Digital Commons Network^™

Advancing Risk Assessment: Mechanistic Dose-Response Modelling Of Listeria Monocytogenes Infection In Human Populations, Ashrafur Rahman, Daniel Munther, Aamir Fazil, Ben Smith, Jianhong Wu

Mathematics and Statistics Faculty Publications

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. The utility of characterizing the effects of strain variation and individual/subgroup susceptibility on dose-response outcomes has motivated the search for new approaches beyond the popular use of the exponential dose-response model for listeriosis. While descriptive models can account for such variation, they have limited power to extrapolate beyond the details of particular outbreaks. By contrast, this study exhibits dose-response relationships from a mechanistic basis, quantifying key biological factors involved in pathogen-host dynamics. An …

Word Recognition In Nutrition Labels With Convolutional Neural Network, Anuj Khasgiwala

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nowadays, everyone is very busy and running around trying to maintain a balance between their work life and family, as the working hours are increasing day by day. In such hassled life people either ignore or do not give enough attention to a healthy diet. An imperative part of a healthy eating routine is the cognizance and maintenance of nourishing data and comprehension of how extraordinary sustenance and nutritious constituents influence our bodies. Besides in the USA, in many other countries, nutritional information is fundamentally passed on to consumers through nutrition labels (NLs) which can be found in all packaged …

Novel Relative Spontaneous Ignition Temperature Determination Using Carbon Dioxide Onset With Sta/Ir, Antonio David Trevino

Electronic Theses and Dissertations

Simultaneous thermal analysis, coupled with infrared spectroscopy (STA/IR), was utilized to monitor the evolution of gaseous products during the thermal degradation of samples from Triadica sebifera (Chinese tallow), Ligustrum sinense (Chinese privet), and Ilex vomitoria (yaupon) plants. Identification of carbon dioxide was successful with a spectral match of 90.2 percent and further used in the determination of relative spontaneous ignition temperature, or RSIT. The RSIT value during the growing season for Chinese tallow, Chinese tallow stem, Chinese privet, and Yaupon were 208.4°C, 250.3°C, 210.1°C, and 232.3°C respectively. During the dormant seasons, the values for Chinese tallow stem, Chinese privet, and …

Glutathione: A Small Molecule With Big Sense, Cristina E. Raya, Debasish Bandyopadhyay

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Glutathione, a peptide found in microbes, plants and animals including human plays a key role in maintaining healthy cells. The peptide exists in both reduced and oxidized forms. Synthesis of GSH occurs in the cytosol of cells, and the extent of glutathione synthesis relies on various factors, such as amino acid availability, protein activity etc. Once synthesized, glutathione exists in both forms: oxidized (GSSG) and reduced (GSH). Oxidized glutathione characterized by its disulfide linkage. On the other hand, presence of a thiol group characterizes the reduced glutathione. This thiol makes the tripeptide an essential component of health; it makes glutathione …

Benthic Invertebrate Communities Of Barnegat Bay New Jersey : Effects Of Hard-Clam (Mercenaria Mercenaria L.) Aquaculture Grow-Outs On Benthic Communities, Rebecca Shell

Theses, Dissertations and Culminating Projects

Plots of three treatment types (industry-standard screens with clams, screens without clams, and control) were installed at Sedge Island, Barnegat Bay, in 2012. 177 species from eight phyla were collected. Hard-clam plots had lower Shannon-Weiner Index values and higher sedimentary sorting coefficients as compared to both control treatments. ANOSIM identified benthic communities inside hard clam plots as statistically distinct from the two control treatments. There was no significant effect of treatment on functional groups assigned by burrowing depth. Seasonal peaks in May are clear for Polydora cornuta and Tritia obsoleta, as well as for suspension feeders and omnivores. All burrowing-depth …

The Energy Yield Of Global Crops 1961-2016, Quinn Montana

Graduate Theses and Dissertations

It is often suggested that world food production must increase by 70%-100% or more by the year 2050 if we are to feed the anticipated world population at that time. To evaluate this claim, global crop production from 1961 to 2016 was inventoried using publicly available data from the United Nations Food and Agriculture Organization (FAO). To determine the adequacy of global crop output for humanity, annual global food crop production data (T y-1) were converted to energy yield in kilojoules (KJ y-1). These data were then compared to the annual metabolic energy requirement of the global human population. The …

Methane Emissions From Rice Production On A Silt-Loam Soil In Arkansas, Joshua Jeffry Humphreys

Graduate Theses and Dissertations

Methane (CH4) emissions from rice (Oryza sativa L.) production are a source of concern in the environmental and agricultural communities. New and/or revised agronomic methodologies will be needed to identify production practice combinations that reduce CH4 emissions without decreasing yields. The objective of this multi-year study was to evaluate the effects of water management (i.e., full-season flood and mid-season drain) (2015), cultivar (i.e., pure-line cultivar ‘LaKast’ and the RiceTec hybrid “XP753”) (2015), soil organic matter (SOM) concentration (2016), and tillage [conventional tillage (CT) and no-tillage (NT)] and urea-based fertilizers [N-(n-butyl) thiophosphoric triamide (NBPT)-coated urea and non-coated urea] (2017) on CH4 …

Plant And Microbial Responses To Repeated Cu(Oh)2 Nanopesticide Exposures Under Different Fertilization Levels In An Agro-Ecosystem, Marie Simonin, Benjamin P. Colman, Weiyi Tang, Jonathan D. Judy, Steven M. Anderson, Christina M. Bergemann, Jennifer D. Rocca, Jason M. Unrine, Nicolas Cassar, Emily S. Bernhardt

Plant and Soil Sciences Faculty Publications

The environmental fate and potential impacts of nanopesticides on agroecosystems under realistic agricultural conditions are poorly understood. As a result, the benefits and risks of these novel formulations compared to the conventional products are currently unclear. Here, we examined the effects of repeated realistic exposures of the Cu(OH)₂ nanopesticide, Kocide 3000, on simulated agricultural pastureland in an outdoor mesocosm experiment over 1 year. The Kocide applications were performed alongside three different mineral fertilization levels (Ambient, Low, and High) to assess the environmental impacts of this nanopesticide under low-input or conventional farming scenarios. The effects of Kocide over time were …

Towards Sustainable Aquafeeds: Evaluating Substitution Of Fishmeal With Lipid-Extracted Microalgal Co-Product (Nannochloropsis Oculata) In Diets Of Juvenile Nile Tilapia (Oreochromis Niloticus), Pallab K. Sarker, Anne R. Kapuscinski, Ashley Y. Bae, Emily Donaldson, Devin S. Fitzgerald, Oliver F. Edelson

Dartmouth Scholarship

Microalgae companies increasingly seek markets for defatted biomass that is left over after extracting omega-3 rich oil for human nutraceuticals and crude oil for fuels. Such a protein-rich co-product is a promising alternative to unsustainably sourced fishmeal in aquaculture diets. We report the first evaluation of co-product of the marine microalga Nannochloropsis oculata(N. oculata co-product) for replacing fishmeal in diets of Nile tilapia, a globally important aquaculture species. We conducted a nutrient digestibility experiment with N. oculata dried whole cells and N. oculata co-product, followed by an 84-day nutritional feeding experiment with N. oculata co-product. N. oculata co-product, more nutrient-dense …

Design, Development And Construct Validation Of The Children’S Dietary Inflammatory Index, Samira Khan, Micheal D. Wirth, Andrew Ortaglia, Christian R. Alvarado, Nitin Shivappa, Thomas Hurley, James R. Hébert

Faculty Publications

Objective: To design and validate a literature-derived, population-based Children’s Dietary Inflammatory Index (C-DII)TM. Design: The C-DII was developed based on a review of literature through 2010. Dietary data obtained from children in 16 different countries were used to create a reference database for computing C-DII scores based on consumption of macronutrients, vitamins, minerals, and whole foods. Construct validation was performed using quantile regression to assess the association between C-reactive protein (CRP) concentrations and C-DII scores. Data Sources: All data used for construct validation were obtained from children between six and 14 years of age (n = 3300) who participated in …

Responses Of Non-Native Earthworms To Experimental Eradication Of Garlic Mustard And Implications For Native Vegetation, Kristina A. Stinson, Serita D. Frey, M. R. Jackson, E. Coates-Connor, Mark A. Anthony, K. Martinez

Faculty Publications

Recent studies in invasion biology suggest that positive feedback among two or more introduced organisms facilitate establishment within a new range and drive changes in native plant communities. Here, we experimentally tested for relationships between native plants and two non-native organisms invading forest habitats in North America: garlic mustard (Alliaria petiolata, Brassicaceae) and earthworms. In two forested sites, we compared understory vegetation and earthworm biomass in plots where garlic mustard was removed for three years, plots without garlic mustard invasion, and plots invaded by garlic mustard that was not removed. Earthworm biomass was highest in the plots with garlic mustard, …

The Global Food-Energy-Water Nexus, Paolo D’Odorico, Kyle Frankel Davis, Lorenzo Rosa, Joel A. Carr, Davide Chiarelli, Jampel Dell’Angelo, Jessica Gephart, Graham K. Macdonald, David A. Seekell, Samir Suweis, Maria Cristina Rulli

United States Geological Survey: Staff Publications

Abstract Water availability is a major factor constraining humanity’s ability to meet the future food and energy needs of a growing and increasingly affluent human population. Water plays an important role in the production of energy, including renewable energy sources and the extraction of unconventional fossil fuels that are expected to become important players in future energy security. The emergent competition for water between the food and energy systems is increasingly recognized in the concept of the “food-energy-water nexus.” The nexus between food and water is made even more complex by the globalization of agriculture and rapid growth in food …

Point-Of-Sale Specific Willingness To Pay For Quality-Differentiated Beef, Kar Ho Lim, Michael Vassalos, Michael R. Reed

Agricultural Economics Faculty Publications

Despite the growing interest of producers and consumers toward grass-fed, local, and organic beef, the supply chain for these products to reach consumers is not always clear-cut. Among the available options are direct-to-consumers and the conventional food supply chain. Although consumers may pay a premium for beef differentiated by quality attributes, the willingness to pay (WTP) difference across point-of-sales is unclear. In this study, we contrast the WTPs for conventional, grass-fed, local, and organic beef by brick-and-mortar supermarkets (B&Ms), farmers’ markets, and via online stores. We conduct a choice experiment with a nationwide online sample of American consumers. The findings …

Evolving Paradigms In Biological Carbon Cycling In The Ocean, Chuanlun Zhang, Hongyue Dang, Farooq Azam, Ronald Benner, Louis Legendre, Uta Passow, Luca Polimene, Carol Robinson, Curtis A. Suttle, Nianzhi Jiao

Faculty Publications

Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO₂, CaCO₃, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO₂. The concepts of the biological carbon pump (BCP) …

Litter Identity Affects Assimilation Of Carbon And Nitrogen By A Shredding Caddisfly, Adam C. Siders, Zacchaeus G. Compson, Bruce A. Hungate, Paul Dijkstra, George W. Koch, Adam S. Wymore, A. Stuart Grandy, Jane C. Marks

Faculty Publications

Ecologists often equate litter quality with decomposition rate. In soil and sediments, litter that is rapidly decomposed by microbes often has low concentrations of tannin and lignin and low C:N ratios. Do these same traits also favor element transfer to higher trophic levels in streams, where many insects depend on litter as their primary food source? We test the hypothesis that slow decomposition rates promote element transfer from litter to insects, whereas rapid decomposition favors microbes. We measured carbon and nitrogen fluxes from four plant species to a leaf-shredding caddisfly using isotopically labeled litter. Caddisflies assimilated a higher percentage of …

Rapid Screening Of Ellagitannins In Natural Sources Via Targeted Reporter Ion Triggered Tandem Mass Spectrometry, Jeremiah J. Bowers, Harsha P. Gunawardena, Anaëlle Cornu, Ashwini S. Narvekar, Antoine Richieu, Denis Deffieux, Stéphane Quideau, Nishanth Tharayil

Publications

Complex biomolecules present in their natural sources have been difficult to analyze using traditional analytical approaches. Ultrahigh-performance liquid chromatography (UHPLC-MS/MS) methods have the potential to enhance the discovery of a less well characterized and challenging class of biomolecules in plants, the ellagitannins. We present an approach that allows for the screening of ellagitannins by employing higher energy collision dissociation (HCD) to generate reporter ions for classification and collision-induced dissociation (CID) to generate unique fragmentation spectra for isomeric variants of previously unreported species. Ellagitannin anions efficiently form three characteristic reporter ions after HCD fragmentation that allows for the classification of unknown …

Perils Of The Fungal Kingdom: Mycotoxins In Food And Feed, Adrianna Isobel Pribil

LSU Master's Theses

Humans and fungi have a complex relationship, especially in regards to the many fungal secondary metabolites that can be produced. When secondary metabolites are toxic to animals and humans they are defined as mycotoxins. Fungi can grow on crops pre-harvest and post-harvest, and have the potential to produce mycotoxins which occur regularly in animal feed and food for human consumption. In high doses, mycotoxins cause variety of problems that result in economic losses and extreme health issues. However, multiple mycotoxins will co-occur in nature and commonly occur in low doses. Thus chronic low daily doses of multiple mycotoxins overtime may …

Mooring Impacts On Zostera Marina Meadows And Associated Epifauna In Nantucket Harbor, Massachusetts, Usa, Andrew Wright Mccandless

Dissertations and Theses

Seagrass ecosystems are some of the most productive in the world and provide a variety of ecosystem services but are facing global decline chiefly due to anthropogenic disturbance. Mechanical disturbances to seagrass meadows from anchoring, propeller scars, and mooring scars result in losses or damage to both shoots and the underlying rhizome. I conducted a literature synthesis on the extent of, recovery from, and ecological impacts of these mechanical disturbances to seagrass meadows. The literature suggests that anchoring damage tends to be worst in deeper water where larger vessels anchor and can cause large (>100m²) loss per …

Educational Resources: Magnets, Emily Knight

Chemistry & Biochemistry Student Projects

No abstract provided.

Production Of Bioactive Isothiocyanates By Bacterial Myrosinase, Juan Isaiz, Xiaoji Liu, Michael J. Miller

PRECS student projects

Isothiocyanates (ITCs) are bioactive products found in several plants belonging to the Brassicaceae family, and are produced as defense upon disruption of the tissue by herbivores or pathogens, but in humans they have shown anti-cancer and anti-inflammatory properties.

Although we know gut microbes can hydrolyze GSL into ITC, the mechanism is not known. With improved detection methods, the aim of this experiment is to explore whether the gut microbial myrosinase β-glucosidase found within the genome of E. coli Nissle 1917 can hydrolyze glucosinolates (GSLs) into detectable ITCs.

An Evaluation Of Deterrent Methods Utilized To Prevent Crop Raiding By African Elephants (Loxodonta Africana) In The Kasigau Wildlife Corridor, Kenya, Rebecca Lynn Von Hagen

Masters Theses & Specialist Projects

Escalating human elephant conflict (HEC) continues to be a contributing factor

towards elephant decline, and crop raiding is the most common form of negative

human-elephant interactions. For communities that cannot reverse or prevent crop

raiding, it is necessary to contain HEC events through deterrent measures. Few

deterrent measures exist that combine practicality and affordability while also

preventing habituation by elephants. This project focused on comparing the efficacy of

deterrent methods to assess which was the most successful at preventing elephants

from entering crops in the farming community of Sasenyi, Kenya. In this paired-control

study, four deterrent methods were evaluated: acacia …

Bayesian Testing, Variable Selection And Model Averaging In Linear Models Using R With Bayesvarsel, Gonzalo Garcia-Donato, Anabel Forte

The R Journal

In this paper, objective Bayesian methods for hypothesis testing and variable selection in linear models are considered. The focus is on BayesVarSel, an R package that computes posterior probabilities of hypotheses/models and provides a suite of tools to properly summarize the results. We introduce the usage of specific functions to compute several types of model averaging estimations and predictions weighted by posterior probabilities. BayesVarSel contains exact algorithms to perform fast computations in problems of small to moderate size and heuristic sampling methods to solve large problems. We illustrate the functionalities of the package with several data examples.

Association Tests For Genetic Effect And Its Interaction With Environmental Factors, Zhengyang Zhou

Statistical Science Theses and Dissertations

My research is in the area of statistical genetics, and it contains three projects: (1) Differentiating the Cochran-Armitage (CA) trend test and Pearson’s chi-square test: location and dispersion; (2) Decomposing Pearson’s chi-square test: a linear regression and its departure from linearity; (3) Testing nonlinear gene-environment (GxE) interaction through varying coefficient and linear mixed models.

(1) In genetic case-control association studies, a standard practice is to perform the CA trend test with 1 degree-of-freedom (df) under the assumption of an additive model. However, when the true genetic model is recessive or near recessive, it is outperformed by Pearson’s chi-square test with …

Using Transboundary Wildfire Exposure Assessments To Improve Fire Management Programs: A Case Study In Greece, Palaiologos Palaiologou, Alan A. Ager, Max Nielsen-Pincus, Cody Evers, Kostas Kalabokidis

Environmental Science and Management Faculty Publications and Presentations

Numerous catastrophic wildfires in Greece have demonstrated that relying on fire suppression as the primary risk-management strategy is inadequate and that existing wildfire-risk governance needs to be re-examined. In this research, we used simulation modelling to assess the spatial scale of wildfire exposure to communities and cultural monuments in Chalkidiki, Greece. The study area typifies many areas in Greece in terms of fire regimes, ownership patterns and fire-risk mitigation. Fire-transmission networks were built to quantify connectivity among land tenures and populated places. We found that agricultural and unmanaged wildlands are key land categories that transmit fire exposure to other land …

Reorganizing School Lunch For A More Just And Sustainable Food System In The Us, Jennifer Gaddis, Amy K. Coplen

Urban Studies and Planning Faculty Publications and Presentations

Public school lunch programs in the United States are contested political terrains shaped by government agencies, civil society activists, and agri-food companies. The particular organization of these programs has consequences for public health, social justice, and ecological sustainability. This contribution draws on political economy, critical food studies, and feminist economics to analyze the US National School Lunch Program, one of the world's oldest and largest government-sponsored school lunch programs. It makes visible the social and environmental costs of the "heat-and-serve" economy, where widely used metrics consider only the speed and volume of service as productive work. This study demonstrates that …

Extended Poisson Models For Count Data With Inflated Frequencies, Monika Arora

Mathematics & Statistics Theses & Dissertations

Count data often exhibits inflated counts for zero. There are numerous papers in the literature that show how to fit Poisson regression models that account for the zero inflation. However, in many situations the frequencies of zero and of some other value k tends to be higher than the Poisson model can fit appropriately. Recently, Sheth-Chandra (2011), Lin and Tsai (2012) introduced a mixture model to account for the inflated frequencies of zero and k. In this dissertation, we study basic properties of this mixture model and parameter estimation for grouped and ungrouped data. Using stochastic representation we show …

Safety Implications Of Plasma-Induced Effects In Living Cells – A Review Of In Vitro And In Vivo Findings, Daniela Boehm, Paula Bourke

Articles

Cold atmospheric plasma is a versatile new tool in the biomedical field with applications ranging from disinfection, wound healing and tissue regeneration to blood coagulation, and cancer treatment. Along with improved insights into the underlying physical, chemical and biological principles, plasma medicine has also made important advances in the introduction into the clinic. However, in the absence of a standard plasma ‘dose’ definition, the diversity of the field poses certain difficulties in terms of comparability of plasma devices, treatment parameters and resulting biological effects, particularly with regards to the question of what constitutes a safe plasma application. Data from various …

Integrated Soil Fertility Management Sequences For Reducing Climate Risk In Smallholder Crop Production Systems In Southern Africa, Hatirarami Nezomba, Florence Mtambanengwe, Jairos Rurinda, Paul Mapfumo

All Peer-Reviewed Publications

Climate change, increased climate variability and poor soil fertility are major bio-physical constraints to cropping on smallholder farms in southern Africa. We used the Agricultural Production Systems sIMulator (APSIM) to assess maize yield response to integrated soil fertility management (ISFM) rotational sequences of low-quality organic resources, nitrogen-fixing green manure and grain legumes, and mineral fertilizers under baseline (1960–2005) and projected (2040–2069) climates. APSIM was also employed to evaluate the response of maize yield to the ISFM sequences under a combination of a changing climate, and typical sowing dates and mineral fertilizer application rates for smallholder households of varying resource endowment. …

Cchs: An R Package For Stratified Case-Cohort Studies, Edmund Jones

The R Journal

The cchs package contains a function, also called cchs, for analyzing data from a stratified case-cohort study, as used in epidemiology. For data from this type of study, cchs calculates Estimator III of Borgan et al. (2000), which is a score-unbiased estimator for the regression coefficients in the Cox proportional hazards model. From the user’s point of view, the function is similar to coxph (in the survival package) and other widely used model-fitting functions. Convenient software has not previously been available for Estimator III since it is complicated to calculate. SAS and S-Plus code-fragments for the calculation have been published, …

A Cyber-Physical System Framework For Early Detection Of Paroxysmal Diseases, Zuxing Gu, Yu Jiang, Min Zhou, Xiaoyu Song, Lui Sha

Computer Science Faculty Publications and Presentations

Paroxysmal diseases of inpatients are globally recognized as one of the top challenges in medicine. Poor clinical outcomes are primarily caused by delayed recognition, especially due to diverse clinical diagnostic criteria with complex manifestations, irregular episodes, and already overloaded clinical activities. With the proliferation of measuring devices and increased computational capabilities, cyber-physical characterization plays an increasingly important role in many domains to provide enabling technologies. This paper presents a cyber-physical system (CPS) framework to assist physicians in making earlier diagnoses of paroxysmal sympathetic hyperactivity based on existing medical knowledge. We propose a configurable diagnostic knowledge model to characterize clinical criteria …