Digital Commons Network^™

Reproductive Trade-Offs In The Colorado Checkered Whiptail Lizard (Aspidoscelis Neotesselatus): An Examination Of The Relationship Between Clutch And Follicle Size, Hannah E. Caracalas, S. S. French, S. B. Hudson, B. M. Kluever, A. C. Webb, D. Eifler, A. J. Lehmicke, Lise M. Aubry

United States Department of Agriculture Wildlife Services: Staff Publications

Life history theory predicts that there should be an inverse relationship between offspring size and number, because individuals cannot simultaneously maximize both when resources are limited. Although extensively studied in avian species, the occurrence and determinants of reproductive tradeoffs in oviparous reptiles are far less understood, particularly in parthenogenetic species. We studied this trade-off in the Colorado Checkered Whiptail, Aspidoscelis neotesselatus, a female-only parthenogenetic lizard. Using data previously collected in 2018 and 2019, we tested for clutch and egg size trade-offs and determined whether this relationship could be influenced by female size and aspects of physiological condition. Physiological condition …

Modelling The Factors Affecting The Probability For Local Rabies Elimination By Strategic Control, Johann L. Kotzé, John Duncan Grewar, Aaron M. Anderson

United States Department of Agriculture Wildlife Services: Staff Publications

Dog rabies has been recognized from ancient times and remains widespread across the developing world with an estimated 59,000 people dying annually from the disease. In 2011 a tri-partite alliance consisting of the OIE, the WHO and the FAO committed to globally eliminating dog-mediated human rabies by 2030. Regardless of global support, the responsibility remains with local program managers to implement successful elimination programs. It is well known that vaccination programs have a high probability of successful elimination if they achieve a population-coverage of 70%. It is often quoted that reducing population turnover (typically through sterilizations) raises the probability for …

Marginal Warming Associated With A Covid-19 Quarantine And The Implications For Disease Transmission, P. W. Miller, C. Reesman, M. K. Grossman, S. A. Nelson, V. Liu, P. Wang

Faculty Publications

During January-February 2020, parts of China faced restricted mobility under COVID-19 quarantines, which have been associated with improved air quality. Because particulate pollutants scatter, diffuse, and absorb incoming solar radiation, a net negative radiative forcing, decreased air pollution can yield surface warming. As such, this study (1) documents the evolution of China's January-February 2020 air temperature and concurrent particulate changes; (2) determines the temperature response related to reduced particulates during the COVID-19 quarantine (C19Q); and (3) discusses the conceptual implications for temperature-dependent disease transmission. C19Q particulate evolution is monitored using satellite analyses, and concurrent temperature anomalies are diagnosed using surface …

Developing A New Analytical Model For Combatting Crises: A Comprehensive Review, Seth Spire

Research Awards

As the world emerges from the COVID-19 pandemic, it is critical to reflect on the lessons learned and prepare for potential future health crises. While data analytics and artificial intelligence (AI) played a pivotal role in managing the pandemic, there is much room for improvement and further use. This study examines the current state of data science tools employed during COVID-19, evaluating their advantages, limitations, and challenges in their broader implementation. We also review literature on future directions for AI in healthcare. Our findings highlight significant challenges, including difficulties in accessing usable data and common distrust of AI models for …

Grappling With Covid-19 By Imposing And Lifting Nonpharmaceutical Interventions In Sri Lanka: A Modeling Perspective, Mahesh Jayaweera, Chamath Dannongoda, Dilum Dilshan, Janith Dissanayake, Hasini Perera, Jagath Manatunge, Buddhika Gunawardana

Physics & Astronomy Faculty Publications

The imposition and lifting of non-pharmaceutical interventions (NPIs) to avert the COVID19 pandemic have gained popularity worldwide and will continue to be enforced until herd immunity is achieved. We developed a linear regression model to ascertain the nexus between the time-varying reproduction number averaged over a time window of six days (Rts) and seven NPIs: contact tracing, quarantine efforts, social distancing and health checks, hand hygiene, wearing of facemasks, lockdown and isolation, and health-related supports. Our analysis suggests that the second wave that emerged in Sri Lanka in early October 2020 continued despite numerous NPIs. The model indicates that the …

Count Data Time Series Models And Their Applications, Yi Zhang

Doctoral Dissertations

“Due to fast developments of advanced sensors, count data sets have become ubiquitous in many fields. Modeling and forecasting such time series have generated great interest. Modeling can shed light on the behavior of the count series and to see how they are related to other factors such as the environmental conditions under which the data are generated. In this research, three approaches to modeling such count data are proposed.

First, a periodic autoregressive conditional Poisson (PACP) model is proposed as a natural generalization of the autoregressive conditional Poisson (ACP) model. By allowing for cyclical variations in the parameters of …

Comparison Of Clinically Approved Molecules On Sars-Cov-2 Drug Target Proteins: A Molecular Docking Study, Hasan Çubuk, Mehmet Özbi̇l

Turkish Journal of Chemistry

The new type of coronavirus, SARS-CoV-2 has affected more than 22.6 million people worldwide. Since the first day the virus was spotted in Wuhan, China, numerous drug design studies have been conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SARS-CoV-2, which is known to bind to the human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus' replication. However, there might be a third target, human furin protease, which cleaves the virus' S1-S2 domains playing an active role in its entry into the host cell. In this study, we docked …

Synthesis, Spectral Characterization, And Biological Studies Of 3,5-Disubstituted- 1,3,4-Oxadiazole-2(3h)-Thione Derivatives, Tuğçe Özyazici, Fi̇kretti̇n Şahi̇n, Meri̇ç Köksal Akkoç

Turkish Journal of Chemistry

The reaction of 3,4-dichlorophenyl-1,3,4-oxadiazole-2(3H)-thione with piperidine derivatives via Mannich reaction was used to generate eleven novel compounds in moderate to good yields. Synthesized molecules were characterized according to their structure with 1H NMR, 13C NMR and FT-IR spectral foundations, which were compatible with literature informations. Antimicrobial activity and cytotoxicity studies were done by disc diffusion and NCI-60 sulphordamine B assay methods. The antimicrobial test results revealed that synthesized compounds have better activity against gram-positive species than gram-negative ones. A total analysis of the antibacterial, antifungal, and antiyeast activity revealed that newly synthesized compounds were really active against Bacillus cereus, Bacillus …

Novel Mannich Bases With Strong Carbonic Anhydrases And Acetylcholinesterase Inhibition Effects: 3-(Aminomethyl)-6-{3-[4-(Trifluoromethyl)Phenyl]Acryloyl}-2(3h)- Benzoxazolones, Si̇nan Bi̇lgi̇ner, Bariş Anil, Mehmet Koca, Yeli̇z Demi̇r, İlhami̇ Gülçi̇n

Turkish Journal of Chemistry

In this study, a new series of Mannich bases, 3-(aminomethyl)-6-{3-[4-(trifluoromethyl)phenyl]acryloyl}-2(3H)- benzoxazolones (1a-g), were synthesized by the Mannich reaction. Inhibitory effects of the newly synthesized compounds towards carbonic anhydrases (CAs) and acetylcholinesterase (AChE) enzymes were evaluated to find out new potential drug candidate compounds. According to the inhibitory activity results, Ki values of the compounds 1 and 1a-g were in the range of 12.3 ± 1.2 to 154.0 ± 9.3 nM against hCA I, and they were in the range of 8.6 ± 1.9 to 41.0 ± 5.5 nM against hCA II. Ki values of acetazolamide (AZA) that was used as …

Detection Of Bacteria Using Antimicrobial Polymer Derived Via Ring-Opening Metathesis (Romp) Pathway, N Ceren Süer, Tüli̇n Arasoğlu, Hüsnü Cankurtaran, Mustafa Okutan, Markus Gallei, Tarik Eren

Turkish Journal of Chemistry

There is growing interest in the detection of bacteria in consumables, for example, in the food and water sectors. In this study, the aim was to produce a polymer-based bacteria biosensor via ROMP (ring opening metathesis polymerization). In the first part of the study, block and random copolymers were synthesized, and their biocidal activities were tested on the glass surface. Interdigitated electrode arrays coated with the polymers possessing the highest activity were used to screen the affinity towards different bacterial strains by monitoring impedance variations in real-time. The polymer-coated electrode could detect gram-positive and gram-negative bacteria strains at a concentration …

Green Biosynthesis, Characterization, And Cytotoxic Effect Of Magnetic Iron Nanoparticles Using Brassica Oleracea Var Capitata Sub Var Rubra (Red Cabbage) Aqueous Peel Extract, Ömer Erdoğan, Sali̇h Paşa, Gülen Meli̇ke Demi̇rbolat, Özge Çevi̇k

Turkish Journal of Chemistry

The green method of nanoparticle synthesis, which is an environment and living-friendly method, is an updated subject that has appeared as an alternative to conventional methods such as physical and chemical synthesis. In this presented study, the green synthesis of magnetic iron oxide nanoparticles (IONPs) from iron (III) chloride by using Brassica oleracea var. capitata sub.var. rubra aqueous peel extract has been reported. The prepared IONPs were characterized with fourier-transform infrared spectroscopy (FT-IR), ultraviolet-visible spectroscopy (UV-VIS), zeta potential, scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDX). The cytotoxic effects of IONPs on MCF-7 breast cancer cell line were studied …

Structural Rearrangement Of Neisseria Meningitidis Transferrin Binding Protein A (Tbpa) Prior To Human Transferrin Protein (Htf) Binding, Gi̇zem Nur Duran, Mehmet Özbi̇l

Turkish Journal of Chemistry

Gram-negative bacterium Neisseria meningitidis, responsible for human infectious disease meningitis, acquires the iron (Fe3+) ion needed for its survival from human transferrin protein (hTf). For this transport, transferrin binding proteins TbpA and TbpB are facilitated by the bacterium. The transfer cannot occur without TbpA, while the absence of TbpB only slows down the transfer. Thus, understanding the TbpA-hTf binding at the atomic level is crucial for the fight against bacterial meningitis infections. In this study, atomistic level of mechanism for TbpA-hTf binding is elucidated through 100 ns long all-atom classical MD simulations on free (uncomplexed) TbpA. TbpA protein underwent conformational …

Antiinfective Properties Of Ursolic Acid-Loaded Chitosan Nanoparticles Againststaphylococcus Aureus, Fatemeh Ghasemzadeh, Ghasem Najafpour, Maedeh Mohammadi

Turkish Journal of Chemistry

The present study aimed to synthesize ursolic acid-loaded chitosan nanoparticles (UA-Ch-NPs) as an antiinfective agent against 21 Staphylococcus aureus isolates. The UA-Ch-NPs were synthesized by a simple method and then characterized by TEM, FTIR, DLS-zeta potential, and XRD analyses. According to the characterization results, highly dispersed spherical nanoparticles with a mean diameter of 258 nm and a zeta potential of + 40.1 mV were developed. The antibacterial properties of UA-Ch-NPs were investigated and their inhibitory effect on biofilm formation was demonstrated by AFM. Finally, the expression levels of icaA and icaD were measured using real-time PCR. Results indicated that the …

Cyclodextrin-Active Natural Compounds In Food Applications: A Review Of Antibacterial, Bingren Tian, Yumei Liu

Turkish Journal of Chemistry

Many natural compounds have excellent activity against different bacteria. However, their food use to inhibit the bacteria is often limited by poor water solubility, or instability to light, heat, oxygen, and other environmental factors. Cyclodextrin combines with these natural compounds could not only overcome these shortcomings, but also increase the antibacterial ability of active compounds. This review focuses on the following aspects of active natural compounds in cyclodextrin-based food: the preparation, food applications, and their possible antibacterial mechanisms of different systems. Both cyclodextrin and its derivatives are able to selectively combine with different guest molecules, such as terpenes, phenols and …

Polymer-Based And Functionalized 3d Microelectrode Array (Mea) Biosensors, Nilab Azim

Electronic Theses and Dissertations, 2020-2023

Microphysiological systems are three-dimensional (3D) in vitro systems that recapitulate crucial biological aspects of cell heterogeneity and native tissue architecture by mimicking complex structures that are impossible in two-dimensional (2D) cell cultures. Microelectrode arrays (MEAs) are biosensors used to spatially and temporally monitor the activity of microphysiological systems by transducing cellular signals into electronic signals to provide quantitative data on the in vitro system. Conventional MEAs are typically planar in nature, however, 3D MEAs offer several advantages such as better simulation of an in vivo cellular environment and improved signal-to-noise ratio and cell-electrode coupling. MEA fabrication utilizing traditional cleanroom methods …

Continental-Scale Dynamics Of Avian Influenza In U.S. Waterfowl Are Driven By Demography, Migration, And Temperature, Erin E. Gorsich, Colleen T. Webb, Andrew A. Merton, Jennifer A. Hoeting, Ryan S. Miller, Matthew Farnsworth, Seth R. Swafford, Thomas J. Deliberto, Kerri Pedersen, Alan B. Franklin, Robert G. Mclean, Kenneth R. Wilson, Paul Doherty

United States Department of Agriculture Wildlife Services: Staff Publications

Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlife has been conducted at local scales, yet fully understanding their spread and distribution requires assessing the mechanisms acting at both local, (e.g., intrinsic epidemic dynamics), and continental scales, (e.g., long-distance migration). Here, we combined a large, continental-scale data set on low pathogenic, Type A AIV in the United States with a novel network-based …

Avian Use Of Exotic Street Treescapes In Metropolitan Areas Of Phoenix, Arizona, Brian E. Washburn, Karen Hoss, David L. Bergman

United States Department of Agriculture Wildlife Services: Staff Publications

Urban areas are highly modified environments that are strongly influenced by a variety of anthropogenic factors. Consequently, these areas contain unique wildlife communities typically dominated by species that are generalist in nature or highly adaptable. We examined the use of five species of exotic treescapes by exotic and native birds in metropolitan areas of Phoenix, Arizona. House Sparrows [Passer domesticus (37%)], European Starlings [Sturnus vulagris (27%)], Mourning Doves [Zenaida macroura (11%)], and Great-tailed Grackles [Quiscalus mexicanus (7%)] were the most frequently observed species during the study. Approximately two-thirds (67%) of the birds observed during the study were exotic species. Avian …

Biological Activity Of Saussurea Amara (L.) Dc., Shagjjav Oyungerel

Erforschung biologischer Ressourcen der Mongolei / Exploration into the Biological Resources of Mongolia, ISSN 0440-1298

The medicinal application of specific plants over the long period in traditional medicine, suggests the presence of biologically active substances in those plant species. Saussurea amara (L.) DC. is a wild plant with a high feeding value because of its high protein content, vitamins, and minerals. S. amara is used in the traditional Mongolian medicine for the treatment of hepato-biliary disorders. The goal of this study was to evaluate the antioxidant and antimicrobial activities of S. amara. The antioxidant capacity of a methanol extract of plants was evaluated by analyzing its DPPH free-radical scavenging activity and reducing power …

In Memoriam Prof. H.C. Dr. Mathias Kiefer † (1943 – 2019), Michael Stubbe, Annegret Stubbe

Erforschung biologischer Ressourcen der Mongolei / Exploration into the Biological Resources of Mongolia, ISSN 0440-1298

Am 15.06.2019 vollendete sich nach langer schwerer Krankheit der Lebenszyklus von Mathias Kiefer. Seiner Frau und seinem Sohn Daniel sind wir für wertvolle Daten aus der Vita des Verstorbenen zu großem Dank verbunden. Mathias Kiefer wurde am 25. März 1943 im slowakischen Kežmarok geboren, wo er auch seine Schulausbildung erhielt. Von 1961 bis 1966 erfolgte an der Naturwissenschaftlichen Fakultät der Comenius-Universität von Bratislava sein Biologiestudium, das er mit dem Diplom (Fachrichtung Parasitologie) abschloss.

How Does Atg 10 Regulate The Autophagic Process? An Investigation Into The Atg12-5 Conjugation Pathway, Ayanda Brydie

Senior Honors Theses and Projects

Autophagy is a highly conserved eukaryotic cellular recycling process in which the degradation of proteins and cytoplasmic organelles occurs to recycle broken down products throughout the cell. This process plays a critical role in cell survival and maintenance. Once initiated by either nutrient deficiency (bulk autophagy) or recognition of damaged organelles (selective autophagy) this process is mediated by autophagy-related proteins (Atg proteins). The Atg proteins function to form a double-membrane vesicle, the autophagosome, to target part of the cytoplasm and deliver it to the vesicle for breakdown. In bulk autophagy, the presence of these proteins at the phagophore assembly site …

Evaluation Of A Warfarin Bait For Controlling Invasive Wild Pigs (Sus Scrofa), James C. Beasley, Lindsay M. Clontz, Allison Rakowski, Nathan P. Snow, Kurt C. Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

BACKGROUND: Wild pigs (Sus scrofa) cause widespread environmental and economic damage, and as a result are subjected to extensive control. Current management strategies have proven insufficient, and there is growing interest in use of toxicants to control invasive populations of this species. In 2017 a low-dose warfarin bait was federally approved for use in controlling wild pigs in the United States. However, no states have allowed use of this bait due to unanswered questions regarding welfare concerns, field efficacy, and non-target impacts.

RESULTS: All captive wild pigs fed 0.005% warfarin baits in no choice feeding trials succumbed in an average …

An Evaluation Of The Bighorn Sheep Population In Badlands National Park, Austin J. Wieseler

Electronic Theses and Dissertations

Within the last century, bighorn sheep (Ovis canadensis) in the badlands ecosystem of western South Dakota have been subjected to complete extirpation, reintroduction, disease die-offs, genetic bottlenecking, and population augmentation. Subsequently, the population in Badlands National Park (BNP) appears to have recovered, but it was unknown to what degree past events had influenced the population. From 2017-2019, we conducted research on 5 subherds within 2 management units in BNP to 1) survey for the presence of respiratory pathogens and estimate the prevalence of other potentially infectious diseases; 2) assess adult and lamb survival and cause-specific mortality; 3) estimate population size …

Use Of Lymesim 2.0 To Assess The Potential For Single And Integrated Management Methods To Control Blacklegged Ticks (Ixodes Scapularis; Acari: Ixodidae) And Transmission Of Lyme Disease Spirochetes, Shravani Chitineni, Elizabeth R. Gleim, Holly D. Gaff

Undergraduate Honors Theses

Annual Lyme disease cases continue to rise in the U.S. making it the most reported vector-borne illness in the country. The pathogen (Borrelia burgdorferi) and primary vector (Ixodes scapularis; blacklegged tick) dynamics of Lyme disease are complicated by the multitude of vertebrate hosts and varying environmental factors, making models an ideal tool for exploring disease dynamics in a time- and cost-effective way. In the current study, LYMESIM 2.0, a mechanistic model, was used to explore the effectiveness of three commonly used tick control methods: habitat-targeted acaricide (spraying), rodent-targeted acaricide (bait boxes), and white-tailed deer targeted acaricide (4-poster …

Addressing The Ecological Fallacy With Lagrangian Inference, Michael Schwob

Calvert Undergraduate Research Awards

Most epidemiologists elect to use statistical models that use population-level data to make inference on the spread of some virus or disease. This has become commonplace in the fields of epidemiology and biostatistics since most data used to construct and verify epidemic models are recorded at the population-level. Obtaining inference from a population-level model may be beneficial in studying the spread of disease in a homogeneous population, but the use of such models to describe a heterogeneous population results in inadequate inference. The inaccuracy of these models is further amplified when one tries to make individual-level inference from these population-level …

R2u3d: Recurrent Residual 3d U-Net For Lung Segmentation, Dhaval D. Kadia, Md Zahangir Alom, Ranga Burada, Tam Nguyen, Vijayan K. Asari

Computer Science Faculty Publications

3D Lung segmentation is essential since it processes the volumetric information of the lungs, removes the unnecessary areas of the scan, and segments the actual area of the lungs in a 3D volume. Recently, the deep learning model, such as U-Net outperforms other network architectures for biomedical image segmentation. In this paper, we propose a novel model, namely, Recurrent Residual 3D U-Net (R(2)U3D), for the 3D lung segmentation task. In particular, the proposed model integrates 3D convolution into the Recurrent Residual Neural Network based on U-Net. It helps learn spatial dependencies in 3D and increases the propagation of 3D volumetric …

Towards An Ontology-Based Approach To The "New Normality" After Covid-19:The Spanish Case During Pandemic First Wave, Evelio Gonzalez

Turkish Journal of Electrical Engineering and Computer Sciences

The impact of the pandemic caused by COVID-19 has been immense in all fields of human activity. In most of the affected countries, the authorities have decreed a series of legal measures to try to stop the growth of the disease and the number of people affected by it. These legal measures involved, in most cases, restrictions on the free movement of people and on work and trade activities, new hygiene procedures, and social distancing. In the particular case of Spain, the rapid evolution of the pandemic led to the declaration of a so-called state of alarm and a period …

Small Business Owner App To Showcase Covid Prevention Policies And Reopening Guidelines, Christopher Duran

Theses, Dissertations and Culminating Projects

Almost a year after the emergence of the Coronavirus, the pandemic still negatively affects the world’s economy and quality of life. In the U.S., Covid-19 has shut down nearly 100,000 businesses.

The goal of this project is to develop an app that can assist business owners to accurately display their coronavirus prevention methods so that people can feel safe while using their services. This project will focus on how the business owner (Vendor) will be able to interact, utilize, and display important information for the customer (Patron) to use.

The vendor will be able to create an individual profile for …

Evaluating The Incidence Of Melanoma And Lung Cancer Of Current And Former Active-Duty U.S. Military Who Were Deployed In Support Of Operation Enduring Freedom And Operation Iraqi Freedom, Brian Kovacic

Theses and Dissertations--Epidemiology and Biostatistics

The incidence of melanoma and lung cancer has been gradually increasing in the United States over the past three decades with the reputed causes due to etiological and environmental exposures, and tobacco usage. There has been concern that melanoma and lung cancer incidence among military personnel may be associated with deployment to environments with intense sun exposure and increased smoking rates due to post-traumatic stress disorder. The aim of this study was to examine associations between deployment in support of Operation Enduring Freedom (OEF) or Operation Iraqi Freedom (OIF), from 2001 through 2015, with subsequent melanoma and lung cancer incidence. …

A Deep Transfer Learning Based Model For Automatic Detection Of Covid-19from Chest X-Rays, Prateek Chhikara, Prakhar Gupta, Prabhjot Singh, Tarunpreet Bhatia

Turkish Journal of Electrical Engineering and Computer Sciences

Deep learning in medical imaging has revolutionized the way we interpret medical data, as high computational devices' capabilities are far more than their creators. With the pandemic causing havoc for the second straight year, the findings in our paper will allow researchers worldwide to use and create state-of-the-art models to detect affected persons before it reaches the R number. The paper proposes an automated diagnostic tool using the deep learning models on chest x-rays as an input to reach a point where we surpass this pandemic (COVID-19 disease). A deep transfer learning-based model for automatic detection of COVID-19 from chest …

On The Local And Global Stability Of An Sirs Epidemic Model With Logistic Growth And Information Intervention, İrem Çay

Turkish Journal of Mathematics

In this study, we investigate an susceptible-infected-recovered-susceptible (SIRS) epidemic model with logistic growth and information intervention. Firstly, the basic reproduction number $R_0$ is defined and the main results are given in terms of local stability. Then, sufficient conditions for the global stability of endemic equilibrium are obtained. Finally, some numerical simulations are given to validate our theoretical conclusions.