Physical Sciences and Mathematics Commons^™

Sediment Metagenomics Reveals The Impacts Of Poultry Industry Wastewater On Antibiotic Resistance And Nitrogen Cycling Genes In Tidal Creek Ecosystems, Miguel Semedo, Bongkeun Song

VIMS Articles

The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the …

From Field To Shore: Policy Improvements To Better Protect Ecosystem And Human Health From Poultry Wastes In Virginia, Rachael A. King

Dissertations, Theses, and Masters Projects

Commercial poultry production is a large industry with economic importance in Virginia. However, mismanagement of manures and wastes generated from the poultry industry can be a serious threat to ecosystem and human health. Primarily, there is a concern about nutrient pollution related to runoff and infiltration of poultry wastes. High nutrient loading can cause groundwater contamination, eutrophication, and harmful algal blooms (HABs). Additional concerns include metals, antibiotics, and pesticides that can be found in poultry wastes. To determine existing threats to ecosystem and human health from the poultry industry, Virginia policies regulating the industry are reviewed and their strengths and …

Voting Rules And Properties, Zhuorong Mao

Undergraduate Honors Theses

This thesis composes of two chapters. Chapter one considers the higher order of Borda Rules (Bp) and the Perron Rule (P) as extensions of the classic Borda Rule. We study the properties of those vector-valued voting rules and compare them with Simple Majority Voting (SMV). Using simulation, we found that SMV can yield different results from B1, B2, and P even when it is transitive. We also give a new condition that forces SMV to be transitive, and then quantify the frequency of transitivity when it fails.

In chapter two, we study the `protocol paradox' of approval voting. In approval …

Increasing Use Of Natural And Nature-Based Features To Build Resilience To Storm-Driven Flooding, Final Report, Center For Coastal Resources Management, Virginia Institute Of Marine Science, Pamela Mason, Jessica Hendricks, Julie Herman, Karen Duhring, Carl Hershner

Reports

In coastal Virginia today, local governments are dealing with recurrent flooding driven by coastal storms, exacerbated by rising sea level and increased frequency of intense rain events. At the same time, they are confronted with increasing demands on limited resources to address issues coastal flooding in concert with water quality, wetlands management, shoreline erosion, habitat, and community needs such as infrastructure, flood insurance and open space. One solution is to maximize the protection of existing and implement new natural and nature-based features (NNBFs) to capitalize on the provision of multiple benefits to address many of these coastal issues.

There are …

Gis Data: St. Mary’S County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Gis Data: Charles County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

Shoreline Situation Reports (SSR) were first generated by VIMS in the 1970s to report the condition and status of the shore lands. The SSR series were published in hardcopy on a county by county basis for each of the Tidewater Virginia localities. The reports were intended to assist planners, managers, and regulators in decisions pertaining to management of coastal areas and natural resources therein. The techniques developed for Virginia's shoreline are used to create similar reports for the Maryland shoreline. Data collected describes conditions in the immediate riparian zone, the bank, and along the shore.

Gis Data: Worcester County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Gis Data: Somerset County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

New Guidance To Build Resiliency And Mitigate For Sea Level Rise As Elements Of The Chesapeake Bay Preservation Act, Pamela Mason, Julie Herman, Christine Tombleson, Jessica Hendricks, Karen Duhring

Reports

The Center for Coastal Resources Management (CCRM), Virginia Institute of Marine Science (VIMS), worked in collaboration with the Virginia Department of Environmental Quality (DEQ) and the Virginia Coastal Policy Center (VCPC) to develop guidance to inform the implementation of Chesapeake Bay Preservation Act (CBPA) regulations promulgated in 2021. The 2021 regulations added provisions to require local governments to consider climate changes, specifically flooding, sea level rise and storms, and the preservation of mature trees in the administration of the CBPA program. Specifically, CCRM developed analytical data using criteria specified in the CBPA regulations, of the National Oceanic and Atmospheric Administration …

Gis Data: Baltimore County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Gis Data: Baltimore City, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Gis Data: Wicomico County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Gis Data: Queen Anne’S County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Gis Data: Kent County, Maryland Shoreline Situation Report, Karinna Nunez, Tamia Rudnicky, Sharon Killeen, Jessica Hendricks, Catherine R. Duning, Evan Hill

Data

No abstract provided.

Norfolk, Virginia Federal Flood Risk Management Study, Jian Shen, Rico Wang, Mac Sisson

Reports

The City of Norfolk and Norfolk District, U.S. Army Corps of Engineers (USACE), are partnering to conduct a Coastal Storm Risk Management Study (CSRM) study to determine the Federal interest and feasibility of alternatives to mitigate coastal flooding risk in the City. The CSRM is in the Feasibility Study (FS) phase in which alternatives are proposed and developed to conceptual/preliminary design level, benefit/cost analyses are conducted, and environmental studies are completed to comply with the National Environmental Policy Act (NEPA). The magnitude of the feasibility study will require an Environmental Impact Statement (EIS).

A component of the FS/EIS is the …

Influence Of Oyster Genetic Background On Levels Of Human-Pathogenic Vibrio Spp., Corinne Audemard, Kimberly S. Reece, Robert J. Latour, Lydia M. Bienlien, Ryan B. Carnegie

VIMS Articles

Human-pathogenic Vibrio bacteria are common inhabitants of oyster tissues, but our understanding of factors driving the wide range of concentrations found in individual oysters is extremely limited. We examined the influence of oyster sex and parasitism in light of their profound effects on oyster tissues against a backdrop of eastern oysters, Crassostrea virginica, from two diploid and two triploid aquacultured lines. This allowed us to examine not only the effect of oyster ploidy but also of oyster genetics, a factor never investigated with regard to human-pathogenic Vibrio species. We measured levels of total Vibrio vulnificus (vvhA), and of …

Chesapeake Bay National Estuarine Research Reserve In Virginia Management Plan: 2022-2027, W. G. Reay, J. Baber, H. Brooks, A. Demeo, C. T. Friedrichs, C. Gonzales, J. Kuriawa, T. Hooper, S. Lerberg, E. J. Miles, B. Neikirk, S. Nuss, L. Ott, D. Parrish, T. Rudo, E C. Shields, S. Snyder, S. Wood

Reports

Established through the Coastal Zone Management Act, the National Estuarine Research Reserve System (NERRS) represents a partnership program between the National Oceanic and Atmospheric Administration (NOAA) and the coastal states to promote informed management of the Nation’s estuaries and habitats. Designated in 1991, and administered by the Virginia Institute of Marine Science (VIMS) of William & Mary, the Chesapeake Bay National Estuarine Research Reserve in Virginia (CBNERR-VA or Reserve) is one of 30 protected areas, which encompass over 1.3 million acres and make up the NERRS.

As the nation's largest estuary, the Chesapeake Bay contains a diverse collection of habitats …

Shear Turbulence In The High-Wind Southern Ocean Using Direct Measurements, Laur Ferris, Carole Anne Clayson, Donglai Gong, Et Al

VIMS Articles

The ocean surface boundary layer is a gateway of energy transfer into the ocean. Wind-driven shear and meteorologically forced convection inject turbulent kinetic energy into the surface boundary layer, mixing the upper ocean and transforming its density structure. In the absence of direct observations or the capability to resolve sub-grid scale 3D turbulence in operational ocean models, the oceanography community relies on surface boundary layer similarity scalings (BLS) of shear and convective turbulence to represent this mixing. Despite their importance, near-surface mixing processes (and ubiquitous BLS representations of these processes) have been under-sampled in high energy forcing regimes such as …

Wind-Modulated Western Maine Coastal Current And Its Connectivity With The Eastern Maine Coastal Current, Denghui Li, Zhengui Wang, Huijie Xue, Andrew C. Thomas, Ron J. Etter

VIMS Articles

Using a high-resolution circulation model and an offline particle tracking model, we investigated variations of the Western Maine Coastal Current (WMCC) and its connectivity with the Eastern Maine Coastal Current (EMCC). The models showed that the weak, broad, and sinuous WMCC is generally southwestward with an offshore and a nearshore core, fed by the extension of the EMCC and runoff from the Penobscot and Kennebec–Androscoggin Rivers, respectively. A sea-level dome can form offshore of Casco Bay in late fall and early winter as the northeastward alongshore wind sets up a seaward sea-level gradient from the coast to meet the shoreward …

Vims Marine Science Day, Virginia Institute Of Marine Science

Miscellaneous

Brochure describing demonstrations and activities on this day of community outreach.

Sediment Characteristics Of The Chesapeake Bay And Its Tributaries, Virginia Province: Data Files, Gary F. Anderson

Data

During the 1990’s, Dr. Maynard Nichols and colleagues at the Virginia Institute of Marine Science compiled digital databases of sediment observations in the Chesapeake Bay and other coastal bays and rivers. These projects were performed under several cooperative agreements with NOAA, EPA and USGS. This particular dataset covers the Chesapeake Bay for bulk properties and contaminants. Additional references are provided below. The original files and filenames are provided without edit. See the readme.txt file for overall explanation of the datasets and individual .DOC files for the data dictionary and further data processing information for each waterbody.

The Probability Mass Function Of The Kaplan-Meier Product-Limit Estimator, Yuxin Qin, Heather Sasinowska, Lawrence Leemis

Arts & Sciences Articles

Kaplan andMeier’s 1958 article developed a nonparametric estimator of the survivor function from a right censored dataset. Determining the size of the support of the estimator as a function of the sample size provides a challenging exercise for students in an advanced course in mathematical statistics. We devise two algorithms for calculating the support size and calculate the associated probability mass function for small sample sizes and particular probability distributions for the failure and censoring times.

Bayesian Spatial Model Development Of Soil Core Organic Matter As A Proxy For Blue Carbon Stocks Within The Chesapeake Bay, Christian Longo

Undergraduate Honors Theses

Blue carbon is carbon captured and stored within bodies of water and their ecosystems. Blue carbon stocks are very important due to their ability to store carbon away from the atmosphere. The destruction of these stocks can accelerate climate change. In particular, we wish to assess blue carbon stock within the Chesapeake Bay. Previous studies have only used geographical features to predict blue carbon stock levels. The big picture question this thesis was meant to answer is: What is the best approach for building a statistical model that factors in both spatial parameters and geographical features to predict blue carbon …

Gas-Phase Proton Affinities For Twenty Of The Proline-Containing Dipeptides, Henry Cardwell

Undergraduate Honors Theses

Peptide fragmentation plays a crucial role in the analysis of proteins through mass spectrometry-based proteomics. Most proteomics experiments take place in the low-energy regime and are governed by the mobile proton model which predicts random cleavages along the peptide backbone; however, there sometimes arise circumstances where the mobile proton model fails causing sequencing algorithms to misidentify peptides. One such example is noted in the “proline effect” wherein proline-containing peptides preferentially fragment N-terminal. While it has been established that the “proline effect” is due to the rigidity and basicity of the proline N-terminus, a further understanding of the factors influencing the …

Modern Theory Of Copositive Matrices, Yuqiao Li

Undergraduate Honors Theses

Copositivity is a generalization of positive semidefiniteness. It has applications in theoretical economics, operations research, and statistics. An $n$-by-$n$ real, symmetric matrix $A$ is copositive (CoP) if $x^T Ax \ge 0$ for any nonnegative vector $x \ge 0.$ The set of all CoP matrices forms a convex cone. A CoP matrix is ordinary if it can be written as the sum of a positive semidefinite (PSD) matrix and a symmetric nonnegative (sN) matrix. When $n < 5,$ all CoP matrices are ordinary. However, recognizing whether a given CoP matrix is ordinary and determining an ordinary decomposition (PSD + sN) is still an unsolved problem. Here, we give an overview on modern theory of CoP matrices, talk about our progress on the ordinary recognition and decomposition problem, and emphasis the graph theory aspect of ordinary CoP matrices.

Alkali Linewidths Under High Temperatures And Pressures Of 3he, Michael Parker

Undergraduate Honors Theses

Current research at Thomas Jefferson National Accelerator Facility is being conducted to study the spin structure of the neutron through collisions with polarized 3He nuclei. The helium is contained in high pressure glass vessels (called cells) along with nitrogen, rubidium, and potassium. To deduce the spin structure from collisions, we need to know the precise number density of 3He in the cell. The process of polarizing 3He through spin-exchange optical pumping requires nitrogen and alkali metal. We can use the absorption linewidths of rubidium and potassium to more accurately determine the density of helium. Throughout my research, I collected absorption …

Climate Change And Conservation Of Milkweed: Evidence Of Extensive Admixture Between Common Milkweed And Poke Milkweed, Elizabeth Davies

Undergraduate Honors Theses

Global climate change can drive many changes in species interactions. One primary way it affects species is by changing climates, causing species to expand their ranges and allowing them to interact with species from whom they were previously isolated. In plants, new species interactions can result in hybridization – the creation of hybrid offspring between two separate species. This hybridization can increase gene flow between the species and lead to introgression, the transfer of genetic material from one species to another through hybrid backcrossing with the parent species. My thesis investigates hybridization in the model system Asclepias (milkweed) by analyzing …

Co-Planar Waveguides For Microwave Atom Chips, Morgan Logsdon

Undergraduate Honors Theses

This thesis describes research to develop co-planar waveguides (CPW) for coupling microwaves from mm-scale coaxial cables into 50 μm-scale microstrip transmission lines of a microwave atom chip. This new atom chip confines and manipulates atoms using spin-specific microwave AC Zeeman potentials and is particularly well suited for trapped atom interferometry. The coaxial-to-microstrip coupler scheme uses a focused CPW (FCPW) that shrinks the microwave field mode while maintaining a constant 50 Ω impedance for optimal power coupling. The FCPW development includes the simulation, design, fabrication, and testing of multiple CPW and microstrip prototypes using aluminum nitride substrates. Notably, the FCPW approach …

Chemical Analysis Of Organic Compounds In Dew Water, Monica Dibley

Undergraduate Honors Theses

Water films on outdoor surfaces, such as dew, can act as a reservoir for organic molecules deposited from the atmosphere and they present a potential reactive medium for chemical transformations. To better understand the flux of volatile organic compounds from evaporating films, the composition and reactivity of the complex mixture of dissolved organic material (DOM) found in these films need to be characterized. Previous studies have measured the salts and the small organic molecules in dew collected on clean Teflon surfaces or condensers. Here, we expand on this by probing the organic chemicals found on natural outdoor surfaces covered in …

Investigation Of Tertiary Impact Cratering And Relation To Impact Physics Theory, Mikayla Huffman

Undergraduate Honors Theses

Extraterrestrial impact crater formation is important in many subfields of planetary science, including geochronology, planetary formation, and dynamic fragmentation theory. Current dynamic fragmentation theory lacks scale dependence and relies heavily on terrestrial data. Exploring a range of impact and ejecta velocities as is produced by cratering events on the Moon may bridge the gap between heavily terrestrial-based theory and planetary data. The secondary craters of secondary craters deemed “tertiary craters,” have been theorized, but planetary images have not been of sufficient resolution to effectively search for them until recently. Tertiary craters are formed by relatively low-velocity fragments ejected by nearby …