Digital Commons Network^™

High-Resolution Detection Of Change-Point With Low Coverage Single-Cell Sequencing Data, Huan Qi

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

Advances in next-generation sequencing technologies are revolutionizing our ability to detect copy number variations (CNVs). Single-cell sequencing technology allows for the genome wide copy number analysis within a single nucleus which is isolated form mixed population of cells. It can avoid the disadvantage of genomic differences in complex mixtures of cells. Many statistical methods and tools have been developed for CNVs detection using high-throughput sequencing data, but most methods are not designed for low-coverage sequencing data. In this article, we present a new Bayesian based change-point Model which has never been used for CNVs detection before and propose two similarity …

Towards Application Of One- And Two-Dimensional Nanomaterials For Reinforcement Of Polymeric Nanocomposite Bone Grafts, Behzad Farrshid

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

One- and two-dimensional (1-D and 2-D) nanomaterials possess extraordinary physiochemical properties such as large surface area, excellent mechanical properties, high surface energy and good dispersivity in organic and biological solvents, therefore, they have been extensively used as reinforcing agents to improve the mechanical properties of polymeric scaffolds for bone tissue engineering applications. Carbon nanomaterials such as carbon nanotubes and graphene have been used as reinforcing agents for biodegradable polymeric scaffolds and composites, however, their short- and long-term in vitro cytotoxicity and in vivo biocompatibility is an area of extensive debate. In this study, we have systematically investigated the effects of …

On The Route To Chaos For Two-Dimensional Modestly Area-Contracting Analytic Maps, Ying Chi

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

It has long been conjectured that the two-dimensional dissipative maps, like their one-dimensional counterparts, experience the period-doubling cascade to chaos. In [CEK], Collet, Eckmann and Koch proved this conjecture for highly dissipative families. In this dissertation, we introduce the notion of nested systems that generalizes Henon maps, and construct two operators acting on the space of nested systems based on the idea of the return maps. We use the two operators to show that if a dissipative nested system satisfies some apriori bounds, then they can be replaced with simpler but dynamically equivalent nested systems. We prove that the total …

Transverse Momentum Distribution For Drell Yan Process, Yikun Wang

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

The Drell-Yan process is the production of massive lepton pairs in hadronic collisions. In this thesis, we investigate the transverse momentum distribution of the intermediate vector bosons for the Drell-Yan process. This distribution can be predicted by perturbative QCD. However, one difficulty of the calculation is large logarithms that occur in the calculation of the differential cross section which come from the soft and collinear structure of the phase space. The large logarithmic terms in the differential cross section spoil the validity of perturbative expansion in the region of small transverse momentum. Transverse momentum resummation can give convergent results and …

Non-Adiabatic Dynamics Of Gene Regulatory Network, Cong Chen

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

Gene regulatory network is a mathematical model of gene expression and regulation in cell environment. The concept of network comes from network in math and computer science. In gene network each node is a gene that has different expression level and links between nodes represent direct regulation (activation or repression). Gene network is stochastic with intrinsic noise from biochemical reactions involved and extrinsic noise from environment. It is non-equilibrium with frequent matter/energy exchange and active entropy production. One crucial character of gene network is the involvement of multiple timescales: timescale of protein synthesis/degradation and timescale of regulation processes. Conventional studies …

The Empowerment Of Women In Candomblé Through The Lens Of Pierre Verger | The Empowerment Of Women In Candomblã© Through The Lens Of Pierre Verger, Luiza Teixeira-Vesey

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

This thesis will address matters of gender and race in Pierre Verger’s photographs of Brazilian Candomblé. Candomblé religion subverts not only race oppression, but gender oppression as well. It is one of the few social spaces where Afro-Brazilians, especially women, assume positions of power. In analyzing Verger's pictures, I will define the extent to which he is successful in translating this subversion to an exterior audience not familiar with the traditions of the religion. | This thesis will address matters of gender and race in Pierre Verger’s photographs of Brazilian Candomblé. Candomblé religion subverts not only race oppression, but gender …

Structure And Dynamics Of The Gulf Stream's Interannual Migration East Of Cape Hatteras, Alejandra Sanchez Franks

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

The Gulf Stream's (GS) main mode of interannual variability, its latitudinal migration, has been shown to be atmospherically forced by the North Atlantic Oscillation (NAO), taking a 2 year lag into account. Observational and model data were used here to examine the structure of the GS's migration and the dynamics linking it to atmospheric forcing. The structure of the GS's interannual variability was investigated from different measures of GS position and transport at 38°N and 27°N (i.e. the Florida Current). Using a zonally averaged index, the local measurements of GS position at 38°N proved good representations of overall meridional shifting …

Design And Analysis Of Parallel Algorithms For Multiscale Modeling Of Platelets, Na Zhang

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

This work presents multiscale models and efficient numerical algorithms for analyzing the activation mechanisms of platelets under blood flow conditions at disparate spatiotemporal scales on supercomputers, with applications in initial thrombogenicity study and medical device optimization. Modeling the multiscale structures of platelets and the dynamics of their motion in viscous blood plasma require multiple time stepping (MTS) algorithm to optimally utilize the computing resources. This MTS algorithm improves the computational efficiency while maintaining stability and prescribed precisions. Our study of the dynamic properties of flipping platelets adapts the hybridized dissipative particle dynamics and coarse-grained molecular dynamics methods, which resolve the …

Specificity In The Regulation And Inhibition Of Src And Related Tyrosine Kinases, Saadat Aleem

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

Dysregulation in the enzymatic activity of Src-family kinases (SFKs) is implicated in multiple disease states, including cancer. SFKs have been intensely investigated as targets for cancer therapeutics. Achieving selectively among the SFKs, and other related non-receptor tyrosine kinases (nRTKs), has proven challenging due to the high similarity in their catalytic domains. Side effects arising from nonspecific binding are common in anticancer therapies, and underscore the need to identify, and exploit differences in these proteins to develop more specific inhibitors. In this study, we have identified differences between the regulatory partners of Src and Brk (Breast Tumor Kinase). We also discuss …

Genetic Alterations To Cx26 Causing Palmoplantar Keratoderma And Hearing Loss Modify Cx43 Channel Behavior, Zunaira Shuja

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

Junctional-mediated intercellular communication in vertebrates is primarily achieved by clusters of connexin proteins which form gap junctions at the plasma membrane. It is believed connexins are crucial to the regulation of physiological homeostasis in various tissues such as the cochlea, and epidermis. Mutations in the GJB2 gene encoding connexin26 (Cx26) cause either deafness, or deafness associated with skin diseases. The fact that very different disorders can be caused by distinct mutations within the same gene suggests that unique channel activities are influenced by each class of mutation. We have examined the functional characteristics of two human mutations, Cx26-H73R and Cx26-S183F, …

Development And Characterization Of High-Resolution Modular Pet Imaging Systems, Michael Budassi

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

Engineering in positron emission tomography contains within it a design for its application. The compact modular detector technology used in the Rat Conscious Animal PET (RatCAP) is specifically designed for awake rat imaging, but is versatile enough for its use in the construction of different preclinical systems. PET scanners based on the RatCAP system include the PET Insert for PET / MR Studies, the Whole-Body Rodent PET Scanner, the BNL PET Imaging System for Plant Science, and the Wrist PET Scanner. This dissertation concerns the development and characterization of these scanners, both specific to their particular use, and common in …

Remembering The Remote: Family, Memory, And Television In Post-Pinochet Chilean Culture, Elizabeth Osborne

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

This dissertation explores how television, its programs, its status as a domestic material object, its technologies, and its presence as a motif in literature, TV series and film, contribute to theorizations and representations of memory of the dictatorship in post-Pinochet Chile. At the same time, individual and collective memories affect television’s representations of the past. Specifically, I look at intersections between familial, generational and medial memory practices of addressing trauma in essays, feature film, television, novels, and documentary films. I identify a range of self-referential and performative techniques of (post)memory particular to the Chilean “children of the dictatorship.†Although the …

Criollo Haitiano Y Español Estudio Comparativo: Los Posesivos Y Los Clíticos | Criollo Haitiano Y Espaã±Ol Estudio Comparativo: Los Posesivos Y Los Clã­Ticos, Wilson Douce

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

Haitian Creole (HC) and Spanish display linguistic traits that are typologically different. These differences are studied through the possessives and the clitics of both languages in a contact situation or possible encounters. The study emphasizes the uniquely post nuclear position of possessives in HC. These two languages have had a past and a present punctuated by a historic and linguistic coexistence that warrants the pedagogical value of a contrastive study of their distinctive features. Conclusively, pronominal and possessive clitics when compared and contrasted in these two languages, due to their range of differences, have necessarily a didactic and pedagogical implication …

Preparation And Characterization Of Stimuli-Responsive Star-Shaped Triblock Copolymers For Gene Delivery, Tianyuan Wu

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

Amphiphilic block copolymers with both a hydrophobic domain and a hydrophilic domain can thermodynamically self-assemble into ordered structures such as spherical micelles, worm-like micelles or vesicles in selective solvents which have great potential for biomedical applications such as drug/gene delivery. Stimuli-responsive amphiphilic block copolymers which can change morphology in response to internal or external stimulus have great potential to achieve controlled release of drugs or genes at specific sites. In this dissertation, two types of stimuli-responsive star-shaped triblock copolymers PEO-S(CKn)-PLA and PEO-(PDEAm)-PLA were synthesized and studied. Amphiphilic cationic star-shaped triblock copolymers with poly(ethylene oxide), poly(D,L-lactide), and poly(L-lysine arms) (PEO-S(CKn)-PLA) were …

Ccn Forwarding Strategies, Ahmed Waliullah Kazi

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

An active area of Future Internet Architectures research is Information Centric Networking (ICNs). Content Centric Networking (CCN) is one of the widely known ICN proposals. ICNs propose a communication paradigm in which named content is the focal point. A fundamental component of ICNs is “in-network caching†, whereby routers act as content caches. The routers implement a “forwarding strategy†for packets that makes intelligent decisions taking several factors into account, not the least of which is leveraging the presence of cached content in the network. From early on, two basic forwarding strategies were proposed for CCN, CCN-Flooding and CCN-Publication. We …

Synthesis Of Novel Conjugated Materials – Push-Pull Conjugated Diynes And 1,7-Phenanthroline Derivatives | Synthesis Of Novel Conjugated Materials €“ Push-Pull Conjugated Diynes And 1,7-Phenanthroline Derivatives, Xiuzhu Ang

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

This thesis is composed of two separate sections, focusing on developing novel conjugated materials. The first section describes attempts towards synthesis of push-pull polydiacetylenes (PDAs), substituted by alternating electron-rich and electron-poor groups. These polymers are expected to have extensive conjugation and low energy band gaps, and therefore potential application in organic photovoltaic cells and nonlinear optics. We targeted push-pull PDAs by solid-state polymerization of appropriate diyne monomers. Oxalamide host molecules containing Lewis acidic or basic side groups are introduced to pre-organize the push-pull diynes in a co-crystal scaffold through Lewis acid-base interactions. Several novel diynes with iodine as electron donor …

Response Of Early Life Stage Bivalves To Diurnal Changes In Carbon Dioxide And Dissolved Oxygen Concentrations, Hannah Rose Clark

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

Highly productive and shallow coastal systems often experience metabolically-driven, diurnal variations in pH and dissolved oxygen (DO) concentrations. It has been suggested that worsening acidification and eutrophication-driven hypoxia will intensify the magnitude of diurnal changes by decreasing baseline pH and DO levels. Few studies, however, have investigated the concurrent effects of low pH and low DO on ecologically and socioeconomically important marine organisms inhabiting coastal ecosystems. My thesis was designed to assess the effects of diurnal patterns in acidification and hypoxia on the survival, growth, and development of the early life stages of three bivalves indigenous to the East Coast …

Analyzing Spatial And Temporal Trends In The Community Structure Of The Peconic Bay Estuary, Tyler Rose Abruzzo

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

Understanding the temporal and spatial trends in community structure of a bay is critical to elucidating drivers of ecosystem change and developing management policies. In order to analyze the spatial and temporal trends in the fish and mobile invertebrate assemblage of Peconic Bay, New York, we utilized data from the NYDEC bottom trawl survey. Beginning in 1987, the survey has been conducted monthly from May through October and averaged 381 stations annually. Twenty two taxa were analyzed using multivariate semivariance on Hellinger transformed abundance data. Temporal trends in community structure revealed strong seasonal patterns typical of a temperate estuarine system. …

Developmental And Receptor-Mediated Pathways Define Acinar Cell Plasticity, Christopher James Halbrook

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

Pancreatic cancer is the fourth leading cause of cancer related death in the United States with most patients succumbing to the disease within a year of diagnosis. Kras mutations are present in the vast majority of pancreatic cancers, though the full mechanism behind Kras induced tumorigenesis is not well defined. Both the EGFR and Notch signaling pathways have been implicated in the formation of precursor lesions from normal acinar cells in a process known as acinar to ductal metaplasia (ADM). Inhibition of MEK kinase downstream of either EGFR or mutant Kras has been shown to be required for ADM formation …

Denitrifying Bioreactors: A Solution To Groundwater Nitrate Pollution At The Forge River?, Christine Jean Gurdon

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

Denitrifying bioreactors are an approach to remediate groundwater contaminated with nitrate. Their popularity as a remediation system has increased due to their unnecessary maintenance, low cost, and longevity. While field trials on their performance have been conducted, few have been completed in a marine coastal environment. In this study, a denitrification wall was designed to be installed and monitored along the shore of a coastal environment, namely, the Forge River, New York. Prior to the design phase, a groundwater plume of elevated nitrate-nitrite concentrations needed to be identified. Groundwater nitrate-nitrite concentrations ranged from 0.01-17.68 mg/L along Riviera Drive, a road …

Advancing Numerical Prediction Of Physical And Biological Processes In Long Island Sound, Ling Liu

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

The occurrence and spread of hypoxia in coastal waters is known to depend strongly on nutrients, primary production, water column structure, wind and tidal mixing. Accurate prediction of the onset, intensity and areal extent of hypoxia remains a challenge. Previous modeling efforts have needed to ‘tune’ vertical mixing or phytoplankton respiration in order to obtain results that agree with field observations of dissolved oxygen (DO). We use a one-dimensional physical model coupled with a biogeochemical model to establish mechanistic links between factors involved in the evolution of seasonal hypoxia in western Long Island Sound. The coupled model includes bacterial dynamics, …

Exploring Model Error Through Post-Processing And An Ensemble Kalman Filter On Fire Weather Days, Michael Jon Erickson

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

The proliferation of coupling atmospheric ensemble data to models in other related fields requires a priori knowledge of atmospheric ensemble biases specific to the desired application. In that spirit, this dissertation focuses on elucidating atmospheric ensemble model bias and error through a variety of different methods specific to fire weather days (FWDs) over the Northeast United States (NEUS). Other than a handful of studies that use models to predict fire indices for single fire seasons (Mölders 2008, Simpson et al. 2014), an extensive exploration of model performance specific to FWDs has not been attempted. Two unique definitions for FWDs are …

Effective Communication Of Critical Radiology Results: The Implementation Of Panic Alert Mechanism, Mumtaz Malik, Sidrah Nausheen

Department of Radiology

Objective: To establish an effective channel of timely communication of life-threatening emergencies to primary physicians by radiology team.Methods: The observational study was conducted at Aga Khan Hospital for Women and Children, Kharadar, Karachi. Data was collected from the log book from July 2012 to June 2013.Amultidisciplinary "Panic Alert" protocol was formulated and implemented in the Radiology unit. All radiological examinations were screened as soon as possible and panic alerts [provisional findings] were communicated to their primary care taker/relevant nursing staff, attendants within 30 minutes from the time of completion of examination. Complete log was maintained. Data was analysed on SPSS …

Real-Time Virtual Teaching: Lessons Learned From A Case Study In A Rural School, Michael K. Barbour

Education Faculty Publications

Due to the challenges facing rural schools, many jurisdictions have resorted to the use of virtual school programs to provide curricular opportunities to their students. While the number of virtual schools that rely on synchronous instruction as a primary or significant method of delivery is quite small, there are some programs that do (and a growing number of virtual schools that use it with small groups or individuals). This case study examined the use of synchronous online instruction by one virtual school with students in a single rural school in Newfoundland and Labrador. The data from a variety of collection …

Una Legua Cuadrada: Exploring The History Of Swanton Pacific Ranch And Environs, Jeanine Marie Scaramozzino

Master's Theses

Swanton Pacific Ranch is an educational and research facility owned by the Cal Poly Corporation and managed by the Cal Poly State University (Cal Poly) College of Agriculture, Food and Environmental Sciences. Located about 180 miles north of campus and just 14 miles north of Santa Cruz, California on Highway 1, the property was first leased to and then donated to Cal Poly by the late Albert E. Smith in 1993. The rancho’s original inhabitants included Native Americans, Spaniards, Mexicans, as well as various European immigrants and their descendants; currently, the staff, faculty, and students of Cal Poly occupy the …

Analyzing General-Purpose Computing Performance On Gpu, Fanfu Meng

Master's Theses

ABSTRACT

Analyzing General-Purpose Computing Performance on GPU

Graphic Processing Unit (GPU) has become one of the most important components in modern computer systems. GPUs have evolved from a single -purpose graphic rendering hardware to a powerful processor that is capable of handling many different kinds of computing tasks. However, GPUs don’t perform well on every application, and it takes a lot of design effort to get good performance on a GPU.

This thesis aims to investigate the relative performance of a GPU vs. CPU. Design effort is held minimum for both CPU implementations and GPU implementations. Matrix multiplication, Advance Encryption …

Methodology And Misdirection: Custom And The Icj, Harlan G. Cohen

Popular Media

Associate Professor Harlan G. Cohen published "Methodology and Misdirection: Custom and the ICJ" on the European Journal of International Law's blog EILJ: Talk! on December 1, 2015.

University Honors Program Newsletters, Honors Program, Georgia Southern University

Honors College: News & Publications (2008-2020)

• Congratulations Fall 2015 Graduates!
• Connor Rentz’s Film Career Takes Flight with Virgin America
• Honors Research Symposium

Donor Platelet Plasma Components Inactivate Sensitive And Multidrug Resistant Acinetobacter Baumannii Isolates, Chelsea M. Edelblute, Olga N. Pakhomova, Fanying Li, Barbara Y. Hargrave, Loree C. Heller

Bioelectrics Publications

Acinetobacter baumannii is an environmentally resilient healthcare-associated opportunistic pathogen responsible for infections at many body sites. In the last 10 years, clinical strains resistant to many or all commonly used antibiotics have emerged globally. With few antimicrobial agents in the pharmaceutical pipeline, new and alternative agents are essential. Platelets secrete a large number of proteins, including proteins with antimicrobial activity. In a previous study, we demonstrated that donor platelet supernatants and plasma significantly inhibited the growth of a reference strain of A. baumannii in broth and on skin. This inhibition appeared to be unrelated to the platelet activation state. In …

The Role Of Entertainment Media In Perceptions Of Police Use Of Force, Kathleen Donovan, Charles Klahm Iv

Political Science Faculty/Staff Publications

Scholars have long noted the importance of the media in shaping citizens’ attitudes about crime and justice. Most studies have focused on the impact of news and particularly local TV news, yet Americans spend far more time watching entertainment media. We examine the portrayal of police misconduct in crime dramas, and how exposure to these portrayals affects perceptions of the police. We find that viewers of crime dramas are more likely to believe the police are successful at lowering crime, use force only when necessary, and that misconduct does not typically lead to false confessions. In contrast, perceptions regarding the …