Digital Commons Network^™

Repairing Gaps In Kinari-2 For Large Scale Protein And Flexibility Analysis Applications, Magdalena Metlicka, Mojtaba Nouri Bygi, Ileana Streinu

Computer Science: Faculty Publications

Pebble game rigidity analysis is a combinatorial method, implemented in our free web server KinariWeb, for extracting protein rigidity and flexibility information without performing costly molecular dynamics simulations. Due to the idiosynchrasies of the data in the Protein Data Bank (PDB), Kinari succeeds only on a fraction of the available files. Motivated by large scale applications, aiming at processing almost all the PDB files, we have recently developed a faster and more robust version, the phased pebble game algorithm. It is specifically designed to take advantage of the sequential structure of biopolymers. However, the structural data available in the Protein …

A Role For Δ-Catenin In Synaptic Regulation, Li Yuan

Theses & Dissertations

The cadherin-catenin complex regulates cell-cell adhesion and signal transduction in epithelial cells. It is becoming increasingly evident that components of the complex regulate various aspects of neuronal architecture and function. δ-catenin is a cytosolic component of the cadherin-catenin complex and is predominantly expressed in the central nervous system. Loss of CTNND2, which encodes δ-catenin, is associated with intellectual disability and mutations in CTNND2 have been identified in autism, suggesting that δ-catenin is a critical component of the molecular machinery underlying neural circuit function. We have previously demonstrated that δ-catenin regulates multiple aspects of synaptic and dendritic development, including dendritic …

Identifying The Role Of Janus Kinase 1 In Mammary Gland Development And Breast Cancer, Barbara Swenson

Theses & Dissertations

The development of the postnatal mammary gland is tightly controlled by peptide hormones and cytokines. The signaling of these extracellular ligands through their corresponding receptors rely on Janus Kinases (JAKs) that activate downstream Signal Transducers and Activators of Transcription (STATs). The JAK/STAT signaling pathway is crucial for processes such as growth, proliferation, and cell survival of the epithelial tissue, but also for the breakdown and remodeling of the mammary gland via IL-6 class inflammatory cytokines (e.g. LIF and OSM). JAK1 and JAK2, which are expressed in the mammary gland, are thought to have redundant functions. However, our previous studies demonstrated …

Exploring Perceptions And Experiences With Resources Among Rural Alzheimer's Dementia Family Caregivers In The Midwest, Rita M. Million

Theses & Dissertations

Exploring PERCEPTIONS AND EXPERIENCES WITH RESOURCES AMONG RURAL Alzheimer’s Dementia Family Caregivers in the Midwest

Rita M. Million

University of Nebraska, 2017

Supervisor: Karen Schumacher, Ph.D., RN

Background. Despite vast amounts of research on informal caregiving in the Alzheimer’s dementia (AD) population, research on the experience and perceptions of rural caregivers is limited. A better understanding of rural caregivers’ knowledge, use, and nonuse of resources is essential to offset the impact of caregiving. Purpose. This study explored Alzheimer’s dementia family caregivers’ experiences and perceptions with resources in rural Midwest communities. Design. A descriptive qualitative approach with one-time semi-structured interviews was …

Metabolic Reprogramming Of Pancreatic Ductal Adenocarcinoma Cells In Response To Chronic Low Ph Stress, Jaime Abrego

Theses & Dissertations

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal of all cancers with a 5-year survival rate of only 8.2%. This is because PDAC is diagnosed in its advanced stages and is characterized by radio and chemotherapy resistance. Aggressiveness of PDAC tumors is attributed to its high metabolic phenotype, which is characterized by increased glycolysis rate and lactate secretion, while oxidative metabolism is reduced. These metabolic features are required to fulfill the biosynthetic demands of proliferating PDAC cells. However, this increase in metabolic activity results in acidification of the extracellular space because the dense fibrotic stroma of PDAC tumors limits …

Assessing And Enhancing Nuclear Safety And Security Culture For Small Facilities That Handle Radioactive Material, Solymosi Máté

International Journal of Nuclear Security

The use of radioactive sources is expanding all over the world and abreast the necessity of the enhancement of its safe and secure application is increasing too. In the nuclear industry, the safety and security are top priorities since decades. They share the same goal, to protect humans from the negative affect of the ionizing radiation. The human component of them is a significant factor and technical solutions can protect us so far and thus the culture for safety and security become a major focus. On the other hand, there are still some contradiction between recommendations and international guidance of …

Development Of A Formalized Mentorship Program For Newly Licensed Registered Nurses At A Large Community Medical Center, Quynh-Hoa Nguyen

Master's Projects and Capstones

Retention, competency, job satisfaction, and lateral violence are issues facing the nursing workforce, especially newly licensed registered nurses (NLRNs). The United States is facing a nursing shortage; therefore it is important to develop strategies to retain qualified registered nurses (RNs). The Master of Science in Nursing/Clinical Nurse Leader (MSN/CNL) student team conducted a literature review on how to address these issues. A mentorship program is the proposed intervention to assist novice nurses during their transition into the nursing role. The student team performed a needs assessment through surveys and interviews to gain valuable data on the medical center. The assessment …

Intercultural Communication: Pre-Departure Orientation For Study Abroad Students, Christopher Hanson

Master's Projects and Capstones

International education in the United States has become increasingly diverse. No longer is study abroad in higher institutions only accessible to the affluent, white privileged class. With this changing demographic in our student population, so does the need of how we prepare our student cohorts for their study abroad experience. The Intercultural Communication: Pre-Departure Orientation for Study Abroad Students is a project designed to start the process of intercultural communication skills building prior to a student’s departure. After exploring the literature about cross-cultural communication, identity formation and cultural humility, this project provides educators with an intercultural communication skill building pre-departure …

Board Of Trustees Meeting Minutes, December 15, 2017

Board of Trustees Minutes

Minutes from the Wright State University Board of Trustees Meeting held on December 15, 2017.

Habitat Selection, Survival, And Movement Ecology Of The American Woodcock (Scolopax Minor) In Louisiana Usa, Elisa Constancia Elizondo

LSU Master's Theses

The American Woodcock (Scolopax minor) is a migratory upland game species occurring across much of eastern North America. Across its breeding range in the northern U.S. and southern Canada, this species has experienced significant, pervasive declines over the last half century. As woodcock populations continue to decline, active habitat management for this species has become increasingly important.

The state of Louisiana has substantial amounts of woodcock habitat and receives wintering birds from across the woodcock range. However, few data exist regarding survival rates, habitat utilization, and movement patterns across the state.

In order to better manage for woodcock …

Defining The Role Of Neuropilin-2 In Macrophages: Implications In Tumor Associated Macrophages In Pancreatic Cancer, Sohini Roy

Theses & Dissertations

Macrophages are extremely heterogeneous and highly plastic hematopoietic cells that reside in all tissues and act as a bridge between the innate and adaptive arms of the immune responses. Besides, they undertake a wide array of housekeeping functions like, clearance of cellular debris that arise due to regular turnover in tissues, iron homeostasis, immune surveillance as well as tissue repair processes post inflammation. They are also causally associated with several clinical conditions, including cancer where the infiltration of macrophages contribute to disease progression, metastasis and therapy resistance, and thereby poor clinical outcome.

Neuropilins (NRPs) are non-tyrosine kinase cell surface glycoproteins …

Focus: A Graph Approach For Data-Mining And Domain-Specific Assembly Of Next Generation Sequencing Data, Julia Sommer

Theses & Dissertations

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the …

Dreams: A Unified Theory Approach, Chance Mcdermott

Dissertations, 2014-2019

Henriques (2011) proposed a new unified theory of psychology (UT) which he argued could assimilate and integrate divergent lines of thought into a coherent whole. An implication of this claim is that the system can be applied to phenomena that was not addressed in the original work and the current work tests this proposition. Specifically, the current work utilized the UT and its components to examine the dream literature, especially psychodynamic, physiological and evolutionary approaches. Following a brief introduction, the project reviews the various lines of research and interpretations of why we dream and what they may mean for us. …

Strength Analysis For The Rudders Of Power-Free Underwater Vehicle In Kuroshio Subjected To Typhoon Waves, Chuan-Tsung Lee, Ray-Yeng Yang, Huang Hsing Pan, Li-An Kuo

Journal of Marine Science and Technology–Taiwan

In this study, a 1/25 hydraulic model of a power-free vehicle was developed. Typhoon waves and Kuroshio current flow in a wave-current flume (200 x 2 x 2 m3 ) were applied to the model for determining the net flow velocity and mooring forces. Through hydraulic experiments with a wave period of 16 s, wave height of 10 m, and ocean current speed of 1.0 m/s, a net flow velocity of up to 3.81 m/s was measured. The maximum lift and drag forces acting on each rudder were calculated through computational fluid dynamics as -245.6 and 151.6 kN, respectively, when …

Cascaded Uuv Trajectory Tracking Control Based On Model Predictive And Sliding Mode Control, Bing Sun, Wenyang Gan, Man Mei, Daqi Zhu, Simon X Yang

Journal of Marine Science and Technology–Taiwan

This paper describes a cascaded dynamic trajectory tracking control approach based on model predictive control (MPC) and sliding mode control for unmanned underwater vehicles (UUVs). The proposed method combines kinematic and dynamic controllers to achieve robust control. First, MPC is employed to realize tracking control kinematically. The MPC algorithm is proposed as a solution to the speed jump problem. Considering the computational burden for nonlinear UUV dynamic models, the MPC method is used in conjunction with sliding mode control to achieve dynamic tracking control, which solves problems of modeling uncertainty and external disturbances. Experimental results showed that the proposed method …

Investigation Of Effects Of Wave Directions On Hull Wave Loads By Hydroelastic Experimental Method, Zhanyang Chen, Jialong Jiao

Journal of Marine Science and Technology–Taiwan

This paper focuses on the hydroelastic responses of ultralarge vessels under different wave directions. Segmented ship model experiments provide an invaluable tool in naval applications. However, most model tests are performed on heading waves. Therefore, a segmented model with variable cross-section steel backbones was designed and the oblique wave tests were performed in a comprehensive test tank. The oblique wave test system was introduced in detail. Time histories of bending moments in oblique waves were given. In order to analyze the influence of structural elastic effect on hydroelastic responses, the number of segments of the model was changed, and the …

Factors Affecting Faculty Use Of Video Conferencing In Teaching: A Mixed-Method Study, Juhong Christie Liu, Rob Alexander

Journal of Educational Technology Development and Exchange (JETDE)

Teaching and learning can now utilize a variety of real-time technologies to build online social presence and learning interactions. However, teachers and students must effectively prepare for this experience; and the identification of contextual and perceptual influences become evolving and necessary (Lehman & Conceição, 2010; Liu & Kaye, 2016). In this paper, the authors explore factors that impact faculty use of synchronous video conferencing (VC) in teaching. The two-phase mixed-method study spanned a year, converging qualitative and quantitative approaches through observations and recordings during a 6-week faculty professional development program, a campus-wide survey, and focus groups. Thematic analysis was used …

Understanding The Paradox Of Genetic Diversity In Uropathogenic E. Coli: The Uncommon Evolution Of A Common Pathogen, Henry Louis Schreiber

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are the second most common bacterial infection of people in the U.S.A and are frequently recurrent, as an initial UTI is quickly followed by a second episode in 30-35% of cases despite appropriate antibiotic treatment and clearance of the bacteria from the urine. The vast majority, >80%, of UTIs are caused by uropathogenic Escherichia coli (UPEC). UPEC that colonize the bladder are thought to originate in the gut, where they live as commensal organisms. UPEC can be shed in feces to colonize the vagina and/or periurethral area, and then can ascend into the bladder to start …

Knowledge Driven Approaches And Machine Learning Improve The Identification Of Clinically Relevant Somatic Mutations In Cancer Genomics, Benjamin John Ainscough

Arts & Sciences Graduate Student Theses and Dissertations

For cancer genomics to fully expand its utility from research discovery to clinical adoption, somatic variant detection pipelines must be optimized and standardized to ensure identification of clinically relevant mutations and to reduce laborious and error-prone post-processing steps. To address the need for improved catalogues of clinically and biologically important somatic mutations, we developed DoCM, a Database of Curated Mutations in Cancer (http://docm.info), as described in Chapter 2. DoCM is an open source, openly licensed resource to enable the cancer research community to aggregate, store and track biologically and clinically important cancer variants. DoCM is currently comprised of 1,364 variants …

New Ventures In Amidine-Based Catalyst Design, Nicholas Alan Ahlemeyer

Arts & Sciences Graduate Student Theses and Dissertations

Two new cascade transformations of α,β-unsaturated thioesters catalyzed by amidine-based catalysts have been developed. First, a reagent-free transformation of o-formylaryl cinnamoyl thioesters catalyzed by HBTM-2 to produce 2-substituted thiochromenes achieved high enantioselectivities and yields while forming carbon dioxide as the only byproduct. Second, a highly diastereo- and enantioselective tandem rearrangement of less reactive enone thioesters into tricyclic thiochromanes in the presence of electron-rich amidine-based catalysts was developed. These catalysts were designed with the help of DFT calculations. H-PIP, the first chiral amidine-based catalyst synthesized in our group, performed the best overall in the thiochromane synthesis.The second chapter of this thesis …

Roles Of Peroxisomes And Peroxisome-Derived Products In Controlling Plant Growth And Stress Responses, Elizabeth May Frick

Arts & Sciences Graduate Student Theses and Dissertations

The peroxisome is a vital organelle conserved through the entire eukaryotic lineage. In all examined species, peroxisomes are responsible for such essential processes as fatty acid beta-oxidation and metabolism of reactive oxygen species (ROS). In plants, peroxisomes have taken on additional specialized roles, such as production of some plant hormones and vitamins. In this work, I have uncovered novel factors regulating peroxisome number in model species Arabidopsis thaliana, and novel mechanisms governing how peroxisomes respond to salt stress. I discovered a role for Arabidopsis MAP KINASE17 (MPK17) as a negative regulator of peroxisome division that acts in the salt-stress response …

A Generalized Biophysical Model Of Transcription Factor Binding Specificity And Its Application On High-Throughput Selex Data, Shuxiang Ruan

Arts & Sciences Graduate Student Theses and Dissertations

The interaction between transcription factors (TFs) and DNA plays an important role in gene expression regulation. In the past, experiments on protein–DNA interactions could only identify a handful of sequences that a TF binds with high affinities. In recent years, several high-throughput experimental techniques, such as high-throughput SELEX (HT-SELEX), protein-binding microarrays (PBMs) and ChIP-seq, have been developed to estimate the relative binding affinities of large numbers of DNA sequences both in vitro and in vivo. The large volume of data generated by these techniques proved to be a challenge and prompted the development of novel motif discovery algorithms. These algorithms …

Longitudinal Cerebrospinal Fluid Biomarkers Of Alzheimer Disease: Movement Toward The Diagnosis, Prognosis And Staging Of Disease, Courtney Sutphen

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer’s disease (AD) is a devastating neurodegenerative disease that slowly claims the memories and experiences that comprise the life experiences of individuals that suffer from the disease. Despite a continually accelerating pace of research and discovery, a viable therapeutic intervention for AD has yet to be realized. There are a multitude of factors that may contribute to this difficulty including the challenge of separating the overall disease of Alzheimer’s from the clinically recognizable memory loss that occurs in what is now known to be the end-stage of the disease. Efforts to treat AD have increasingly turned toward very early disease …

Untangling The Mechanics Of Co-Entangled Cytoskeletal Networks, Shea Ricketts

Undergraduate Honors Theses

Active networks of interlinked protein filaments comprising the cytoskeleton largely control cellular mechanics and cell architecture. By forming cytoskeleton networks that combine motile, semiflexible actin with rigid, supportive microtubules, cells maintain structural integrity and shape while being able to flow and move. To elucidate the complex mechanical processes that arise between interacting networks of actin and microtubules within cells, we create a suite of randomly-oriented, well mixed networks of actin and microtubules by co-polymerizing varying ratios of both proteins in situ. We use optical tweezer microrheology in order to characterize the nonlinear mesoscale mechanics of in vitro co-entangled actin-microtubule composites. …

Comparison Of Complete Bouguer Anomalies From Satellite Marine Gravity Models With Shipborne Gravity Data In East Sea, Korea, Dong Ha Lee, Tri Dev Acharya

Journal of Marine Science and Technology–Taiwan

This paper describes the results of complete bouguer anomalies (B.A) computed from the free-air anomalies (F.A) of Sandwell and DTU13 marine gravity models that derived from satellite altimetry observations in the area of East Sea, South Korea. In order to confirm the usefulness of satellite-derived gravity anomalies to analyze the geophysical, geological and geographical characteristics in East Sea, the results of marine gravity models have been compared with shipborne gravity anomalies obtained from KHOA (Korea Hydrographic and Oceanographic Agency). To calculate the complete B.A, we applied complete bouguer correction which consists of three steps: the bouguer slab correction (Bullard A), …

Determination Of Vertical Datum Level For Tidal Bench Mark Using Gnss Buoy Observations, Jae Young Roh, Kyung Wan Yoo, Yong Cheol Suh, Moon Seung Shin, Dong Ha Lee

Journal of Marine Science and Technology–Taiwan

Coastal areas are the most vulnerable areas to sea level fluctuations. Such areas comprise approximately 4% of South Korea's total land; therefore, monitoring these fluctuations is crucial. The present study determined the vertical datum level using a global navigation satellite system (GNSS). Unlike traditional sea level measurements, which are performed using fixed-type gauge observations, a GNSS has an accuracy of a few millimetres and no spatiotemporal constraints. For this purpose, a set of buoys containing GNSS devices was installed in coastal waters, and observations were performed for more than 8 h. The processed GNSS buoy data were compared with tidal …

Next Generation Sequencing Technologies For Real-Time Genotyping And Targeted Sequencing For Precision Medicine, Priyanka Rawat

Biomedical Engineering ETDs

Astounding success of Human genome project and accelerating success of sequencing technologies have enabled $ 1000 genome goals possible. But, this is still far-fetched from the reach of many resource refrained populations with high genetic variations causing lethal genetic diseases. Based on present technology principles, I have developed prototypes for affordable, scalable and customizable point-of-care genotyping and targeted sequencing. Ion-sensitive field effect transistors with novel read-out and signal amplification techniques are used for laying foundation of possible ISFET based allele-arrays. Sequencing-by-synthesis based full-fledge sequencer is made with novel immobilization, flow-cell and data acquisition methods for massive sequenciing.

Breadcrumbs: Privacy As A Privilege, Prachi Bhardwaj

Capstones

Breadcrumbs: Privacy as a Privilege Abstract

By: Prachi Bhardwaj

In 2017, the world saw more data breaches than in any year prior. The count was more than the all-time high record in 2016, which was 40 percent more than the year before that.

That’s because consumer data is incredibly valuable today. In the last three decades, data storage has gone from being stored physically to being stored almost entirely digitally, which means consumer data is more accessible and applicable to business strategies. As a result, companies are gathering data in ways previously unknown to the average consumer, and hackers are …

Teaching Efl/Esl College-Level Learners Through Current Global Topics: Integrated Lessons For Efl/Esl Teachers, Chaiyeon Sylvia Lee

Master's Projects and Capstones

The importance of educating effective English users competent in communicating and interacting in a variety of social settings is highlighted in today’s highly globalized world. Being able to understand and discuss complex global topics related to current cultural, social, and business issues and events has become an integral skill of English learners to achieve greater international connectivity. Unfortunately, many EFL/ESL college-level students, specifically Korean EFL students, do not seem to have sufficient preparation to build English communicative competence and cultural awareness necessary to cope with various situations in which they need to communicate meaningfully and purposefully as effective English users. …

Development Of A Curriculum Analysis And Simulation Library With Applications In Curricular Analytics, Michael S. Hickman

Electrical and Computer Engineering ETDs

Higher education institutions are currently investing significant resources in attempts to improve student success by improving instruction quality, implementing tutoring programs, and providing other services to help students. While these are all worth- while, one area that tends to be overlooked is the structure of the curricula that are offered. When viewing curricula as data, or more specifically, a graph, it is intuitive to see how its structure can influence a student’s ability to move through it. How- ever, there are currently no tools to analyze a curriculum’s structural properties and how they might affect student success. This thesis describes …