Digital Commons Network^™

The Effects Of Isolation On Endemic Cozumel Island Rodents: A Test Of The Island Rule, Brittany Marie Nuttall

Theses and Dissertations

Island isolation can cause changes in body size, cranial characteristics, and genetic variation in mammals. We use geometric morphometrics to test skull and mandible shape and size change across three species of endemic Cozumel Island rodents in order to test the “island rule” of larger size in isolated rodents. We also sequenced the D-Loop and cytochrome b region of the mitochondrial genome and tested for differences in genetic variation between island and mainland groups, as well as population structure and gene flow in order to assess the effect of island isolation on these three rodents. We found that the three …

Application Of Next-Generation Transcriptomic Tools For Non-Model Organisms: Gene Discovery And Marker Developmentwithin Plecoptera (Insecta), Nicholas Gregory Davis

Theses and Dissertations

Phylogenetic research on non-model organisms has been hindered by limited marker availability. Next generation sequencing techniques are eliminating that barrier. Using Illumina sequencing technology, Trinity assembly software, custom Perl reciprocal BLAST scripts, and Primer3 primer prediction software, we produced and analyzed 7 Plecopteran transcriptomes, representing 7 of the 16 total families, in an attempt to identify and develop conserved orthologous genetic markers. The transcriptomes were used to reconstruct a gene content phylogeny using a simple distance matrix generated from reciprocal blastn data. By producing and filtering a reciprocal blast network we identified and aligned over 450 putative orthologs. Out of …

The Effects Of Wrist Orthoses On The Stiffness Of Wrist Rotations, Daniel Brad Seegmiller

Theses and Dissertations

Wrist orthoses are the most common upper limb orthoses, being used by thousands of individuals each year to stabilize, immobilize, or support the wrist joint. Wrist orthoses achieve their function by altering the stiffness of the wrist joint (Figure 1-1). However, there is no quantitative understanding of how wrist orthoses affect wrist stiffness, and consequently, wrist orthosis development often relies on feel, intuition, or empirical heuristics rather than a methodical, quantitative approach. Because wrist movement control is dominated by wrist joint stiffness (Charles and Hogan 2011) a quantitative understanding of how wrist orthoses alter the stiffness of the wrist is …

Parenting Skills As Predictors Of Child And Adolescent Psychotherapy Outcomes: Examining Change In Usual Care Settings, Alicia Ann Henderson

Theses and Dissertations

Youth psychotherapy literature is in need of more research related to understanding psychotherapy process and outcome in child psychotherapy in community settings. The purpose of this study was to examine how key parenting skills were associated with child and adolescent symptoms and outcomes over the course of treatment in an outpatient community mental health system. Much of the research on child and adolescent outcomes has been conducted in controlled research settings, which raises the importance of more research needing to be done in representative clinical practice conditions (Weisz & Jensen, 2001). Further, few child and adolescent studies have examined potential …

Population Genetic Structure Of Bromus Tectorum In The American Desert Southwest, Desiree Rochelle Eldon

Theses and Dissertations

Following its introduction to North America in the late nineteenth century, Bromus tectorum L., an inbreeding invasive winter annual grass, has become dominant on millions of hectares of sagebrush steppe habitat throughout Intermountain Western North America. It appears that within the last 30-40 years, B. tectorum has expanded its range southward into the Mojave Desert and also into more climatically extreme salt desert environments. Previous research using microsatellite markers and experimental studies has suggested that lineages found in desert habitats are genetically distinct from those found in the sagebrush-steppe habitat and possess suites of traits that pre-adapt them to these …

Service Provider And Beneficiary Perceptions Of Collectivist Domestic Violence Social Issues, Annie Mohsen Samhouri

Theses and Dissertations

In this research I have focused on beneficiary and service providers' perceptions toward Arab social obstacles to help-seeking, appropriate intervention methods and obstacles to reintegration into the community after seeking assistance. Through semi-structured interviews and content analysis of local policies, laws and specific service offerings, I sought to contribute to the limited literature that explores how formal institutions that originate from a Western context are adapted to meet the unique needs of Arab victims of domestic violence. I found that the main social obstacles to help-seeking were attributed to a dearth of knowledge about existing services, a lack of confidence …

Habitat Selection By Two K-Selected Species: An Application To Bison And Sage Grouse, Joshua Taft Kaze

Theses and Dissertations

Population growth for species with long lifespans and low reproductive rates (i.e., K-selected species) is influenced primarily by both survival of adult females and survival of young. Because survival of adults and young is influenced by habitat quality and resource availability, it is important for managers to understand factors that influence habitat selection during the period of reproduction. My thesis contains two chapters addressing this issue for K-selected species in Utah. Chapter one evaluates habitat selection of greater sage-grouse (Centrocercusurophasianus) on Diamond Mountain during the critical nesting and brood-rearing period. Chapter two address selection of birth sites by bison (Bison …

Exploring Post-Fire Recovery Of Biocrusts And Desert Ecosystem Services, Jason R. Bahr

Theses and Dissertations

Biocrusts and the ecosystem services they provide are becoming more susceptible to fire as exotic annual grass invasions facilitate the spread of desert wildfires. Further, precipitation patterns across the western United States are predicted to change over the next century, and have the potential to dramatically influence fire regimes and the recovery of burned biocrusts. Despite these changes to desert fire and precipitation cycles, our understanding of post-fire biocrust recovery is limited, especially regarding the first two years after fire. To investigate biocrust recovery, we created burn manipulations (i.e., unburned and burned) and tracked crust form and function over two …

Sudden Gains: A Pluralistic Approach To The Patient And Therapist Experience, Brian P. Hansen

Theses and Dissertations

Qualitative and quantitative research methods were used to study instances of sudden gains within the case load of a private practice practitioner. Five clients whose progress was marked by such changes were contrasted with the views of five clients whose progress was marked by significant setbacks. Results from the quantitative analyses indicated that clients who experienced sudden gains during therapy tended to retain their therapeutic gains over a 2-year time period. In contrast, individuals who experienced setbacks in therapy generally continued to be distressed at the 2-year reassessment. Clients who experienced sudden gains were more distressed prior to treatment and …

Importance Of Placement Depth In Evaluating Soil Nitrogen, Phosphorus, And Sulfur Using Ion Exchange Resin Capsules In Semi-Arid, Low Fertility Soils, Rachel Lynn Buck

Theses and Dissertations

Ion exchange resin capsules provide a possible alternative to conventional soil testing procedures. Previous studies with semi-arid, low fertility soils observed poor relationships with poorly mobile nutrients such as phosphorus (P). We propose that placement depth may improve those relationships. Our objective was to (1) determine if placement depth could improve resin capsule estimation of the bioavailability of nitrogen (N), P, and sulfur (S) and (2) to determine if resin capsules can effectively estimate S availability in semi-arid, low fertility soils. Field sites were established in Rush and Skull Valleys, Utah on loam and sandy loam soils, respectively. Fertilizer was …

Involvement Of Ampk And Ap-1 Biochemical Pathways In Il-6 Regulation Of Steroidogenic Enzymes In The Adrenal Cortex, Matharage Shenali De Silva

Theses and Dissertations

The adrenal cortex is a crucial endocrine gland in the mammalian stress response. In chronic inflammatory stress, cortisol is elevated whereas adrenal androgens are decreased. Furthermore, ACTH levels have poor correlation with the plasma cortisol in these conditions, thus suggesting that other factors are driving the stress response during chronic inflammatory stress. Interleukin-6 (IL-6), a cytokine which is released during chronic inflammatory stress, is assumed to be one such factor. Thus the biochemical pathways by which IL-6 increases cortisol release from the zona fasciculata (ZF), and decreases adrenal androgen release from the zona reticularis (ZR) were investigated. Since IL-6 activates …

Ferritin-Based Photo-Oxidation Of Biomass For Nanoparticle Synthesis, Bioremediation, And Hydrogen Evolution, Oscar Petrucci

Theses and Dissertations

The cell is the basic unit of all living organisms. It is an amazing machine capable of self-replicating, growing, and synthesizing and shuttling thousands of compounds. To perform all of these activities the cell needs energy. The original source of energy for all living beings is the Sun. The energy of the sun is collected by the autotrophs (mostly plants) through photosynthesis and stored in the chemical bonds of carbohydrates and lipids through carboxylic acid intermediates; animals use these compounds to obtain the energy for their cells. Most of the energy extracted by the cell comes from the citric acid …

Fgf4 Induced Wnt5a Gradient In The Limb Bud Mediates Mesenchymal Cell Directed Migration And Division, John C. Allen

Theses and Dissertations

The AER has a vital role in directing embryonic limb development. Several models have been developed that attempt to explain how the AER directs limb development, but none of them are fully supported by existing data. I provide evidence that FGFs secreted from the AER induce a gradient of Wnt5a. I also demonstrate that limb mesenchyme grows toward increasing concentrations of Wnt5a. We hypothesize that the changing shape of the AER is critical for patterning the limb along the proximal to distal axis. To better understand the pathway through which Wnt5a elicits its effects, we have performed various genetic studies. …

The Effects Of Video Prompting Via An Ipad On Vocational Skill Development Of Secondary Students With Developmental Disabilities, Patricia D. Lund

Theses and Dissertations

Current laws stress the importance of using research-based practices to teach transition and vocational skills to students with disabilities. Some of the evidence-based practices include the use of videos to prompt students through a task. Much research has been done concerning the effectiveness of video prompts to teach daily living skills, academic skills and social skills. Transitional skills that have been taught often include simple, entry level skills such as watering plants, cooking soup in the microwave or setting a table. To date, there is little research regarding the use of video prompts to teach complex employment skills that can …

Investigating The Impact Of Orientation And Detected Characteristics Of First-Time Online Students On Their Success Rate In A Community College Setting, Reginald C. Akpom

Dissertations

It is evident that the failure rate is higher among online students than in-class students at Hopkinsville Community College. An analysis of the academic records of students who enrolled in online courses for the first time at Hopkinsville indicated a 13% higher withdrawal and failure rate than those who took in-class courses over the same period between 2000 and 2010. Colleges are taking potentially all of the necessary steps to reduce the student failure rates among online students because high withdrawal and failure rates often reflect badly on the quality of education by the providing institutions (C. Segura, personal communication, …

Nature Of Science Conceptions, Attitudes Towards Evolution And Global Climate Change, And Course Achievement In An Introductory Biology Course, Benjamin Elijah Carter

Theses - ALL

Many researchers have studied student attitudes toward and knowledge of evolutionary science, attitudes towards global climate change (GCC), conceptions about the nature of science (NOS), and course success. However, at the time of this writing, no studies explicitly link these topics.

It is overwhelmingly acknowledged by the scientific community that evolution and global climate change (GCC) are undeniably supported by physical evidence. And yet, both topics remain very politically contentious in the United States. Efforts to mitigate the disconnects between the scientific community and the general public on these issues are imperative to science education. Such undertakings need to examine …

Reducing Digestible Tidbits From Meaty Stock: Satisfying Varied Tastes With An Attractive Instructional Assessment Menu, Erika Bennett, Jennie Simning, Kim Staley

LOEX Conference Proceedings 2011

Do you collect streams of data that never see the light of day? Libraries are more frequently being held accountable for metrics via scorecards, dashboards, and other short snapshots of performance. Information Literacy practitioners have meanwhile moved away from tick-marks to a learning outcome assessment culture. This means that the full array of evaluative, formative and summative approaches-- competencies, tests, self-reports and rubrics-- can leave new librarians' heads spinning.

Learning outcomes data are hard to wrangle, let alone, in a digestible format, but fresh assessment approaches can fully illustrate the benefits of our varied media and modes of instruction. Instead …

Influence Of Hydrogel Substrate On Cell Growth And Virus Infection, Fan Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The interaction of cells with their extracellular matrix is of great importance when cells adapt to their environment. The purpose of this thesis is to design substrates with controllable properties and to study cellular interaction on these substrates. Firstly, enzymatically cross-linked gelatin hydrogels with different elastic modulus were prepared. Then, we studied the condition of cell growth and virus infection on these hydrogels as a followed-up. In the first part of the study, we made enzymatically cross-linked gelatin hydrogels with five different elastic modulus. As a parameter of stiffness, elastic modulus varies from 2.4 KPa to 7.5 KPa based on …

A Distributed Mac Protocol For Efficient Channelization In Wireless Networks, Seyed Kaveh Fayazbakhsh

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

There is a significant interest in designing new wireless multiple access protocols that split a wide frequency channel into multiple sub-channels and assign these sub-channels to competing transmissions. Doing this adaptively depending on the number of competing transmissions has a tremendous potential both in high-speed and white-space networks. While such protocols have been developed, they suffer from limitations such as considerable protocol overheads, dependence on a centralized controller, and assumptions about the network being static, etc. In this work, we develop a new multiple access protocol, Ez-Channel, that adaptively and efficiently channelizes the spectrum for improving throughput, without encountering the …

Reproduction, Sexual Swellings And Mating Behavior In Sanje Mangabeys (Cercocebus Sanjei), David Fernandez Sobrado

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Inter-sexual conflict, or the opposing reproductive strategies of males and females, has become a primary structural factor in current models of social organization as it drives an evolutionary arms-race between the sexes. In many primates living in polygynandrous groups, the mating strategy of dominant males is to guard fertile females, while females develop sexual swellings that provide males with information regarding the approximate, but not exact, timing of ovulation. This allows females to mate promiscuously, confusing paternity, while concentrating paternity on males with the best competitive ability, i.e. | those that are able to mate guard during the peak swelling …

(I) Synthesis And Application Of Chiral Biphenol-Based Phosphorus Ligands To Catalytic Asymmetric Synthesis; (Ii) Rhodium-Catalyzed Cycloaddition Reactions For Rapid Construction Of Polycyclic Skeletons Of Biological Interest, Chih-Wei Chien

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Chiral ligand design is crucial for the asymmetric transformations. In our laboratory, libraries of fine-tunable phosphorus ligands based on axially chiral biphenol have been well developed. These ligands exhibit excellent enantioselectivity in various transition-metal catalyzed asymmetric reactions. We present here the application of the monodentate phosphoramidite (MPN) ligand library to the Pd-catalyzed intramolecular asymmetric allylic amination (AAA) for the formation of chiral 1-vinyltetrahydroiso-quinoline skeleton, a versatile key intermediate in the synthesis of natural products such as isopyruthaline and (− )-O-methylthaicanine. We also studied the Pd-catalyzed inter-molecular AAA reaction using our bidentate diphosphonite (BOP) ligands. The BOP ligands exhibit excellent efficacy …

Molecular Movie Magic: Real-Time Picosecond To Microsecond Structural Dynamics Of Photoactive Flavoproteins, Richard James Brust

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Femtosecond (fs) excitation of photoreceptors results in protein structural changes that occur on the microsecond to millisecond timescale or longer. It is thus of fundamental interest to understand how these fast timescale events dictate large scale protein dynamics that occur on much longer (106 orders of magnitude) timescales. AppA is a blue light using FAD (BLUF) protein which acts as a transcriptional antirepressor in Rhodobacter sphaeroides. The ultrafast photocycle and IR spectra are well characterized and involve a near instantaneous (<100 fs) response of the protein matrix that surrounds the chromophore. While there has been extensive study on the ultrafast time scales there has never been an observation of the kinetics of the light induced structural changes in the protein. Here we investigated the ultrafast (ps) to ms structural dynamics through transient IR. The data show that significant structural changes occur on the sub microsecond timescale following photoactivation. In addition our work has expanded to other BLUF proteins. BlsA is a BLUF protein found in the pathogenic bacterium Acinetobacter baumannii. Vibrational data together with homology modeling identify significant differences in β 5 strand caused by photoactivation, a region of BLUF photoreceptors proposed to be essential for signal modulation, that are unique for BlsA. In addition, the BLUF protein PixD, from Synechocystis, was characterized by transient IR, where photoexcitation results in radical pair formation, an event not observed in AppA. Transient IR also revealed that light state formation is complete within nanoseconds for PixD, suggesting a unique mechanism for single and multidomain BLUF systems. | 254 pages

System Evaluation And Design Of Delay-Sensitive Wireless Networks, Xi Deng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Wireless networks have now been widely used and enjoyed in many aspects of human life and the society. Delay-sensitive wireless network, in a strict sense, is not a particular type of wireless networks. It represents a large number of wireless networks whose performance is greatly affected by the packet end-to-end delay, defined as the duration between a packet's generation at the source node and its delivery to the destination. Such network has been growing rapidly in recently years due to the tremendous demands from network applications. Emerging multimedia applications including Video-on-demand (VOD) and Voice-over-IP (VoIP) have become one of the …

Biomimetic Calcium Phosphate Coatings Synthesized By Electrochemical Deposition And Air Plasma Spray: Morphology, Composition And Bioactive Performance, Ling Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this project, with the aim to develop bioactive biomimetic coatings for dental and orthopedic applications, calcium phosphate based coatings deposited by electrochemical deposition and plasma spray were investigated. Different combinations of process parameters were used to achieve coatings with various chemical compositions and morphologies. The obtained coating composition was investigated by energy dispersive X-ray spectroscopy and X-ray diffraction. The microstructure of the coatings were studied through scanning electron microscopy while the cytocompatibility and bioactivity of the strontium-doped calcium phosphate coatings were evaluated using bone cell culture using MC3T3-E1 osteoblast-like cells. A set of designed experiments were performed to study …

Real Attitudes, Fictional Crime: How Crime Dramas Impact Policy Attitudes, Kathleen Donovan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Previous research shows that citizens' primary source of information about crime is through the media. These empirical investigations have generally focused on the link between news – particularly the content of local television news – and perceptions of and attitudes about crime. Local television news programming, however, comprises a small and diminishing proportion of all televised media consumed by Americans. And while scholars have long suspected violence on television affects viewers' perceptions of the world, only recently have political scientists turned their attention to the role non-news media might play in political attitudes. The present study expands on this nascent …

Scalable Particle And Mesh Algorithms For Elliptic Components Of Multiphase Problems, Tongfei Guo

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

New mesh and meshless algorithms for elliptic boundary and elliptic interface problems have been developed. By utilizing the embedded boundary method, a mesh based algorithm to solve elliptic interface problem is implemented as an extension of hybrid Eulerian-Lagrangian hydrodynamic library FronTier which employs the method of front tracking for interface propagation and this implementation is parallelized for distributed memory clusters. The use of embedded boundary method supports arbitrary discontinuities of density and other physics properties across the interfaces and significantly improves methods that smear interface discontinuities across several grid cells. This code has been applied to process simulation for heat …

An Ex Vivo Femoral Artery Model To Demonstrate Inflammatory Response And Monocyte Response Following Increased Vascular Wall Shear Stress, Aparna Kadam Baldwin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Background Vascular remodeling reestablishes blood flow in the case of occlusions and can save tissue that would otherwise become hypoxic and necrotic. Vascular growth in an adult can occur in two ways: angiogenesis and/or arteriogenesis. While some pathways that govern the two are similar, the triggers have been found to be distinct. This study focuses on arteriogenesis- believed to be triggered by increases in wall shear stress (WSS) due to arterial occlusion. Hypothesis Inflammatory response will be initiated in an ex vivo femoral artery model in response to an increase in WSS. The inflammatory response will be detected by increases …

The Design, Synthesis And Biological Evaluation Of Novel Taxoid Anticancer Agents And Their Tumor-Targeted Drug Conjugates, Joshua Seitz

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Cancer is the second leading cause of death in the United States and is responsible for one in eight deaths worldwide. Traditional chemotherapeutics target the processes involved in cell division and consequently produce dangerous and dose-limiting side effects. In an effort to identify the therapeutic windown of these drugs, tumor targeted drug conjugates (TTDCs) are currently under development. The Ojima lab has developed and extensive panel of next-generation taxoids that possess the requisite sub-nanomolar potency for incorporation into effective conjugates. A small library of 17 taxoids was synthesized and their cytotoxicity investigated. Selected taxoids were synthesized on the half-gram to …

Integration Of Regenerative Shock Absorber Into Vehicle Electric System, Chongxiao Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

For cars with combustion engine, fuel is wasted on powering electric devices and conquering resistant forces from the road while driving forward. Regenerative shock absorber can help to harvest kinetic energy from vehicle suspension and power on-car electric system. One innovative design of energy harvesting shock absorber with mechanical motion rectifier is used in this thesis to harvest power and to be integrated with existing vehicle electric system. Interfacing circuits are developed and tested to regulate unstable power and achieve input current control for damping adjustment purpose. The overall integration of car alternator, electric load and regenerative shock absorber is …

Proteomic Profiling Of Burkholderia Cenocepacia Clonal Isolates With Different Virulence Potential Retrieved From A Cystic Fibrosis Patient During Chronic Lung Infection., Siobhan Mcclean, Máire Callaghan, Jean Tyrrell, Isabelle Sa Correia

Articles

Respiratory infections with Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) are associated with a worse prognosis and increased risk of death. In this work, we assessed the virulence potential of three B. cenocepacia clonal isolates obtained from a CF patient between the onset of infection (isolate IST439) and before death with cepacia syndrome 3.5 years later (isolate IST4113 followed by IST4134), based on their ability to invade epithelial cells and compromise epithelial monolayer integrity. The two clonal isolates retrieved during late-stage disease were significantly more virulent than IST439. Proteomic profiling by 2-D DIGE of the last isolate recovered …