Digital Commons Network^™

The Effect Of Hydroxychloroquine On Mortality In Hospitalized Covid-19 Patients, Misha Suresh, Jeff Abraham

Physician Assistant Capstones, 2020-current

As of October 2020, there are no commonly accepted or proven effective treatments for coronavirus disease 2019 (COVID-19). Hydroxychloroquine (HCQ) is an established anti-malarial drug with demonstrated action against SARS-CoV-2 (the virus that causes COVID-19) in-vitro and early observational studies and anecdotal evidence supported its use in treatment of COVID-19. In this review, three of largest and most statistically powerful studies to date (two cohort studies and one randomized controlled trial [RCT]) are synthesized for the purpose of determining whether HCQ is effective in reducing mortality in patients hospitalized with COVID-19. All three studies found no statistically significant difference in …

Environmental Influence On Size Frequency Distributions Of The Pacific Blue Mussel (Mytilus Trossulus) In Two Glacially Inlfuenced Estuaries, Amy Dowling

Marine Biology

The Pacific blue mussel (Mytilus trossulus) is a foundation species in high-latitude intertidal and estuarine systems that can create complex habitats, provide sediment stability, serve as food for top predators, and act as connectors between the water column and the benthos. M. trossulus also makes an ideal model species to assess biological responses to environmental variability, as its size frequency distributions can be influenced by the environment in which it lives. Size frequency distributions can provide valuable information about ecological systems that are experiencing environmental change (e.g., increased global temperatures). M. trossulus populations in high latitude estuaries receive freshwater runoff …

The Role Of Micrornas In The Pathophysiology Of Neonatal Hypoxic-Ischemic Brain Injury, Eric S. Peeples

Theses & Dissertations

Neonatal hypoxic-ischemic brain injury (HIBI) is a devastating injury resulting from impaired blood flow and oxygen delivery to the brain at or around the time of birth. The subsequent metabolic failure and cellular injury in the brain can be partially attenuated by rapid initiation of therapeutic hypothermia, but even with prompt induction of hypothermia, more than one in four survivors suffer from major developmental disabilities – an indication of the critical need for more effective therapies. MicroRNAs (miRNA) may be able to act as therapeutic targets in neonatal HIBI; however, very little is known about the endogenous expression of miRNAs …

Giving Birth At A Critical Time: Assessing Perinatal Depression Among Syrian Refugees In Low Resource Settings, Nada Alnaji

Theses & Dissertations

Refugee mothers are at an increased risk of suffering from stress and mental health conditions during the first year after giving birth to a child. The objective of this study is to enhance the early identification of treatable mental health conditions among perinatal women living within humanitarian settings. The central hypothesis is that a culturally specific approach can be helpful for the long-term success of mental health efforts. In this study, we use qualitative interview methods to understand the cultural paradigms and predisposing factors for perinatal depression related to being a Syrian refugee in Lebanon during the COVID-19 pandemic. In …

The Effect Of Orthodontic Treatment With Extraction On The Upper Airway Dimensions And Three-Dimensional Morphology: A Retrospective Study Using Cone-Beam Computed Tomography Technique, Ehsan Mostaghni

Theses & Dissertations

The purpose of this study was to evaluate the effect of orthodontic treatment with and without extractions of teeth on the upper airway dimension and morphology. Records of 40 consecutively treated patients who received orthodontic treatment with or without dental extractions were evaluated. Pre-and post-treatment volumes, minimum cross-sectional areas, and linear dimensions of oropharyngeal airways were quantified using InVivo Dental 6.0 (Anatomage, San Jose, CA). Additionally, pre and post CBCT images of the upper airways were superimposed on each other using voxel-based registration and fixed coordinate system using 3D Slicer 4.1.1 (www.Slicer.org) and ITK-SNAP (http://www.itksnap.org). While the …

Design And Synthesis Of Small Molecular Probes For Cns And Kidney Disorders, Swagat H. Sharma

Theses & Dissertations

The G protein regulated inwardly rectifying potassium channels (GIRK) are a family of inwardly rectifying potassium channels and are key effectors in signaling pathways. GIRK 1/2 channel subunit, predominantly found in the brain, is involved pathophysiology of various neurological disorders including, but not limited to, epilepsy, anxiety, Parkinson's, pain, reward, and addiction. Previously, our laboratory had identified a series of urea containing molecules as GIRK1/2 preferring activators. Unfortunately, the urea series suffers from significant PK liabilities (solubility, brain penetration and high clearance). The chapter 1 of the dissertation describes our efforts in developing three new series of activators with improved …

Characterization Of Aerosols Produced By Common Orthodontic Procedures, Anna R. Schoettger

Theses & Dissertations

Introduction: Aerosols can harbor active viruses, including SARS-CoV-2, making it vital that clinical protocols implemented in the orthodontic office be based on which procedures produce aerosols. Research shows that various procedures in the field of orthodontics generate aerosols, however, there is a lack of consensus as to which procedures should be deemed aerosol-generating procedures (AGPs). The current study aimed to better understand aerosol production of various orthodontic procedures. Methods: Orthodontic procedures were performed in a closed-room dental operatory on acrylic teeth mounted onto a dental manikin. Procedures performed included: debonding, bonding, and repositioning of one bracket. Variations introduced included: high-speed …

Alignment Of Cervical Vertebrae And Reliability Of Cephalometric Measurements, Ece Agirgol

Theses & Dissertations

Cervical vertebrae are in close relationship with dentofacial structures due to their anatomical position. In previous studies, the inclination of cervical vertebrae was measured by mostly Nasion-Sella line as the reference plane to evaluate the relationship with dentofacial structures.

The aim of this study is to observe the correlation between cervical vertebrae inclination and lateral cephalometric measurements. 124 lateral cephalograms taken in Natural Head Position of subjects over 18 years of age were traced with Dolphin Imaging Software 11.95 Premium. Cervical vertebrae inclination was measured by using the lines passing from landmarks on second, third and forth cervical vertebrae. Correlation …

Integrative Analysis Of Multi-Omics Kinome Data And Virtual Screening Of Identified Targets With Pan-Cancer Application, Siddesh Southekal

Theses & Dissertations

Cancer is a heterogeneous disease characterized by the uncontrolled growth and dissemination of abnormal cells. Unfortunately, it is also challenging to treat due to the heterogeneous nature of the tumors and the lack of known drugs that are effective against all tumor subpopulations.

The human protein kinases represent an essential and diverse family of enzymes and are often dysregulated in cancer. The human kinome comprises only around 2% of all coding genes of the human genome but phosphorylates about 30% of cellular proteins critical for regulating various biological processes such as cell proliferation, cell cycle progression, apoptosis, motility, growth, differentiation, …

Glad To Be Out. I Was Running Out Of Womb: A Study Of Omega-6 And Omega-3 Fatty Acid Metabolites At Delivery And Their Relationship To Infant Growth, Prematurity, And Admission To The Neonatal Intensive Care Unit, Maranda Thompson

Theses & Dissertations

Normal pregnancy relies on inflammation for implantation, placentation, and parturition, but uncontrolled it can lead to poor infant outcomes. Maternal diet is one modifiable factor that can impact inflammation. Omega-3 and omega-6 fatty acids have been shown to be metabolized into bioactive metabolites that effect inflammation. The presence and importance of these metabolites at the time of delivery are not well understood. Therefore, the purpose of this dissertation was to first quantify omega-3 and omega-6 metabolites in maternal plasma, cord plasma, and placental tissue. Then the relationships between metabolites and infant outcomes, including birth weight percentile, length percentile, head circumferences …

Relationships Between Dress And Gender Identity: Lgbtqia+, Alyssa Dana Adomaitis, Diana Saiki, Kim K. P. Johnson, Rafi Sahanoor, Arsha Attique

Publications and Research

No abstract provided.

The Contribution Of Bioethics To Home Healthcare (Hhc) In Saudi Arabia, Saeed Alghamdi

Electronic Theses and Dissertations

This dissertation examines the contribution of bioethics to Home Healthcare (HHC) In Saudi Arabia (SA). Through exploring the critical bioethical issues that have influenced the implementation of home health care, the dissertation highlights the significance of incorporating bioethics in home health care. Organizational ethics has led to the regulation of healthcare professionals, patients, and the stakeholders within clinical care settings. Healthcare organizations and other stakeholders, such as global health bodies, should formulate laws and policies that promote bioethics in contemporary healthcare. The Kingdom of Saudi Arabia, through the Ministry of Health, should promote the adoption of home health care services …

Does Speech-To-Text Assistive Technology Paired With Graphic Organizers Improve The Written Expression Of Students With Traumatic Brain Injuries?, Kayla Cuifolo

Electronic Theses and Dissertations

A traumatic brain injury (TBI) can range from mild to severe and can cause debilitating outcomes that require children to need specialized medical or educational services post-injury. Outcomes vary and are dependent on the location of injury, age, severity, and environmental factors. Some common deficits that happen as a result of a brain injury are fine motor and executive functioning skill difficulties. Fine motor and executive functioning skills are an important component of written expression. Therefore, this current study utilized a brief experimental analysis in order to determine the effects that speech-to-text assistive technology along with a graphic organizer has …

Identifying And Knocking Out Non-Visual Opsins In The Optic Tectum Of Zebrafish Larvae, Sarah Jarrett

Undergraduate Honors Theses

Deep brain photoreceptors (DBPs) are non-visual photoreceptors found in the brains of non-mammalian vertebrates like zebrafish. While using optogenetic techniques in our lab to photo-activate the ear (by expressing the light-gated channel: channelrhodopsin) in efforts of identifying optic tectum (OT) neurons that respond to and integrate auditory and visual stimuli, we found that violet light was able to elicit OT neuronal activity. OT activity was also detected in cases when visual and auditory stimulation was not possible due to removal of the eyes and absence of the exogenously expressed channelrhodopsin, respectively. Analyzing OT single-cell sequencing data of 7day post fertilization …

Using Eugenecid And Eugenecim Computational Tools For Synthetic Biology, Wheaton L. Schroeder, Anna S. Baber, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Synthetic biology often relies on the design of genetic circuits, utilizing ‘‘bio parts’’ (modular DNA pieces) to accomplish desired responses to external stimuli. While such designs are usually intuited, detailed here is a computational approach to synthetic biology design and modeling using optimization-based tools named Eukaryotic Genetic Circuit Design and Modeling. These allow for designing and subsequent screening of genetic circuits to increase the chances of in vivo success and contribute to the development of an application development pipeline. For complete details on the use and execution of this protocol, please refer to Schroeder, Baber, and Saha (2021).

Ultrasound Modulation Of Macaque Prefrontal Cortex Selectively Alters Credit Assignment–Related Activity And Behavior, Davide Folloni, Elsa Fouragnan, Marco K. Wittmann, Lea Roumazeilles, Lev Tankelevitch, Lennart Verhagen, David Attali, Jean François Aubry, Jerome Sallet, Matthew F.S. Rushworth

School of Psychology

Credit assignment is the association of specific instances of reward to the specific events, such as a particular choice, that caused them. Without credit assignment, choice values reflect an approximate estimate of how good the environment was when the choice was made—the global reward state—rather than exactly which outcome the choice caused. Combined transcranial ultrasound stimulation (TUS) and functional magnetic resonance imaging in macaques demonstrate credit assignment–related activity in prefrontal area 47/12o, and when this signal was disrupted with TUS, choice value representations across the brain were impaired. As a consequence, behavior was no longer guided by choice value, and …

Characterization Of Phase Behavior In Idp Solutions By Uv-Vis Spectrophotometry And Phase Volume Fraction Measurements In Capillaries, Qing Sun

Biomedical Engineering ETDs

Intrinsically disordered proteins (IDPs) play vital roles in cell signaling and regulation by changing conformation dynamically under various stimulus. Thus, it is crucial to understand their physical properties in vitro especially liquid-liquid phase separation (LLPS). Here, we first used UV-vis spectrophotometry to investigate two of IDPs' physical properties – transition temperature (Tt) and coacervate size. This deeper insight allows us to further understand the dynamics of phase growth. We then constructed a binodal curve in the phase diagram by measurement of volume ratios in phase separated IDP solution in glass capillaries.

An Analysis Of University Students’ Self-Labeling And Perception Of Feminism, Emilie Seibert

Honors Projects

This project investigates students’ perceptions of feminism, whether or not they identify as feminist, and how closely their ideals align with basic feminist ideals. There is currently no research that investigates self-labeling as a feminist among the current generation of college students in the United States. Despite the immense benefits to holding a feminist identification, it is estimated that only about 21% of the United States population identifies as feminist (Swirsky & Angelone, 2014, p. 230). Understanding the perspectives of current students is important as they have the potential to become activists and impact the future of the feminist movement. …

A Literature Review Of Wetland Treatment Systems Used To Treat Runoff Mixtures Containing Antibiotics And Pesticides From Urban And Agricultural Landscapes, Emily R. Nottingham, Tiffany L. Messer

Biosystems and Agricultural Engineering Faculty Publications

Wetland treatment systems are used extensively across the world to mitigate surface runoff. While wetland treatment for nitrogen mitigation has been comprehensively reviewed, the implications of common-use pesticides and antibiotics on nitrogen reduction remain relatively unreviewed. Therefore, this review seeks to comprehensively assess the removal of commonly used pesticides and antibiotics and their implications for nitrogen removal in wetland treatment systems receiving non-point source runoff from urban and agricultural landscapes. A total of 181 primary studies were identified spanning 37 countries. Most of the reviewed publications studied pesticides (n = 153) entering wetlands systems, while antibiotics (n = 29) had …

Decreasing Maternal Breastfeeding Dissatisfaction During The Night Shift Related To Lactation Support, Robyn Caston

Master's Projects and Capstones

Abstract

Problem

This paper will discuss the Clinical Nurse Leader (CNL) project's specific aim: to decrease maternal dissatisfaction during the night shift related to lactation support in a high-risk maternal department.

Context

Research has shown that adding lactation support improves the decision to exclusively breastfeed and increases the duration. Breastfeeding for all infants starting at birth and continuing until at least 6 months of age has been recommended by the World Health Organization, UNICEF, and the American Academy of Pediatrics. Many studies about lactation support have demonstrated the health benefits to mothers and their infants.

Interventions

A baseline survey will …

Nitrogenase Iron Protein Classification Using Cnn Neural Network, Amer Rez

Master's Projects

The nitrogenase iron protein (NifH) is extensively used to study nitrogen fixation, the ecologically vital process of reducing atmospheric nitrogen to a bioavailable form. The discovery rate of novel NifH sequences is high, and there is an ongoing need for software tools to mine NifH records from the GenBank repository. Since record annotations are unreliable, because they contain errors, classifiers based on sequence alone are required. The ARBitrator classifier is highly successful but must be initialized by extensive manual effort. A Deep Learning approach could substantially reduce manual intervention. However, attempts to build a character-based Deep Learning NifH classifier were …

Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen

Master's Projects

he trip to Mars and back is planned for the next 20 years. Improvement in technology and research has allowed data analysis, at a larger scale, on spaceflight specimen. However, research involving spaceflight is decentralized, as research is spread across laboratories with different methodologies. NASA’S GeneLab is a public repository for spaceflight-related omics data and promotes centralizing spaceflight RNA-Seq studies using NASA’s RNA-Seq pipeline. Jonathan Oribello, a SJSU’s Bioinformatics graduate and now an employee at GeneLab, has implemented Nextflow to NASA’s RNA-Seq pipeline. The Nextflow RNA-Seq pipeline was ran on San Jose State University’s College of Science High Performance Computing …

An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo

Master's Projects

Spaceflight poses many risks to human health due to the harsh conditions of microgravity, cosmic radiation, and confinement. One of the impacts that spaceflight entails is bone loss, which is a risk to astronauts as future space missions will require long travel durations. To elucidate the role of genetics in spaceflight bone loss, in this study differential gene expression analysis was performed using Nextflow-RCP, an adaptation of NASA Genelab’s RNA-Seq Consensus pipeline. The dataset for this project was GLDS-241, which contained samples from mice femoral skin. To gain a comprehensive understanding of the genes involved in bone loss, the results …

Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han

Master's Projects

Endothelial cells (ECs) line the insides of blood vessels and play a key role in the coagulation and vascular repair system. Under normal circumstances, ECs are constantly expressing anticoagulants to prevent clots and maintain healthy blood flow. But when there is an injury to the vessel, endothelial cells become centrally involved in orchestrating the complex series of events that would lead to the clotting of the wound. Thus, ECs are dynamic and respond accordingly based on changes in their local environment. Unfortunately, endothelial cells can sometimes misinterpret cues from the environment and initiate coagulation when there is no vessel damage …

Mindfulness And Meditation To Reduce Test And Evaluation Anxiety In Doctoral Nurse Anesthesia Students, Jenna L. Tebbenkamp

Doctor of Nursing Practice Projects

Abstract

Mindfulness and Meditation to Reduce Test and Evaluation Anxiety in Doctoral Nurse Anesthesia Students

Background/Information

A significant number of university students report experiencing test anxiety. Extreme anxiety has been reported as a cause of withdrawal from university studies. Certified Registered Nurse Anesthetists are required to complete an intense curriculum with tests and evaluations prior to passing a national board certifying exam, which is anxiety provoking.

Purpose

The primary objective of this project was to provide mindfulness intervention information to be utilized by the DNP students and assess desires of having a mindfulness meditation practice to alleviate academic anxiety.

Methods …

Implementation Of A Risk Assessment Tool To Increase Screening For Extragenital Gonorrhea And Chlamydia In Men Who Have Sex With Men, Andrew P. Tharp

Doctor of Nursing Practice Projects

INTRODUCTION: Gonorrhea and chlamydia account for the majority of sexually transmitted infections (STIs) in the United States and are often thought to infect only the urogenital tract. Infections can also be harbored at extragenital sites (rectum and oropharynx), and these infections can increase susceptibility to HIV. Extragenital screening recommendations exist for populations deemed high risk, including men who have sex with men (MSM); yet, routine screening is not consistently completed.

PURPOSE: To improve screening rates for extragenital gonorrhea and chlamydia in MSM within a primary care setting by using an STI risk assessment tool.

METHODS: Clinicians completed a baseline knowledge …

Viloxazine In The Treatment Of Attention Deficit Hyperactivity Disorder, Amber N. Edinoff, Haseeb A. Akuly, John H. Wagner, Megan A. Boudreaux, Leah A. Kaplan, Shadman Yusuf, Elisa E. Neuchat, Elyse M. Cornett, Andrea G. Boyer, Adam M. Kaye, Alan David Kaye

School of Pharmacy Faculty Articles

Attention deficit hyperactivity disorder (ADHD) is the most common neurodevelopmental disorder in children. Over the past twenty years, research on the disease and its characteristics and treatment options has grown exponentially. The first-line pharmacologic treatment of ADHD is stimulants, which have a response rate of ~70%. With the support of four phase 3 studies involving more than 1,000 pediatric patients 6–17 years old, the FDA has approved the non-stimulant, serotonin-norepinephrine modulating agent (SNMA) viloxazine in an extended-release capsule (viloxazine ER) for treatment of ADHD in children aged 6–17. Viloxazine modulates serotonergic activity as a selective 5-HT22B receptor antagonist and 5-HT2C …

Coyote Management In San Francisco, Matthew Greer

Master's Projects and Capstones

As cities in North America grow, coyotes have become progressively more important species in urban ecosystems. Moreover, as coyotes increasingly use these urban spaces, human-coyote conflicts have become more common, creating a need for new management strategies. This paper will explore how the city of San Francisco could create a new coyote management plan for its highly visible coyote population. San Francisco has had a persistent coyote population since the early 2000s (Todd, 2018). Currently, the coyote population is close to 100 individuals and is still growing (J. Young, Presidio Trust, pers. comm.). To explore this topic a literature review …

Poor Acclimation To Experimental Field Drought In Subalpine Forest Tree Seedlings, Alex Goke, Patrick H. Martin

Biological Sciences: Faculty Scholarship

The ability of tree species to acclimate and tolerate projected increases in drought frequency and intensity has fundamental implications for future forest dynamics with climate change. Inquiries to date on the drought tolerance capacities of tree species, however, have focused almost exclusively on mature trees with scant in situ work on seedlings, despite the central role that regeneration dynamics play in forest responses to changing conditions. We subjected naturally established seedlings of co-dominant subalpine conifer species (Abies lasiocarpa and Picea engelmannii) in the southern Rocky Mountains to 2 years of in situ summer precipitation exclusion, simulating summer drought …

Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung

Master's Projects

Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interaction which promotes enhancer-promoter interactions for transcriptional activities. Alterations of chromatin states in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth. Resulting phenotypic changes are correlated to underlying changes in higher-order chromatin structure such as topologically associating domains (TADs) and compartments. In cancer cells, TAD structure is usually altered to facilitate the communication between enhancers and promoters in addition to higher …