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Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …

Using Machine Learning Classification And Esa Sentinel 2 Multispectral Imager Data To Delineate Marsh Vegetation And Measure Ecotone Movement In Coastal Georgia, Thomas A. Pudil

College of Graduate Studies: Theses & Dissertations

Tidal marshes are unique communities that are subjected to environmental stressors including sea level rise, salinity change, and drought, resulting in constant change. It is important to monitor these changing areas because of the ecosystem services they provide to us, such as protection from storms and carbon sequestration. The proposed work for this thesis project is focused on the study of tidal marshes and the dynamics between the vegetation species within them. The aim of this project is to use geospatial technology and analyses, along with machine learning classification methods, to monitor change in these valuable ecosystems. The Georgia coast …

Abmr: An R Package For Agent-Based Model Analysis Of Large-Scale Movements Across Taxa, Benjamin Gochanour, Javier Fernández-López, Andrea Contina

School of Integrative Biological & Chemical Sciences Faculty Publications

1. Agent-based modelling (ABM) shows promise for animal movement studies. However, a robust, open-source and spatially explicit ABM coding platform is currently lacking.
2. We present abmR, an R package for conducting continental-scale ABM simulations across animal taxa. The package features two movement functions, each of which relies on the Ornstein–Uhlenbeck (OU) process.
3. The theoretical background for abmR is discussed and the main functionalities are illustrated using example populations.
4. Potential future additions to this open-source package may include the ability to specify multiple environmental variables or to model interactions between agents. Additionally, updates may offer opportunities for disease ecology and integration with …

Socio‑Economic Inequalities In Minimum Dietary Diversity Among Bangladeshi Children Aged 6–23 Months: A Decomposition Analysis, Satyajit Kundu, Pranta Das, Ashfikur Rahman, Hasan Al Banna, Kaniz Fatema, Akhtarul Islam, Shobhit Srivastava, T. Muhammad, Rakhi Dey, Ahmed Hossain

Department of Statistics: Faculty Publications

This study aimed to measure the socio-economic inequalities in having minimum dietary diversity (MDD) among Bangladeshi children aged 6–23 months as well as to determine the factors that potentially contribute to the inequity. The Bangladesh Demographic and Health Survey (BDHS) 2017–2018 data were used in this study. A sample of 2405 (weighted) children aged 6–23 months was included. The overall weighted prevalence of MDD was 37.47%. The concentration index (CIX) value for inequalities in MDD due to wealth status was positive and the concentration curve lay below the line of equality (CIX: 0.1211, p < 0.001), where 49.47% inequality was contributed by wealth status, 25.06% contributed by the education level of mother, and 20.41% contributed by the number of ante-natal care (ANC) visits. Similarly, the CIX value due to the education level of mothers was also positive and the concentration curve lay below the line of equality (CIX: 0.1341, p < 0.001), where 52.68% inequality was contributed by the education level of mother, 18.07% contributed by wealth status, and 14.69% contributed by the number of ANC visits. MDD was higher among higher socioeconomic status (SES) groups. Appropriate intervention design should prioritize minimizing socioeconomic inequities in MDD, especially targeting the contributing factors of these inequities.

Larval Ecology Of Atlantic Bluefin Tuna (Thunnus Thynnus): New Insights From Otolith Microstructure, Biotic, And Abiotic Analyses From The Gulf Of Mexico And Mediterranean Sea, Estrella Malca

All HCAS Student Capstones, Theses, and Dissertations

Atlantic bluefin tuna (ABT), Thunnus thynnus, spawn in the Gulf of Mexico (GoM) and the Mediterranean Sea (MED). Spawning occurs within narrow temporal and environmental parameters. Efforts to characterize growth of ABT in wild conditions revealed a wide range of growth variability during the early life stages. This series of studies examined potential biotic and abiotic influences of larval growth from seven ABT cohorts, and identified several key drivers of growth for this commercially valuable species. A detailed investigation of larval dynamics using otolith microstructure was conducted as follows. First, companion growth curves and stable isotope analysis from the same …

Forest Structure And Composition Alleviate Human Thermal Stress, Loïc Gillerot, Dries Landuyt, Rachel Oh, Winston T. L. Chow, Et Al

Research Collection College of Integrative Studies

Current climate change aggravates human health hazards posed by heat stress. Forests can locally mitigate this by acting as strong thermal buffers, yet potential mediation by forest ecological characteristics remains underexplored. We report over 14 months of hourly microclimate data from 131 forest plots across four European countries and compare these to open-field controls using physiologically equivalent temperature (PET) to reflect human thermal perception. Forests slightly tempered cold extremes, but the strongest buffering occurred under very hot conditions (PET >35°C), where forests reduced strong to extreme heat stress day occurrence by 84.1%. Mature forests cooled the microclimate by 12.1 to …

The Significance Of Cephalopod Beaks As A Research Tool: An Update, José C. Xavier, Alexey V. Golikov, José P. Queirós, Catalina Perales-Raya, Rigoberto Rosas-Luis, José Abreu, Giambattista Bello, Paco Bustamante, Juan C. Capaz, Valerie H. Dimkovikj, Angel F. González, Hugo Guímaro, Airam Guerra-Marrero, José N. Gomes-Pereira, Jorge Hernández-Urcera, Tsunemi Kubodera, Vladimir Laptikhovsky, Evgenia Lefkaditou, Fedor Lishchenko

Marine Science

The use of cephalopod beaks in ecological and population dynamics studies has allowed major advances of our knowledge on the role of cephalopods in marine ecosystems in the last 60 years. Since the 1960’s, with the pioneering research by Malcolm Clarke and colleagues, cephalopod beaks (also named jaws or mandibles) have been described to species level and their measurements have been shown to be related to cephalopod body size and mass, which permitted important information to be obtained on numerous biological and ecological aspects of cephalopods in marine ecosystems. In the last decade, a range of new techniques has been …

Spatial Variation In Hard Bottom Coral Communities Of The Coastal West Florida Shelf, Nicole Blank, Sandra D. Brooke, Brian K. Walker

Marine & Environmental Sciences Faculty Articles

Hard bottom coral and sponge communities differ along portions of the West Florida Shelf (WFS) in species occurrence, diversity, and/or size. However, the composition and spatial distribution of these communities are not well understood. Community transitions have been proposed in the central portion of the WFS around Tampa Bay, Cedar Key, and as far south as Charlotte Harbor, but supporting data are sparse. Fifteen sites in three regions of Florida were surveyed for species distribution, density, and demographics. Distinct communities were found between St Teresa, Hudson, and Tarpon Springs. Coral and sponge densities were highest off Tarpon Springs followed by …

Poster Session, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Evaluating the Effects of Beaver Dam Removal on the Hydrology, Water Quality, and Bioindicators of a Restored Wetland
• Predictive Sediment Flux Modeling of a Karst Spring Using High Resolution Sensors and Stable Carbon and Nitrogen Isotopes
• Development and Validation of qPCR Assays for Use in eDNA Detection of Four Species of Semiaquatic Salamanders .
• Analyzing Recent Spatio-Temporal Rainfall Erosivity Patterns and Trends Across Kentucky
• Development of eDNA Protocols for Detection of Four Darter (Percidae: Etheostomatinae) Species in Central Kentucky Streams
• Assessing Change in the Seasonality of Stable Isotopes δ18O and δ2H for Meteoric and Terrestrial Waters of Central Kentucky
• Coupling …

Montezuma Quail In The Edwards Plateau Of Texas: Detection, Occurrence, And Habitat, Zachary J. Pearson, Eric D. Grahmann, Fidel Hernández, Robert Perez, Leonard A. Brennan, Humberto L. Perotto-Baldivieso

National Quail Symposium Proceedings

Montezuma quail (Cyrtonyx montezumae) were historically found throughout nearly every county in the Edwards Plateau region of Texas, USA. Over the last century, shifting land use, reduction of fire on the landscape, and the subsequent encroachment of woody vegetation have constricted the distribution of Montezuma quail to a few counties in the southern portion of the Edwards Plateau. A renewed interest in management for Montezuma quail over the last decade has been met with a lack of information regarding their habitat requirements in this region. This lack of general information and increased sightings of this elusive species in …

Winter Survival And Resource Use Of Translocated Northern Bobwhite In The Mid-Atlantic United States, Kaili Stevens, Christopher K. Williams, Theron Terhune, Philip Coppola, John Parke, John Cecil

National Quail Symposium Proceedings

Northern bobwhite (Colinus virginianus; hereafter, bobwhite) in the Mid-Atlantic United States have been experiencing precipitous population declines due to a combination of habitat deterioration, urban and suburban sprawl, change in forest management regimes, and farming practices. In recent years, restocking of bobwhite through translocation efforts has gained interest to rebuild local populations. However, empirical studies are warranted to understand the limitations of translocation as it relates to its potential use for long-term population recovery and persistence in this region. Further, few studies nation-wide have evaluated resource use and survival during the non-breeding season on translocated sites. As such, …

Effect Of Food Distribution On Northern Bobwhite Resource Selection, Rachel R. Gardner, John Maerz, Theron M. Terhune Ii, Ira B. Parnell, James A. Martin

National Quail Symposium Proceedings

Supplemental feeding is a common management tactic used to increase survival and reproduction of northern bobwhite (Colinus virginianus; hereafter, bobwhite). Different supplemental feeding methods alter the distribution of resources across a landscape in unique ways and may influence the space use and resource selection of target species differently. Predators may concentrate their movements near fed sites, and different distributions of supplemental feed may encourage bobwhite to concentrate their movements closer to feed than other areas, thereby altering the potential for predator-prey interactions near feed. We used radio-tracked locations and movements in areas with stationary feeders (“feeder fed”) and …

Nsf Supported Socio-Environmental Research: How Do Crosscutting Programs Affect Research Funding, Publication, And Citation Patterns?, Kendra E. Kaiser, Anna E. Braswell, Megan L. Fork

Geosciences Faculty Publications and Presentations

Recognizing the continued human domination of landscapes across the globe, social-ecological systems (SES) research has proliferated, necessitating interdisciplinary collaborations. Although interdisciplinary research started gaining traction in academic settings close to 50 years ago, formal frameworks for SES research did not develop until the late 1990s. The first National Science Foundation (NSF) funding mechanism specifically for interdisciplinary SES research began in 2001 and the SES-specific Coupled Natural Human (CNH) Systems program began in 2007. We used data on funded NSF projects from 2000 to 2015 to examine how SES research was funded, where the research is published, and the scholarly impact …

Spatial Analysis Of Seven Islands In Indonesia To Determine Stunting Hotspots, Tiopan Sipahutar, Tris Eryando, Meiwita Budiharsana

Kesmas

Indonesia is a vast country struggling to reduce its stunting prevalence. Hence, identifying priority areas is urgent. In determining areas to prioritize, one needs to consider geographical issues, particularly correlations among areas. This study aimed to discover whether stunting prevalence in Indonesia occurs randomly or in clusters; and, if it occurs in clusters, which areas are the hotspots. This ecological study used aggregate data from the 2018 National Basic Health Research and Poverty Data and Information Report from the Statistics Indonesia. This study analyzed 514 districts/cities across 34 provinces on seven main islands in Indonesia. The method used was the …

Limited Rigor In Studies Of Raptor Mortality And Mitigation At Wind Power Facilities, Tara J. Conkling, Christopher J.W. Mcclure, Sandra Cuadros, Scott R. Loss, Todd E. Katzner

United States Geological Survey: Staff Publications

Wind power is an expanding source of renewable energy. However, there are ecological challenges related to wind energy generation, including collisions of wildlife with turbines. Lack of rigor, and variation in study design, together limit efforts to understand the broad-scale effects of wind power infrastructure on wildlife populations. It is not clear, however, whether these types of limitations apply to groups of birds such as raptors that are particularly vulnerable to negative effects of wind energy. We reviewed 672 peer-reviewed publications, unpublished reports, and citations from 321 wind facilities in 12 countries to evaluate methods used to monitor and mitigate …

Spatial Analysis Of Burn Severity And Streamflow Response In The Western Conus, Will Brendan Long

Dissertations and Theses

Wildfire increases the magnitude of runoff in catchments, which can lead to the degradation of ecosystems, risk to infrastructure, and loss of life. The Labor Day Fires of 2020 provided an opportunity to compare multiple large and severe wildfires with the objective of determining potential changes to hydrologic processes in Oregon Cascades watersheds. Geographic information systems (GIS) were implemented to determine the total percentage burned and percentage of high burn severity class of six watersheds on the west-slope of the Oregon Cascade Range. In addition, two control watersheds were included to contrast the influence of climatic effects. Spatial arrangement of …

Absence Of Visitors During Lockdown Reveals Natural Variation In Carbon Dioxide Level In The Glowworm Cave, Waitomo, New Zealand, David J. Merritt, Chris Hendy Dr, Shannon Corkill Ms

International Journal of Speleology

Waitomo Glowworm Cave is a highly visited cave where the highlight is viewing the bioluminescence display of a large colony of glowworms. Anthropogenic carbon dioxide build-up in the cave is prevented by management of chimney-effect ventilation aided by a network of microclimate sensors. A cave door prevents ventilationunder drying conditions and promotes it when necessary to clear CO₂ and when inflowing air has high relative humidity. A COVID-19-related nationwide “lockdown” in New Zealand from March 2020 resulted in neither staff nor visitors being present in the cave for 60 days, and provided an opportunity to assess the natural microclimate …

Rock Climbing And Conservation In Land Management: Can They Coexist?, Marissa Heller

Geography ETDs

As participation in outdoor recreation is growing in the U.S., a dilemma is presented for conservation planners and land area managers who must manage the increasing demand for recreation while simultaneously working to protect species. Rock climbers and other outdoor recreationalists have asserted that a relationship exists between recreation and the conservation of public lands. However, mounting evidence suggests that rock climbing continues to cause a multitude of negative impacts to ecosystems. Here, I investigate the extent to which land management practices allow for rock climbing and conservation to coexist, and how it is that well developed plans protect ecologically …

Competing Behaviors Of Thermoregulation And Ambush Foraging In The Timber Rattlesnake (Crotalus Horridus Horridus): A Mechanistic Assessment Of Thermal Conduction, Larry K. Kamees

Graduate Theses and Dissertations

The interaction between the biophysical environment and ectotherm morphology elicits behaviors designed to maintain internal body temperature (Tb) within a range that promotes physiological functions. The short-term requirements of mass (energy requirements) and heat balance are subject to tradeoffs imposed by the organisms current physiological (heat and mass budgets) and environmental (biophysical, demographic, social, and predation) constraints and available resources. In temperate forests, extreme temperatures are common in summer even with intermittent sun exposure due to dense canopy cover. In Spring and Fall, temperatures can range from below freezing to 35 ℃ in 24 hrs. An ambush predator like the …

Growth And Reproduction In Gulf Of Mexico Black Corals (Antipatharians) In Field And Laboratory Studies, Victoria E. Salinas

Theses and Dissertations

Black corals provide an important ecosystem of marine life and are found throughout all the oceans of the world at depths between 2 and 8,600 m. However, little is understood about their life history and the factors that control the distribution of black corals, particularly in the Gulf of Mexico (GoM). Given the impacts of the Deepwater Horizon oil spill on soft corals (e.g., black corals and octocorals) in the GoM, studies of their growth and reproductive biology in both natural and aquaculture environments are crucial for restoration efforts. The objectives of this study were to examine reproductive processes, compare …

Spotted Fever Group Rickettsioses In Central America: The Research And Public Health Disparity Among Socioeconomic Lines, Kyndall C. Dye-Braumuller, Marvin S. Rodriguez Aquino, Stella C.W. Self, Mufaro Kanyangarara, Melissa Nolan Ph.D., Mph

Faculty Publications

Tick-borne diseases including rickettsial diseases are increasing in incidence worldwide. Many rickettsial pathogens can cause disease which is commonly underdiagnosed and underreported; Rickettsia pathogens in the spotted fever group (SFGR) are thus classified as neglected bacterial pathogens. The Central American region shoulders a large proportion of the global neglected disease burden; however, little is known regarding SFGR disease here. Although development varies, four of the seven countries in this region have both the highest poverty rates and SFGR disease burdens (El Salvador, Honduras, Guatemala, and Nicaragua), compared to Belize, Panama, and Costa Rica. Utilizing the Human Development Index (HDI), we …

Amplification Of Black Vulture (Coragyps Atratus) Dna From Regurgitated Food Pellets, Daniel R. Taylor, Bryan M. Kluever, John S. Humphrey, Iona M. Hennessy, Amber Sutton, William E. Bruce, Antoinette J. Piaggio

United States Department of Agriculture Wildlife Services: Staff Publications

Studies that rely on noninvasive collection of DNA for birds often use feces or feathers. Some birds, such as vultures, regurgitate undigested matter in the form of pellets that are commonly found under roost sites. Our research demonstrates that regurgitated pellets are a viable, noninvasive source of DNA for molecular ecology studies of vultures. Our objectives were to amplify 5 microsatellite loci designed for distinguishing Turkey Vultures (Cathartes aura) and Black Vultures (Coragyps atratus) in a single, multiplexed PCR, and to determine how long the target nuclear DNA persists after a vulture pellet is regurgitated and …

Using An Affinity Analysis To Identify Phytoplankton Associations, Weiju Zhu, Zhaojian Ding, Yangdong Pan, Quanxi Wang

Environmental Science and Management Faculty Publications and Presentations

Phytoplankton functional traits can represent particular environmental conditions in complex aquatic ecosystems. Categorizing phytoplankton species into functional groups is challenging and time-consuming, and requires high-level expertise in species autecology. In this study, we introduced an affinity analysis to aid the identification of candidate associations of phytoplankton from two data sets comprised of phytoplankton and environmental information. In the Huaihe River Basin with a drainage area of 270,000 km2 in China, samples were collected from 217 selected sites during the low-water period in May 2013; monthly samples were collected during 2006–2011 in a man-made pond, Dishui Lake. Our results indicated that …

A Gis Suitability Model Evaluating Habitat Characteristics Influencing Beaver (Castor Canadensis) Lodge Site Selection And Lodge Occupancy In Central Adirondacks, New York, Amanda K. Jacobs

Theses - ALL

The North American beaver (Castor canadensis) represents a quintessential example of an "ecosystem engineer." Yet the species' landscape-scale impacts on hydrology, geomorphology, and ecosystem ecology are not uniformly distributed through landscapes or time. Understanding beaver lodge site selection and lodge fidelity through time can help to predict where the greatest effects of beaver activity may occur. In this research project, I seek to understand the relationships between beaver habitat suitability, the habitat variables that currently define suitable areas, and lodge occupancy over time. Using Geographic Information Systems (GIS) to model habitat suitability, I use hydrologic, vegetative, and physiographic variables to …

Efficiency In The Upper Deschutes Basin: Understanding The Hydrosocial Implications Of Irrigation Canal Piping, Rebecca Anderson

Dissertations and Theses

In response to water scarcity, irrigation efficiency projects aim to conserve water for in-stream flow and agricultural use. Piping irrigation canals is a common irrigation efficiency method which reduces the loss of incidental recharge, resulting in trade-offs within a hydrosocial system. Few studies have focused on the consequences of canal piping and none have integrated a critical analysis of the social factors involved in deciding what constitutes 'efficient' water use. This study seeks to fill this gap by combining natural and social science to give attention to the scales and perspectives involved in irrigation efficiency canal piping and the material …

Biological Hydrogen Gas Production From Food Waste As A Sustainable Fuel For Future Transportation, Pitiporn Asvapathanagul, Leanne Deocampo, Nicholas Banuelos

Mineta Transportation Institute

In the global search for the right alternative energy sources for a more sustainable future, hydrogen production has stood out as a strong contender. Hydrogen gas (H2) is well-known as one of the cleanest and most sustainable energy sources, one that mainly yields only water vapor as a byproduct. Additionally, H2 generates triple the amount of energy compared to hydrocarbon fuels. H2 can be synthesized from several technologies, but currently only 1% of H2 production is generated from biomass. Biological H2 production generated from anaerobic digestion is a fraction of the 1%. This study aims to enhance biological H2 production …

"We've Created Cheap Energy Off The Backs Of Salmon": Dam Removal Politics And Alliances In The Lower Snake River Basin, Krista Harrington

Dissertations and Theses

Dams, once considered by many to be good for water development in the Western U.S., might not be a part of a climate resilient future. Dams have come under increasing scrutiny due to undesirable ecological implications. Although dam removal proposals are growingly popular in recent decades, they are controversial since they impact different stakeholders in different ways. In the Pacific Northwest, the Lower four Snake River dams have long been criticized for their negative impacts on salmon. In February 2021, US Congressman Mike Simpson (R-Idaho) proposed a comprehensive framework to deconstruct the Lower four Snake River dams as an attempt …

In Situ Observations Of Fish Attraction To Light-Emitting Diodes On An Undersea Observation Deck, Makoto Tomiyasu, Yoko Tanouchi, Yasuzumi Fujimori, Minato Kaji, Takuma Hayashi, Naoto Matsubara, Hiroki Yasuma, Susumu Shimizu, Seiji Katakura

Journal of Marine Science and Technology–Taiwan

Many fisheries employ fishing lights to manipulate the behaviors of target fish and to attract them toward the light; however, relatively few long-time observations of fish attraction have been performed in the field. Here, an underwater observation deck was used to examine the differences in the fish-attracting effect of light-emitting diode (LED) lights on the number of attracted fish and on their behavior in the field, using white-edged rockfish as the target species. A total of 604 ± 324, 307 ± 203 and 171 ± 106 white-edged rockfish individuals were attracted to the observation window when it was illuminated with …

Loggerhead Shrike Detectability And Occurrence In Coastal South Carolina Urban Areas, Michelle Krauser

Electronic Theses and Dissertations

Grassland birds, such as the loggerhead shrike (Lanius ludovicianus), are threatened by extensive land-use change, including urbanization. Loggerhead shrikes have been declining since the early 1900s and are rare or extirpated in portions of their former range. Obtaining reliable population estimates of loggerhead shrikes is important to identify demographic trends and ensure conservation decisions are based on an accurate assessment of their current status. Imperfect detection, or the inability to detect every shrike during a survey, can result in biased population estimates. Estimating detection probability is labor-intensive and requires assumptions that are difficult to satisfy in most field studies. Understanding …

The Identification And Quantification Of Organophosphate Flame Retardants In Raw Materials Utilized In Polyurethane Production, Lindsay Tudor

Master of Science in Chemical Sciences Theses

Flame retardant additives are utilized in various polyurethane applications to comply with industry and flammability standards. Federal regulations and restrictive standards continue to tighten controls on certain impurities found in flame retardant blends. These restrictions include the limitation of organophosphates. Extensive research has been conducted to examine the effects of organophosphates in humans. To date, researchers have predominantly focused on the final product, mainly furniture and bedding products, rather than the raw materials utilized in production. Industrial chemists continue to grapple with the development of an effective method for detecting and quantifying organophosphate compounds in various flame retardant mixtures as …