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Characterization Of Bacteriophage Targeting Bacillus Licheniformis In Milk Processes And Thermal Stability Of Bacteriophage During Htst Pasteurization, Jeremy Robert Arbon

Theses and Dissertations

An array of Bacillus licheniformis strains were isolated from a commercial powdered milk process. Bacteriophages exhibiting activity against B. licheniformis were isolated from cattle manure and effluent samples destined for a lagoon at a dairy farm. After sequencing, 8 of the 10 phages were found to be novel and genetically differentiated. Transmission electron scanning microscopy (TSEM) was performed. All bacteriophages were of the family Herelleviridae with contractile tail sheaths ranging from 80µm to 150µm and, surprisingly, survived a common fluid milk processing treatment used to inactivate vegetative cells. The survival of the phage after high temperature short time pasteurization of …

Multicenter Randomized Phase Ii Trial Of Atezolizumab With Or Without Cobimetinib In Biliary Tract Cancers, Mark Yarchoan, Andrea Wang-Gillam, Et Al

Open Access Publications

BACKGROUNDMEK inhibitors have limited activity in biliary tract cancers (BTCs) as monotherapy but are hypothesized to enhance responses to programmed death ligand 1 (PD-L1) inhibition.METHODSThis open-label phase II study randomized patients with BTC to atezolizumab (anti-PD-L1) as monotherapy or in combination with cobimetinib (MEK inhibitor). Eligible patients had unresectable BTC with 1 to 2 lines of prior therapy in the metastatic setting, measurable disease, and Eastern Cooperative Oncology Group (ECOG) performance status less than or equal to 1. The primary endpoint was progression-free survival (PFS).RESULTSSeventy-seven patients were randomized and received study therapy. The trial met its primary endpoint, with a …

Investigating Antimicrobial Properties Of Snake Venoms Against B. Cereus, B. Subtilis, E. Coli, And P. Vulgaris, Savannah Elaine Berger

Honors Program Theses and Research Projects

The increasing incidence of antibiotic resistant bacterial infections has provoked the attention of health officials and scientists as a major threat to global public health. Antibiotic resistance is the product of overprescription by doctors, ineffective or shortened dosing by the patient, and more. When a bacterial infection is ineffectively treated as such, persistent pathogenic cells are given the opportunity to proliferate and spread their resistance to other cells. With bacteria utilizing such tools to fight and ultimately resist our current treatment methods, investigation towards the next novel mechanism of inhibition is essential. Venom is of particular interest to many scientists …

The Binary Oppositions In Joseph Conrad's Novel Heart Of Darkness, Huda Kadhim Alwan

Alustath Journal for Human and Social Sciences

The novel Heart of Darkness is regarded as one of Joseph Conrad's highly skilled works and seen as an important tale written between the years of 1898 - 1899, and also viewed as an assault on imperialism and unethical behaviors of the European colonizers in Africa in the nineteenth century. The novel displays the author's humanity towards the crimes of the colonists and imperialists throughout the world. In Heart of Darkness, Conrad shows the cruelty of colonialism in Africa through his major character, Charlie Marlow, who realizes the cruel manners of Belgian colonialism during his journey to the Congo …

Levels Of Influence: How Teacher Self-Efficacy Reflects Individual, School, And Country Level Variables, Rachel B. Goldberg

Seton Hall University Dissertations and Theses (ETDs)

This study investigates relationships between teacher self-efficacy and associated factors not previously studied at an international level. This study used the data gathered through the Programme for International Student Assessment (PISA) assessment conducted in 2018, with an initial sample size of 107,367 participating teachers from 6,128 schools across 19 countries to gain a global perspective regarding the individual and environmental factors that impact teacher self-efficacy. A blocked hierarchical regression model was chosen to support the theoretical structure of the analysis by examining the relationships between three levels of independent variables and teacher self-efficacy. The model predicted over 30 percent of …

Office Of Research, Economic Engagement And Outreach Update, December 15, 2021, Office Of Research, Economic Engagement And Outreach

Office of Research, Economic Engagement and Outreach

No abstract provided.

A Case Study On Hls Portability From Intel To Xilinx Fpgas, Zhili Xiao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Field-programmable gate arrays (FPGAs) are a hardware accelerator option that is growing in popularity. However, FPGAs are notoriously hard to program. To this end, high-level synthesis (HLS) tools have been developed to allow programmers to design hardware accelerators with FPGAs using familiar software languages. The two largest FPGA vendors, Intel and Xilinx, support both C/C++ and OpenCL C to construct kernels. However, little is known about the portability of designs between these two platforms. In this work, we evaluate the portability and performance of Intel and Xilinx kernels. We conduct a case study, porting the Needleman-Wunsch application from the Rodinia …

Mapping Neural Responses Onto Innate And Acquired Behavior: From Insect Olfaction To Realizing A Bio-Hybrid Chemical Recognition System, Rishabh Chandak

McKelvey School of Engineering Graduate Student Theses & Dissertations

In many organisms, the sense of smell, driven by the olfactory system, serves as the primary sensory modality that guides a plethora of behaviors such as foraging for food, finding mates, and evading predators. Using an array of biological sensors, the olfactory system converts volatile chemical inputs from an organism’s environment into well-patterned neural responses that inform downstream motor neurons to drive appropriate behaviors (e.g., moving towards food or away from danger). For many external cues, the elicited neural responses are often determined by the genetic makeup of the organism, which assigns an innate preference, or valence, for these different …

Identification Of Candidate Microbial Biomarkers Of Disease And Design Of Engineered Microbial Therapeutics For The Gut Microbiome, Aura Lucia Ferreiro

McKelvey School of Engineering Graduate Student Theses & Dissertations

The human gut microbiome is a compositionally and functionally diverse community of microorganisms that profoundly influences the health of the host. Deep characterization of gut microbiomes via high-throughput sequencing has identified associations between the gut microbiome and disease states, and spurred development of engineered microbial therapeutics. Successful translation of these research efforts to the clinic will involve i) consideration of how engineered microbes behave and adapt in the gut, towards the implementation of biosafety mechanisms, and ii) identification and validation of microbial biomarkers of disease. This dissertation describes both investigative (Chapter 2) and engineering (Chapters 3 and 4) approaches to …

Photoacoustic Imaging Of Colorectal Cancer And Ovarian Cancer, Xiandong Leng

McKelvey School of Engineering Graduate Student Theses & Dissertations

Photoacoustic (PA) imaging is an emerging hybrid imaging technology that uses a short-pulsed laser to excite tissue. The resulting photoacoustic waves are used to image the optical absorption distribution of the tissue, which is directly related to micro-vessel networks and thus to tumor angiogenesis, a key process in tumor growth and metastasis. In this thesis, the acoustic-resolution photoacoustic microscopy (AR-PAM) was first investigated on its role in human colorectal tissue imaging, and the optical-resolution photoacoustic microscopy (OR-PAM) was investigated on its role in human ovarian tissue imaging.Colorectal cancer is the second leading cause of cancer death in the United States. …

Identifying Structures For Ion Channel Kinetic Models, Kathryn Mangold

McKelvey School of Engineering Graduate Student Theses & Dissertations

Voltage-gated ion channels carry transmembrane current and underlie the voltages changes seen during the action potential. The ion channels open and close precisely, or gate, in response to voltage to create the specific cellular action potential waveform. The first models of voltage-gated ion channels gating dynamics were described by Hodgkin and Huxley when studying the neuronal action potential in the squid giant axon. While the probabilistic gating variables cleverly imagined by Hodgkin and Huxley to describe channel gating are still used today to describe cardiac ionic currents, Markov (or state-dependent) models provide a more accurate representation of channel dynamics. As …

Laser Stimulated Dynamic Thermal Imaging System For Tumor Detection, Hongyu Meng

McKelvey School of Engineering Graduate Student Theses & Dissertations

Laser stimulated dynamic thermal imaging system for tumor detectionby Hongyu Meng Doctor of Philosophy in Biomedical Engineering Washington University in St. Louis, 2021 Professor Samuel Achilefu, Chair Recent advances in infrared sensor technology have enabled the rapid application of thermal imaging in materials science, security and medicine. Relying on the infrared characteristics of living systems, thermal imaging has been used to generate individual heat maps, detect inflammation and tumor. As an imaging system, thermal imaging has the advantages of portability, real-time, non-invasive, and non-contact. But the low specificity of thermal imaging hinders its wide clinical application.

Unfortunately, label-free DTI is …

Acoustic Radiation Force And Its Application For Cell Manipulation And Ion Channels Activation, Xiangjun Peng

McKelvey School of Engineering Graduate Student Theses & Dissertations

Sound is a stress wave that carries energy and momentum flux. Scattered sound waves can generate acoustic radiation force that can be used to manipulate particles or cells. This dissertation demonstrates the physics behind cell manipulation by ultrasound. The work begins with a detailed analysis of the mechanics of using standing surface acoustic waves to fabricate acoustic tweezers for contactless particle manipulation using acoustic radiation force. Models to design and analyze acoustic radiation force have traditionally relied on plane wave theories that cannot predict how standing surface acoustic waves can levitate cells in the direction perpendicular to the substrate. We …

Quantifying Components Of Protein Translation And Metabolite Heterogeneity In Isogenic Microbial Populations, Alexander Schmitz

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cell-to-cell variation in gene expression and metabolite levels have a significant impact on ensemble productivity of microbial bioproduction. New metabolic engineering tools and approaches are needed that consider cell cultures as an amalgam of uniquely behaving individuals to improve the slow commercialization of metabolically engineered systems. Stochastic cellular process including gene expression, metabolism, and growth lead to phenotypic variation between genetically identical cells. Understanding and the ability to control microbial phenotypic variation is key to improving microbial bioproduction metrics. During protein translation, codon usage strongly influences ensemble gene expression but the effect on the variation of gene expression was not …

Zebrafish Models Of Katp Channelopathies, Soma S. Singareddy

McKelvey School of Engineering Graduate Student Theses & Dissertations

Much work has been carried out to understand the composition, structure, and function of ATP-sensitive potassium (KATP) channels in mammalian tissues, as well as the molecular basis of the channelopathies that result from loss-of-function or gain-of-function mutations in these channels. These studies have also highlighted that the available pharmacology to treat such diseases is limited. To overcome such limitations, a better understanding of the tissue specificity of expression, the exact mechanisms linking the molecular dysfunction to the development of complex pathophysiology, the potential for reducing cross-reactivity of drugs, and ultimately more specific therapies are needed. The work described in this …

Anion Exchange Membranes In Electrochemical Energy Systems, Yunzhu Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Non-CO2-emitting sources of renewable energy, such as solar and wind, have become quite popular in recent years, and their electricity generation cost at scale has become comparable with that of gas- and coal-fired power plants. However, their intermittent output makes the resultant electricity hard to dispatch in a reliable manner in the absence of grid-scale electrical energy storage (EES) technologies. Redox-flow batteries (RFBs) are promising devices for medium- to large-scale electric energy storage. They are safe, reliable, and portable, and are designed with decoupled power and energy modules, which makes it easy and cost-effective to scale their output to meet …

Short-Term Memory And Olfactory Signal Processing, Lijun Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Modern neural recording methodologies, including multi-electrode and optical recordings, allow us to monitor the large population of neurons with high temporal resolution. Such recordings provide rich datasets that are expected to understand better how information about the external world is internally represented and how these representations are altered over time. Achieving this goal requires the development of novel pattern recognition methods and/or the application of existing statistical methods in novel ways to gain insights into basic neural computational principles. In this dissertation, I will take this data-driven approach to dissect the role of short-term memory in olfactory signal processing in …

Racial/Ethnic Differences In The Relationship Between Wealth And Health, Sicong Sun

Brown School Graduate Student Theses and Dissertations

Racial wealth inequity is one of the most pressing social and economic issues in the United States, historically and contemporarily. Primarily due to unequal distribution of opportunity for economic advancement and mobility in addition to the accumulation of historic disadvantage endured by Black and Latinx Americans, U.S. racial wealth inequity leads to substantial racial health disparities. It is widely acknowledged that socioeconomic position (SEP) is a fundamental cause of disease and health disparities. Centering around three key constructs—race/ethnicity, wealth, and health—this dissertation had two overarching aims: (a) to investigate the relationship between wealth and health, delineating the effects of wealth …

A Study On The Hormonal Regulation And Novel Role Of Na+ Leak Channel, Non-Selective (Nalcn) In Human Myometrial Smooth Muscle Cells, Chinwendu Amazu

Arts & Sciences Graduate Student Theses and Dissertations

During pregnancy, the uterus transitions from a quiescent state to an excitable, highly contractile state to deliver the fetus. Two important contributors essential for this transition are progesterone (P4) and estrogen (E2), which promote quiescence or contraction, respectively, by acting on the myometrial smooth muscle cells (MSMCs). While these hormones regulate uterine contractions, it is unclear how they affect electrical activity of MSMCs, which underlies uterine contractile activity. Our lab recently identified Na+ leak channel, non-selective (NALCN) as a component of the leak current in human MSMCs and showed that mice lacking NALCN in the uterus have dysfunctional labor. In …

Quantitative Characterization Of Microbial Ecologies In Dysbiosis And Infection, Eric Keen

Arts & Sciences Graduate Student Theses and Dissertations

In 1973, Theodosius Dobzhansky famously wrote that nothing in biology makes sense except in the light of evolution. Today, nearly 50 years later, little in microbiology – or in biology, for that matter – makes sense except in the light of genomics. Microbial genomics populates the field with innumerable testable hypotheses for evaluation in vitro and in vivo, allows us to monitor microbial populations in real time and at a massive scale, and underpins our approach to entire domains of microbiology, including microbial evolution. In this Thesis, I present three studies from my graduate research united by their common theme …

Computational Methods For Analysis Of Data For Conformational And Phase Equilibria Of Disordered Proteins, Jared Michael M Lalmansingh

Arts & Sciences Graduate Student Theses and Dissertations

Intrinsically disordered proteins and regions (IDPs / IDRs) are a class of proteins with diverse conformational heterogeneity that do not fold into a tertiary structure due to the lack of a native structural state. Consequently, disordered proteins are remarkably flexible and exhibit multivalent properties that enable them to adopt myriad functional roles within the cell such as: signaling transduction, transcription, enzymatic catalysis, translation, and many more. Due to their multivalency, some IDPs undergo monomeric and heterotypic interactions which can drive phase separation. Such IDPs can form membraneless organelles with specific regulatory roles within the cell which include, but are not …

Using Single-Particle Fluorescence Microscopy To Elucidate The Role Of Structural Distortions And Defects In The Chemical Reactivity And Photophysics Of Cesium Lead Halide Perovskite Nanocrystals, Dong Wang

Arts & Sciences Graduate Student Theses and Dissertations

Colloidal cesium lead halide perovskite nanocrystals (CsPbX3, X = Cl, Br or I) are attractive for optoelectronic applications due to their unique chemical and physical properties including high photoluminescence quantum yield, tunable bandgaps, high defect tolerance, and low-cost processibility. A facile method to tune the emission wavelength of perovskite nanocrystals is through anion exchange. For light emission applications, it is desirable to prepare CsPbX3 nanocrystals of uniform size and composition. However, the complex reaction kinetics of this chemical transformation may limit the compositional uniformity and color purity of the CsPbX3 nanocrystals produced by anion exchange when the transformation is scaled …

The Effects Of Molecular Chaperone Modulation On Protein Folding, Prion Formation, And Prion Propagation In Saccharomyces Cerevisiae, Leeran Blythe Dublin Ryan

Arts & Sciences Graduate Student Theses and Dissertations

Proper and efficient protein folding is vital for cell survival. Many factors affect protein folding fidelity and prion formation, including molecular chaperone availability and activity. Research has shown that modulating chaperone availability and function can affect protein misfolding and aggregation, as well as de novo prion formation and propagation. However, the factors involved and underlying mechanisms influencing prion formation and protein folding are largely unknown. The following work aims to elucidate these areas. The Nascent Polypeptide-Associated Complex (NAC) is the first point of chaperone contact for nascent polypeptides. Previous work has shown that disruption of the NAC leads to improved …

Deconvolving Genomic Regulatory Heterogeneity With Self-Reporting Transposons, Arnav Moudgil

Arts & Sciences Graduate Student Theses and Dissertations

A cell’s identity is a function of the genes expressed in that cell, which are in turn regulated by transcription factors. Over the last decade, single-cell RNA sequencing (RNA-seq) has emerged as a powerful class of techniques to characterize cellular diversity in heterogeneous tissues. These methods barcode transcripts by their cell-of-origin and assign them to specific genes. The resulting high-dimensional data are further processed to reveal clusters of cells sharing transcriptional states. Annotating these clusters, based on either known or discovered marker genes, offers a glimpse into the dynamic composition of an organ or biological process. While single-cell RNA-seq excels …

Surveillance And Dynamics Of Bacteria And Resistance Genes In Humans And Hospitals, Alaric Wences D'Souza

Arts & Sciences Graduate Student Theses and Dissertations

Bacteria live in, on, and around us. These bacteria affect human health through beneficial commensal interactions that promote normal development and through harmful infections or perturbations leading to disease. Understanding the prevalence, spread, and resilience of these bacteria in humans and human environments is critical to clinical medicine and epidemiology. I investigated environmental and human resident bacteria to understand dynamics in bacterial communities and how these dynamics may impact human health.Hospitals are one critical location of human-bacterial interactions. Bacteria can contaminate hospital surfaces from patients or environmental sources and subsequently transmit from surfaces to vulnerable patients. I analyzed bacteria from …

Iron And Manganese Oxidation By Oxyhalogen Species: Implications For Paleoenvironmental Reconstruction On Mars, Kaushik Mitra

Arts & Sciences Graduate Student Theses and Dissertations

As the nearest planetary neighbor with potential earlier habitable conditions, Mars is replete with minerals that hold clues to its past chemistry and evolution of the aqueous systems. Oxidized iron (Fe) and manganese (Mn) minerals on Mars are geochemical markers of such environments in which they formed and record past pH, redox conditions, and intensity of water-rock interaction. Fe and Mn oxides can therefore be used to reconstruct past Martian environmental conditions from settings where aqueous fluids were active. Various processes that form Fe and Mn oxide minerals on Mars have been previously proposed, including chemical oxidation using molecular oxygen …

On Arousal And The Internal Regulation Of Brain Function: Theory And Evidence Across Modalities And Species, Ryan Raut

Arts & Sciences Graduate Student Theses and Dissertations

The brain is an organ. It is subject to the same physiological regulatory processes that engage the rest of the body’s organs, sculpted over hundreds of millions of years to sustain life so effectively. The central message of this thesis is that the holistic functioning of the brain, rather than operating at some level above or independent from these systemic regulatory processes, is deeply related to them. In short, as our limited attention spans might suggest: brain function is internally regulated. I propose that this internal regulation is a primary function of intrinsic brain activity. Chapter 2 provides a theoretical …

A Rapid Screening Method For Ecological Risks Posed By Different Land Use Intensities: Case Study Of Marikina City’S River System, Maria Aileen Leah Guzman, Charlotte Kendra Gotangco Gonzales, Rene Juna Claveria, Philippe Joshua Evardo, Jean Jardeleza Mijares

Journal of Management for Global Sustainability

Land use plays an important role in environmental and sustainability research because of its potential contribution to ecosystem protection or degradation. However, most risk maps used in comprehensive land use planning only identify areas at risk, for example, to various geophysical or climate- and weather-related hazards. It would also be useful to identify land areas that pose a risk to ecological systems. In this study, a simplified method adapted from the source-habitat approach and the relative risk model was used to explore the potential ecological risk of exposure to water pollutants posed by land uses on the river system in …

A Large West Antarctic Ice Sheet Explains Early Neogene Sea-Level Amplitude, J. W. Marschalek, L. Zurli, F. Talarico, De Flierdt T Van, P. Vermeesch, A. Carter, F Beny, V. Bout-Roumazeilles, F. Sangiorgi, S. R. Hemming, L. F. Pérez, F. Colleoni, J. G. Prebble, Peer Te Van, M. Perotti, A. E. Shevenell, I Browne, Dk Kulhanek, R. Levy, D Harwood, N. B. Sullivan, S. R. Meyers, E. M. Griffith, C. D. Hillenbrand, E. Gasson, M. J. Siegert, B Keisling, K. J. Licht, G. Kuhn, Jp Dodd, C. Boshuis, Santis L De, Rm Mckay, Jeanine Ash, F Beny, Im Browne, Giuseppe Cortese, Santis L De, Jp Dodd, Oliver M. Esper, Jenny A. Gales, Dm Harwood, Saki Ishino, Ba Keisling, S Kim, S Kim, Dk Kulhanek, Jan Sverre Laberg, R. Mark Leckie, Rm Mckay, J Müller, Mo Patterson, Bw Romans, Oe Romero, F. Sangiorgi, O Seki, Ae Shevenell, Sm Singh, De Sousa Im Cordeiro, St Sugisaki, T Van De Flierdt, Peer Te Van, W Xiao, Z Xiong

School of Biological and Marine Sciences

Early to Middle Miocene sea-level oscillations of approximately 40–60 m estimated from far-field records are interpreted to reflect the loss of virtually all East Antarctic ice during peak warmth2. This contrasts with ice-sheet model experiments suggesting most terrestrial ice in East Antarctica was retained even during the warmest intervals of the Middle Miocene. Data and model outputs can be reconciled if a large West Antarctic Ice Sheet (WAIS) existed and expanded across most of the outer continental shelf during the Early Miocene, accounting for maximum ice-sheet volumes. Here we provide the earliest geological evidence proving large WAIS expansions occurred during …

Beach Hazards: Riu Funana, Cape Verde, C Stokes, G Masselink, T Scott, L Brodie

School of Biological and Marine Sciences

No abstract provided.