Digital Commons Network^™

Glcms Based Multi-Inputs 1d Cnn Deep Learning Neural Network For Covid-19 Texture Feature Extraction And Classification, Elaf Ali Abbood, Tawfiq A. Al-Assadi

Karbala International Journal of Modern Science

Coronavirus disease 2019 epidemic (COVID-19) is an infectious disease that appeared because of the newest version of discovered coronavirus. The advent and rapid spread of this disease over the world necessitated a concerted effort to contain and eradicate it. Computer Tomography (CT) imaging and X-Ray images are considered as one of the important medical examinations used for disease diagnosis. To speed up and confirm the correctness of the medical diagnosis, many artificial intelligence techniques and machine learning methods are proposed. In this paper, a new and efficient proposed system is introduced to extract appropriate and meaningful features for CT scans …

Hyperparameter Optimization For Covid-19 Chest X-Ray Classification, Ibraheem Hamdi, Muhammad Ridzuan, Mohammad Yaqub

Computer Vision Faculty Publications

Despite the introduction of vaccines, Coronavirus disease (COVID-19) remains a worldwide dilemma, continuously developing new variants such as Delta and the recent Omicron. The current standard for testing is through polymerase chain reaction (PCR). However, PCRs can be expensive, slow, and/or inaccessible to many people. X-rays on the other hand have been readily used since the early 20th century and are relatively cheaper, quicker to obtain, and typically covered by health insurance. With a careful selection of model, hyperparameters, and augmentations, we show that it is possible to develop models with 83% accuracy in binary classification and 64% in multi-class …

Dispersed Crude Oil Induces Dysbiosis In The Red Snapper Lutjanus Campechanus External Microbiota, Andrew M. Tarnecki, Christelle Miller, Tracy A. Sherwood, Robert J. Griffitt, Ryan W. Schloesser, Dana L. Wetzel

Faculty Publications

The fish external microbiota competitively excludes primary pathogens and prevents the proliferation of opportunists. A shift from healthy microbiota composition, known as dysbiosis, may be triggered by environmental stressors and increases host susceptibility to disease. The Deepwater Horizon (DWH) oil spill was a significant stressor event in the Gulf of Mexico. Despite anecdotal reports of skin lesions on fishes following the oil spill, little information is available on the impact of dispersed oil on the fish external microbiota. In this study, juvenile red snapper (Lutjanus campechanus) were exposed to a chemically enhanced water-accommodated fraction (CEWAF) of Corexit 9500/DWH …

Evidence For A Semisolid Phase State Of Aerosols And Droplets Relevant To The Airborne And Surface Survival Of Pathogens, Erik Huynh, Anna Olinger, David Woolley, R. K. Kohli, J. M. Choczynski, J. F. Davies, K. Lin, L. C. Marr, Ryan D. Davis

Chemistry Faculty Research

The phase state of respiratory aerosols and droplets has been linked to the humidity-dependent survival of pathogens such as SARS-CoV-2. To inform strategies to mitigate the spread of infectious disease, it is thus necessary to understand the humidity-dependent phase changes associated with the particles in which pathogens are suspended. Here, we study phase changes of levitated aerosols and droplets composed of model respiratory compounds (salt and protein) and growth media (organic-inorganic mixtures commonly used in studies of pathogen survival) with decreasing relative humidity (RH). Efflorescence was suppressed in many particle compositions and thus unlikely to fully account for the humidity-dependent …

Indole-3-Glycerol Phosphate Synthase From Mycobacterium Tuberculosis: A Potential New Drug Target, Nikolas Esposito, David W. Konas, Nina M. Goodey

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Tuberculosis (TB), caused by the pathogen Mycobacterium tuberculosis, affects millions of people worldwide. Several TB drugs have lost efficacy due to emerging drug resistance and new anti-TB targets are needed. Recent research suggests that indole-3-glycerol phosphate synthase (IGPS) in M. tuberculosis (MtIGPS) could be such a target. IGPS is a (β/α)8-barrel enzyme that catalyzes the conversion of 1-(o-carboxyphenylamino)-1-deoxyribulose 5’-phosphate (CdRP) into indole-glycerol-phosphate (IGP) in the bacterial tryptophan biosynthetic pathway. M. tuberculosis over expresses the tryptophan pathway genes during an immune response and inhibition of MtIGPS allows CD4 T-cells to more effectively fight against M. tuberculosis. Here we review the published …

Synthesis And Biosynthesis Of 3-Hydroxy-Β-Lactam Antibiotics, Wei Wei

Arts & Sciences Graduate Student Theses and Dissertations

Novel treatments for tuberculosis (TB) are urgently needed to conquer this global health crisis. Unlike canonical β-lactam antibiotics that target transpeptidases by hydrolyzing the lactam ring, tabtoxinine-β-lactam (TβL) functions as a potent glutamine synthetase (GS) inhibitor by forming a transition state mimic. TβL has the potential to be used as an anti-TB agent by targeting the nitrogen metabolic pathway of pathogenic mycobacteria. This work reported an innovative, convergent, and flexible cross-metathesis method to obtain the fully protected TβL scaffold. The trans-olefin intermediate provides possibilities for synthesizing various derivatives through alkene functionalization reactions. We also developed and optimized a solid phase …

Challenges In Covid-19 Chest X-Ray Classification: Problematic Data Or Ineffective Approaches?, Muhammad Ridzuan, Ameera Ali Bawazir, Ivo Gollini Navarrete, Ibrahim Almakky, Mohammad Yaqub

Computer Vision Faculty Publications

The value of quick, accurate, and confident diagnoses cannot be undermined to mitigate the effects of COVID-19 infection, particularly for severe cases. Enormous effort has been put towards developing deep learning methods to classify and detect COVID-19 infections from chest radiography images. However, recently some questions have been raised surrounding the clinical viability and effectiveness of such methods. In this work, we carry out extensive experiments on a large COVID-19 chest X-ray dataset to investigate the challenges faced with creating reliable solutions from both the data and machine learning perspectives. Accordingly, we offer an in-depth discussion into the challenges faced …

Modeling And Simulation Of Emergency Medical Resources Allocation In Shanghai During Covid-19, Changjia Fan, Yanqiu Du, Liang Di, Hu Kai, Jiayan Huang

Journal of System Simulation

Abstract: Modeling and simulating on the allocation of emergency medical resources in Shanghai with COVID-19 is carried out. Based on the SEIR model of infectious diseases, combined with the process of outpatients visiting and inpatients treatment, a SEIOWHR(susceptible-exposed-infected-outpatients- waiting to hospitalized-hospitalized-removed) system dynamics model is established. If the Wuhan epidemic occurred in Shanghai, based on the model, the amount of emergency medical resources needed, the gap time of medical resources and the disease progression of patients who are waiting to hospitalized under the different supply of medical resources is simulated, and the key factors in the allocation of medical …

Iron Dysregulation In Covid-19 And Reciprocal Evolution Of Sars-Cov-2: Natura Nihil Frustra Facit, Yash Gupta, Dawid Maciorowski, Brian Medernach, Daniel P. Becker Ph.D., Ravi Durvasula, Claudia R. Libertin, Prakasha Kempaiah

Chemistry: Faculty Publications and Other Works

After more than a year of the COVID-19 pandemic, SARS-CoV-2 infection rates with newer variants continue to devastate much of the world. Global healthcare systems are overwhelmed with high positive patient numbers. Silent hypoxia accompanied by rapid deterioration and some cases with septic shock is responsible for COVID-19 mortality in many hospitalized patients. There is an urgent need to further understand the relationships and interplay with human host components during pathogenesis and immune evasion strategies. Currently, acquired immunity through vaccination or prior infection usually provides sufficient protection against the emerging variants of SARS-CoV-2 except Omicron variant requiring recent booster. New …

Using A Stochastic Continuous-Time Markov Chain Model To Examine Alternative Timing And Duration Of The Covid-19 Lockdown In Kuwait: What Can Be Done Now?, Mustafa Al-Zoughool, Tamer Oraby, Harri Vainio, Janvier Gasana, Joseph C. Longenecker, Walid Al Ali, Mohammad Alseaidan, Susie Elsaadany, Michael G. Tyshenko

School of Mathematical & Statistical Sciences Faculty Publications

Background

Kuwait had its first COVID-19 in late February, and until October 6, 2020 it recorded 108,268 cases and 632 deaths. Despite implementing one of the strictest control measures-including a three-week complete lockdown, there was no sign of a declining epidemic curve. The objective of the current analyses is to determine, hypothetically, the optimal timing and duration of a full lockdown in Kuwait that would result in controlling new infections and lead to a substantial reduction in case hospitalizations.

Methods

The analysis was conducted using a stochastic Continuous-Time Markov Chain (CTMC), eight state model that depicts the disease transmission and …

Raw Garlic (Allium Sativum) Improves Nonspecific Immune Responses And Resistance Against Vibrio Alginolyticus Infection In Grouper (Epinephelus Coioides), Huai-Ting Huang, Po-Tsang Lee, Zhen-Hao Liao, Cheng-Ting Huang, Hsiang-Yin Chen, Zhi-Gu Huang, Fan-Hua Nan, Yu-Sheng Wu

Journal of Marine Science and Technology–Taiwan

Garlic contains various nutrients and healthful ingredients. The content of garlic products is closely related to their processing methods, and each compound has specific biological effects. Allicin, a heat labile compound, is considered the most important factor in garlic. Garlic powder is commonly prepared by subjecting raw garlic to thermal processing before being grounded into powder,and it is of interest to compare the biological activity of garlic powder with raw garlic in fish. This study investigated immune effects of raw garlic and garlic powder on groupers (Epinephelus coioides). Although raw garlic and garlic powder did not promote growth performance of …

Legacy And Emerging Contaminants In Water And Wastewater, P. Chakraborty, Daniel D. Snow

School of Natural Resources: Faculty Publications

No abstract provided.

Public Search Interests Related To Covid-19: Insights From Google Search Trends In Bangladesh, M. Ahamad, M. Ahmed, Daniel R. Uden

School of Natural Resources: Faculty Publications

No abstract provided.

Nonlinear Mixed-Effects Models For Hiv Viral Load Trajectories Before And After Antiretroviral Therapy Interruption, Incorporating Left Censoring, Sihaoyu Gao, Lang Wu, Tingting Yu, Roger Kouyos, Huldrych F. Gunthard, Rui Wang

Harvard University Biostatistics Working Paper Series

Characterizing features of the viral rebound trajectories and identifying host, virological, and immunological factors that are predictive of the viral rebound trajectories are central to HIV cure research. In this paper, we investigate if key features of HIV viral decay and CD4 trajectories during antiretroviral therapy (ART) are associated with characteristics of HIV viral rebound following ART interruption. Nonlinear mixed effect (NLME) models are used to model viral load trajectories before and following ART interruption, incorporating left censoring due to lower detection limits of viral load assays. A stochastic approximation EM (SAEM) algorithm is used for parameter estimation and inference. …

Σ-Ary, Minnesota State University Moorhead, Mathematics Department

Math Department Newsletters

No abstract provided.

Towards Water Literacy: An Interdisciplinary Analysis Of Standards For Teaching And Learning About Humans And Water, Silvia‑Jessica Mostacedo‑Marasovic, Brooke Colleen Mott, Holly White, Cory T. Forbes

School of Natural Resources: Faculty Publications

Water is critical to sustain human existence. Water literacy involves understanding the interactions within and between natural and human dimensions of water systems to support informed decision-making, an important outcome for learners of all ages. It is therefore critical to foster water literacy in today’s global citizens, particularly through formal education. The purpose of this study, in tandem with a parallel study focusing on natural dimensions of water systems (Mostacedo-Marasovic et al., in press), is to examine water-related K-12 standards for teaching and learning about human dimensions of water systems to develop a comprehensive and transdisciplinary perspective on water education. …

Genome-Wide Association Study Of Disease Resilience Traits From A Natural Polymicrobial Disease Challenge Model In Pigs Identifies The Importance Of The Major Histocompatibility Complex Region, Jian Cheng, Rohan Fernando, Hao Cheng, Stephen D. Kachman, Kyusang Lim, John C.S. Harding, Michael K. Dyck, Frederic Fortin, Graham S. Plastow, Piggen Canada Research Consortium, Jack C.M. Dekkers

Department of Statistics: Faculty Publications

Infectious diseases cause tremendous financial losses in the pork industry, emphasizing the importance of disease resilience, which is the ability of an animal to maintain performance under disease. Previously, a natural polymicrobial disease challenge model was established, in which pigs were challenged in the late nursery phase by multiple pathogens to maximize expression of genetic differences in disease resilience. Genetic analysis found that performance traits in this model, including growth rate, feed and water intake, and carcass traits, as well as clinical disease phenotypes, were heritable and could be selected for to increase disease resilience of pigs. The objectives of …

No Panacea Attractant For Wild Pigs (Sus Scrofa), But Season And Location Matter, Nathan P. Snow, Caitlin A. Kupferman, Michael J. Lavelle, Kim M. Pepin, Madeline H. Melton, Whitney J. Gann, Kurt C. Vercauteren, James C. Beasley

United States Department of Agriculture Wildlife Services: Staff Publications

Wild pigs (Sus scrofa) are a prolific invasive species throughout many regions of the world that cause extensive economic and environmental damage. Trapping is a common strategy for reducing their populations with baits (i.e., food) and attractants (e.g., scents) used to lure wild pigs into traps. However, there is little information on which scent attractants may attract wild pigs more readily and rapidly across regions and seasons. We examined 60 scent attractants for wild pigs that could be used to increase trapping success across three seasons (winter, spring, and fall) and in two geographic regions, including a warm …

Predation Thresholds For Reintroduction Of Native Avifauna Following Suppression Of Invasive Brown Treesnakes On Guam, Robert M. Mcelderry, Eben H. Paxton, Andre V. Nguyen, Shane R. Siers

United States Department of Agriculture Wildlife Services: Staff Publications

The brown treesnake (BTS) (Boiga irregularis) invasion on Guåhan (in English, Guam) led to the extirpation of nearly all native forest birds. In recent years, methods have been developed to reduce BTS abundance on a landscape scale. To help assess the prospects for the successful reintroduction of native birds to Guåhan following BTS suppression, we modeled bird population persistence based on their life history characteristics and relative sensitivity to BTS predation. We constructed individual-based models and simulated BTS predation in hypothetical founding populations for each of seven candidate bird species. We represented BTS predation risk in two steps: …

Conserving Endangered Black-Footed Ferrets: Biological Threats, Political Challenges, And Lessons Learned, Travis M. Livieri, Steven C. Forrest, Marc R. Matchett, Stewart Breck

United States Department of Agriculture Wildlife Services: Staff Publications

There may be few stories in the annals of wildlife management that are as dramatic as the near demise and comeback of the black-footed ferret (Mustela nigripes). Endemic only to North America, this charming little carnivore found only in the continent’s central grasslands was hardly known to science until the mid-20th century. By then, vast colonies of the prey it depended on for food and shelter, the prairie dog (Cynomys spp.), had been wiped out through disease (sylvatic plague) and an agricultural industry with little tolerance for burrowing and grazing rodents. At its low point, the species’ …

Disability And Climate Change: A Critical Realist Model Of Climate Justice, Molly M. King, Maria A. Gregg

Sociology

Existing literature on climate change as an issue of environmental justice documents the heightened vulnerability of people with disabilities to the effects of climate change. Additionally, there are numerous studies showing that access to information is a prerequisite for perceiving risk and taking action. Building on this work, our review seeks to understand how physical disability relates to perceptions of climate-related risk and adaptations to climate-related events. We introduce a critical realist model of climate justice to understand the relationships between the environmental features that disable, risk perception and information seeking, and adaptive capacity and resilience to climate change. In …

Comparison Of The Mental Burden On Nursing Care Providers With And Without Mat-Type Sleep State Sensors At A Nursing Home In Tokyo, Japan: Quasi-Experimental Study, Sakiko Itoh, Hwee-Pink Tan, Kenichi Kudo, Yasuko Ogata

Research Collection School Of Computing and Information Systems

Background: Increasing need for nursing care has led to the increased burden on formal caregivers, with those in nursing homes having to deal with exhausting labor. Although research activities on the use of internet of things devices to support nursing care for older adults exist, there is limited evidence on the effectiveness of these interventions among formal caregivers in nursing homes. Objective: This study aims to investigate whether mat-type sleep state sensors for supporting nursing care can reduce the mental burden of formal caregivers in a nursing home. Methods: This was a quasi-experimental study at a nursing home in Tokyo, …

Population Persistence And Disease Invasion In Heterogenous Networks, Poroshat Yazdanbakhshghahyazi

Electronic Theses and Dissertations, 2020-2023

The problem of understanding how biological species and infectious diseases can persist and spread in heterogeneous networks has brought a wide attention, recently highlighted due to the COVID-19 pandemic. This dissertation investigates the connection between the structures of heterogeneous networks and population persistence/disease invasion. To do so, we propose a new index for network heterogeneity by employing the Laplacian matrix of population dispersal and its corresponding group inverse. The network growth rate and reproduction number can be evaluated using the network average and the network heterogeneity index as the first and second order approximation, respectively. We also illustrate the impact …

Development Of Peg-B-Pla Based Micelles For Neutralization Of A Toxic Peptide, Giselle Campos

Graduate Theses/Dissertations

I herein report the preparation and characterization of PEG-b-PLA block copolymer micelles and PEG-b-PLA/PLA mixed micelles as potential “plastic antidotes” for a toxic peptide, melittin. PEG-b-PLA micelles have been used in a number of biomedical applications for their biodegradability and biocompatibility. Along these lines, I investigated the colloidal stability and the peptide absorption properties of PEG-b-PLA/PLA mixed micelles. A series of PEG-b-PLA block copolymer micelles and PEG-b-PLA/PLA mixed micelles were prepared, and their colloidal stability was studied. The hydrodynamic diameters of stable micelles were determined by using Dynamic …

Deep Features To Analyze Pulmonary Abnormalities In Chest X-Rays Due To Covid-19, Supriti Ghosh

Dissertations and Theses

Artificial Intelligence (AI) has contributed a lot since the beginning. Healthcare is no exception. Detecting anomaly/abnormality in (bio)medical image is crucial. In this thesis, we aim at detecting/screening pulmonary abnormalities due to Covid-19 in chest X-rays using deep features. We study CheXNet, DenseNet169, ResNet50 and VggNet16 to analyze CXRs to detect the evidence of Covid-19 in this research. CheXNet was primarily designed for radiologist-level pneumonia detection in Chest X-rays (CXRs). We created a benchmark dataset size of 4,716 CXRs (2,358 Covid-19 positive cases and 2,358 non-Covid cases (Healthy and Pneumonia cases)) and with k(=5) fold cross-validation technique, using the DenseNet, …

Analyzing Cough Sounds For The Evidence Of Covid-19 Using Deep Learning Models, Muntasir Mamun

Dissertations and Theses

Early detection of infectious disease is the must to prevent/avoid multiple infections, and Covid-19 is an example. When dealing with Covid-19 pandemic, Cough is still ubiquitously presented as one of the key symptoms in both severe and non-severe Covid-19 infections, even though symptoms appear differently in different sociodemographic categories. By realizing the importance of clinical studies, analyzing cough sounds using AI-driven tools could help add more values when it comes to decision-making. Moreover, for mass screening and to serve resource constrained regions, AI-driven tools are the must. In this thesis, Convolutional Neural Network (CNN) tailored deep learning models are studied …

Foot Injuries In Michigan, Usa, Gray Wolves (Canis Lupus), 1992–2014, Daniel J. O'Brien, Dean E. Beyer Jr., Erin Largent, Julie R. Melotti, Caitlin N. Ott-Conn, Donald H. Lonsway, Thomas M. Cooley, Robert Atkinson, Michelle Clayson, Kelly A. Straka

United States Department of Agriculture Wildlife Services: Staff Publications

The range of gray wolves (Canis lupus) in the contiguous US is expanding. Research and monitoring to support population recovery and management often involves capture via foothold traps. A population-level epidemiologic assessment of the effect of trap injuries on wolf survival remains needed to inform management. We describe the baseline rate, type, and severity of foot injuries of wolves born 1992–2013 in Michigan’s Upper Peninsula, evaluate the reliability of field-scoring trap-related injuries, and the effect of injuries on wolf survival. We assessed foot injuries by physical and radiographic exam at postmortem and/or time of capture for 351 wolves using the …

Olfactory Lures In Predator Control Do Not Increase Predation Risk To Birds In Areas Of Conservation Concern, Page Klug, Amy A. Yackel Adams, Robert N. Reed

United States Department of Agriculture Wildlife Services: Staff Publications

Context. Lethal control of predators is often undertaken to protect species of conservation concern. Traps are frequently baited to increase capture efficacy, but baited traps can potentially increase predation risk by attracting predators to protected areas. This is especially important if targeted predators can escape capture due to low trap success. Snake traps using live mouse lures may be beneficial if traps effectively remove snakes in the presence of birds and do not attract additional snakes to the area.

Aims. The present study evaluated whether mouse-lure traps in areas occupied by birds (simulated by deploying birdlure traps) could influence predation …

Wild Pig Removal Reduces Pathogenic Bacteria In Low-Order Streams, Sara A. Bolds, B. Graeme Lockaby, Latif Kalin, Stephen S. Ditchkoff, Mark D. Smith, Kurt Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

Invasive wild pig populations have undergone enormous increases in the United States and particularly across the southern U.S. in recent years. High fecundity rates and abilities to adapt quickly to varied habitats have enabled pig populations to become entrenched and difficult to eliminate. The pigs cause many negative impacts on ecosystems including degradation of water quality through infusion of fecal contamination and other non-point source pollutants. Our goal was to determine the effects of pig removal on water quality in streams that were known to be significantly polluted by pig activity Bolds (J Environ Qual 50: 441–453, 2021). We compared …

Plague Risk In The Western United States Over Seven Decades Of Environmental Change, Colin J. Carlson, Sarah N. Bevins, Boris V. Schmid

United States Department of Agriculture Wildlife Services: Staff Publications

After several pandemics over the last two millennia, the wildlife reservoirs of plague (Yersinia pestis) now persist around the world, including in the western United States. Routine surveillance in this region has generated comprehensive records of human cases and animal seroprevalence, creating a unique opportunity to test how plague reservoirs are responding to environmental change. Here, we test whether animal and human data suggest that plague reservoirs and spillover risk have shifted since 1950. To do so, we develop a new method for detecting the impact of climate change on infectious disease distributions, capable of disentangling long-term trends (signal) and …