Digital Commons Network^™

Microchip Thermal Gradient Gas Chromatography, Anzi Wang

Theses and Dissertations

Although the airbath oven is a reliable heating method for gas chromatography (GC), resistive heating is needed for higher analytical throughput and on-site chemical analysis because of size, heating rate and power requirements. In the last thirty years, a variety of resistive heating methods were developed and implemented for both benchtop and portable GC systems. Although fast heating rates and low power consumption have been achieved, losses in column efficiency and resolution, complex construction processes and difficulties experienced in recovering damaged columns have also become problematic for routine use of resistively heated columns. To solve these problems, a new resistively …

Cheatgrass Die-Off Phenomena: What Are The Short And Long Term Recovery Factors Of Bromus Tectorum Stand Failure?, Joshua Alan Nicholson

Theses and Dissertations

Observations of Bromus tectorum L. (cheatgrass or downy brome) monocultures have shown that populations are susceptible to stand die-off or replacement failures. Die-offs, where the seed bank from the previous year fails to emerge, occurs in cheatgrass stands and it is unclear the trigger or cause. The fungus Fusarium has been identified in plant and seed samples from die-offs and may drive die-off activity through pathogenicity. Die-off recovery may take several years but cheatgrass populations eventually reestablish. The purpose of our study was to determine whether Fusarium is a potential player in a die-off, and understand how die-offs recover after …

Framework To Implement Authentication, Authorization And Secure Communications In A Multiuser Collaborative Cax Environment, Francis Mensah

Theses and Dissertations

Computer Aided Design (CAD) applications have historically been based on a single user per application architecture. Although this architecture is still popular to date, it does have several drawbacks. First of all the single user CAD architecture inhibits a concurrent engineering design process where several designers can work on the same model simultaneously. This limitation introduces time inefficiency especially when a project involves geographically dispersed designers. A solution to these drawbacks could be a transition from the traditional single user CAD architecture to a multiuser collaborative architecture. Advances in computer networking technologies, especially relating to the Internet, have provided the …

Fuel Response To Mechanical Mastication Of Pinyon-Juniper Woodlands In Utah, Alan Wyatt Shakespear

Theses and Dissertations

Pinyon-juniper woodland encroachment threatens ecosystem function and diversity on sagebrush steppe. Decreased fire frequency likely favors proliferation of pinyon-juniper woodlands and subsequent decline in desirable understory species. Increased tree cover produces hazardous canopy fuel loads that contribute to severe crown fires and threaten life and property at the wildland-urban-interface. Mechanical mastication converts large canopy fuels into small woody debris, altering wildfire dynamics from a potential crown fire to a more controllable surface fire. We measured fuel loading and cover on untreated, masticated, and masticated + burned treatments on 30-m transects within 30 X 33-m subplots, representing 45 different sites throughout …

Fire And Ungulate Herbivory Differentially Affect The Sexual Reproduction Of Generalist And Specialist Pollinated Plants, Andrew Hollis Lybbert

Theses and Dissertations

Currently the size and frequency of wildfires are increasing at a global scale, including arid ecosystems that exhibit great sensitivity to disturbance. Fire effects on plant pollination and reproductive success in deserts are largely unknown. Plant dependence on animal pollinators for reproduction can increase the risk of reproductive failure if pollination services are hindered or lost. Species that depend on few taxonomically related pollinator species are expected to be most negatively affected by disturbances that disrupt pollination interactions. To assess fire and isolation effects on reproductive success in desert plant communities, and how wildfire influences the pollination success of generalist …

The Bioluminescence Heterozygous Genome Assembler, Jared Calvin Price

Theses and Dissertations

High-throughput DNA sequencing technologies are currently revolutionizing the fields of biology and medicine by elucidating the structure and function of the components of life. Modern DNA sequencing machines typically produce relatively short reads of DNA which are then assembled by software in an attempt to produce a representation of the entire genome. Due to the complex structure of all but the smallest genomes, especially the abundant presence of exact or almost exact repeats, all genome assemblers introduce errors into the final sequence and output a relatively large set of contigs instead of full-length chromosomes (a contig is a DNA sequence …

A Desk Study Of The Education Policy Implications Of Using Data From Multiple Sources: Example Of Primary School Teacher Supply And Demand In Malawi, Moses Khombe

Theses and Dissertations

Malawi, as a country with very limited resources, needs to have educational policies in place to maximize effectiveness of the public education system. Policymakers depend on accurate data, but variations in data between sources leaves policymakers uncertain as they attempt to craft policies to address the growing educational crisis in Malawi. A desk study was performed to evaluate the policy implications of employing data from multiple sources using primary school teacher supply and demand in Malawi as an illustration. This study examined one national organization, Malawi's Ministry of Education, Science, and Technology (MoEST); three international aid and assistance organizations (IAAOs), …

Pets In The City: Managing Surplus Dogs In Syracuse, New York, Kristin A. Cutler

Theses - ALL

This thesis contributes to the growing interest in animals in geography. Specifically, it situates pets within the geographic literature and addresses the causes and consequences of pet love in the United States. Using Syracuse, New York as a case study, this thesis illuminates the critical yet understudied existence of pets in the city, paying particular attention to the historical and contemporary foundations, management, and geographies of surplus dogs. Further, it explores major shifts in Americans' attitudes toward pets over the last two centuries, details the necessity for and establishment of animal management in the city, and explains the consequences (namely, …

The Effect Of Surface Roughness On The Fretting Corrosion Of 316l Stainless Steel Biomaterial Surfaces, Aarti Shenoy

Theses - ALL

The medical device industry is still seeking answers to the mechanically-assisted corrosion (MAC) problem, which becomes increasingly important due to modularity in design. MAC manifests in various forms, some of which are fretting corrosion, crevice corrosion and stress corrosion. Several studies have been conducted to understand the causes and the factors that affect fretting corrosion. Some of the factors are the applied load, surface potential, oxide film characteristics and solution chemistry near the interface. Surface properties such as surface roughness determine the topography of the surface and the nature of asperity-asperity contact, which is a factor that would determine the …

The Effects Of Watershed Liming On Mercury Concentrations And Stocks In Soil Of Woods Lake, New York, Zhenni Xie

Theses - ALL

Abstract

In acid-impacted forests, lime has been applied to neutralize acidity and mitigate acidification of soil and surface waters. However, few studies have evaluated the effects of liming on watershed mercury processes and transport. I investigated the effects of liming on mercury, organic carbon, and sulfur concentrations and stocks in forest soil 19 years after the application of lime to the Woods Lake Watershed, Adirondack Park, New York, USA (42o52' N, 71o58' W). The mercury, organic carbon, and sulfur stocks were significantly greater in the forest floor of limed areas (24.5 vs. 11.1 Hg g/ha for Oe and 31.6 vs. …

The Conservation Genetics Of Two Emydid Turtles: Emydoidea Blandingii And Malaclemys Terrapin, Charlotte Lizana Petre

Master's Theses

Conservation of turtles is complicated by their sensitivity to habitat degradation and overexploitation. I used microsatellites and standard population genetic analyses to explore genetic diversity, population structure, paternity and demographic history in two emydid turtles that are currently experiencing threats to their survival. The Blanding’s turtle, Emydoidea blandingii, has experienced habitat fragmentation throughout its range, and this study focuses on a population in Massachusetts where hatchlings from one population are being translocated to establish a new population. I found evidence of multiple paternity within clutches and found no significant reduction in genetic diversity when comparing the source population and …

A Comparison Of Passive And Active Acoustic Sampling For A Bat Community Impacted By White-Nose Syndrome, Laci S. Coleman, W. Mark Ford, Chris A. Dobony, Eric R. Britzke

KIP Articles

In the summers of 2011 and 2012, we compared passive and active acoustic sampling for bats at 31 sites at Fort Drum Military Installation, New York. We defined active sampling as acoustic sampling that occurred in 30-min intervals between the hours of sunset and 0200 with a user present to manipulate the directionality of the microphone. We defined passive sampling as acoustic sampling that occurred over a 12-h period (1900–0700 hours) without a user present and with the microphone set in a predetermined direction. We detected seven of the nine possible species at Fort Drum, including the federally endangered Indiana …

Front Tracking Method With High-Order Enhancement And Its Application In Two-Phase Micromixing Of Incompressible Viscous Fluids, Yijie Zhou

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

We develop a front tracking method based on the hydrodynamic library FronTier for the solution of the governing equations of motion for two-phase micromixing of incompressible, viscous, liquid-liquid solvent extraction processes. The method is used for accurate simulation of the turbulent micromixing dynamics of an aqueous and an organic phase exposed to intense centrifugal force and shearing stress. The onset of mixing is the result of the combination of the classical Rayleigh-Taylor and Kelvin-Helmholtz instabilities. We demonstrate verification and convergence results for one-phase and unmixed, two-phase flows. For mixed, two-phase flow a mixing environment that emulates a sector of the …

Protein Dimerization Mechanisms Study With Molecular Dynamics Simulation, Yuan Yao

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

Protein dimerization is involved in many essential biological processes like gene expression, allosteric regulation, enzymatic activation and signal transduction. However, our understanding about dimerization mechanisms is limited despite of the progress made. In this work, we applied molecular dynamics simulation with all-atom structure-based model to the investigation often commonly studied regulatory dimers. Through the combinational analysis of intrinsic energy funnels, density of states, thermodynamic free energy landscapes, phi-values of transition states, and kinetic simulations, new and detailed mechanisms of dimerization and their coupling with monomer folding are revealed, in good agreements with existing experimental evidences and suggestions. We found five …

Graphene Nanoribbons Elicit Cell Specific Uptake And Drug Delivery Via Activation Of Epidermal Growth Factor Receptors, Sayan Mullick Chowdhury

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

Ligands such as peptides, antibodies or other epitopes bind and activate specific cell receptors, and can be employed for targeted cellular delivery of pharmaceuticals such as drugs, genes and imaging agents. In this dissertation, I investigate the in vitro and hematological compatibility of oxidized graphene nanoribbons, non-covalently functionalized with PEG-DSPE (1, 2-distearoyl-sn-glycero-3-phosphoethanolamine-N[amino(polyethyleneglycol)]) (O-GNR-PEG-DSPE) and evaluate its potential as a drug delivery agent. Although, O-GNR-PEG-DSPE was found to interact with RBC membrane and induce structural changes in them, they did not affect other hematological parameters. In vitro studies showed that these particles activate epidermal growth factor receptors (EGFRs) and elicit cell …

Representations Of Gender In Young Adult (Ya) Literature, 1960-2010, Maria I. Cipriani

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

This dissertation focuses the lens of queer studies and trauma studies on YA literature published in the United States between 1960 and 2010 to demonstrate that authors embed cultural messages in YA texts. Those messages for YA readers intend to model behavior considered appropriate and teach about normative sex and gender roles. Individuals between the ages of 10 and 20 comprise YA readership, and the means of teaching these readers cultural norms include imagery and cautionary tales. The content of the literature inculcates views of acceptable behaviors with respect to sexuality and gender roles and generally conflates sex and gender. …

Exploring The Erp And Facial Response To Cocaine And Emotional Cues, Hojin Choi

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

With the advancement of affective computing technologies, spontaneous and complex emotions that were difficult or even impossible to recognize in the past are rapidly becoming the focus of many research. One intriguing example of these non-basic emotions is drug craving, a sophisticated concept which neuroscientists have studied for a long time. Nevertheless, it is not yet known whether craving is accompanied by a characteristic expressive behavior when it occurs, and only little work has been done on exploring the relationship between craving and facial expressions. In this thesis, we assume that drug-related stimuli can induce craving-related emotional states in drug …

An Examination Of Candida Albicans Mannosylation Mutants And Their Cw Structures, Frank August Mindlin

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

Candida albicans is the most important human pathogenic fungus. Due to rising rates of infection and limited treatment options, it has become increasingly vital to identify the structures of the cell wall (CW) that can serve as ligands for anti-fungal drug recognition. Recently, a number of studies have focused their attention to the outer portion of the CW, which is comprised of glycoproteins modified with asparagine (N)-linked or serine or threonine (O)-linked mannan. Current models have shown N-linked mannan to be one of the key structures responsible for immune-cell recognition. Mutations in construction of the N-linked mannan outer chain, which …

Low Intensity Vibrations Mitigate Cancer-Induced Bone Loss With Indications Of Reduced Tumor Progression, Gabriel M. Pagnotti

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

Osteopenia is a comorbidity frequently observed in patients being treated for and recovering from cancer treatment, elevating their risk of fracture. These skeletal losses are compounded by chemotherapy and irradiation, damaging both bone and contents of the marrow, thereby undermining recovery efforts. Exercise is commonly prescribed as a non-pharmacological means of maintaining bone mass. However, in those with compromised bone strength, the loads imposed by rigorous exercises may facilitate a fracture it was intended to prevent. Low intensity vibrations (LIV), a mechanical signal demonstrated as anabolic to bone by biasing mesenchymal stem cells (MSCs) towards an osteogenic endpoint, may represent …

Synthesis Of Thermally-Responsive Amphiphilic Tri-Arm Star Copolymers, Menglan Jiang

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

Amphiphilic block copolymers have attracted much research interest due to their potential applications in various areas, such as drug delivery and gene therapy and. Those polymers usually contain hydrophobic and hydrophilic blocks, which allow them to undergo self-assemby in aqueous solution. Thermally-responsive amphiphilic copolymers have been investigated by our group. Thermally-responsive blocks which have a lower critical solution temperature (LCST) will become insoluble in aqueous solution upon heating and induce the morphological changes in copolymer assembly. In this project, amphiphilic tri-arm star copolymer which contains one hydrophilic polyethylene glycol (PEG) block, one hydrophobic polylactide (PLA) block and one thermally-responsive Poly(N,N-diethylacrylamide) …

Validating The Use Of Fluorescent Proteins As Molecular Probes In Vivo And In Vitro, Laura Elizabeth Dougherty

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

Fluorescent proteins are widely used in cell biology as molecular probes to observe a protein of interests location and movement and also to study protein-protein interactions. The study of protein-protein interactions is observed using a technique called fluorescent resonance energy transfer (FRET). FRET is used as a way to approximate distances between proteins in vivo and requires at least two fluorescent proteins in order to utilize the process. The most popular pairing is enhanced cyan and yellow fluorescent (eCFP/eYFP) proteins. To view protein localization, fluorescent proteins are attached to the protein of interest. PSD-95, a scaffolding protein in the post …

Computational Modeling And Analysis Of Cardiac Excitation, Abhishek Murthy

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

Modeling, analysis, and control of cardiac excitation, the biological process cardiac cells undergo on a periodic basis, is indispensable for understanding and countering life-threatening electrical disturbances of the heart, such as atrial and ventricular fibrillation. Modeling involves the derivation of a mathematical/computational representation of the dynamics of cardiac cells and their diffusivity. The key to effective modeling lies in striking a balance between i) precision, the ability of the model to replicate the underlying biological phenomena, and ii) performance, in terms of amenability to automated analysis techniques, such as simulation and formal verification. The techniques of abstraction and compositionality have …

Deformation Behavior Of Honeycomb Foams In Compression, Doo Hee Lee

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

In the present work, poly lactic acid (PLA) is used as a model system to investigate the deformation behavior of honeycomb foams under compression loads. Solid PLA tension specimens and foams made of PLA were fabricated using fused deposition 3-D printing technique. The solid PLA tension specimens were characterized for their densities and found to be about 10% lower in density as compared to their bulk counter parts. The honeycomb foams had a relative density of about 47%. The deformation mechanisms leading to the crushing of the honeycomb foams under compression were characterized. Furthermore, simple finite element models were developed …

Oceanic And Atmospheric Influences On The Interannual Variability Of The Madagascar Phytoplankton Bloom, Lindsay Roupe

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

Approximately every other year during the austral summer a larger phytoplankton bloom propagates off of the southeast tip of Madagascar. The cause of the interannual variability of this distinct oceanic feature remains unclear, so here we improve the analysis of the interannual variability of the bloom with a longer ocean color dataset, re-examine the existing mixed layer depth and iron fertilization hypotheses formerly used to explain bloom formation and analyze the variability in the larger ocean-atmosphere system in the region in relation to bloom formation. To resolve the forcings on the bloom, relevant satellite and reanalysis data were examined using …

Molecular Characterization Of Quahog Parasite Unknown (Qpx), A Thraustochytird Pathogen Of The Hard Clam, Mercenaria Mercenaria, Ewelina Rubin

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

The hard clam or northern quahog, Mercenaria mercenaria, is one of the most valuable seafood products in the United States. Severe episodes of hard clam mortality have been consistently associated with infections caused by a thraustochytrid parasite called Quahog Parasite Unknown (QPX). Studies in the present dissertation examined the molecular bases of QPX virulence towards clams. Investigation of QPX transcriptome libraries generated a database of QPX putative virulence factors and other molecules potentially involved in interactions with the clam host. Multiple differential gene expression profiles were generated using oligoarray technology for QPX strains isolated from different geographic locations and for …

Nitrogen Loading To The South Shore, Eastern Bays, Ny: Sources, Impacts, And Management Options, Isabelle Stinnette

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

The excessive delivery of nitrogen from land into coastal waters can lead to a host of environmental problems including algal blooms, hypoxic zones, habitat loss, and acidification. While many of these environmental problems have manifested themselves within Long Island's coastal bays, the quantity and sources of nitrogen are largely unknown in much of this region, making the development of effective management plans to ameliorate these problems exceedingly difficult. This study was designed to quantify nitrogen loads and sources to Moriches, Quantuck and Shinnecock Bays within the eastern extent of Long Island's South Shore Estuary Reserve. Further this study assessed water …

The Effect Of Patch Dynamics And Nutrient Availability On The Production Of Zostera Marina Seeds Within Shinnecock Bay, Ny, Lisa Jackson

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

Exposing Zostera marina to fertilized porewater has been shown to increase vegetative shoot density and leaf growth rates, as well as affect morphological shoot characteristics including increasing leaf length, leaf area and the number of leaves per shoot. However, aside from changes in shoot density, records of morphological changes in reproductive shoots subjected to increased nutrient availability are lacking. To address this, five replicate ambient and nutrient enriched patches, each between 0.5 and 2.0 m2, were selected within a developing Z. marina meadow in Shinnecock Bay, NY. Fertilizer stakes, with a N:P:K of 15:3:3, were used to amend enriched patches …

Mathematical Modeling Of G-Protein-Coupled Receptor Signaling Pathways, Tao Jiang

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

G-protein-coupled receptor (GPCR) signaling plays an important role in converting extracellular stimuli into cellular responses. Many biological functions are regulated by GPCR signaling, and nearly 40\% of current pharmaceuticals target GPCRs. In this work, mathematical modeling is used to investigate the initial steps of GPCR signaling with two major aims: 1) to understand the causes for non-canonical signaling behaviors; 2) to understand how signaling specificity is reacted to in the individual reactions of the pathway. The classic ternary complex model describing the interaction between a single ligand, receptor and G-protein served as our basic model for the initial investigation. Dose …

The Dp Category And Serbian Nominal Structure, Ivana Laterza

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

This thesis investigates nominal structure in Serbian, focusing on the issue of DP paramaterization. Since the introduction of DP as a syntactic category in the late 1980s (Fukui and Speas (1986), Abney (1987)), various investigators have questioned its universality on the basis of " article-less" languages, such as Japanese and Serbian. Two proposals have emerged. The Universal DP-Hypothesis holds that all languages project DP (Progovac (1998), Rappaport (2001), Basic (2004), Cinque (2005), i.a.). The Parameterized DP-Hypothesis claims that languages without (definite) articles do not project DP (Fukui (1986), Corver (1992), Zlatic (1997), Boskovic (2005), Despic (2011), i.a.). The second view …

Gender, Number, Nouns & Adjectives: A Study Of Grammatical Agreement In Second Language Learners Of Arabic & Spanish, Anne-Marie Marguerite Poulos

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

This thesis investigates the causes of gender and number agreement errors in learners of both Arabic and Spanish as second languages. Data was collected from each of these groups during beginner level language courses at a university. There were a total of eight tests. The first six were adjective selection activities focusing on a specific noun phrase or sentence structure. The last two were written tests, elicited by images, where students had to produce their own nouns and adjectives. The common first language (L1) of the majority of participants is English, which lacks adjective agreement and does not have the …