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Nanostructured Surface Enhanced Raman Spectroscopy Sensor For Marine Pollutants, Timo Küster

Open Access Master's Theses

Excess concentrations of nitrate and phosphate in seawater can lead to harmful algae blooms that damage coastal ecosystems, pose health risks and adversely impact commercial activity. Early in situ detection of over-nutrification is necessary for rapid response and mitigation plans. Commercial nitrate and phosphate sensors utilize UV-Vis spectroscopy methods. Those sensors show interference with ions present in seawater and are prone to biofouling, necessitating new approaches for in situ monitoring. Surface enhanced Raman spectroscopy (SERS) is a technique theoretically capable of single molecule detection, and therefore may be a promising approach for nitrate and phosphate detection. However, there are clear …

Evaluation Of Ifqs In The Pacific Halibut Fishery In Alaska: Were The Management Safeguards Successful?, Jessica Menges

Open Access Master's Theses

Alaskan fisheries are steeped in centuries of tradition and decades of innovative management. The Pacific halibut fishery is the oldest fishery in the United States managed under an individual fishing quota (IFQ) system. As such, the Pacific halibut fishery serves as an ideal system to study the long-term impacts of an IFQ system. A frenzy of research focused on the system after its implementation in 1995, which created an excellent baseline. However, interest in the halibut fishery faded as other IFQ programs began popping up around the world.

Over two decades later, the Pacific halibut fishery remains understudied in its …

Stakeholder Input To The Development Of The Santa Clara County Lgbtq-Focused Shelter: A Process And Policy Analysis, Anthony Montalvo

Master's Projects

Due to elevated homelessness and growing hate crimes, an LGBTQ-focused shelter was developed and implemented by Office of Supportive Housing (OSH), along with the OLGBTQ (Office of Lesbian, Gay, Bisexual, Transgender, Queer). The following research investigated whether the process to design the LGBTQ-focused shelter program in Santa Clara county took the necessary steps to ensure that the program represents the community it intends to serve. Using process evaluation to identify the problem and proposed solutions, and policy analysis to examine the alternative solutions, the research answered the question: Did the approved design of the LGBTQ-focused shelter represent the stakeholder planning …

Table Of Contents

Human–Wildlife Interactions

This is the table of contents.

Efficacy Of An Online Native Snake Identification Search Engine For Public Use, Scott E. Henke, Samantha S. Kahl, David B. Wester, Gad Perry, David Britton

Human–Wildlife Interactions

Visual methods of species identification are used both in research and recreational contexts because they are inexpensive, non-invasive, and believed to be effective among uniquely identifiable individuals. We examined the ability of the general public to identify live snakes (Serpentes) that are native to the United States using an online snake identification search engine (SISE) produced by the North America Brown Tree Snake Control Team (NABTSCT) website, http://www.nabtsct.net. The SISE consisted of participants answering 7 descriptive questions concerning a snake and then reviewing photographs of snakes that matched that description. Using 3 species of snakes native to Texas, USA, 21% …

A Review Of Rat Lungworm Infection And Recent Data On Its Definitive Hosts In Hawaii, Chris N. Niebuhr, Susan I. Jarvi, Shane R. Siers

Human–Wildlife Interactions

Rat lungworm (Angiostrongylus cantonensis) is a zoonotic nematode that causes rat lungworm disease (angiostrongyliasis), a potentially debilitating form of meningitis, in humans worldwide. The definitive hosts for rat lungworm are primarily members of the genus Rattus, with gastropods as intermediate hosts. This parasite has emerged as an important public health concern in the United States, especially in Hawaii, where the number of human cases has increased in the last decade. Here we discuss the current knowledge of the rat lungworm, including information on the life cycle and host species, as well as updates on known infection levels. Three …

Numbers Of Human Fatalities, Injuries, And Illnesses In The United States Due To Wildlife, Michael R. Conover

Human–Wildlife Interactions

I reviewed published and unpublished papers, government reports, and websites to estimate how many people are injured or killed each year by wildlife or stricken by a zoonotic disease. Over 47,000 people annually in the United States sought medical attention after being attacked or bitten by wildlife, and approximately 8 people died annually. Most bites were by snakes, birds, rodents, and raccoons (Procyon lotor). Each year, wildlife–vehicle collisions resulted in >59,000 human injuries and >440 human fatalities, while wildlife–aircraft collisions added 16 more injuries and 10 fatalities. I also found that >68,000 people each year sought medical …

Application Strategy For An Anthraquinone-Based Repellent And The Protection Of Soybeans From Canada Goose Depredation, Scott J. Werner, Matthew Gottlob, Charles D. Dieter, Joshua D. Stafford

Human–Wildlife Interactions

Agricultural crops can sustain extensive damage caused by Canada geese (Branta canadensis) when these crops are planted near wetlands or brood-rearing sites. From 2000 to 2015, South Dakota Game, Fish and Parks spent >$5.6 million to manage damages caused by Canada geese to agricultural crops (primarily soybeans) in South Dakota, USA. For the purpose of developing a repellent application strategy for nonlethal goose damage management, we comparatively evaluated the width of anthraquinone applications (i.e., 9.4 L Flight Control^® Plus goose repellent/ha [active ingredient: 50% 9,10-anthraquinone] at 0–36 m versus 0–73 m perpendicular to the edge of wetlands …

Temporal Variation Of Moose–Vehicle Collisions In Alaska, Lucian R. Mcdonald, Terry A. Messmer, Michael R. Guttery

Human–Wildlife Interactions

Collisions between vehicles and wildlife have long been recognized to pose threats to motorists and wildlife populations. In addition to the risk of injury or mortality faced by the motorists involved in wildlife-vehicle collisions (WVCs), other drivers are also put at risk due to road obstructions and traffic congestions associated with WVCs. Most WVCs in Alaska involve moose (Alces alces), an animal that is sufficiently large to pose a threat to property and human life when involved in collisions. We analyzed the temporal variation in the number of moose–vehicle collisions (MVCs) reported in the 4 most populous boroughs …

Stories And Personalities: Program Notes For Graduate Recital, Erinn Komschlies

Research Papers

No abstract provided.

Optimization Of Reproductive Success In Beef Cattle By Implementation Of Estrus Resynchronization, Nutritional Management, And Evaluation Of Disease Prevalance, Kaitlin M. Epperson

Electronic Theses and Dissertations

The beef industry is a unique community of operations that employ different management techniques to accomplish a similar goal. Like other facets of animal agriculture, profitability of the beef industry is heavily reliant upon the implemented management practices. Reproductive efficiency is an area of management that has great potential to positively influence the success of beef production. Through the use of reproductive technologies such as estrus synchronization and AI, a greater percentage of females can become bred to superior sires, breeding and calving seasons can be shortened, calf uniformity increased, and economic return maximized (Odde, 1990; Rodgers et al., 2012; …

Nodule Zone-Specific Gene Expression In Soybean, Sadikshya Aryal

Electronic Theses and Dissertations

Nitrogen is one of the most limiting nutrients for plant growth and yield. Leguminous plants such as soybean (Glycine max) have developed the ability to form a symbiotic association with nitrogen fixing rhizobia. This symbiotic association results in the formation of unique structures called nodules that originate from root cortex via de novo cell differentiation. During soybean nodule development, two major nodule zones, the Nodule primordium (Npr) in the center and the nodule parenchyma (Npa) in the periphery, are clearly distinguishable. Npr gives rise to infection zone (IZ), and the Npa holds vascular bundles. However, it is not clear what …

Improvement Of Dried Distillers’ Grains With Solubles Utilizing Pretreatments And Fungal Fermentation, Burgandy Zschetzsche

Electronic Theses and Dissertations

Limited inclusion of distillers’ grains in animal feed is primarily due to low protein and high fiber content. Other elements, such as phytate phosphorus levels in DDGS are still an issue for monogastric animals such as swine, poultry, and fish. Furthermore, unabsorbed phytic acid in manure poses a high risk for environmental pollution, because bacteria can hydrolyze phytic acid into free phosphorus that can result in algal blooms and eutrophication of surface or ground water. The objective of this thesis was to improve the nutritional value of corn dried distillers’ grains with solubles (DDGS). This was done utilizing submerged fungal …

Applying Machine Learning Algorithms For The Analysis Of Biological Sequences And Medical Records, Shaopeng Gu

Electronic Theses and Dissertations

The modern sequencing technology revolutionizes the genomic research and triggers explosive growth of DNA, RNA, and protein sequences. How to infer the structure and function from biological sequences is a fundamentally important task in genomics and proteomics fields. With the development of statistical and machine learning methods, an integrated and user-friendly tool containing the state-of-the-art data mining methods are needed. Here, we propose SeqFea-Learn, a comprehensive Python pipeline that integrating multiple steps: feature extraction, dimensionality reduction, feature selection, predicting model constructions based on machine learning and deep learning approaches to analyze sequences. We used enhancers, RNA N6- methyladenosine sites and …

Effects Of A Low Allergenic Soybean Variety On Gut Permeability, Digestibility And Growth Performance In Pigs, Katelyn M. Zeamer

Electronic Theses and Dissertations

Soybeans are the ‘gold standard’ protein source in pig diets, with lower inclusion levels in weaned pig diets due to transient inflammatory and hypersensitivity responses. This study evaluated a low allergenic (LA) soybean seed containing low Trypsin inhibitors, lectins, and P34 protein. The objective was to determine the impact of weaned pig diets containing LA soybean in both meal (LASBM) and full fat ground (LAGR) forms on the intestinal permeability and gut microbial composition, digestibility of protein and amino acids, and growth performance, in comparison to conventional (CON) soybeans and animal proteins (ANIM). In study 1, 60 weaned barrows (20.9 …

Role Of Glial Glutamate Transporter In Animal Model Of Acute And Chronic Inflammatory Pain, Ghallab Alotaibi

Electronic Theses and Dissertations

No abstract provided.

A Seed Dormancy Gene-Mediated Biotechnology To Mitigate Transgene Flow Into Weedy Rice, Luai Nahar Muhammad

Electronic Theses and Dissertations

Transgene flows into wild/weedy relatives may cause ecological and economic problems. Seed dormancy is an adaptive trait that distributes germination over time and promotes persistence of weeds in agroecosystems. Silencing natural genes controlling seed dormancy (SD) could promote germination and reduce weed adaptability. The goal of this project was to develop a transgenic mitigation (TM) technology by linking to a primary transgene with an SD gene-silencing structure, as a tandem construct for transformation, to reduce the risk of gene flow into weed populations. In this research, the Bar (Bialaphos) gene for resistance to the glufosinate herbicide was used as a …

Identifying Critical Genes For Cholesterol Metabolism In Macrophages Using Crispr-Cas9 Whole-Genome Screens, Kevin Wanniarachchi

Electronic Theses and Dissertations

Macrophage foam cells contribute to atherosclerotic plaque formation, a pathology that underlies heart disease, peripheral arterial disease and stroke. Foam cells form when macrophages take up excessive amounts of low-density lipoprotein (LDL) leading to elevated cellular levels of neutral lipids, which are packaged into lipid droplet organelles. Despite the high public health priority motivating research of cardiovascular disease processes, current understanding of macrophage cholesterol metabolism including mechanisms of LDL uptake, cholesterol trafficking, lipid droplet biogenesis, lipid droplet degradation and cholesterol efflux is limited. Here, we implemented a CRISPR-Cas9 whole genome screening strategy to identify critical genes regulating macrophage cholesterol metabolism. …

Mice, Acorns, And Lyme Disease: A Case Study To Teach The Ecology Of Emerging Infectious Diseases, Laurieann Klockow

Biomedical Sciences Faculty Research and Publications

Ebola, Zika, the recall of contaminated lettuce - these are just a few recent outbreaks making headlines. Students should be able to connect what they learn in their biology courses to explain these events happening around them. Unfortunately, students do not necessarily make those connections. Therefore, it is important, as instructors, to provide opportunities where students engage with societal issues and problems related to course content and case studies, using headlines from the news are one way to do this.

Here I describe a case study about Lyme disease that engages students in learning about the ecology of infectious disease. …

Deep Patient Representation Of Clinical Notes Via Multi-Task Learning For Mortality Prediction, Yuqi Si, Kirk Roberts

Faculty, Staff and Student Publications

We propose a deep learning-based multi-task learning (MTL) architecture focusing on patient mortality predictions from clinical notes. The MTL framework enables the model to learn a patient representation that generalizes to a variety of clinical prediction tasks. Moreover, we demonstrate how MTL enables small but consistent gains on a single classification task (e.g., in-hospital mortality prediction) simply by incorporating related tasks (e.g., 30-day and 1-year mortality prediction) into the MTL framework. To accomplish this, we utilize a multi-level Convolutional Neural Network (CNN) associated with a MTL loss component. The model is evaluated with 3, 5, and 20 tasks and is …

Is Apremilast 30mg Effective In Lowering Dlgi Scores In Patients With Plaque Psoriasis In 16 Weeks Of Therapy?, Hunter N. Dennard

PCOM Physician Assistant Studies Student Scholarship

Objective: The objective of this selective EBM review is to determine whether or not “Is Apremilast 30 mg effective in lowering DLQI scores in patients with plaque psoriasis in 16 weeks of therapy?”

Study Design: Review of three randomized, blind, placebo-controlled clinical trials published between the years 2013 and 2016.

Data Sources: All studies were published in peer-reviewed journals that were located using PubMed database searches.

Outcome Measured: The DLQI is a 10-item questionnaire that assesses the impact of skin disease on health-related quality of life (HRQOL) over the previous week. Scores for each item range from 0 (not at …

Is Tribulus Terrestris Effective At Increasing Sexual Desire In Adult Women Suffering From Hypoactive Sexual Desire Disorder?, Trevene T. Bell

PCOM Physician Assistant Studies Student Scholarship

Objective: The objective of this selective evidence-based medicine (EBM) review is to determine whether or not Tribulus terrestris is effective at increasing sexual desire in adult women suffering from hypoactive sexual desire disorder (HSDD).

Study Design: Review of three randomized controlled trials published in 2014, 2016, and 2017; selection was based on their relevance to the clinical question and on their patient-oriented outcomes.

Data Sources: Three peer-reviewed primary studies comparing the use of Tribulus terrestris to placebo in the treatment of HSDD were found on PubMed. Outcome(s) Measured: For each trial, patients were divided into either Tribulus terrestris treatment or …

Does Adjuvant Therapy With Omega-3 Fatty Acids (Fish Oil) Improve Joint Tenderness In Patients With Rheumatoid Arthritis?, Eileen Fauteux

PCOM Physician Assistant Studies Student Scholarship

OBJECTIVE: The objective of this selective EBM review is to determine whether or not adjuvant therapy with Omega-3 fatty acids (fish oil) improves joint tenderness in patients with Rheumatoid Arthritis.

STUDY DESIGN: Review of 3 double-blind, randomized controlled trials from 2010- 2017.

DATA SOURCES: Three peer-reviewed journal articles written in English were found using PubMed. Articles were selected based on their relevance to the question and whether the outcome measured was patient-oriented evidence that matters.

OUTCOME(S) MEASURED: All articles analyzed the effectiveness of adjunctive treatment with omega-3 fatty acids on the improvement of joint tenderness in patients with rheumatoid arthritis. …

Are Probiotics Effective In Reducing Symptoms Of Atopic Dermatitis?, Samuel H. Kim

PCOM Physician Assistant Studies Student Scholarship

OBJECTIVE: The objective of this selective EBM review is to determine whether or not probiotics are effective in reducing symptoms of atopic dermatitis.

STUDY DESIGN: Selective EBM review of three randomized, double-blind, placebo-controlled trials published after 2009, all English language.

DATA SOURCES: All three studies were published in peer-reviewed journals found on PubMed and selected based on relevance to the proposed clinical question.

OUTCOMES MEASURED: The main outcome measured was the percentage change in SCORAD index to determine severity of atopic dermatitis before and after trial through objective and subjective findings. Additional outcomes included DLQ index which was evaluated via …

Are Plasma Rich Platelets More Effective In Decreasing Chronic Lower Back Pain As Compared To Epidural Injections In Young Adults?, Linda M. Leones

PCOM Physician Assistant Studies Student Scholarship

Objective: The objective of this selective EBM review is to determine whether or not PRP injections are more effective in decreasing chronic lower back pain as compared to epidural injections in young adults.

Study Design: Systematic review of three English language randomized controlled trials (RCTs), all published after 2012.

Data Sources: Two double-blind RCTs and one randomized open blinded end point (PROBE), which analyzed the effectiveness of PRP and epidural injections in young adults with chronic lower back pain. All studies were found using PubMed.

Outcome(s) Measured: Each of the articles analyzed the pain relief and function ability stated by …

Is Curcumin An Effective Treatment For Major Depressive Disorder?, Virginia Hoptman

PCOM Physician Assistant Studies Student Scholarship

OBJECTIVE: The objective of this selective EBM review is to determine whether or not curcumin is an effective treatment for Major Depressive Disorder (MDD).

STUDY DESIGN: A systematic review of three peer-reviewed studies published between 2014 and 2017.

DATA SOURCES: Two of the studies were randomized, double-blind, and placebo controlled. The third study was a randomized controlled trial. All three studies were chosen due to relevance to the clinical question and if they included patient oriented outcomes. The studies were found using PubMed.

OUTCOMES MEASURED: The outcomes of the studies were measured using self-report scales on each patient’s mood. The …

Is Tildrakizumab Monotherapy Effective In Treating Moderate To Severe Plaque Psoriasis?, April L. Wiseman

PCOM Physician Assistant Studies Student Scholarship

Objective: The objective of this selective EBM review is to determine whether or not tildrakizumab monotherapy is effective in treating moderate to severe plaque psoriasis.

Study Design: Systemic review of three randomized placebo controlled clinical trials published in 2015 and 2017.

Data Sources: Three randomized controlled trials published in peer-reviewed journals comparing the effects of IV or subcutaneous tildrakizumab to a visually matched placebo for the treatment of moderate to severe plaque psoriasis. Data sources were found using the PubMed database.

Outcomes Measured: The reduction of psoriatic lesions following treatment was measured using the Psoriasis Area and Severity Index 75 …

Does Grounding To The Earth Reduce Subjective Experience Of Pain?, Adam Umbro

PCOM Physician Assistant Studies Student Scholarship

OBJECTIVE: The objective of this selective EBM review is to determine whether or not grounding to the earth reduces subjective experience of pain.

STUDY DESIGN: This paper evaluates one double-blind, randomized placebo-controlled trial, one randomized placebo-controlled trial, and one prospective cohort trial investigating the efficacy of grounding in reducing subjects’ experience of pain.

DATA SOURCES: All articles were published in English language peer-reviewed journals and accessed through PubMed.

OUTCOMES MEASURED: The outcome measured in this review is the subjective experience of pain by study participants. Pain levels are measured using a visual-analog pain scale or pain survey.

RESULTS: Two studies …

Does Probiotic Supplementation Help Decrease Pain And Number Of Tender Joints In Adults With Rheumatoid Arthritis?, Brittany Snyder

PCOM Physician Assistant Studies Student Scholarship

OBJECTIVE: The objective of this selective EBM review is to determine whether or not “probiotic supplementation helps decrease pain and number of tender joints in adults with rheumatoid arthritis?”

STUDY DESIGN: Review of three double-blind, randomized control trials published between 2008 and 2018. All studies were published in English in peer reviewed journals.

DATA SOURCES: Three double-blind, randomized control trials were found via PubMed.

OUTCOMES MEASURED: The outcomes measured included number of tender joints from baseline to end of study counted by an investigator, visual analog scale (VAS) for pain severity, and a Stanford Health Assessment Questionnaire visual analog scale …

Does Secukinumab Improve Self-Reported Quality Of Life In Patients With Moderate-To-Severe Ankylosing Spondylitis When Taken Regularly?, Ryan Yenovkian

PCOM Physician Assistant Studies Student Scholarship

Objective: The objective of this selective EBM review is to determine whether or not secukinumab improves self-reported quality of life in patients with moderate-to-severe ankylosing spondylitis when taken regularly.

Study design: A systematic review of three randomized placebo-controlled trials (RCTs), published in peer-reviewed journals between 2013 and 2015, all in the English language. Data sources: All three studies were found and accessed on PubMed.

Outcomes measured: Patient quality of life was assessed in all three studies using the Ankylosing Spondylitis Quality of Life (ASQoL) questionnaire and reported as mean change from baseline. ASQoL is scored from 0-18 with a higher …