Digital Commons Network^™

Comparison Of Two Trap Net Designs For Sampling Muskellunge, Brian G. Blackwell, Todd M. Kaufman, Tyrel S. Moos, David O. Lucchesi

The Prairie Naturalist

Sampling adequate numbers of muskellunge (Esox masquinongy) is necessary to evaluate stocking success and to collect information on various population metrics (e.g., growth, condition, relative abundance). However, muskellunge are often difficult to sample with standard fish sampling gears. We collected muskellunge in trap nets of two different designs (large trap nets [1.5-m × 1.8-m frames, 1.5-m diameter hoops, double throated, single 1.5-m × 30.5-m lead and 19-mm knotless mesh] and small trap nets [0.9-m × 1.5-m frames, 0.9-m diameter hoops, single throat, single 0.9-m × 15.2-m lead and 19-mm knotted mesh]. We also estimated abundance of muskellunge (>600 mm …

Peptides: A Package For Data Mining Of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, Rodrigo Torres

The R Journal

Antimicrobial peptides (AMP) are a promising source of antibiotics with a broad spectrum activity against bacteria and low incidence of developing resistance. The mechanism by which an AMPexecutes its function depends on a set of computable physicochemical properties from the amino acid sequence. The Peptides package was designed to allow the quick and easy computation of ten structural characteristics own of the antimicrobial peptides, with the aim of generating data to increase the accuracy in classification and design of new amino acid sequences. Moreover, the options to read and plot XVG output files from GROMACS molecular dynamics package are included.

News From The Bioconductor Project, Bioconductor Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 1024 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/. Navigate packages using ‘biocViews’ terms and title search. Each package has an html page with a description, links to vignettes, reference manuals, and usage statistics. Start using Bioconductor version 3.1 by installing R 3.2.1 and evaluating the commandS

Book Review [Of At Home And At Large In The Great Plains: Essays And Memories], Janis Paseka

Nebraska Bird Review

Nebraska birders may remember reading some of the 14 essays published in this book, since they appeared previously in Prairie Fire, the monthly Great Plains public policy newspaper. Topics of the short and engaging essays range from changing bird life to outstanding birding areas to conservation in the Great Plains. We read about sediment deposits, the “gifts of glaciers past,” which were left by retreating rivers of ice thousands of years ago and resulted in the creation of the prairie potholes so important now to our waterfowl and wading birds. One essay marvels at the variety of animal skeletons, including …

I Know I Can: Feeling Confident About Discussing Cancer May Help Couples' Cancer Management, Kate Magsamen-Conrad, Maria K. Venetis, M. G. Checton, K. Greene

School of Media and Communication Faculty Publications

Managing chronic illness, especially something like cancer, affects more than the diagnosed person. Cancer also affects partners, families, and loved ones. In our study, we were interested in how cancer affects communication patterns between survivors and their partners. We wanted to apply a model that explains chronic illness management in couples to see if we could determine how parts of a relationship, uncertainty about cancer prognosis, and the confidence people have in talking with partners about the cancer affect couples’ ability to manage the disease.

Personality Traits And Prior Academic Learning As Predictors Of Student Success In High School Math Courses, Wilson Morris

Doctor of Education (EdD)

Academic institutions continue to find that the cost of a student’s failure of a core class has significant implications for that student’s overall academic success, from middle school through university level programs. Many intervention programs are retroactively planned as they are activated after the student has failed a number of core classes. This research investigated three measures of self-control, grit, and attitude toward math as possible predictors of student performance in a math class. Surveys were administered toward the beginning of the trimester to 46 high school students enrolled in four different geometry and algebra courses at a rural Oregon …

Titan International Couples Share Joy, Challenges, Anna Deters ’04

News and Events (Discontinued Series)

No abstract provided.

The Effect Of Osm On Mc3t3-E1 Osteoblastic Cells In Simulated Microgravity With Radiation, Jake Goyden, Ken Tawara, Danielle Hedeen, Jeffrey S. Willey, Julia Thom Oxford, Cheryl L. Jorcyk

Biomedical Research Institute Publications and Presentations

Bone deterioration is a challenge in long-term spaceflight with significant connections to patients experiencing disuse bone loss. Prolonged unloading and radiation exposure, defining characteristics of space travel, have both been associated with changes in inflammatory signaling via IL-6 class cytokines in bone. While there is also evidence for perturbed IL-6 class signaling in spaceflight, there has been scant examination of the connections between microgravity, radiation, and inflammatory stimuli in bone. Our lab and others have shown that the IL-6 class cytokine oncostatin M (OSM) is an important regulator of bone remodeling. We hypothesize that simulated microgravity alters osteoblast OSM signaling, …

Activity Of The Porcine Gonadotropin-Releasing Hormone Receptor Gene Promoter Is Partially Conferred By A Distal Gonadotrope Specific Element (Gse) Within An Upstream Enhancing Region, Two Proximal Gses And A Retinoid X Receptor Binding Site, Rebecca Cederberg, Jacqueline Smith, Emily A. Mcdonald, Chanho Lee, Amy R. Perkins, Brett R. White

Department of Animal Science: Faculty Publications

Background: Regulation of gonadotropin-releasing hormone (GnRH) receptor (GnRHR) numbers on gonadotropes within the anterior pituitary gland represents a critical point for control of reproductive function. Binding of GnRH to its receptor regulates follicle stimulating hormone (FSH) and luteinizing hormone (LH) release and levels of this G-protein coupled receptor on the surface of gonadotropes determines their sensitivity to GnRH pulses. While transcriptional regulation of this gene has been studied in mice, rats, humans and sheep, little is known about its regulation in the pig, an important agricultural species and human research model.

Methods: We isolated 5118 bp of 5′ flanking …

The Characterization Of A Vital Wisconsin Waterway: A Biological Assessment Of The Lower Fox River From 2006-2014, Emily L. Kiehnau

Lawrence University Honors Projects

The Lower Fox River has historically been used as a navigational crossroads, a waste disposal system, and source of hydroelectric power. Over the years, heavy use of the river has negatively affected water quality and the overall health of the system. Unhealthy rivers cannot function properly. Biological assessment based on animal surveys are often used to determine river health. I used data from the Lawrence University and Fox River Navigational System Authority invasive species-monitoring project to explore how the distribution of animals in the Fox River has changed over time and across locations. Monitoring surveys have taken place between June …

Sustainable Treatment Of Landfill Leachate, Mohamad Anuar Kamaruddin, Mohd. Suffian Yusoff, Hamidi Abdul Aziz, Yung-Tse Hung

Civil and Environmental Engineering Faculty Publications

Landfill leachate is a complex liquid that contains excessive concentrations of biodegradable and non-biodegradable products including organic matter, phenols, ammonia nitrogen, phosphate, heavy metals, and sulfide. If not properly treated and safely disposed, landfill leachate could be an impending source to surface and ground water contamination as it may percolate throughout soils and subsoils, causing adverse impacts to receiving waters. Lately, various types of treatment methods have been proposed to alleviate the risks of untreated leachate. However, some of the available techniques remain complicated, expensive and generally require definite adaptation during process. In this article, a review of literature reported …

Kayardild Morphology And Syntax, By Erich R. Round (Review), Gregory Stump

English Faculty Publications

No abstract provided.

The Broken Ring: Reduced Aromaticity In Lys-Trp Cations And High Ph Tautomer Correlates With Lower Quantum Yield And Shorter Lifetimes, Azaria Solomon Eisenberg, Laura J. Juszczak

Publications and Research

Several nonradiative processes compete with tryptophan fluorescence emission. The difficulty in spectral interpretation lies in associating specific molecular environmental features with these processes and thereby utilizing the fluorescence spectral data to identify the local environment of tryptophan. Here, spectroscopic and molecular modeling study of Lys-Trp dipeptide charged species shows that backbone-ring interactions are undistinguished. Instead, quantum mechanical ground state isosurfaces reveal variations in indole π electron distribution and density that parallel charge (as a function of pK1, pK2, and pKR) on the backbone and residues. A pattern of aromaticity-associated quantum yield and fluorescence lifetime changes emerges. Where quantum yield is …

Process Monitoring And Fault Detection In Nonlinear Chemical Process Based On Multi-Scale Kernel Fisher Discriminant Analysis, Norazwan Md Nor, Mohd Azlan Hussain, Che Rosmani Che Hassan

Research Publications (2011 to 2015)

This paper presents a multi-scale kernel Fisher discriminant analysis (MSKFDA) algorithm combining Fisher discriminant analysis (FDA) and its nonlinear kernel variation with the wavelet analysis. This approach is proposed for investigating the potential integration of wavelets and multi-scale methods with discriminant analysis in nonlinear chemical process monitoring and fault detection system. In this paper, a discrete wavelet transform (DWT) is applied to extract the dynamics of the process at different scales. The wavelet coefficients obtained during the analysis are used as input for the algorithm. By decomposing the process data into multiple scales, MSKFDA analyse the dynamical data at different …

Transformer Incipient Fault Prediction Using Combined Artificial Neural Network And Various Particle Swarm Optimisation Techniques, Hazlee Azil Illias, X.R. Chai, A.H. Abu Bakar, Hazlie Mokhlis

Research Publications (2011 to 2015)

It is important to predict the incipient fault in transformer oil accurately so that the maintenance of transformer oil can be performed correctly, reducing the cost of maintenance and minimise the error. Dissolved gas analysis (DGA) has been widely used to predict the incipient fault in power transformers. However, sometimes the existing DGA methods yield inaccurate prediction of the incipient fault in transformer oil because each method is only suitable for certain conditions. Many previous works have reported on the use of intelligence methods to predict the transformer faults. However, it is believed that the accuracy of the previously proposed …

Virulence Gene Expression Of Vibrio Parahaemolyticus In The Viable But Nonculturable State, Tiffany Pui-Yun Tse

Master's Theses

Vibrio parahaemolyticus is a food-borne pathogen commonly associated with the consumption of raw or undercooked seafood resulting in primary infections of the human gastrointestinal tract. It is estimated to cause about 4500 illnesses each year in the United States. However, infection from this food-borne pathogen can be avoided if this organism is detected in the implicated food, prior to consumption. Current standard methods of detecting this organism are dependent on the culturability of the bacteria. Detection based on an organism’s culturability may be problematic as V. parahaemolyticus has been known to exist in a viable but nonculturable (VBNC) state. Bacteria …

Physiological Factors Affecting The Bactericidal Activity Of The Western Fence Lizard (Sceloporus Occidentalis) For The Lyme Disease Spirochete, Borrelia Burgdorferi, Kyle Russell Weichert

Master's Theses

The Western Fence Lizard (Sceloporus occidentalis) is a major host of juvenile stages of the Western Black-legged Tick (Ixodes pacificus), which is the vector for the Lyme disease causative spirochete bacterium Borrelia burgdorferi in the western United States. Because S. occidentalis is reservoir incompetent and capable of eliminating spirochetes from infected ticks, it has been implicated as a major factor in the ecology of Lyme disease in the West. Although complement proteins in lizard blood have been established as the borreliacidal factor, no studies have examined intraspecific variability in host lizard borreliacidal capacity. In Chapter 1 …

Adaptive Molecular Evolution Of Phye In Primulina, A Karst Cave Plant, Junjie Tao, Qingwen Qi, Ming Kang

KIP Articles

Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection …

A Cultural Diffusion Model For The Rise And Fall Of Programming Languages, Sergi Valverde, Ricard V. Solé

Human Biology Open Access Pre-Prints

Our interaction with complex computing machines is mediated by programming languages (PLs) which constitute one of the major innovations in the evolution of technology. PLs allowed a flexible, scalable and fast use of hardware and are largely responsible for shaping the history of information technology since the rise of computers in the 1950s. The rapid growth and impact of computers was followed closely by the development of programming languages. As it occurs with natural, human languages, they emerged and got extinct. There has been always a diversity of coexisting PLs that somewhat compete among them, while occupying special niches. Here …

Quantifying Unnecessary Normal Tissue Complication Risks Due To Suboptimal Planning: A Secondary Study Of Rtog 0126., Kevin L. Moore, Rachel Schmidt, Vitali Moiseenko, Lindsey A. Olsen, Jun Tan, Ying Xiao, James Galvin, Stephanie Pugh, Michael J Seider, Adam P. Dicker, Walter Bosch, Jeff Michalski, Sasa Mutic

Department of Radiation Oncology Faculty Papers

PURPOSE: The purpose of this study was to quantify the frequency and clinical severity of quality deficiencies in intensity modulated radiation therapy (IMRT) planning in the Radiation Therapy Oncology Group 0126 protocol.

METHODS AND MATERIALS: A total of 219 IMRT patients from the high-dose arm (79.2 Gy) of RTOG 0126 were analyzed. To quantify plan quality, we used established knowledge-based methods for patient-specific dose-volume histogram (DVH) prediction of organs at risk and a Lyman-Kutcher-Burman (LKB) model for grade ≥2 rectal complications to convert DVHs into normal tissue complication probabilities (NTCPs). The LKB model was validated by fitting dose-response parameters relative …

Msu Reports On Racine Research On Impulsivity And Binge Eating, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

A Finite Element Analysis Of Tibial Stem Geometry For Total Knee Replacements, Aaron Isidro Bautista

Master's Theses

The purpose of this study was to investigate the influence of tibial stem geometry on stress shielding of the tibia for patients with a total knee replacement. Finite element analysis was used to study different tibial stem geometry types, as well as a vast array of different geometric sizes. Both a peg and stem type geometry were analyzed and compared in order to determine what type geometry causes the least amount of stress shielding. A static loading condition with a dynamic loading factor of three was used for the system and the stress responses were analyzed at regions of interest …

Clarification Of Recreational Pool Water Using Biological Additives Produced By Biowish(Tm), Reese Nathaniel Wilson

Master's Theses

Effects of commercially available bacterial products were investigated on two common recreational pool contaminants: sunscreen and cyanuric acid (CYA). Microbial products developed by BiOWiSH Technologies, Inc. were tested for enhancing mechanical filtration and water clarification in bench-scale bioreactors, with conditions mimicking those of recreational pool water. Bacterial consortia included proprietary mixes of Bacillus, Lactobacillus and Pseudomonas, and other genera of bacteria. BiOWiSH products are either fermented on a solid substrate consisting of rice bran and soy meal, or they are mixed with a soluble diluent. Twenty-nine BiOWiSH products were tested throughout forty experiments.

Experiments were carried out to determine both …

Bishop Peak Natural Reserve Conservation Plan Update, Douglas J. Bush

Master's Theses

My master's project is updating the Conservation Plan for the Bishop Peak Natural Reserve (BPNR) in San Luis Obispo, California. It is a professional project for the City of San Luis Obispo, supported by City policy that requires continued management of its open space network through management plans unique to each property. As one of the city's most visited open spaces and one of its most visible natural landmarks, the Bishop Peak Natural Reserve is in need of continued management and oversight. While much of the work in developing the plan focused on identifying issues and developing responsive policy, this …

Structural Micrometeoroid And Radiation Shielding For Interplanetary Spacecraft, Jared Allen Ruekberg

Master's Theses

This paper focused on two significant space forces that can affect the success of a spacecraft: the radiation and micrometeoroid environments. Both are looked at in the context of the region of space between Earth and Mars. The goal was create reference environments, to provide context to results of environmental modeling, and to provide recommendations to assist in early design decisions of interplanetary spacecraft. The radiation section of this report used NASA's OLTARIS program to generate data for analysis. The area of focus was on the radiation effects for crewed missions, therefore effective dose equivalent was the metric used to …

Development Of A Human Tibiofemoral Joint Finite Element Model To Investigate The Effects Of Obesity And Knee Malalignment On Joint Contact Pressure, Meghan Sylvia

Master's Theses

Obesity is a known risk factor for osteoarthritis (OA). Excess body weight generates greater joint contact forces at the knee; however, obese individuals alter their gait to decrease joint contact forces. Knee malalignment has been identified as a strong mediating factor between obesity and knee OA progression. Excess body weight acting on a varus malaligned knee would have an additive effect on cartilage stress and could cause stress levels to exceed the threshold limit for damage and loss of cartilage matrix.

A finite element (FE) model of the human tibiofemoral joint was developed and validated in order to investigate changes …

Locating Optimal Water Quality Monitoring Locations Using Demand Coverage Index Method, Jeffrey Scott Brake

Master's Theses

Water quality regulations are always expanding especially in the field of water quality monitoring; however, threats to our water distribution systems still remain. Components of water distribution systems are susceptible to intentional and accidental contamination; therefore, they represent highly vulnerable aspects of our vital infrastructure.

An analysis was performed on a city in California with a population of 30,000 to 40,000 residents. The analysis is performed to determine the optimal locations of monitoring stations throughout the water distribution system. The method presented by Liu and colleagues (Liu et al, 2012) selects the optimal monitoring locations for the virtual California city …

Crotalus Snake Venom Preconditioning To Prevent Surgical Brain Injury, Cherine Hee-Sun Kim

Loma Linda University Electronic Theses, Dissertations & Projects

Preventive measures are increasingly relevant to medical practice. Preconditioning, a preemptive therapy that administers mildly harmful stimuli to induce endogenous protective mechanisms before major injury, has been shown to minimize injury in many animal models. Given the elective nature of most neurosurgical procedures, the surgical brain injury (SBI) rodent model provides an ideal platform for preconditioning. Our work shows that preconditioning with Crotalus rattlesnake venom, known for its hemorrhagic and inflammatory effects, mitigates some harmful effects of SBI. We have identified two proteins of interest in Crotalus venom: snake venom metalloproteinase (SVMP), an enzyme with hemorrhagic effects, and phospholipase A2 …

Chlorinated Tyrosine Species As Markers Of Inflammation: A Kinetic Study, Matthew Peter Curtis

Loma Linda University Electronic Theses, Dissertations & Projects

Chronic inflammation is associated with numerous human diseases. During inflammation, leukocytes release the enzyme myeloperoxidase (MPO) which generates reactive oxygen species such as hypochlorous acid (HOCl). Additionally, MPO generates reactive nitrogen species. These reactive species can damage host fats, proteins, and DNA, contributing to disease pathology. Because of the reactivity and short half-lives of reactive species, measurement of surrogate markers is necessary to determine their extent and source. Chlorination of the tyrosine phenol ring by HOCl to produce 3-chlorotyrosine (3ClTyr) or nitration of the phenol ring by reactive nitrogen species to produce 3-nitrotyrosine (NO2Tyr) are two such markers. Both are …

Lipid Regulation As A Critical Factor In The Development Of Alzheimer's Disease, Michael A. Castello

Loma Linda University Electronic Theses, Dissertations & Projects

Alzheimer’s disease (AD) is the most common form of dementia in the United States, representing around eighty percent of all cases. For more than two decades, researchers have been led by the amyloid cascade hypothesis, which assumes that accumulation of the amyloid peptide Aβ, derived by proteolytic processing from the amyloid precursor protein (APP), is the key pathogenic trigger in AD. To date, therapies have largely focused on removing Aβ from the brain, an approach that has produced disappointing clinical outcomes. I present an alternative hypothesis in which Aβ production and aggregation is a symptom of a larger, systemic disease …