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A Trait‐Based Framework For Assessing The Vulnerability Of Marine Species To Human Impacts, Nathalie Butt, Benjamin S. Halpern, Casey S. O'Hara, A. Louise Allcock, Beth Polidoro, Samantha Sherman, Maria Byrne, Charles Birkeland, Ross G. Dwyer, Melanie Frazier, Bradley K. Woodworth, Claudia P. Arango, Michael J. Kingsford, Vinay Udyawer, Pat Hutchings, Elliot Scanes, Emily Jane Mcclaren, Sara M. Maxwell, Guillermo Diaz-Pulido, Emma Dugan, Blake Alexander Simmons, Amelia S. Wenger, Christi Linardich, Carissa J. Klein

Biological Sciences Faculty Publications

Marine species and ecosystems are widely affected by anthropogenic stressors, ranging from pollution and fishing to climate change. Comprehensive assessments of how species and ecosystems are impacted by anthropogenic stressors are critical for guiding conservation and management investments. Previous global risk or vulnerability assessments have focused on marine habitats, or on limited taxa or specific regions. However, information about the susceptibility of marine species across a range of taxa to different stressors everywhere is required to predict how marine biodiversity will respond to human pressures. We present a novel framework that uses life-history traits to assess species’ vulnerability to a …

Identification Of A Rickettsial Endosymbiont In A Soft Tick Ornithodoros Turicata Americanus, Lichao Liu, Daniel E. Sonenshine, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Bacterial endosymbionts are abundantly found in both hard and soft ticks. Occidentia massiliensis, a rickettsial endosymbiont, was first identified in the soft tick Ornithodoros sonrai collected from Senegal and later was identified in a hard tick Africaniella transversale. In this study, we noted the presence of Occidentia species, designated as Occidentia-like species, in a soft tick O. turicata americanus. Sequencing and phylogenetic analyses of the two genetic markers, 16S rRNA and groEL confirmed the presence of Occidentia-like species in O. turicata americanus ticks. The Occidentia-like species was noted to be present in all developmental stages …

Streaminghub: Interactive Stream Analysis Workflows, Yasith Jayawardana, Vikas G. Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Reusable data/code and reproducible analyses are foundational to quality research. This aspect, however, is often overlooked when designing interactive stream analysis workflows for time-series data (e.g., eye-tracking data). A mechanism to transmit informative metadata alongside data may allow such workflows to intelligently consume data, propagate metadata to downstream tasks, and thereby auto-generate reusable, reproducible analytic outputs with zero supervision. Moreover, a visual programming interface to design, develop, and execute such workflows may allow rapid prototyping for interdisciplinary research. Capitalizing on these ideas, we propose StreamingHub, a framework to build metadata propagating, interactive stream analysis workflows using visual programming. We conduct …

Completing Single-Cell Dna Methylome Profiles Via Transfer Learning Together With Kl-Divergence, Sanjeeva Dodlapati, Zongliang Jiang, Jiangwen Sun

Computer Science Faculty Publications

The high level of sparsity in methylome profiles obtained using whole-genome bisulfite sequencing in the case of low biological material amount limits its value in the study of systems in which large samples are difficult to assemble, such as mammalian preimplantation embryonic development. The recently developed computational methods for addressing the sparsity by imputing missing have their limits when the required minimum data coverage or profiles of the same tissue in other modalities are not available. In this study, we explored the use of transfer learning together with Kullback-Leibler (KL) divergence to train predictive models for completing methylome profiles with …

Spaghetti Tracer: A Framework For Tracing Semiregular Filamentous Densities In 3d Tomograms, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D …

Refinement Of Alphafold2 Models Against Experimental And Hybrid Cryo-Em Density Maps, Maytha Alshammari, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Recent breakthroughs in deep learning-based protein structure prediction show that it is possible to obtain highly accurate models for a wide range of difficult protein targets for which only the amino acid sequence is known. The availability of accurately predicted models from sequences can potentially revolutionise many modelling approaches in structural biology, including the interpretation of cryo-EM density maps. Although atomic structures can be readily solved from cryo-EM maps of better than 4 Å resolution, it is still challenging to determine accurate models from lower-resolution density maps. Here, we report on the benefits of models predicted by AlphaFold2 (the best-performing …

Odu Research Is Showcased In ‘Waters Rising’ Exhibition At The Chrysler Museum Of Art, Amber Kennedy

News Items

No abstract provided.

Monarch Science Observer, Volume 12, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Winter 2021 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

Analytical Approach To Biometric Security And How It Affects Privacy, Torré A. Williams

Cybersecurity Undergraduate Research Showcase

In this time where the world is using technology every day, there is going to be a need for some type of security to take place to protect its citizens from unwanted harm or danger. The use of any authentication methods is becoming very essential for a lot of companies and even for your own personal belongings. The use of biometric technology has offered companies the chance to upgrade their security system. This has also provided easier ways that people authenticate themselves as who they say they are. Due to their growth of usage, there is a privacy and security …

The Investigations Of Nps Modulated Immunity And Immunometabolism, Brittney Leigh Ruedlinger

Biomedical Sciences Theses & Dissertations

Cancers remain in the top noncommunicable diseases responsible for premature mortality. The heterogeneity among cancers and within tumors makes treating them ever more challenging. Our misfortune for developing cures is mocked by cancer, with the lowest probability of success (PoS) through clinical trials and FDA approval. At the basic level, there are generally two broad gaps impeding cancer eradication: the unidentified shared mechanism(s) exploited by all cancers and the therapeutic approach to intervene. Nanosecond pulse stimulation (NPS) offers a unique approach since its broad impacts intersect those often hijacked by oncogenesis. Metabolic pathways, known for dysfunctions among cancers, share a …

Assessment Of The Hydrograv® Adapt Variable Height Secondary Clarifier Inlet At Hrsd Nansemond Treatment Plant, Matthew Poe

Civil & Environmental Engineering Theses & Dissertations

The Hampton Roads Sanitation District (HRSD) recently completed the first North American and center driven installation of the Hydrograv® Adapt Variable Height Secondary Clarifier Inlet (Adapt) at HRSD’s Nansemond Treatment Plant. This is a variable height inlet structure designed to decrease clarifier effluent turbidity and maintain low turbidity during high flow events. Low turbidity is achieved by feeding the secondary clarifier influent within the solids blanket during dry weather conditions and lifting the inlet structure during wet weather conditions to avoid disrupting the blanket. The Adapt clarifier was monitored alongside an identical fixed inlet clarifier to assess performance. Both clarifiers …

Tunable Compressive Mechanical Behavior Of Ice-Templated Materials, Sashanka Akurati

Mechanical & Aerospace Engineering Theses & Dissertations

The inherent hierarchical microstructural organization in natural materials is responsible for their excellent mechanical properties beyond that predicted by the simple rule-of-mixtures. Further exhibit synergy between strength and toughness, otherwise mutually exclusive in brittle materials. Conventional processing methods are unable to replicate hierarchical microstructures in engineering ceramics akin to that observed in natural materials. Ice-templating has emerged as a potential technique to fabricate bioinspired hierarchical materials. This process involves simultaneous unidirectional solidification and phase segregation of aqueous suspensions. Ice-templated porous ceramic materials have received significant attention for overcoming several limitations of conventional ceramic foams currently used in numerous engineering applications. …

Intention-Behavior Discrepancies For Alcohol Consumption Among College Students, Emily Kaye Junkin

Psychology Theses & Dissertations

Unplanned drinkers may experience elevated risk for drinking-related harm. Research examining unplanned drinking focuses on the unplanned nature of a drinking episode (i.e., did the student drink when no drinking was planned), yet this does not capture the importance of the unintended quantity consumed. For instance, a discrepancy between drinking intentions and actual consumption has the potential to differentially impact alcohol-related outcomes beyond what is accounted for by unplanned drinking episodes. Further, research has not investigated how college students’ unintended drinking is associated with alcohol-related consequences. Moreover, utilization of protective behavioral strategies (PBS) has been shown to decrease negative outcomes …

Integrated Processing Of Municipal Solid Waste For Maximizing Waste Reduction, Carbon Recovery And Fuel Production, Kameron J. King

Civil & Environmental Engineering Theses & Dissertations

Nationally and internationally, waste generation is increasing and along with it negative environmental impacts. Many people think waste ends at disposal; however, environmental impacts have already begun. Unfortunately, 50% of waste ends up in a landfill which is the third largest source of human related methane emissions and a leading cause of global climate change. This study investigated a novel waste management strategy in hopes of mitigating negative environmental effects caused by conventional waste management practices. The novelty of the study lies in the development of an integrated method of hydrothermal carbonization and an anaerobic digestion (HTC + AD) process …

Hydrothermal Processes For Extraction And Conversion Of Biomass To Produce Biofuels And Value-Added Products, Anuj Hemant Thakkar

Civil & Environmental Engineering Theses & Dissertations

An integrated biorefinery approach based on subcritical hydrothermal processes was developed to maximize utilization of biomass components by producing multiple products. Biomass from various sources like agricultural waste (lignocellulose), food waste (spent yeast), and dedicated cultivation (micro-algae) was used in this research.

Corn stover (agricultural waste) was hydrothermally pretreated to remove lignin and xylan while preserving most of the glucan. The pretreated corn stover was utilized to produce levulinic acid (thermochemically) and fermentable sugars (biochemically). The solid residue generated during levulinic acid production was utilized to produce biocarbon electrode material. The results generated from the experiments were used for designing …

Estimating The Risk Of Future Plastic Marine Debris Resulting From The Urban Coastal Built Environment, Kelly C. Jones

OES Theses and Dissertations

The growing urban built environment in the coastal zone poses an unknown risk to the marine biosphere as a source of marine debris. Plastic, since its introduction in the mid- 1900s, is now used in nearly all aspects of human life. Growth in human population and urbanization in coastal zones has resulted in the accumulation of large stocks of plastic in the coastal built environment, and these stocks are still growing exponentially. The coastal zone is exposed to a number of hazards including storms, tsunamis, and sea level rise, and most of these hazards are expected to change in the …

Covid-19, Technology, And The Math Classroom: Changes, Obstacles, And Victories Integrating Digitally, Lauren Fifield Bellamy

Teaching & Learning Theses & Dissertations

Secondary math teachers faced new experiences and struggles this past virtual school year due to the global COVID-19 pandemic. Nine secondary math teachers from a school division in southeastern Virginia participated in this qualitative single case study. Data collection included individual semi-structured interviews and technology integration artifacts. Through a three round coding process, ten themes emerged to answer the following three research questions: 1) In terms of curriculum, teaching methods, and assessments, how did teachers describe their pedagogical change in virtual learning? 2) How do teachers perceive student performance has changed within the virtual learning space? 3) From teachers’ perspectives, …

Genetically Engineered Thermosynechococcus Elongatus Bp1: Assessment Of Potential Biorisks And Biofuel Production, Thu Ho Anh Nguyen-Jones

Chemistry & Biochemistry Theses & Dissertations

According to the International Energy Outlook 2019, released by the U.S. Energy Information Administration, it is projected that the energy consumption will increase up to 50% between 2018 and 2050 worldwide. As fossil fuel being a finite source of energy with the risk of depletion, many countries are now facing an energy security crisis. Therefore, it is important to develop other renewable and sustainable energy sources that will allow countries to shift away from depending on fossil fuels. Among several types of renewable energy, biofuel production using genetically engineered cyanobacteria is capturing much interest due to its many advantages. Different …

Synthesis And Characterization Of 4,6-Protected Glucosamine Derivatives And Branched Glycoconjugates, Jonathan Bietsch

Chemistry & Biochemistry Theses & Dissertations

Low molecular weight gelators (LMWGs) are small molecules that self-assemble in appropriate solvents to form three dimensional networks that immobilize the solvent, creating a supramolecular gel. The self-assembly of LMWGs occurs through non-covalent interactions such as hydrogen bonding, aromatic interactions, donor-acceptor interactions, Van der Waals interactions, hydrophobic forces, halogen bonding, etc. Due to self-assembly occurring through reversible non-covalent interactions, supramolecular gels can undergo a gel to solution transformation. Because of this, these materials can be sensitive to external stimuli such as temperature changes, pH changes, and other stimuli that effect non-covalent interactions. This makes the synthesis of LMWG’s an appealing …

Design, Synthesis And Characterization Of Carbohydrate Based Macrocycles, Photo Responsive Derivatives, And Glycoconjugates Based Low Molecular Weight Gelators, Surya Bahadur Adhikari

Chemistry & Biochemistry Theses & Dissertations

Functional glycoconjugates are important classes of compounds with many applications in different research fields. Our lab has been studying the synthesis and applications of different classes of glycoconjugates ranging from macrocycles to sugar heterocycle derivatives. Due to the importance of these compounds, our research is based on development of synthetic methods for various carbohydrate derivatives. This dissertation includes introduction and overview of projects, followed by the synthesis and studies of several different series of glycomacrolactones. The second project focuses on two classes of photoresponsive molecules, the coumarins and diarylethenes. The third project involves the synthesis and self-assembling properties of isoxazole-based …

Emotion Regulation Variability And Relationship Functioning In Emerging Adulthood, Laura B. Kenneally

Psychology Theses & Dissertations

Emotion regulation is a transdiagnostic factor that functions as a crucial contributor to individual well-being and social functioning. Research seeking to identify adaptive or maladaptive strategies of emotion regulation has often focused on individual strategies, though emerging evidence suggests that what constitutes “adaptive” regulation is often context-dependent. Having a large repertoire of emotion regulation strategies that one is willing to use at different rates has been termed “emotion regulation variability,” and has been linked to positive individual outcomes. While the benefits of emotion regulation variability have been demonstrated on an individual level, the impact on romantic relationships has yet to …

Phytoplankton Community Response To Upwelling Events: Distribution And Abundance Investigated Using Genomic Methods, Sveinn V. Einarsson

OES Theses and Dissertations

Upwelling events are known to support blooms of phytoplankton, important primary producers at the base of the oceanic food web. Phytoplankton community structure changes in response to upwelling support higher trophic level growth and increased efficiency of carbon export from the euphotic zone. While these events occur globally, this study examined upwelling in coastal regions, where alongshore winds can drive Ekman transport and upwelling of deeper waters. The two upwelling regimes examined were the California Current System and the Alaskan Beaufort Sea. In the California Current System, the relative diatom community composition was examined using 18S sequencing to determine how …

Experiences With Flood And Perceptions Of Flood Risk Among Members Of The Filipino American Community In Virginia Beach, Virginia, Anjelica Pascual Petsch

Institute for the Humanities Theses

The Filipino Americans living in Hampton Roads, Virginia have comprised of almost 2% of the region’s overall population, and 5.3% of the population in Virginia Beach, Virginia (United States Census Bureau, 2019) (Greater Hampton Roads Connects, 2021). Filipino Americans in Hampton Roads, like the rest of the population, are equally vulnerable to experiencing flooding when commuting to and from work or simply traveling around town, but previous research and surveys from the Hampton Roads Region have failed in their ability to capture this cultural diversity within perception of flood risk. In this paper, a qualitative research design was used to …

Efficacy Of Sediment Contaminant Remediation Of The Benthos In A Segment Of The Southern Branch Of The Elizabeth River, Colton Martin

Biological Sciences Theses & Dissertations

The bottom sediment of the Southern Branch of the Elizabeth River, a tributary of Chesapeake Bay, was historically contaminated with hydrocarbons from industrial sources especially wood treatment facilities. The Elizabeth River Project selected a section of the bottom off Money Point in the Southern Branch for a sediment contaminant remediation effort. Prior to initiation of remediation efforts, a survey occurred in summer 2010 to characterize the ecological condition of the benthic communities off Money Point compared to benthic communities of a benthic region across the channel and northwest of Money Point near Blows Creek. That study characterized the benthos of …

The Influence Of Emotion Regulation And Neural Cognitive Control On Distress Tolerance, Alicia L. Milam

Psychology Theses & Dissertations

Tolerance of negative emotions has been associated with transdiagnostic negative mental health outcomes. Theory and research implicate emotion regulation and cognitive control as factors in tolerance of negative emotions. But their unique contributions to tolerance of negative emotions and interdependency have been unclear due to methodological limitations. This study aimed to explicate cognitive and emotional factors affecting distress tolerance in a non-clinical sample of emerging adults. Undergraduate psychology students completed self-report measures of emotion regulation ability and tolerance of negative emotions. The N2 ERP component elicited by a Go-NoGo task was also used as a neurophysiological marker of cognitive control …

Mechanisms Of Stress Survival In Gram Positive Bacterial Pathogens, Asia Poudel

Chemistry & Biochemistry Theses & Dissertations

Anaerobic Gram-positive bacteria are not a well-characterized group but include many human pathogens that are resilient against stresses caused by the human immune system or by antibiotic treatment. This dissertation investigated the survival mechanisms of two clinically relevant Gram-positive organisms, Clostridioides difficile and Cutibacterium acnes under extracellular stresses. The response of the opportunistic skin pathogen Cutibacterium acnes to nanosecond electric pulses is characterized and found that growth in a biofilm, which usually protects bacteria from stress, renders this species more killable by this treatment. In addition, the stringent response (SR), a conserved bacterial stress survival mechanism, is studied in the …

A Copula Model Approach To Identify The Differential Gene Expression, Prasansha Liyanaarachchi

Mathematics & Statistics Theses & Dissertations

Deoxyribonucleic acid, more commonly known as DNA, is a complex double helix-shaped molecule present in all living organisms and hosts thousands of genes. However, only a few genes exhibit differential expression and play a vital role in a particular disease such as breast cancer. Microarray technology is one of the modern technologies developed to study these gene expressions. There are two major microarray technologies available for expression analysis: Spotted cDNA array and oligonucleotide array. The focus of our research is the statistical analysis of data that arises from the spotted cDNA microarray. Numerous models have been proposed in the literature …

Sleeping With The Enemy: Examining The Relationship Between Sleep And Pain In Post-9/11 Veterans, John L. Schwartz Jr.

Psychology Theses & Dissertations

United States veterans are a diverse group of individuals, yet as a result of their service, they share a unique set of customs, traditions, and values. Post-9/11 veterans are more likely to experience elevated levels of pain and poor sleep quality compared to their civilian counterparts; however, little is known about how beliefs related to veterans’ pain impact their sleep and how levels of pain acceptance influence the sleep-pain association. This study examined relationships between sleep and pain in a sample of 102 post-9/11 veterans. Results support associations between pain and sleep identified in other populations. Positive correlations were found …

Shipboard Lidar As A Tool For Remotely Measuring The Distribution And Bulk Characteristics Of Marine Particles, Brian Leigh Collister

OES Theses and Dissertations

Light detection and ranging (lidar) can provide remote estimates of the vertical distribution of optical properties in the ocean, potentially revolutionizing our ability to characterize the spatial structure of upper ocean ecosystems. However, challenges associated with quantifying the relationship between lidar measurements and biogeochemical properties of interest have prevented its adoption for routinely mapping the vertical structure of marine ecosystems. To address this, we developed a shipboard oceanographic lidar that measures attenuation (α) and linear depolarization (δ) at scales identical to those of in-water optical and biogeochemical measurements. The instrument’s ability to resolve the distribution of optical and biogeochemical properties …

The Effects Of Depression, Anxiety, And Stress On College Students: Examining The Role Of Mental Health Self-Efficacy On Willingness To Engage In Mental Health Services, Leeanna L. Golembiewski

Psychology Theses & Dissertations

Relative to younger ages, mental health problems are more prevalent among college students (Pedrelli et al., 2015) and nearly 20% of U.S college students are diagnosed each year with a mental health problem (Blanco et al., 2008). College students’ self-efficacy may influence mental health outcomes by impacting an individual’s decision to change their behavior and execute a course of action (Bresó et al., 2011). Mental health may also be influenced by the degree of willingness that an individual possesses, such that those who are more willing to seek mental health treatment are also more likely to follow through and seek …