Digital Commons Network^™

Network Survivability Analysis: Coarse-Graining And Graph-Theoretic Strategies, Teshome Feyessa

Dissertations

Survivability is the ability of a system to continuously deliver essential services despite attacks, failures, or accidents that damage a significant portion of the system. Most of existing survivability measures evaluate global impact of faults on a network by averaging the loss in performance over the whole network. These approaches undermine the fact that a fault is not expected to impact all parts of the network equally. Impacts of some faults are contained in local neighborhoods while others have a global reach. In addition, graph algorithms are often computationally intensive, and even polynomial time algorithms get impractical for a fair …

Molecular Dynamics Modeling Of Scalable Micro/Nano Manufacturing, Ravindra Damodarrao Kaware

Dissertations

In this research, 'Droplet Based Direct Write' micro/nano manufacturing is investigated using a molecular dynamics modeling and simulation approach. The aim of this investigation is characterization of the direct write inkjet printing process to promote optimization for the enhancement of scalability. The study was completed in four phases; nanodroplet evaporation modeling, substrate-nanodroplet interaction modeling, nanodroplet impingement study and nanodroplet-patterned substrate interaction modeling. For the evaporation study, the two typical solvents water and acetone were used. Under this phase, characterization of nanodroplet evaporation was accomplished including evaluation of droplet size variations at different temperatures and time scales. The results of evaporation …

Biofunctional Coatings Using Direct-Write Fabrication Technique For Surgical Implant Devices, Jessica L. Perkins

Dissertations

Surface modification of biomaterials is of critical value to attain desired functionality of biomedical devices and implants. Many of the conventional manufacturing methods used for the fabrication of thin film coatings lack the ability to precisely dispense biological compounds without compromising its chemical integrity. This research investigates the use of direct-write inkjet technique for the deposition of multi-layer coatings of biodegradable polymers. The Direct Write inkjet method provides selective deposition and patterning capability for depositing multi-material coatings on biomaterials for a vast array of surgical implant devices (e.g. stents for cardiovascular applications and orthopedic implants). In the first phase of …

Synthesis And Photoluminescence (Pl) Of Gold (I) And Silver (I) Metal Complexes With 1-Methylbenzimidazole Diphenylphosphine (Mbdp): Potential Sensing Applications For Volatile Organic Compounds, Darkus Elizabeth Jenkins

Dissertations

Volatile organic compound(s), VOC(s), detection have become a highly demanding area of research due to potential harmful effects to the ecosystem. The search for methods of VOC sensor devices has led to the examination of photoluminescence and photoluminescent materials such as metal complexes. Their luminescent properties markedly with phosphine and/or nitrogen based ligands, bridging ligands, have the ability to accommodate metal atoms with short metal – metal distances. It is of great interest to accomplish short metal interactions as the photoluminescent properties can be altered. We show the synthesis and structural characterization of the bridging ligand, 1-methylbenzimidazole diphenylphosphine. We examined …

A Molecular Perspective On The Ageing Of Marine Dissolved Organic Matter, R. Flerus, O. J. Lechtenfeld, B. P. Koch, S. L. Mccallister, P. Schmitt-Kopplin, Ronald Benner, G. Kattner

Faculty Publications

Dissolved organic matter (DOM) was extracted by solid-phase extraction (SPE) from 137 water samples from different climate zones and different depths along an eastern Atlantic Ocean transect. The extracts were analyzed with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI). Δ14C analyses were performed on subsamples of the SPE-DOM. In addition, the amount of dissolved organic carbon was determined for all water and SPE-DOM samples as well as the yield of amino sugars for selected samples. Linear correlations were observed between the magnitudes of 43 % of the FT-ICR mass peaks and the extract Δ14C …

The Use Of Preoperative Epoetin-Α In Revision Hip Arthroplasty., Lawrence A Delasotta, Ashwin Rangavajjula, Michael L Frank, Jamie Blair, Fabio Orozco, Alvin Ong

Rothman Institute Papers

PURPOSE: To evaluate the efficacy of preoperative epoetin-α on the revision hip arthroplasty patient. We hypothesized that epoetin-α will reduce blood transfusion. A pertinent review of the literature is provided.

METHODS: Forty-six patients were retrospectively reviewed. Sixteen patients received epoetin-α. Patients were case matched by age, preoperative hemoglobin, surgery, gender, and BMI. The clinical triggers for blood transfusion during or after the procedure were determined based on peri- and postoperative hemoglobin levels, ASA score, and/or clinical symptoms consistent with anemia. Blood salvage was not used.

RESULTS: Blood transfusion and length of stay were decreased in the epoetin-α group. Hemoglobin in …

Discovery Of Novel Glycogen Synthase Kinase-3beta Inhibitors: Molecular Modeling, Virtual Screening, And Biological Evaluation, Gang Fu

Electronic Theses and Dissertations

Glycogen synthase kinase-3 (GSK-3) is a multifunctional serine/threonine protein kinase which is engaged in a variety of signaling pathways, regulating a wide range of cellular processes. Due to its distinct regulation mechanism and unique substrate specificity in the molecular pathogenesis of human diseases, GSK-3 is one of the most attractive therapeutic targets for the unmet treatment of pathologies, including type-II diabetes, cancers, inflammation, and neurodegenerative disease. Recent advances in drug discovery targeting GSK-3 involved extensive computational modeling techniques. Both ligand/structure-based approaches have been well explored to design ATP-competitive inhibitors. Molecular modeling plus dynamics simulations can provide insight into the protein-substrate …

Survey Of The Native And Nonnative Vascular Plant Species Of Three Islands In Lake Winnipesaukee, New Hampshire, Mark Gardner Winkler

Electronic Theses and Dissertations

This study examined the long-term patterns in vascular plant composition on three islands in Lake Winnipesaukee, NH. It also tested the role of island biogeography in ecology as it analyzed the effectiveness of a land use plan implemented on the islands. Samplings were made on the islands in the summer of 2011 and were compared to earlier samplings in 1978, 1991, and 2001. The flora was observed and measured in 25 permanent plots that were established on the three islands in 1978. The understory flora was measured by presence and percent cover and the overstory was measured by frequency and …

Geographic And Host-Microbe Symbiotic Influence On Secondary Metabolism, Samuel Hamed Abbas

Electronic Theses and Dissertations

This thesis is composed of studies that regard the advancement to the Arctic region and the importance of host-microbe interactions in natural product discovery. Bioactive metabolites have been reported from a myriad of marine and terrestrial organisms around the world including plants, insects, sponges, tunicates, bacteria, and fungi among others. Many macroorganisms, of which the metabolites are found, depend on the symbiotic relationship of microorganisms for metabolite production. The scope of this work is to investigate secondary metabolism of both marine and terrestrial organisms from different areas of the world as well as search for the importance of host-microbe symbiosis …

Restricting Supervised Learning: Feature Selection And Feature Space Partition, Xiaofei Nan

Electronic Theses and Dissertations

Many supervised learning problems are considered difficult to solve either because of the redundant features or because of the structural complexity of the generative function. Redundant features increase the learning noise and therefore decrease the prediction performance. Additionally, a number of problems in various applications such as bioinformatics or image processing, whose data are sampled in a high dimensional space, suffer the curse of dimensionality, and there are not enough observations to obtain good estimates. Therefore, it is necessary to reduce such features under consideration. Another issue of supervised learning is caused by the complexity of an unknown generative model. …

Bacterial And Sediment Transport In An Artificial Sand Bed Stream During Unsteady Flow, Mary Alexandra Mccaskill

Electronic Theses and Dissertations

Storms cause a substantial increase in the fecal indicator bacteria (FIB) concentrations in stream water. Causes for this concentration increase include FIB-laden stormwater runoff and the release of bacteria from stream-bottom sediments. Studies were carried out to quantify this second cause of water quality impairment. Coliform bacteria are a group of FIB, indicate the presence of pathogenic microorganisms, and have been shown to be transported in streams far from their source areas, especially during storms. FIB transport is dependent on several factors including water velocity, size and transport rates of bed sediments, and the FIB concentration in bed sediment. The …

The Queen Of The Household: Mothers, Other Mothers, And Female Genealogy On The Plantation In Postslavery Women's Fiction, Correna Catlett Merricks

Electronic Theses and Dissertations

In many ways, the plantation defined the U.S. South because it was the primary site of production, and therefore income, for prominent southerners. In addition to being a site of production, the plantation created a complex series of connected relationships that was imagined by the plantocracy to be a large family unit. It functioned according to a specific hierarchical model that was primarily based on a patriarchal understanding of genealogy. Yet Kate Chopin's "Désirée's Baby" and "La Belle Zoraïde," Pauline Hopkins's Contending Forces, Zora Neale Hurston's Their Eyes Were Watching God, Julia Peterkin's Scarlet Sister Mary, Eudora Welty's Delta Wedding, …

Development And Comparative Predictive Validity Of An Outpatient Medication Exposure Measure For Risk Adjustment Using Retrospective Claims Data, Kyle Dennis Null

Electronic Theses and Dissertations

The purpose of this study was to develop and test a measure of outpatient prescription utilization (medication exposure measure, or MEM) that may be coupled with the CMS-HCC and CMS-RxHCC methodologies to improve risk-adjusted payments to Medicare Part C and Part D plans. Studies have identified prescription measures that predict future expenditures; however, many are easily manipulable by health plans or practitioners, thus limiting their utility as risk-adjusters. The addition of a non-manipulable prescription utilization measure to existing risk-adjustment models may improve prediction, reducing adverse risk selection incentives by health plans. A secondary objective of this study was to evaluate …

Virtual Worlds And Conservational Channel Evolution And Pollutant Transport Systems (Concepts), Chenchutta Denaye Jackson

Electronic Theses and Dissertations

Many models exist that predict channel morphology. Channel morphology is defined as the change in geometric parameters of a river. Channel morphology is affected by many factors. Some of these factors are caused either by man or by nature. To combat the adverse effects that man and nature may cause to a water system, scientists and engineers develop stream rehabilitation plans. Stream rehabilitation as defined by Shields et al., states that "restoration is the return from a degraded ecosystem back to a close approximation of its remaining natural potential" [Shields et al., 2003]. Engineers construct plans that will restore streams …

A Role For Mechanosensitive Channels In Chloroplast And Bacterial Fission., Margaret E. Wilson, Elizabeth S. Haswell

Biology Faculty Research

The division site in both chloroplasts and bacteria is established by the medial placement of the FtsZ ring, a process that is in part regulated by the evolutionarily conserved components of the Min system. We recently showed that mechanosensitive ion channels influence FtsZ ring assembly in both Arabidopsis thaliana chloroplasts and in Escherichia coli; in chloroplasts they do so through the same genetic pathway as the Min system. Here we describe the effect of heterologous expression of the Arabidopsis MS channel homolog MSL2 on FtsZ ring placement in E. coli. We also discuss possible molecular mechanisms by which MS channels …

Whole Genome Sequencing Of Mutation Accumulation Lines Reveals A Low Mutation Rate In The Social Amoeba Dictyostelium Discoideum, Gerda Saxer, Paul Havlak, Sara A. Fox, Michael A. Quance, Sharu Gupta, Yuriy Fofanov, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9), with a Poisson confidence interval …

Mscs-Like10 Is A Stretch-Activated Ion Channel From Arabidopsis Thaliana With A Preference For Anions, Grigory Maksaev, Elizabeth S. Haswell

Biology Faculty Research

Like many other organisms, plants are capable of sensing and responding to mechanical stimuli such as touch, osmotic pressure, and gravity. One mechanism for the perception of force is the activation of mechanosensitive (or stretch-activated) ion channels, and a number of mechanosensitive channel activities have been described in plant membranes. Based on their homology to the bacterial mechanosensitive channel MscS, the 10 MscS-Like (MSL) proteins of Arabidopsis thaliana have been hypothesized to form mechanosensitive channels in plant cell and organelle membranes. However, definitive proof that MSLs form mechanosensitive channels has been lacking. Here we used single-channel patch clamp electrophysiology to …

Why Wasp Foundresses Change Nests: Relatedness, Dominance, And Nest Quality, Perttu Seppä, David C. Queller, Joan E. Strassmann

Biology Faculty Research

The costs and benefits of different social options are best understood when individuals can be followed as they make different choices, something that can be difficult in social insects. In this detailed study, we follow overwintered females of the social wasp Polistes carolina through different nesting strategies in a stratified habitat where nest site quality varies with proximity to a foraging area, and genetic relatedness among females is known. Females may initiate nests, join nests temporarily or permanently, or abandon nests. Females can become helpers or egglayers, effectively workers or queens. What they actually do can be predicted by a …

A Pre-Embedding Immunogold Approach Reveals Localization Of Myosin Vi At The Ultrastructural Level In The Actin Cones That Mediate Drosophila Spermatid Individualization, Marta Lenartowska, Mamiko Isaji, Kathryn G. Miller

Biology Faculty Research

Stable actin structures play important roles in the development and specialization of differentiated cells. How these structures form, are organized, and are used to mediate physiological processes is not well understood in most cases. In Drosophila testis, stable actin structures, called actin cones, mediate spermatid individualization, a large-scale cellular remodeling process. These actin cones are composed of two structural domains, a front meshwork and a rear region of parallel bundles. Myosin VI is an important player in proper actin cone organization and function. Myosin VI localizes to the cones' fronts and its specific localization is required for proper actin cone …

A Database For Estimating Organ Dose For Chest And Head Ct Scans For Arbitrary Spectra And Angular Tube Current Modulation, Franco Rupcich, Andreu Badal, Iacovos Kyprianou, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Purpose: The purpose of this study was to develop a database for estimating organ dose in a voxelized patient model for coronary angiography and brain perfusion CT acquisitions with any spectra and angular tube current modulation setting. The database enables organ dose estimation for existing and novel acquisition techniques without requiring Monte Carlo simulations. Methods: The study simulated transport of monoenergetic photons between 5 and 150 keV for 1000 projections over 360◦ through anthropomorphic voxelized female chest and head (0◦ and 30◦ tilt) phantoms and standard head and body CTDI dosimetry cylinders. The simulations resulted in tables of normalized dose …

Movement Function Follows Spatial Form: Coordinate System Implications For Online Visual Feedback Control Of The Hand, Justin Brooks

All Theses and Dissertations (ETDs)

Closed loop visual feedback control of the hand is essential for accurate reaching movements. Without visual signals of either the hand or target position, reaches are inaccurate and imprecise; therefore the brain uses a relative positional signal to control movements online. Previous studies suggest that movements are planned and represented in a polar coordinate system and that the dimensions, direction and extent are independently specified and processed. We were interested to find out whether there was behavioral evidence for the independent control of hand direction and extent as a movement unfolded. We asked subjects to make a reaching movement in …

Taspase1 Is A Non-Oncogene Mediator Of Tumorigenesis And Maintenance, David Chen

All Theses and Dissertations (ETDs)

The clinical success of oncogene-targeted therapies substantiates the continued reliance of certain cancers upon the continued function of apical oncogenes involved in its genesis--a phenomenon known as "oncogene addiction." Though this shift from non-targeted, cytotoxic therapies offers new hope to patients, resistance to oncogene inactivation often remains an eventuality, and it is clear that further investigation is required to more effectively battle cancer using alternative therapeutic targets. Our studies on Taspase1: threonine aspartase 1) reveal its role in coordinating cellular proliferation and apoptosis in cancer. Loss of Taspase1 by shRNA-mediated knockdown decreased cellular proliferation in a diverse set of cancer …

Mechanisms Of Induction And Maintenance Of Constitutive Ptgs2 Expression In Colonic Mesenchymal Stem Cells, Monica Drylewicz

All Theses and Dissertations (ETDs)

Colonic injury and inflammation exhibit high morbidity and mortality in western society and are increasingly diagnosed in human patients. In many models of such gastrointestinal insults, prostaglandin endoperoxide synthetase 2: Ptgs2; cyclooxygenase 2) and its downstream synthetic products, most notably prostaglandin E2, support proliferation and modulate the inflammatory immune response, two functions involved in proper injury response. We identified a primary source of this mediator as a population of stromal cells constitutively expressing Ptgs2 that appear to be required in two different model injury systems: administration of dextran sodium sulfate: DSS) and colonic biopsy. The central role of Ptgs2-expressing cells …

The Role Of Snail Homolog 1 In Embryonic Stem Cell Differentiation, Jennifer Gill

All Theses and Dissertations (ETDs)

During gastrulation, epiblast cells undergo an epithelial-to-mesenchymal transition: EMT) as they ingress through the primitive streak and form mesoderm. To better understand the molecular pathways of EMT during this developmental transition, we developed a model system utilizing mouse embryonic stem: ES) cells. We show that EMT occurs during ES cell differentiation and is dependent on the Wnt signaling pathway. We further show that the Wnt-dependent transcription factor Snail homolog 1: Snail) is expressed and capable of inducing EMT in differentiating ES cells. In addition to EMT, Snail accelerates differentiation, promotes mesoderm commitment, and restricts markers of primitive ectoderm and epiblast. …

Molecular Insights Into The Uropathogenesis Of Enterococcus Faecalis And Escherichia Coli In The Context Of Urinary Catheterization, Pascale Guiton

All Theses and Dissertations (ETDs)

Nosocomial urinary tract infections: UTIs) are a very common result of catheterization with 3 to 7% risk of developing catheter-associated UTIs: CAUTIs) each day catheterized. As multi-drug resistance increases in uropathogens, it is imperative to better understand the effects of catheterization on the urinary tract and pathogenesis. Further, microbial colonization and biofilm production on the surface of urinary catheters are a common component of CAUTIs. Thus, this dissertation focuses on understanding the contribution of known biofilm determinants to urovirulence of Enterococcus faecalis: a common nosocomial uropathogen) and uropathogenic Escherichia coli: UPEC): the most common causative agent of UTI), and the …

Mitofusin 2 Regulated Transport Of Mitochondria Is Necessary For Axonal Integrity, Albert Misko

All Theses and Dissertations (ETDs)

The ubiquitous finding of axonal degeneration in a number of the most prevalent neuropathologies marks the importance of understanding axonal biology and the axonal self-destruct mechanism. Though our understanding of axonal degeneration remains largely incomplete, several down-steam steps of the molecular cascade have been elucidated. While this insight has emerged from models of axon degeneration following physical injury or toxic insult, a more comprehensive understanding of the upstream events may be gained from studying primary axonopathies with defined genetic causes. This dissertation aims to elucidate a molecular mechanism underlying the loss of axons in Charcot-Marie-Tooth Disease type 2A, which is …

Exploring The Role Of Wolbachia Endobacteria In The Biology Of Filarial Nematode Parasites, Samantha Mcnulty

All Theses and Dissertations (ETDs)

Filarial nematodes are vector borne parasitic worms that cause a variety of disfiguring and disabling diseases, including lymphatic filariasis and onchocerciasis. Many filarial species require Wolbachia endobacteria: family: Rickettsiaceae) to carry out their life cycle. Studies using antibiotics to target the endobacteria, thereby interfering with worm fertility and viability, have generated interest in using Wolbachia as an antifilarial drug target. However, the exact mechanisms underpinning this interesting mutualistic interaction are poorly understood. Wolbachia-dependence is not ubiquitous in the filarial family. Some species are able to survive in the absence of an endosymbiont. The inconsistent patterns of Wolbachia-dependence and independence seen …

Novel Sequence-Based Method For Identifying Transcription Factor Binding Sites In Prokaryotic Genomes, Gurmukh Sahota

All Theses and Dissertations (ETDs)

Computational techniques for microbial genomic sequence analysis are becoming increasingly important. With next–generation sequencing technology and the human microbiome project underway, current sequencing capacity is significantly greater than the speed at which organisms of interest can be experimentally probed. We have developed a method that will primarily use available sequence data in order to determine prokaryotic transcription factor binding specificities. The prototypical prokaryotic transcription factor: TF) contains a helix–turn–helix: HTH) fold and bind DNA as homodimers, leading to their palindromic motif specificities. The connection between the TF and its promoter is based on the autoregulation phenomenon noticed in E. coli. …

Calcium-Stimulated Adenylyl Cyclases Are Critical Modulators Of Fear Learning And Experience-Dependent Plasticity, Lindsay Wieczorek

All Theses and Dissertations (ETDs)

Stress can exacerbate psychiatric disease, often resulting in cognitive deficits. Consequently, a better understanding of what modulates stress-facilitated memory processing will help identify new targets for possible therapeutic intervention. Recent evidence suggests a role of the Ca2+-stimulated adenylyl cyclases: AC), AC1 and AC8, in modulating fear memory. Ca2+-stimulated AC activity couples neuronal activity and intracellular Ca2+ increases to the production of cAMP, and therefore, can very tightly regulate signal transduction after learning; yet, the details by which this occurs are not well understood. In this dissertation, I first investigated the temporal and regional importance of Ca2+-stimulated AC activity during different …

Cardiac Pi3kα Signaling And K+ Channel Regulation In Cardiac Hypertrophy And Heart Failure, Kai-Chien Yang

All Theses and Dissertations (ETDs)

Pathologic biomechanical stresses cause cardiac hypertrophy, which is associated with QT prolongation and increased risk of life-threatening ventricular arrhythmias. Previous studies demonstrated that repolarizing K+ current densities are decreased in pressure overload-induced left ventricular hypertrophy, resulting in action potential and QT prolongation. Cardiac hypertrophy also occurs with exercise training, but this "physiological hypertrophy" is not associated with electrical abnormalities or increased arrhythmia risk, suggesting that repolarizing K+ currents are upregulated, in parallel with the increase in myocyte size, to maintain normal cardiac function. To explore this hypothesis directly, two mouse models of physiological hypertrophy, one produced by chronic exercise: swim-) …