Life Sciences Commons^™

Relating Spontaneous Activity And Cognitive States Via Neurodynamic Modeling, Matthew Singh

Arts & Sciences Electronic Theses and Dissertations

Stimulus-free brain dynamics form the basis of current knowledge concerning functional integration and segregation within the human brain. These relationships are typically described in terms of resting-state brain networks—regions which spontaneously coactivate. However, despite the interest in the anatomical mechanisms and biobehavioral correlates of stimulus-free brain dynamics, little is known regarding the relation between spontaneous brain dynamics and task-evoked activity. In particular, no computational framework has been previously proposed to unite spontaneous and task dynamics under a single, data-driven model. Model development in this domain will provide new insight regarding the mechanisms by which exogeneous stimuli and intrinsic neural circuitry …

Modeling Stromatolite Formation With Diffusion-Limited Aggregation, Laura E. Stevens

Graduate Student Theses, Dissertations, & Professional Papers

Stromatolites, microbialites, and other microbially induced sedimentary structures exist in the rock record as far back as 3.6 billion years ago and continue to form in the present day. Better characterizing these structures and better understanding how they form is crucial in distinguishing these biosignatures from similar, abiotic structures, which can help us to understand the conditions of early Earth and early Mars. To that end, I have modified DLA 3D EXT, an open-source stromatolite modeling program, to more closely reflect the process of microbial trapping-and-binding by filamentous microbes in a calcite-precipitating hot spring system. This modified program includes a …

Exposure Assessment Of Emerging Contaminants: Rapid Screening And Modeling Of Plant Uptake, Majid Bagheri

Doctoral Dissertations

"With the advent of new chemicals and their increasing uses in every aspect of our life, considerable number of emerging contaminants are introduced to environment yearly. Emerging contaminants in forms of pharmaceuticals, detergents, biosolids, and reclaimed wastewater can cross plant roots and translocate to various parts of the plants. Long-term human exposure to emerging contaminants through food consumption is assumed to be a pathway of interest. Thus, uptake and translocation of emerging contaminants in plants are important for the assessment of health risks associated with human exposure to emerging contaminants. To have a better understanding over fate of emerging contaminants …

Building Habitat Suitability Models To Examine Distribution Shifts For The Black-Headed Grosbeak, Hairy Woodpecker, And Yellow-Rumped Warbler Due To Drought, Fire, And Bark Beetle Infestation In The Pacific Northwest, Holli Nicole Pruhsmeier

Cal Poly Humboldt theses and projects

Spatial models that describe species distributions are valuable in determining how environmental impacts, such as drought, fire, and bark beetle infestations, have shifted these distributions and guide management decisions. In this thesis, I begin by comparing the utility of two datasets by building habitat suitability models for Black-headed Grosbeak, Hairy Woodpecker, and Yellow-rumped Warbler. By combining the datasets, I created response curves that explain habitat associations I expected from each species. I expanded upon the methods section to compare pre- and post-drought data from the 2011 California multi-year drought and evaluate how the three avian species have shifted their habitat …

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

Costs Of Protected Areas In The United States, Diane Lebouille

Doctoral Dissertations

Protected areas, or land owned in fee by agencies and non-profits to further conservation goals, have traditionally been the go-to choice for conservation interests. The UN Environment World Conservation Monitoring Centre estimates that, currently, close to 15% of all terrestrial and inland water areas are protected. This figure falls short of the Aichi Biodiversity Target of 17% in 2020, that was added to the Convention on Biological Diversity by its 196 signatories in 2010. But as the Convention prepares to set new post-2020 targets, this percentage is expected to keep increasing. Although acquiring a parcel of land is only one …

Analytic Solutions For Diffusion On Path Graphs And Its Application To The Modeling Of The Evolution Of Electrically Indiscernible Conformational States Of Lysenin, K. Summer Ware

Boise State University Theses and Dissertations

Memory is traditionally thought of as a biological function of the brain. In recent years, however, researchers have found that some stimuli-responsive molecules exhibit memory-like behavior manifested as history-dependent hysteresis in response to external excitations. One example is lysenin, a pore-forming toxin found naturally in the coelomic fluid of the common earthworm Eisenia fetida. When reconstituted into a bilayer lipid membrane, this unassuming toxin undergoes conformational changes in response to applied voltages. However, lysenin is able to "remember" past history by adjusting its conformational state based not only on the amplitude of the stimulus but also on its previous …

Modeling The Impact Of Grazing On Water Budgets, Ying Zhao, Stephan Peth, Julia Krümmelbein, Bettina Ketzer, Yingzhi Gao, Christian Bernhofer, Rainer Horn

IGC Proceedings (1997-2023)

No abstract provided.

The Effects Of Elevation On Foraging Behavior Of Bats In Southern Appalachia, Victoria Long

Electronic Theses and Dissertations

There are limited studies on bat activity in higher elevations in the Appalachian region. Levels of bat activity were compared in south central Appalachia at low (< 914.4 m) and high (> 1, 524 m) elevations in open, forest edge, and riparian habitats. Additionally, habitat suitability was modeled for a common species, big brown bat (Eptesicus fuscus). The study started May 27^th 2019, and sites were monitored biweekly until October 2^nd 2019. Six species and one genus were recorded during the study. Species from the Myotis genus were grouped together because of similar call characteristics. Results show that species were significantly more …

Structural Analysis Of The Multifunctional Spoiie Regulatory Protein Of Clostridioides Difficile., Blythe Emily Bunkers

Graduate Theses and Dissertations

Clostridioides (formally Clostridium) difficile is a medically relevant pathogen pertinent to infectious disease research. C. difficile is distinctly known for its ability to produce two toxins, enterotoxin A and cytotoxin B, and the propensity to colonize the mammalian gastrointestinal tract. It is known that metabolism is tightly correlated with sporulation in endospore producers such as C. difficile, but an interesting and novel regulatory relationship found by the Ivey lab has yet to be understood. The relationship explored in this study is observed between the sporulation factor, SpoIIE, which represses expression of an ABC peptide transporter, app. In this study, two …

Evaluating Moose Alces Alces Population Response To Infestation Level Of Winter Ticks Dermacentor Albipictus, Daniel D. Ellingwood, Peter J. Pekins, Henry Jones, Anthony R. Musante

USDA Wildlife Services: Staff Publications

Many wildlife populations are experiencing a variety of environmental pressures due to the direct and indirect consequences of a changing climate. In the northeast, USA, moose Alces alces are declining in large part because of the increasing parasitism by winter tick Dermacentor albipictus, facilitated by high host density and optimal environmental conditions. To test this hypothesis, and better understand the influence of this interaction on the stability of the regional population, we constructed a population viability model using data collected through comprehensive survival and productivity studies in 2002–2005 and 2014–2018 in northern New Hampshire. Years of heavy tick infestation (epizootics) …

The Utility Of Environmental Dna And Species Distribution Models In Assessing The Habitat Requirements Of Twelve Fish Species In Alaskan North Slope Rivers, James B. Eddings

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Subsistence fishing is a vital component of Alaska’s North Slope borough economy and culture that is being threatened by human disturbance. These threats mean the fish must be protected, but the size of the region makes conservation planning difficult. Fortunately, advances in species distribution models (SDMs), environmental DNA (eDNA), and remote sensing technologies provide potential to better understand species’ needs and guide management. The objectives of my study were to: (1) map the current habitat suitability for twelve fish species, occurring in Alaska’s North Slope, (2) determine if SDMs based on eDNA data performed similarly to, or improved, models based …

Forage Inventory And Modeling In Uintah And Ouray Reservation Rangelands, Scott N. Zimmer

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Uintah and Ouray Reservation in northeastern Utah has not been widely studied, and access to non-tribal members is highly restricted. We sampled vegetation to summarize condition in 300,000 acres of unsurveyed Reservation lands in 2017-2018, combining these data with data collected by the Bureau of Indian Affairs from 2010-2015 to complete an initial rangeland vegetation inventory of the Reservation. This survey was designed to inform management of the area by determining cattle stocking rates and overall ecological condition across the Reservation. Both the density of forage available to cattle and appropriate cattle stocking rates vary greatly throughout management units …

Historical And Contemporary Variables Affecting The Range And Distribution Of Aedes Aegypti, The Yellow Fever Mosquito, In The United States, Nicole Mackey

Master's Theses

Aedes aegypti, the primary mosquito vector of the yellow fever virus, threatens global health by passing on this virus, as well as chikungunya, dengue, and Zika viruses. Through its natural tendency to live in highly urban areas and bite human hosts; understanding the factors that affect the historical and current range of the pest is invaluable (Gubler, 1998). Although these viruses are not normally found in the United States, lack of vaccinations and wide-spread presence of the mosquito could lead to these diseases being reintroduced with potentially devastating effects (Monath, 2001). To determine a partial historical range of A. aegypti …

Antibiotic Resistant Bacteria, Antibiotic Resistance Genes And Potential Drivers In The Aquatic Environments, Shuo Shen

Dissertations

As antibiotic resistance genes in aquatic environment have been increasing across the world, affecting water quality and public health, many studies documented concentrations of antibiotic resistance genes and some studies discussed their potential drivers. However, systematic and quantitative reviews that link antibiotic resistance genes (ARGs) to anthropogenic and environmental factors are limited. Nevertheless, this information will be important for developing regulation policy on controlling antibiotic use and therefore reducing potential risks to antibiotic resistance. I conducted meta-analysis of ARGs concentration at a global scale using Bayesian inference to explore climatic and socio-economic factors as drivers. I found local-scale climatic variables …

Economic Trade-Offs Of Novel Forage Use In Livestock Production Systems: Insights From Australia, Marta Monjardino, Neil D. Macleod, Dean K. Revell

IGC Proceedings (1997-2023)

Globally, livestock are a major component of agricultural systems and natural resource management, as well as an important contributor to nutrition and livelihoods, but are often undervalued (Herrero et al., 2009). In Australia, livestock production systems occupy half of the available land and contribute to ~50% of gross agricultural production. The main livestock systems are beef cattle grazing at low intensity in the arid and semi-arid regions of northern and central Australia; and sheep flocks integrated in crop-livestock systems in the temperate zone of southern Australia (Bell et al., 2014). Despite increased physical productivity (changes in outputs relative …

An Ecopath With Ecosim Analysis On Offshore Petroleum Platform Influences On Gulf Of Mexico Red Snapper, Valentin Gomez

LSU Master's Theses

Offshore oil and gas platforms have had a significant presence in the Gulf of Mexico since the 1950s. An important secondary function of these structures is that they provide artificial habitat to fisheries, most notably Red snapper. Policy changes intended to reduce the risk associated with aging infrastructure have reduced the number of standing platforms from 4044 to 1867 from 2001 to 2018. The effect this loss of habitat has on Red snapper was tested by creating three scenarios of platform changes and modeling the perturbation from 2005 to 2050. The simulation was accomplished using the ecological model Ecopath with …

Design And Analysis Of The Cylinder Cam Mechanism Of The Group Cover Machine, Li Gan, Yin Cheng-Long, Jiang De-Fu, Ke Wan

Food and Machinery

The cam profile of the cylindrical cam mechanism of the bottle cap assembly machine is designed, the curve is fitted, the three-dimensional model of the SolidWorks is established, and the cylindrical cam and the cylindrical cam of the sinusoidal curve fitting are simulated in Adams by the cylindrical cam and the sinusoidal curve fitting of the five polynomial curve fitting. The result of the simulation is compared and analyzed, which shows that the design of the cam wheel can be used in the manufacture of the cylindrical cam mechanism of the actual group cover machine.

Multivariate Habitat-Based Predictive Modeling Of Three Demersal Rockfish Species In Central California, Georgia R. Martel

Cal Poly Humboldt theses and projects

Accurate, spatially explicit models of rockfish abundance are critical in implementing ecosystem-based management strategies and designating essential fish habitats and marine protected areas. Multibeam bathymetry methods and visual, non-extractive submersible transect surveys were combined to collect environmental variables and fish abundance data at three distinct sites within the study region. Zero-adjusted models were developed using habitat classification analyses of high-resolution (5 m) digital elevation models. Model accuracies were assessed by using a reserved subset of the original datasets. To demonstrate that a model’s predictive power was linked to its spatial origins, Mean Absolute Error and coefficient of determination values were …

Recolonization Potential For Coho Salmon (Oncorhynchus Kisutch) In Tributaries To The Klamath River After Dam Removal, Max M. Ramos

Cal Poly Humboldt theses and projects

Removal of four major dams on the Klamath River is scheduled to begin in 2023, restoring access to greater than 50 km of historic mainstem habitat for coho salmon. However, mainstem habitat may not be suitable for juvenile coho salmon due to elevated water temperatures and high concentrations of infectious myxospores in the summer and fast water velocities in the winter. Small, cooler tributaries can provide essential habitat for escape from deleterious conditions in the mainstem Klamath River. I used temperature and other physical features of six tributaries to the Klamath River above Iron Gate Dam to assess their capacity …

Tick Control Methods For Amblyomma Americanum In Virginia: Applications And Modeling, Alexis Lynn White

Biological Sciences Theses & Dissertations

Tick-borne diseases continue to increase in the United States, and yet no comprehensive method of tick control currently exists. The lone star tick, Amblyomma americanum, is an aggressive human-biting tick and vector of several pathogens which effect both humans and other animals. Standard control methods do not work as well for A. americanum as they do for the more commonly studied blacklegged tick, Ixodes scapularis. TickBot, a tick-killing robot, is a potential method to control A. americanum that lures ticks to its path with carbon dioxide and the ticks die from contact with a permethrin-treated cloth that is …

Sonification Of Epigenetic Processes, Joelle Strom

Senior Theses

Sonification is the process of creating sound or music from data for investigative or aesthetic purposes. Data sonification has been used in multiple fields to provide an additional layer of analysis to datasets, engage general audiences in a scientific topic, or create an evocative musical piece. Sonification has been extended to biological subjects, including macromolecules such as protein and DNA. Epigenetics, the processes by which gene expression is regulated, is a burgeoning field of molecular biology research. Epigenetic processes have been scarcely sonified, and the process of sonifying DNA base methylation has never been published. DNA methylation is an integral …

The Correlation Between Sleep And Lifespan In Drosophila Melanogaster, Joshua Randall Lisse

Masters Theses

”Adequate sleep is associated with an individual’s health. Too little sleep is associated with many health problems, including cardiovascular disease, obesity, and a general increase in all-cause mortality. Yet the molecular changes that link poor sleep and changes in health are still not well understood. Individuals have a unique daily need for sleep, and deviations from the animal’s regular sleeping patterns can be indicative of, or result in, underlying changes in its health. Therefore, we hypothesize that changes in the sleep architecture in Drosophila melanogaster reflect changes in the fly’s health.

We determined sleep architecture in wild-type male flies over …

Brave Spaces: Augmenting Interdisciplinary Stem Education By Using Quantitative Data Explorations To Engage Conversations On Equity And Social Justice, John R. Jungck, Jon Manon

Numeracy

In workshops and courses involving in-service teachers, participating teachers can engage in problem posing and exploration of difficult issues when they are asked to quantitatively model alternative scenarios, statistically analyze complex data, and visualize these data in multiple formats. Subsequent to these activities, discussions of sensitive issues, some even considered taboo in classrooms, can open up “brave spaces” in these teachers’ classrooms. Without coaching through elaborate facilitation strategies, the in-service teachers grappled openly with the nuances of such difficult issues and raised many alternatives involving quantitative reasoning as well as considering biological, cultural, economic, social, and political factors influencing social …

Evaluation Of A Commercial Model For Predicting Growth Performance Of Pigs With Varying Diet Composition And Stocking Density, M. B. Menegat, F. Wu, J. C. Woodworth, M. D. Tokach, J. M. Derouchey, S. S. Dritz, R. D. Goodband

Kansas Agricultural Experiment Station Research Reports

The objective of this study was to validate the growth performance predictions of a commercial model (CAMERA®; INTL FCStone, New York, NY) by comparing the optimally-solved estimates with observed growth performance from published studies. Three studies were selected to create 3 feeding scenarios: 1) variation in dietary energy concentrations and fiber sources (Nitikanchana et al., 2015); 2) variation in dietary lysine level (Menegat et al., 2017); and 3) variation in space allowance (Carpenter et al., 2018). For each validation scenario, the growth performance of pigs from the best-performing treatment group was first estimated, calibrated using the observed performance, and used …

Contribution Of Juvenile Estuarine Residency In A Bar-Built Estuary To Recruitment Of Chinook Salmon (Oncorhynchus Tshawytscha), Emily Katherine Chen

Cal Poly Humboldt theses and projects

Estuaries are commonly touted as nurseries for out-migrating salmonids, providing higher prey availability than streams, a physiological transition zone, and refugee from marine predators. Yet the diversity of estuaries makes it difficult to generalize the effect they have on salmonid recruitment. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low flow, closing access to the ocean and disrupting outmigration. In this thesis, I evaluated how residency in a bar-built estuary affects the growth, survival, and ultimately recruitment of Chinook salmon (Oncorhynchus tshawytscha) in Redwood Creek, California. I conducted a mark-recapture experiment on out-migrating …

Artificial Neural Models Of Concentrations Of Fungal Spores In The Air For Aerobiological Research, Agnieszka Grinn-Gofron

Turkish Journal of Botany

This article describes in detail an advanced statistical method, the artificial neural network, and the possibilities for its application in aerobiological analyses. The study and models involve the concentration of fungal spores in the air and their relationship with various biological and environmental factors. The author hopes that this work will contribute to a wider use of this method not only in the study of spores but also the concentration of pollen grains.

The Drug Discovery Of Potential Anti-Cancer Agents To Inhibit The Demethylation Catalytic Activity Of The Jmjc Domain Of Kdm3a, Balgees Alshanqeti

Electronic Theses & Dissertations

Lysine demethylase 3A (KDM3A) is an enzyme that specifically catalyzes the removal of 2 or three methyl groups from lysine 9 of histone 3 (KH3). It belongs to the family of histone demethylases that contain the Jumonji C (JmjC) domain, which means cruciform in Japanese. KDM3A also belongs to a family of hydroxylases that are alpha-ketoglutarate dependent. The role of KDM3A in the cell is not yet understood, however, and based on its demethylation of studies have showed that its expression is elevated in embryonic stem cells in humans and in mice. In general, patterns of elevated expression of KDM3A …

Atmospheric Cold Plasma Inactivation Of Salmonella And Escherichia Coli On The Surface Of Golden Delicious Apples, Agnes Kilonzo-Nthenge, Siqin Liu, Sudheer K. Yannam, Ankit Patras

Agricultural and Environmental Sciences Faculty Research

The contamination of fruits with human pathogens is a reoccurring concern in the fresh produce industry. Atmospheric cold plasma (ACP) is a potential alternate to customary approaches for non-thermal decontamination of foods. In this study, the efficacy of a dielectric barrier discharge ACP system against Salmonella (Salmonella Typhimurium, ATCC 13311; Salmonella Choleraesuis, ATCC 10708) and Escherichia coli (ATCC 25922, ATCC 11775) was explored. For each bacteria, a two-strain mixture at 8 log10 CFU/ml was spot inoculated on the surface of Golden Delicious apples, air dried, and exposed to ACP at a fixed distance of 35 mm, input power of 200 …

Modeling The Effect Of Post-Dispersal Seed Predation On Tropical Tree Species In Panama, Justin Tirrell

Fall Student Research Symposium 2018

Palm trees provide a unique opportunity to study what conditions optimize the probability that a seed will grow successfully. The seeds of palm trees, endocarps, are large and easy to locate. When they don't grow, predators leave marks on them that tell the story of their fate. The focus of my experiment is to determine how the current distribution pattern of parent palm trees in Panama Palm trees affects the the future distribution of seedlings. I have programmed a versatile model that takes the assumption that bruchid beetles are the sole predators acting on the seeds, and that these fall …