Digital Commons Network^™

Siderophore-Mediated Zinc Acquisition Enhances Enterobacterial Colonization Of The Inflamed Gut, Judith Behnsen, Hui Zhi, Allegra T. Aron, Venkateswaran Subramanian, William Santus, Michael H. Lee, Romana R. Gerner, Daniel Petras, Janet Z. Liu, Keith D. Green, Sarah L. Price, Jose Camacho, Hannah Hillman, Joshua Tjokrosurjo, Nicola P. Montaldo, Evelyn M. Hoover, Sean Treacy-Abarca, Benjamin A. Gilston, Eric P. Skaar, Walter J. Chazin, Sylvie Garneau-Tsodikova, Matthew B Lawrenz, Robert D Perry, Sean-Paul Nuccio, Pieter C. Dorrestein, Manuela Raffatellu

Pharmacy Nuclear Magnetic Resonance Center Faculty Publications

Zinc is an essential cofactor for bacterial metabolism, and many Enterobacteriaceae express the zinc transporters ZnuABC and ZupT to acquire this metal in the host. However, the probiotic bacterium Escherichia coli Nissle 1917 (or “Nissle”) exhibits appreciable growth in zinc-limited media even when these transporters are deleted. Here, we show that Nissle utilizes the siderophore yersiniabactin as a zincophore, enabling Nissle to grow in zinc-limited media, to tolerate calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. We also show that yersiniabactin’s affinity for iron or zinc changes in a pH-dependent manner, with increased relative zinc binding as the …

Comparative Analysis Of Kmer Counting And Estimation Tools, Ankitha Vejandla

School of Computing: Dissertations, Theses, and Student Research

The rapid development of next-generation sequencing (NGS) technologies for determining the sequence of DNA has revolutionized genome research in recent years. De novo assemblers are the most commonly used tools to perform genome assembly. Most of the assemblers use de Bruijn graphs that break the sequenced reads into smaller sequences (sub-strings), called kmers, where k denotes the length of the sub-strings. The kmer counting and analysis of kmer frequency distribution are important in genome assembly. The main goal of this research is to provide a detailed analysis of the performance of different kmer counting and estimation tools that are currently …

A Linear Dynamical Perspective On Epidemiology: Interplay Between Early Covid-19 Outbreak And Human Mobility, Shakib Mustavee

Electronic Theses and Dissertations, 2020-2023

This research investigates the impact of human activity and mobility (HAM) in the spreading dynamics of an epidemic. Specifically, it explores the interconnections between HAM and its effect on the early spread of the COVID-19 virus. During the early stages of the pandemic, effective reproduction numbers exhibited a high correlation with human mobility patterns, leading to a hypothesis that the HAM system can be studied as a coupled system with disease spread dynamics. This study applies the generalized Koopman framework with control inputs to determine the nonlinear disease spread dynamics and the input-output characteristics as a locally linear controlled dynamical …

Effects Of Il-10 On Local Cell Populations And Functional Recovery Following Vml Injury, Zain Blackwell

Biomedical Engineering Undergraduate Honors Theses

Volumetric muscle loss (VML) injuries are prevalent in both military personnel suffering from battlefield related incidents, and civilians following severe motor accidents. Despite its prevalence, VML has no pro-regenerative clinical treatments in place to recover some of the functional capabilities of the damaged muscle. Free flap grafting, debridement of damaged tissue, and physical therapy are the only clinical standards available that offer little functional recovery benefits, even after years of consistent treatment. In this study, anti-inflammatory cytokine interleukin-10 in conjunction with autologous minced muscle was assessed as a possible treatment for VML injuries and its influences on cellular behavior within …

Data Analytics For Google Trend Search Result Of Illness Symptoms, Md Jakir Hossain

Theses and Dissertations

The outbreak of COVID-19 has escalated from March 2020. Since then, people from all over the world are curiously searching different types of illness symptoms including corona virus. Before the outbreak, people were also searching different types of symptoms at different times. Both diseases share same symptoms, but in the flu season. If certain types of symptoms are visible at summer season, then these symptoms are for corona virus. The main purpose of our study is to find out this discriminative information from these search result. We will discuss some mathematical concepts and then develop an algorithm based on those …

A Integrated Approach Of Deep Learning And Augmented Reality For Pneumonia Detection In Chest X-Ray Images, Jeevarathinam Senthilkumar

Open Access Theses & Dissertations

Pneumonia is a viral or fungal illness that spreads to the lungs of the human body, causing fluid to accumulate in the lungs' air sacs. Millions of people are affected by this disease each year. One of the most common radiological diagnostics for diagnosing and screening this kind of sickness is a chest X-ray. The most commonly available radiological test for diagnosing and screening this kind of illness is a chest X-ray. An inaccurate diagnosis, especially over-diagnosis and under-diagnosis, is a common issue in the medical sector. As another issue, human-assisted diagnosis has limitations like the availability of an expert, …

Development Of Solution Blow Spun Nanofibers As Electrical And Whole Cell Biosensing Interfaces, Craig Levar Miller

All Dissertations

Infectious pathogens place a huge burden on the US economy with more than $120 billion spent annually for direct and indirect costs for the treatment of infectious diseases. Rapid detection schemes continue to evolve in order to meet the demand of early diagnosis. In chronic wound infections, bacterial load is capable of impeding the healing process. Additionally, bacterial virulence production works coherently with bacterial load to produce toxins and molecules that prolongs the healing cycle. This work examines the use of nonwoven polymeric conductive and non-conductive nanofiber mats as synthetic biosensor scaffolds, drug delivery and biosensor interface constructs. A custom-made …

Drug-Based Therapeutic Strategies For Covid-19-Infected Patients And Their Challenges, Khatereh Zarkesh, Elaheh Entezar-Almahdi, Parisa Ghasemiyeh, Mohsen Akbarian, Marzieh Bahmani, Shahrzad Roudaki, Rahil Fazlinejad, Soliman Mohammadi-Samani, Negar Firouzabadi, Majid Hosseini, Fatemeh Farjadian

Manufacturing & Industrial Engineering Faculty Publications

Emerging epidemic-prone diseases have introduced numerous health and economic challenges in recent years. Given current knowledge of COVID-19, herd immunity through vaccines alone is unlikely. In addition, vaccination of the global population is an ongoing challenge. Besides, the questions regarding the prevalence and the timing of immunization are still under investigation. Therefore, medical treatment remains essential in the management of COVID-19. Herein, recent advances from beginning observations of COVID-19 outbreak to an understanding of the essential factors contributing to the spread and transmission of COVID-19 and its treatment are reviewed. Furthermore, an in-depth discussion on the epidemiological aspects, clinical symptoms …

Optimizing Vaccine Supply Chains With Drones In Less-Developed Regions: Multimodal Vaccine Distribution In Vanuatu, Deng Pan

Dissertations

In recent years, many less-developed countries (LDCs) have been exploring new opportunities provided by drones, such as the capability to deliver items with minimal infrastructure, fast speed, and relatively low cost, especially for high value-added products such as lifesaving medical products and vaccines. This dissertation optimizes the delivery network and operations for routine childhood vaccines in LDCs. It analyzes two important problems using mathematical programming, with an application in the South Pacific nation of Vanuatu. The first problem is to optimize the nation-wide multi-modal vaccine supply chain with drones to deliver vaccines from the national depot to all health zones …

Optizimation Of Vaccination Supply Chain Based On Scg In Nanshan District, Zhenning Dong, Shunzhou Huang, Jiajun Chen, Huiqiong Zheng

Journal of System Simulation

Abstract: To optimize the vaccination network, inventory strategy and human resource allocation in Nanshan District, Supply Chain Guru's (SCG) network optimization method is used to select 50 alternative stations to decrease the fixed operating cost. SCG's inventory optimization method is used to set inventory strategy for each station, and simulation method is designed to compare total cost of all schemes. To optimize the opening days of vaccination stations, an medical personnel allocation rule is designed, which reduces some stations' opening days to 2 or 3 days and increases some stations' medical personnel. An simulation method is designed to compare the …

Infectious Disease Modeling And Intervention Planning, Shalome Hanisha Anand Tatapudi

USF Tampa Graduate Theses and Dissertations

Disease outbreaks caused by existing and emerging pathogens pose a serious threat to local and global communities in the form of epidemics and pandemics, respectively. The 2009 H1N1 pandemic and the 2019 COVID-19 pandemic are exemplars of how underprepared both the developed and developing nations are at mitigating pandemics.

Mathematical modeling and simulation of disease outbreaks has served as a powerful tool to understand disease transmission dynamics. They also aid in developing effective intervention strategies. However, existing models are usually particularized to a region, or a specific disease pathogen and interventions used in these models may not translate well to …

Intelligent Internet Of Things Frameworks For Smart City Safety, Dimitrios Sikeridis

Electrical and Computer Engineering ETDs

The emerging Smart City ecosystem consists of a vast edge network of Internet of Things (IoT) devices that continuously interact with mobile devices carried by its citizens. In this setting, the IoT infrastructure, apart from the main communications facilitator, acts as a crowdsourcing mechanism that collects massive amounts of user data, and can support public safety applications for the Smart City. In this thesis, we design and analyze learning mechanisms that extract intelligence from crowd interactions with the wireless IoT infrastructure, and optimize its energy efficiency while operating as a public safety network. First, we deploy a multi-story facility testbed …

Biosensor Devices Based On Graphene And 2d Materials, Suhada Aidrous Poovathy

Theses

Nanomaterials offered new improvements and developments to the bio-sensing field due to their unique physical and chemical properties. Unique and exceptional electronic properties, such as the ultrahigh surface-to-volume ratio and the excellent electrical properties of the 2D materials like in graphene, making these materials promising for future smaller and faster electronics, but an extensive amount of research is still needed. This thesis is concerned with the study of the integration of 2D material graphene in the development of sensitive and rapid biosensors. The main objective of this thesis is to understand the features and characteristics of graphene, evaluate the scope …

Virus Propagation And System Simulation Based On Cellular Automata Model, Lijuan Zhang, Fuchang Wang, Zhengang Li

Journal of System Simulation

Abstract: A susceptible-latent-infected-cured-immune virus spreading model is established according to the characteristics of epidemic transmission and the actual urban spatial map model. Individuals in the environment are regarded as agents, and the spreading mechanism is established according to the principle of cellular. The effects of different strategies and different characteristics of virus spreading on epidemic have been studied. The role and effect of important factors on epidemic prevention and control method are discussed, and the model is validated taking Shijiazhuang epidemic as an example . The results show that the number of initial latent, the infectivity of disease, vaccination proportion …

Increasing The Predictive Capability Of Mapping Technologies For Healthcare In Disaster Management, Simon O.M. Adebola

Online Journal of Space Communication

Health as defined by the WHO/EUROs Health 21 is 'the reduction in mortality, morbidity and disability due to detectable disease and disorder, and an increase in the perceived level of health' (WHO, 1999). Health Impact Assessment (HIA) is a combination of procedures, methods and tools by which a policy, program or project may be judged as to its potential effects on the health of a population, and the distribution of those effects within the population (WHO, 1999).

Remote Sensing And Human Health: New Sensors And New Opportunities, Louisa R. Beck, Bradley M. Lobitz, Byron L. Wood

Online Journal of Space Communication

Remote sensing data enable scientists to study the earth's biotic and abiotic components. These components and their changes have been mapped from space at several temporal and spatial scales since 1972. A small number of investigators in the health community have explored remotely sensed environmental factors that might be associated with disease-vector habitats and human transmission risk. However, most human health studies using remote sensing data have focused on data from Landsat's Multispectral Scanner (MSS) and Thematic Mapper (TM), the National Oceanic and Atmospheric Administration (NOAA)'s Advanced Very High Resolution Radiometer (AVHRR), and France's Système Pour l'Observation de la Terre …

Use Of Google Earth™ To Strengthen Public Health Capacity And Facilitate Management Of Vector-Borne Diseases In Resource-Poor Environments, Saul Lozano-Fuentes

Online Journal of Space Communication

Novel, inexpensive solutions are needed for improved management of vector-borne and other diseases in resource-poor environments. Emerging free software providing access to satellite imagery and simple editing tools (e.g. Google Earth™) complement existing geographic information system (GIS) software and provide new opportunities for: (i) strengthening overall public health capacity through development of information for city infrastructures; and (ii) display of public health data directly on an image of the physical environment.

Collaborators include: Saul Lozano-Fuentes, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Darwin Elizondo-Quiroga, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort …

Satellite Imagery In The Study And Forecast Of Malaria, David J. Rogers, Sarah E. Randolph, Robert W. Snow, Simon I. Hay

Online Journal of Space Communication

More than 30 years ago, human beings looked back from the Moon to see the magnificent spectacle of Earthrise. The technology that put us into space has since been used to assess the damage we are doing to our natural environment and is now being harnessed to monitor and predict diseases through space and time. Satellite sensor data promise the development of early-warning systems for diseases such as malaria, which kills between 1 and 2 million people each year.

The Possible Use Of Telemedicine In Developing Countries, R. Wootton

Online Journal of Space Communication

Since the place of telemedicine in the industrialized world is by no means properly worked out yet, it might seem premature to consider its use in developing countries. Nonetheless, there is interest in the possible use of telemedicine in developing countries, from at least two organizations:

1. The Midjan group, an impromptu committee that was formed following the African Regional Telecommunications Development Conference in Abidjan in March 19963. This European telemedicine collaboration group aims to explore the use of telemedicine in developing countries. At present, the group includes representatives from 22 telecommunication and medical informatics suppliers, telecommunication operators, universities, hospitals and …

Defining The Innate Immune Responses For Sars-Cov-2-Human Macrophage Interactions, Mai M. Abdelmoaty, Pravin Yeapuri, Jatin Machhi, Katherine E. Olson, Farah Shahjin, Vikas Kumar, You Zhou, Jingjing Liang, Kabita Pandey, Arpan Acharya, Siddappa N. Byrareddy, R. Lee Mosley, Howard E. Gendelman

Nebraska Center for Biotechnology: Faculty and Staff Publications

Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end-organ malfunctions. All follow the presence of persistent viral components and virions without evidence of viral replication. To elucidate SARS-CoV- 2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the …

Infrastructure Risk Reduction: The Case Of Drinking Water Emergencies, Mark Paine

Dissertations

Public water systems are an integral part of community infrastructure. Drinking water contamination or service disruptions have the potential to cause economic losses, limit fire suppression capability, and result in human illnesses. Until 2016, the United States federal government had not issued a disaster declaration due to contaminated water. The first federal drinking water disaster declaration due to contaminated water serves as a sentinel event demonstrating the need to increase focus on public water systems during all phases of emergency management: mitigation, preparation, response, and recovery. Previous studies evaluating risks to vulnerable populations associated with drinking water primarily utilized qualitative …

Study Of The Effect Of B-Cell-Intrinsic Mhcii Antigen Presentation On Germinal Center B Cell Evolution Using The Brainbow Mouse Model, Nia Hall

Theses and Dissertations

Major histocompatibility complex class II (MHCII) are molecules that are essential for B cell activation, as well as clonal competition among activated B cell clones during germinal center (GC) reactions. However, it is unknown to what extent MHCII drives the selection of some clones over others. This is of particular importance since MHCII is highly polymorphic with the ability to indirectly alter gutmicrobiome composition by altering the immunoglobulin A (IgA) repertoire. To study this, we utilized a novel triple-transgenic mouse model to assess how B-cellintrinsic MHCII influences GC responses and GC clonal diversity, with an eyeforward to understanding the relevance …

The Immune Modulatory Role Of Endocannabinoid Anandamide To Suppress Inflammation Through Regulation Of Microrna And Microbiome, Muthanna Ali Sultan

Theses and Dissertations

Cannabinoids are group of compounds that exerts their anti-inflammatory action through activation of CB1 and CB2 receptors and other minor receptors. In the current study, we investigated the effect of Anandamide (AEA) on Acute Respiratory Distress Syndrome (ARDS) induced by exposure to Staphylococcus Enterotoxin B (SEB) intranasally. We found that C57BL/6 mice treated with AEA showed improvement in the clinical functions of the lungs, accompanied by a decrease in the infiltration of inflammatory cells in the lung tissue, and a decrease in the secretion of pro-inflammatory cytokines. Furthermore, AEA regulated the miRNA profile of the mononuclear cells in the lungs …

Fate And Transport Of The Microbiome In Built Environments, Dahae Seong

Theses and Dissertations

Buildings are complex ecosystems evolving continuously. Indoor components such as occupants, ventilation system, and building structures influence the microbiome. To shed light on how the microbial population in a building will respond to such a fluid system, the fundamental interactions between microbes and the indoor ecosystem must be understood. Buildings are being designed as air-tight structures to save energy; however, this could lead to degradation of indoor air quality through indoor sources of contaminants and/or containment of pollutants in the room or introduce outdoor pollutants indoors depending on the ventilation conditions. In addition, transmission of infectious microbes in indoors threaten …

The Effect Of Low Dose Penicillin On Tumor Development In ApcMin/+ Mice, Kinsey Ann Sierra Meggett

Theses and Dissertations

Antibiotics have been our most effective weapon against bacterial infections since their discovery in the early 1900s. Their use has been critical in reducing mortality rate from infectious diseases. However, in the last few decades, the overuse of antibiotics, beginning at an early age and into adulthood, has become a growing concern globally. Penicillin is one of many extensively used antibiotics in early childhood that has been used to treat childhood infections. Recent studies showed that exposure to low dose penicillin can have adverse effects leading to chronic illness such as diabetes, allergies, inflammation, and susceptibility to obesity, with the …

The Role Of Vidura Chatbot In The Diffusion Of Knowcovid-19 Gateway, Kerk F. Kee, Prasad P. Calyam, Hariharan Regunath

Human-Machine Communication

The COVID-19 pandemic is an unprecedented global emergency. Clinicians and medical researchers are suddenly thrown into a situation where they need to keep up with the latest and best evidence for decision-making at work in order to save lives and develop solutions for COVID-19 treatments and preventions. However, a challenge is the overwhelming numbers of online publications with a wide range of quality. We explain a science gateway platform designed to help users to filter the overwhelming amount of literature efficiently (with speed) and effectively (with quality), to find answers to their scientific questions. It is equipped with a chatbot …

Communicative Development And Diffusion Of Humanoid Ai Robots For The Post-Pandemic Health Care System, Do Kyun David Kim, Gary Kreps, Rukhsana Ahmed

Human-Machine Communication

As humanoid robot technology, anthropomorphized by artificial intelligence (AI), has rapidly advanced to introduce more human-resembling automated robots that can communicate, interact, and work like humans, we have begun to expect active interactions with Humanoid AI Robots (HAIRs) in the near future. Coupled with the HAIR technology development, the COVID-19 pandemic triggered our interest in using health care robots with many substantial advantages that overcome critical human vulnerabilities against the strong infectious COVID-19 virus. Recognizing the tremendous potential for the active application of HAIRs, this article explores feasible ways to implement HAIRs in health care and patient services and suggests …

Co-Carriage Of Metal And Antibiotic Resistance Genes In Sewage Associated Staphylococci, Atena Amirsoleimani, Gail M. Brion, Patrice Francois

Civil Engineering Faculty Publications

Controlling spread of resistance genes from wastewater to aquatic systems requires more knowledge on how resistance genes are acquired and transmitted. Whole genomic sequences from sewage-associated staphylococcus isolates (20 S. aureus, 2 Staphylococcus warneri, and 2 Staphylococcus delphini) were analyzed for the presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Plasmid sequences were identified in each isolate to investigate co-carriage of ARGs and MRGs within. BLASTN analysis showed that 67% of the isolates carried more than one ARG. The carriage of multiple plasmids was observed more in CC5 than CC8 S. aureus strains. Plasmid …

Assessment Of A Program For Sars-Cov-2 Screening And Environmental Monitoring In An Urban Public School District, John Crowe, Andy T. Schnaubelt, Scott Schmdit Bonne, Kathleen Angell, Julia Bai, Teresa Eske, Molly Nicklin, Catherine Pratt, Bailey White, Brodie Crotts-Hannibal, Nicholas Staffend, Vicki Herrera, Jeramie Cobb, Jennifer Connor, Julie Carstens, Jonell Tempero, Lori Bouda, Matthew Ray, James V. Lawler, W Scott Campbell, John-Martin Lowe, Joshua Santarpia, Shannon Bartelt-Hunt, Michael Wiley, David Brett-Major, Cheryl Logan, Jana Broadhurst

Department of Civil and Environmental Engineering: Faculty Publications

IMPORTANCE Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in kindergarten through 12th grade settings. OBJECTIVES To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning. DESIGN, SETTING, AND PARTICIPANTS This pilot quality improvement program engaged 3 schools in Omaha, Nebraska, for weekly saliva polymerase chain reaction testing of staff and students participating in in-person learning over a 5-week period from November 9 to December 11, 2020. …

In Situ Imaging Of Bacterial Outer Membrane Projections And Associated Protein Complexes Using Electron Cryo-Tomography, Mohammed Kaplan, Georges Chreifi, Lauren Ann Metskas, Janine Liedtke, Cecily R. Wood, Catherine M. Oikonomou, William J. Nicolas, Poorna Subramanian, Lori A. Zacharoff, Yuhang Wang, Yi-Wei Chang, Morgan Beeby, Megan J. Dobro, Yongtao Zhu, Mark J. Mcbride, Ariane Briegel, Carrie L. Shaffer, Grant J. Jensen

Veterinary Science Faculty Publications

The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs …