly harmful given the importance placed on peer relations and social status during this developmental period. This dissertation evaluated the associations among social victimization, physical health, psychological health, the BDNF Val66Met polymorphism, and inflammatory biomarkers (IL-6 and CRP) in a diverse sample of adolescents (N = 254). Social victimization was related to depressive symptoms, health problems, and inflammation, partially replicating a previous study. BDNF Val66Met moderated the link between social victimization and health outcomes, such …

Synthesis And Application Of Porphyrinated Latex Particles For Photodynamic Therapy, Brian Quang Bui

Physics Dissertations - Archive

Photodynamic Therapy is a cancer treatment that requires a photosensitizer to reach a tumor in order to be excited by electromagnetic radiation sources so that the cancer killing agents such as Singlet Oxygen can be generated. In this work, the photosensitizer Protoporphyrin IX (PPIX) is improved with PS4VP nanoparticles to exhibit better photosensitive properties in aqueous solutions. Improvements include spectroscopic properties like absorption and photoluminescence emissions. In vitro studies showed better cell uptake, dark toxicity and photodynamic action, killing up to 85% of PC3 prostate cancer cells. Typical PPIX characteristics including photo-bleaching and photo-modification were also observed when nanoparticle variations …

The Role Of Hotair In Skeletal Muscle Myogenesis, Fritzlaine Roche

Chemistry & Biochemistry Theses - Archive

Skeletal muscle function is a vital requirement for an enriched healthy life. For years the molecular processes governing myogenesis and the development of skeletal muscle were primarily associated with proteins. In recent years, however, non-coding RNAs including microRNAs (miRNAs) and long non coding RNAs (lncRNAs) have emerged as integral components of gene regulation that take part in cellular differentiation, development and disease. HOTAIR (HOX antisense intergenic RNA) is a long non-coding RNA (lncRNA) that is transcribed from the antisense strand of the homeobox C (HOXC) gene locus present on chromosome 12. HOTAIR has been shown to have a regulatory role …

Antibacterial Drug Design And Discovery Via Vitamin B1 Biosynthetic Pathway, Abu Afzal Mohammad Shakar

Chemistry & Biochemistry Theses - Archive

Antibiotics play a vital role in fighting infectious disease caused by bacterial species. Antimicrobial resistance has been shown for every current antibiotic and poses a major health risk. To combat these growing threats to human health; new molecules must be investigated to treat bacterial infection. Chemical inhibition of the vitamin B1 biosynthetic pathway in the bacterial cell was hypothesized to inhibit the survival of bacteria. A series of synthetic molecules, which resemble metabolites of the vitamin B1 pathway, exhibit the inhibition of specific enzymes within this pathway and display initial activity against bacterial growth and survival. The beneficial activity of …

Gene Expression Differences In Hybrids At Beginning Of Speciation Continuum, Long A. Nicholas

Biology Theses - Archive

The formation of new species results from reproductive isolation, or the barrier to successful mating between organisms of divergent populations. The degree of reproductive isolation can be measured by the reduction in fitness of hybrid offspring that can result from incompatibilities between the genotypes of each parent. In this study, genetic incompatibilities arising at the earliest stage of speciation are examined between intraspecific hybrids in which an effectively sterile hybrid phenotype termed “still” is observed at ~50% frequency in crosses between divergent populations of Tribolium castaneum. Timing and magnitude of gene expression regulation is examined at four stages of development, …

West Florida Shelf Upwelling: Origins And Pathways, Robert H. Weisberg, Lianyuan Zheng, Yonggang Liu

Marine Science Faculty Publications

Often described as oligotrophic, the west Florida continental shelf supports abundant fisheries, experiences blooms of the harmful alga, Karenia brevis, and exhibits subsurface chlorophyll maxima evident in shipboard and glider surveys. Renewal of inorganic nutrients by the upwelling of deeper ocean water onto the shelf may account for this, but what are the origins and pathways by which such new water may broach the shelf break and advance toward the shoreline? We address these questions via numerical model simulations of pseudo-Lagrangian, isopycnic water parcel trajectories. Focus is on 2010, when the west Florida shelf was subjected to an anomalously protracted …

Offshore Forcing On The “Pressure Point” Of The West Florida Shelf: Anomalous Upwelling And Its Influence On Harmful Algal Blooms, Yonggang Liu, Robert H. Weisberg, Jason M. Lenes, Lianyuan Zheng, Katherine Hubbard, John J. Walsh

Marine Science Faculty Publications

Gulf of Mexico Loop Current (LC) interactions with the West Florida Shelf (WFS) slope play an important role in shelf ecology through the upwelling of new inorganic nutrients across the shelf break. This is particularly the case when the LC impinges upon the shelf slope in the southwest portion of the WFS near the Dry Tortugas. By contacting shallow water isobaths at this “pressure point” the LC forcing sets the entire shelf into motion. Characteristic patterns of LC interactions with the WFS and their occurrences are identified using unsupervised neural network, self-organizing map, from 23 years (1993–2015) of altimetry data. …

Alaska Nurse Practitioner Practices Regarding Adolescent Indoor Tanning, Monica H. Perez-Verdia

Student Projects for Graduate Degrees

Skin cancer is the most prevalent form of cancer in the United States and melanoma is the second most common form of cancer in adolescents. Indoor tanning increases the risk of skin cancer especially when exposure begins at an early age. A significant percentage of adolescents indoor tan begining at an early age. Guidelines recommend that clinicians address indoor tanning use and avoidance behaviors with adolescents and their guardians. The purpose of this project is to assess Alaska nurse practitioner practices regarding adolescent indoor tanning and to provide nurse practitioners with evidence‐based tools for counseling that are current with clinical …