Digital Commons Network^™

Learning To See With Minimal Human Supervision, Zezhou Cheng

Doctoral Dissertations

Deep learning has significantly advanced computer vision in the past decade, paving the way for practical applications such as facial recognition and autonomous driving. However, current techniques depend heavily on human supervision, limiting their broader deployment. This dissertation tackles this problem by introducing algorithms and theories to minimize human supervision in three key areas: data, annotations, and neural network architectures, in the context of various visual understanding tasks such as object detection, image restoration, and 3D generation. First, we present self-supervised learning algorithms to handle in-the-wild images and videos that traditionally require time-consuming manual curation and labeling. We demonstrate that …

Landscape Ecology And Conservation Of Freshwater Turtles Across The Eastern United States, H. Patrick Roberts

Doctoral Dissertations

Space use and movement patterns are integral to population dynamics and are often indicative of vulnerability to anthropogenic threats. Spatial ecology research can be fundamental to conservation strategies but is largely biased toward short-term intra- and interannual patterns. Without an understanding of space use over temporal scales commensurate with lifespan and the processes that may influence movement, conservation tools derived from short-term (2–4 yrs) movement patterns may be misguided or ineffective, particularly for long-lived species. The goal of Chapter 1 was to characterize the long-term (multi-decadal) spatial ecology of three long-lived (80–110 yrs) turtle species. We revisited six areas where …

Computational Analysis Of Microbial Sequence Data Using Statistics And Machine Learning, Zhixiu Lu

Doctoral Dissertations

Since the discovery of the double helix of DNA in 1953, modern molecular biology has opened the door to a better understanding of how genes control chemical processes within cells, including protein synthesis. Although we are still far from claiming a complete understanding, recent advances in sequencing technologies, increased computational capacity, and more sophisticated computational methods have allowed the development of various new applications that provide further insight into DNA sequence data and how the information they encode impacts living organisms and their environment. Sequencing data can now be used to start identifying the relationships between microorganisms, where they live, …

Bridging The Digital Divide: Using Ecological Modeling To Enhance Adult Student Recruitment And Retention In Higher Education, Katherine Dawson

Doctoral Dissertations

Higher education is at a crossroads. An enrollment cliff (Kline, 2019) looms and global instability only exacerbates the need for higher and continuing education. The global COVID-19 pandemic of 2020 highlighted the problem, and despite the evolutions in technology and Internet connectivity, there is still a chasm regarding equity of digital access. This applied dissertation study examined the barriers that exist for returning adult students to higher education and the digital divide in Louisiana. The study focused on the potential adult student population of Louisiana who have some college experience but no bachelor’s degree. Designed using archival research methods, the …

Habitat Use And Individual-Based Modeling Of Bald Eagles In Maine Near Current And Potential Wind Energy Facilities, Blake Massey

Doctoral Dissertations

Wind energy facilitates have expanded significantly in the United States over the last few decades due to technological advancements, regulatory incentives, and policies aimed at increasing renewable energy production, but poorly sited turbines may have adverse effects on local and migratory birds, bats, and other wildlife and their habitats. In the northeastern United States, Maine has become the leader in wind energy but also has the greatest density of Bald Eagles in the region. As wind energy production continues to be developed across the state and in coastal waters, research is needed to analyze and assess potential risks, including displacement, …

Cerulean Warbler Full Annual Cycle Ecology: Filling In Critical Knowledge Gaps, Douglas W. Raybuck

Doctoral Dissertations

Cerulean Warblers (Setophaga cerulea) are a declining migratory bird species of conservation concern that breed in mature hardwood forests of eastern North America and spend the stationary non-breeding period in the tropical Andes of South America. To reverse their >50-year population decline, a full annual cycle conservation strategy is needed. However, several important knowledge gaps have limited our understanding of this species’ full annual cycle ecology, including migration ecology, response to forest management on the breeding grounds, and basic ecology during the stationary non-breeding period in Andean forests. From geolocator data, we found a moderate pattern of migratory …

Monitoring Mammals At Multiple Scales: Case Studies From Carnivore Communities, Kadambari Devarajan

Doctoral Dissertations

Carnivores are distributed widely and threatened by habitat loss, poaching, climate change, and disease. They are considered integral to ecosystem function through their direct and indirect interactions with species at different trophic levels. Given the importance of carnivores, it is of high conservation priority to understand the processes driving carnivore assemblages in different systems. It is thus essential to determine the abiotic and biotic drivers of carnivore community composition at different spatial scales and address the following questions: (i) What factors influence carnivore community composition and diversity? (ii) How do the factors influencing carnivore communities vary across spatial and temporal …

The Effects Of Urbanization On The Avian Gut Microbiome, Mae Berlow

Doctoral Dissertations

The gut microbiome influences and is influenced by the host, and can affect the host organism by contributing to health, development and immunity. Similarly, the host can influence this community; it’s makeup can vary with host species, locality, diet, social stressors, and environmental stressors. Some of these environmental stressors have arisen due to human-induced rapid environmental change, like urbanization. The physiology and behaviors of organisms that are able to persist in urban environments are often different from their non-urban congeners. Nutrition, development, and immunity—all of which are affected by the gut microbiome—are important factors that can determine survival in urban …

Evolution And Resurrection Ecology Of A Foundational Coastal Marsh Plant, Jennifer L. Summers

Doctoral Dissertations

Stratified storage of dormant seeds in soil can result in natural archives useful for studying evolutionary responses to environmental change. However, few studies leverage soil-stored seed banks as natural archives, in part because of concerns over attrition, bias, and sediment mixing. Here, I examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to a) determine whether it can serve as a resource for reconstructing demographic and population genetic/genomic variation, b) whether and how evolution may be occurring across a century. After extracting seeds from radionuclide-dated soil cores taken across the Chesapeake Bay, I “resurrected” age …

Fear, Parental Behavior, And Community Structure In Residential Lands, Aaron M. Grade

Doctoral Dissertations

In an urbanizing world, residential lands present an opportunity for conservation of biodiversity right in our backyards. Informed conservation necessitates a mechanistic understanding of how development influences animal populations and communities. Birds nesting in residential lands are less productive in urban yards than rural yards. Urban yards also have higher densities of potential predators, but lower per capita predation, indicating that direct predation is not entirely responsible for lack of productivity. I suggest that fear effects, also known as non-lethal effects, could be a mechanism by which predators exert indirect influence on bird parental behavior and nestling condition in urban …

Characterization Of The Biogeography And Temporal Dynamics Of The Trachymyrmex Septentrionalis Fungus Garden Microbiome, Kevin Lee

Doctoral Dissertations

Like all fungus-growing ants, Trachymyrmex septentrionalis engages in an obligate mutualism with a Basidiomycete fungus that it raises as its primary nutrition source. Therefore, the success of the symbiosis is dependent upon the health of the fungus garden containing this fungus, which may be affected by the composition of its microbiome. Most of what is known about fungus garden microbiomes comes from studies of the Neotropical fungus growing ants, especially the most evolutionarily derived and economically impactful “leaf-cutting” species. Although fungus-farming ants inhabit a vast range, little is known about how dispersal of microbes from their biogeographically and temporally distinct …

Theoretical And Quantitative Methods Connecting Characterizing Micoribal Metabolism Diversity: Implciations From Phylogenetics, Community Diversity, And Organic Geochemistry, Taylor Royalty

Doctoral Dissertations

Biogeochemistry is controlled by microorganisms obtaining nutrients and energy. Thus, microbial metabolisms directly link microbial ecology and geochemistry. The extent that microbial ecology and geochemistry microbial ecology and geochemistry affects the other requires constraint on the spatiotemporal distribution and abundance of microbial metabolisms with respect to geochemistry, or the microbial niches. Elucidating microbial metabolisms was challenging prior to the advent of ‘omics sequencing technologies, as most microbial lineages lack cultured representatives. Although revolutionizing microbial ecology, challenges still exist in fully leveraging information derived from ‘omics technologies. This dissertation attempts to address a small subset of these challenges that include quantifying …

Connecting The Social And Spatial Behaviors Of A Territorial Species (Anolis Carolinensis), Jordan M. Bush

Doctoral Dissertations

Why animals live where they do is a key question in ecology and evolution. An individual’s home range determines the resources they have access to, conspecifics they encounter, and predators and pitfalls they must avoid. Home range behaviors also have an inherently social component; where animals live affects the rivals they compete with and the mates they have access to. This is especially true in territorial species, as defensive displays make up a large portion of their social behaviors. In this dissertation, I sought to understand how territorial behaviors affect the social lives of the green anole lizard (Anolis …

Spatiotemporal Patterns And Burden Of Myocardial Infarction In Florida, Evah Odoi

Doctoral Dissertations

Knowledge of spatiotemporal disparities in myocardial infarction (MI) risk and the determinants of those disparities is critical for guiding health planning and resource allocation. Therefore, the aims of this study were to: (i) investigate the spatial distribution and clusters of MI hospitalization (MIHosp) and MI mortality (MIMort) risks in Florida over time to identify communities with consistently high MI burdens, (ii) assess temporal trends in geographic disparities in MIHosp and MIMort risks (iii) identify predictors of MIHosp risks.Retrospective MIhosp and MImort data for Florida for 2005-2014 and 2000-2014 periods, respectively, were used. Kulldorff’s circular and Tango’s flexible spatial scan statistics …

The Ecology Of Soil Viruses: Abundance, Distribution, Diversity And Impact On Microbial Community Structure, Xiaolong Liang

Doctoral Dissertations

Viruses as a critical biotic component in all ecosystems have exhibited pronounced ecological significance. The global abundance of viruses in the biosphere has been estimated at 1 x 1031, with 90-95% of these viruses residing in soil and/or sedimentary environments. Despite the apparent greater abundance and diversity, soil virology is under-investigated relative to other environments such as marine and freshwater habitats and soil viral genomic data are underrepresented in public repositories of genetic information. In this dissertation, we investigated the viral abundance, diversity, and virus-host interactions in natural soils and the simulated stimulated subsurface bioremediation environments. We used epifluorescence microscopy …

Expanding The Omics Repertoire For Model Studies On A Chlorella-Infecting Giant Virus, Samantha Coy

Doctoral Dissertations

Viruses are the most abundant biological entities in aquatic ecosystems. As top-down controls of plankton abundance and diversity, they are intrinsically linked to biogeochemical cycling, and by proxy, to global climate change. It is thus of great interest for researchers to understand the mechanics of viral infection and persistence among ecologically important phytoplankton assemblages. Viruses which infect eukaryotic algae are observed with diverse nucleic acid types, structures, and sizes, though most isolates to date bear large, dsDNA genomes comprised of genes normally only seen in cellular organisms. The Chlorella viruses are the model system for studying these entities, with many …

Living Life On The Edge: The Role Of Introduction And Range Expansion In Shaping Behavior Of A Non-Native Spider, Angela Chuang

Doctoral Dissertations

Animal personalities describe the behavioral phenotypes of individuals that often remain relatively stable over time and contexts. Since they can account for differential dispersal tendencies, understanding how personality types are distributed across the range can lead to important characterization of expanding invasive populations. Cyrtophora citricola is a colonial tentweb orbweaver spider with an Old World native range that is invasive in Florida. It has experienced a range expansion of over 450 km in 20 years. In my dissertation, I asked whether C. citricola exhibits personality, whether some of its behavioral traits are correlated with dispersal tendencies, and whether personality types …

The Legacy Of Hosting Mega-Sports Events: A Twitter Analysis Of Leisure-Time Physical Activity Communication, Gabriela Baranowski Pinto

Doctoral Dissertations

Routine engagement in Leisure-Time Physical Activity (LTPA) is associated with long-term health, lower mortality, and higher quality of life. Inspiring participation in LTPA is one desired benefit of public investment in mega-events such as the Olympic Games. Whether such inspiration materializes—and, if so, for how long—was examined in three studies that investigated a perception-action process at the level of the interaction between real and virtual environments. The influence of the real environment of the Games in Rio de Janeiro in 2016 was assessed via the virtual environment instantiated in the Twitter social network. Emerging dynamic communication about LTPA in three …

Tree-Ring Evidence Of Climate And Environmental Change, Beartooth Mountains, Wyoming, U.S.A., Maegen Lee Rochner

Doctoral Dissertations

Long-lived, subalpine tree species like whitebark pine and Engelmann spruce may eventually cease to exist due to the combination of climate change and exacerbated native and invasive biological threats. While this loss would have dire consequences for mountain ecosystems, it would also result in the irreversible loss of valuable climatological and ecological data preserved in the growth rings of these trees. The purpose of this dissertation research was to develop extended whitebark pine and Engelmann spruce tree-ring chronologies for use in regional analyses of climate and disturbance, and more importantly to demonstrate the potential of these tree species and the …

Learning With Aggregate Data, Tao Sun

Doctoral Dissertations

Various real-world applications involve directly dealing with aggregate data. In this work, we study Learning with Aggregate Data from several perspectives and try to address their combinatorial challenges. At first, we study the problem of learning in Collective Graphical Models (CGMs), where only noisy aggregate observations are available. Inference in CGMs is NP- hard and we proposed an approximate inference algorithm. By solving the inference problems, we are empowered to build large-scale bird migration models, and models for human mobility under the differential privacy setting. Secondly, we consider problems given bags of instances and bag-level aggregate supervisions. Specifically, we study …

Forecasting Vibrio Parahaemolyticus In A Changing Climate, Meghan Ann Hartwick

Doctoral Dissertations

The distribution, transmission and adaptation patterns of infectious diseases are changing worldwide. Though there are many potential mechanisms that can transmit infectious agents to new areas, the ability of pathogens to persist in new locations can be largely attributed to changing climate conditions, especially in temperate regions. Vibrio parahaemolyticus, a naturally occurring bacteria in most marine and estuarine systems, provides a model example of these globally observed climate-related changes to disease dynamics that are occurring locally in the Northeast, US. Like many Vibrio species, pathogenicity in human hosts is believed to be limited to a subset of strains, whereas the …

Stability, Development, And Function Of A Symbiotic Bacterial Community Associated With The Reproductive System Of The Hawaiian Bobtail Squid, Euprymna Scolopes, Allison H. Kerwin

Doctoral Dissertations

Many aquatic organisms deposit their eggs into an environment where successful embryogenesis depends on minimizing biofouling. The female Hawaiian bobtail squid, Euprymna scolopes, harbors a diverse bacterial community within the accessory nidamental gland (ANG), a symbiotic reproductive organ. This community is hypothesized to be environmentally transmitted, and to be deposited from the ANG into the egg jelly coat (JC). Illumina sequencing of the 16S rRNA V4 gene region demonstrated that the ANG bacterial community (n=29) and that of the JC (n=35) were composed primarily of members of the Rhodobacteraceae and Verrucomicrobia, which together comprised on average 86% of …

Multistage Sampling Strategies And Inference In Health Studies Under Appropriate Linex Loss Functions, Sudeep R. Bapat

Doctoral Dissertations

A sequential sampling methodology provides concrete results and proves to be benefecial in many scenarios, where a fixed sampling technique fails to deliver. This dissertation introduces several multistage sampling methodologies to estimate the unknown parameters depending on the model in hand. We construct both two-stage and purely sequential sampling rules under different situations. The estimation is carried under a loss function which in our case is either a usual squared error loss or a Linex loss. We adopt a technique known as bounded risk estimation strategy, where we bound the appropriate risk function from above by a fixed and known …

The Effects Of Anthropogenic Stress On Nitrogen-Cycling Microbial Communities In Temperate And Tropical Soils, George S. Hamaoui Jr.

Doctoral Dissertations

In this dissertation several research studies are discussed that characterize the effects of anthropogenic, or human-induced, stress on both ammonia-oxidizing and total bacterial soil microbial communities. The disturbances of land-use change in tropical, South American rainforests and artificial warming and nitrogen (N) fertilization in temperate, North American forests were investigated as these disturbances represent past and current disturbances caused by human landscape alteration and climate change. Initially, the response of soil ammonia-oxidizing microbial communities to land-use change from primary rainforest to pasture and, finally, back to secondary forest was determined. Next, these analyses of land-use change effects were expanded to …

Population And Trophic Dynamics Of Striped Bass And Blueback Herring In The Connecticut River, Justin P. Davis

Doctoral Dissertations

Case studies of the ramifications of predator management for prey population dynamics can play a valuable role in developing ecosystem fisheries management. My dissertation focuses on the predator-prey interaction between Striped Bass (Morone saxatilis), an abundant predatory finfish, and an imperiled prey population of anadromous Blueback Herring (Alosa aestivalis). Annual returns of Blueback Herring to the Holyoke Dam on the Connecticut River in southern New England collapsed during the 1980-2000s, coincident with Striped Bass recovery. I studied the abundance and demography of both species in the Connecticut River during 2005-08, measured predation levels, and surveyed the …

The Microbiome Of The Eastern Oyster, Crassostrea Virginica (Gmelin, 1791): Temporal And Spatial Variation, Environmental Influences, And Its Impact On Host Physiology, Melissa L. Pierce

Doctoral Dissertations

Prokaryotic communities are ubiquitous in every environment on earth. In the oceans they are integral to a number of biogeochemical processes and form the base of marine food webs. Microbes have also coevolved with eukaryotes, aiding in a variety of host functions including digestion and nutrient absorption, development of the immune system, and protection against pathogens. The disruption of these microbial communities, especially in the gut, has been linked to altered health statuses and physiological functions in a range of hosts. The eastern oyster, Crassostrea virginica (Gmelin, 1791), is a valuable economic and ecological resource in near-shore environments. As a …

Assessing The Functional Similarity Of Native And Invasive Anolis Lizards In The Food Webs Of Structurally-Simple Habitats In Florida, Nathan W. Turnbough

Doctoral Dissertations

Invasive species often displace ecologically-similar native species, but the extent to which invading and displaced species function similarly in the food web processes of invaded communities is largely unknown. I investigated whether populations and individuals of an invasive Anolis lizard (the brown anole, Anolis sagrei) and the native congener it displaces in Florida (the green anole, Anolis carolinensis) are functionally equivalent in the food webs of open and structurally-simple habitats. In a system of invaded and uninvaded dredge-spoils islands, I found that both arthropod communities and winter bird communities covaried with brown anole abundance (and therefore the identity …

Response Of Microbial Community Structure To Clay Flocculation Of Harmful Algal Blooms, Chunyi Chen

Doctoral Dissertations

Harmful algal blooms are cosmopolitan and can produce extremely dangerous toxins that can sicken or kill people and animals, and create dead zones in the water. The U.S. economic loss caused by algal blooms is $82 million every year. Clay-based flocculation techniques have been developed to mitigate algal blooms; however, the potential impacts on the microbial community are poorly understood. This dissertation includes multi-scale experiments (Jar, field, microcosms) to study the response of microbial community structure and function to clay flocculation of algal blooms.

Jar tests of removal of Microcystis aeruginosa by chitosan and two types of commercially available clays …

Characterizing Early-Life Microbiome Functionality In Premature Infant Gut By A Metaproteomics Approach, Weili Xiong

Doctoral Dissertations

Microbes inhabit all parts of human body that are exposed to the environment and their interactions with human host mutually benefit each other and play significant roles in human health and diseases. The human gastrointestinal tract harbors the largest population of the microbiota and has gained broad research attention and efforts over the past decade. Colonization of the gut by microbes begins at birth and this early-life bacterial establishment can impact infants’ health and even the human health and lifestyle across an entire life span. Recent studies on community structure and composition of infant gut microbiota have revealed the species …

Individual Variation In Plant Traits Drives Species Interactions, Ecosystem Functioning, And Responses To Global Change, Quentin Daniel Read

Doctoral Dissertations

Ecologists have long sought to understand the processes that lead to the riotous diversity in communities of organisms that inhabit disparate climates and landscapes. Such a diversity of traits leads to a diversity of interactions among species in natural communities, which in turn generates a diversity of potential responses to ongoing global change. In this dissertation, I do three things: I explore the forces that structure plant communities and the ecosystem functions that they mediate, I describe patterns of variation among communities, species, and individual organisms across environmental contexts, and I disentangle the direct effects of global change from the …