Digital Commons Network^™

Integrating Comorbidity Knowledge For Alzheimer's Disease Drug Repurposing Using Multi-Task Graph Neural Network, Ko-Hong Lin, Kang-Lin Hsieh, Xiaoqian Jiang, Yejin Kim

Faculty, Staff and Student Publications

Alzheimer's Disease (AD) is a multifactorial disease that shares common etiologies with its multiple comorbidities, especially vascular diseases. To predict repurposable drugs for AD utilizing the relatively well-investigated comorbidities' knowledge, we proposed a multi-task graph neural network (GNN)-based pipeline that incorporates the corresponding biomedical interactome of these diseases with their genetic markers and effective therapeutics. Our pipeline can accurately capture the interactions and disease classification in the network. Next, we predicted drugs that might interact with the AD module by the node embedding similarity. Our candidates are mostly BBB permeable, and literature evidence showed their potential for treating AD pathologies, …

Data Mining Pipeline For Covid-19 Vaccine Safety Analysis Using A Large Electronic Health Record, Yan Huang, Xiaojin Li, Deepa Dongarwar, Hulin Wu, Guo-Qiang Zhang

Faculty, Staff and Student Publications

We developed a novel data mining pipeline that automatically extracts potential COVID-19 vaccine-related adverse events from a large Electronic Health Record (EHR) dataset. We applied this pipeline to Optum® de-identified COVID-19 EHR dataset containing COVID-19 vaccine records between December 11, 2020 and January 20, 2022. We compared post-vaccination diagnoses between the COVID-19 vaccine group and the influenza vaccine group among 553,682 individuals without COVID-19 infection. We extracted 1,414 ICD-10 diagnosis categories (first three ICD10 digits) within 180 days after the first dose of the COVID-19 vaccine. We then ranked the diagnosis codes using the adverse event rates and adjusted odds …

Digital Solutions Observed In Clinical Trials: A Formative Feasibility Scoping Review, Taylor M Harrison, Sungrim Moon, Liwei Wang, Sunyang Fu, Hongfang Liu

Faculty, Staff and Student Publications

Growing digital access accelerates digital transformation of clinical trials where digital solutions (DSs) are increasingly and widely leveraged for improving trial efficiency, effectiveness, and accessibility. Many factors impact DS success including technology barriers, privacy concerns, or user engagement activities. It is unclear how those factors are considered or reported in the literature. Here, we perform a formative feasibility scoping review to identify gaps impacting DS quality and reproducibility in trials. Articles containing digital terms published in English from 2009 to 2022 were collected (n=4,167). 130 articles published between 2016 and 2022 were randomly selected for full-text review. Eligible articles (n=100) …

The Health-Promoting Effects And The Mechanism Of Intermittent Fasting, Simin Liu, Min Zeng, Weixi Wan, Ming Huang, Xiang Li, Zixian Xie, Shang Wang, Yu Cai

Faculty, Staff and Student Publications

Intermittent fasting (IF) is an eating pattern in which individuals go extended periods with little or no energy intake after consuming regular food in intervening periods. IF has several health-promoting effects. It can effectively reduce weight, fasting insulin levels, and blood glucose levels. It can also increase the antitumor activity of medicines and cause improvement in the case of neurological diseases, such as memory deficit, to achieve enhanced metabolic function and prolonged longevity. Additionally, IF activates several biological pathways to induce autophagy, encourages cell renewal, prevents cancer cells from multiplying and spreading, and delays senescence. However, IF has specific adverse …

Deep Learning-Based Technique For The Perception Of The Cervical Cancer, Aya Haraz, Hossam El-Din Moustafa, Abeer Twakol Khaleel, Ahmed H. Eltanboly

Mansoura Engineering Journal

In third-world countries, cervical cancer is the most prevalent and leading cause of death. It is affected by a variety of factors, including smoking, poor nutritional status, immunological inadequacy, and prolonged use of contraception. The Pap smear test, which is intended to prevent cervical cancer, finds preneoplastic changes in cervical epithelial cells. This study framework classified cervical cancer cells from Pap smears into five specified cell types using machine learning-based classification algorithms. The SIPaKMeD database is used in this investigation. This public dataset, which was manually cropped from 966 cluster cell images taken from Pap smear slides, has 4045 isolated …

"You Shouldn't Need To Share Your Data": Perceived Privacy Risks And Mitigation Strategies Among Privacy-Conscious Smart Home Power Users, Anna Lenhart, Sunyup Park, Michael Zimmer, Jessica Vitak

Computer Science Faculty Research and Publications

Fueled by Internet-of-Things technologies and spanning a wide range of sensors, speakers, and cameras, smart homes promise to make our lives easier and automate routine tasks. From speakers to security cameras, smart home devices (SHDs) answer our questions, monitor our home environment, and conserve energy. They also collect significant data, ranging from on/off commands to audio and video data, and they do this in some of our most private spaces. In this paper, we explore the privacy risks associated with SHDs by focusing on privacy-conscious smart home power users--those who spend significant time and money to research, install, and integrate …

Opportunities And Challenges In Augmenting Honey Bee Forage Resources With Pasture Legumes In Southern Australia, M. Kratz, M. Brown, M. T. Newell, R. C. Hayes

IGC Proceedings (1977-2023)

More than 80% of Australian honey is produced from native tree and shrub species. However, with increasing demands on public lands along with production risks posed by drought, floods and wildfires, there is a need to identify alternative forage resources to augment Australian honey production. With over 30 pasture legumes now available for agriculture in southern Australia, opportunity exists to increase the utilisation of some species with co-benefits to multiple production industries. However, there is little understanding of the potential value of most pasture legumes for honey production, and side by side comparisons are complicated by factors such as differences …

Data Curation For Modeling Tall Fescue Biomass Dynamics With Dssat-Csm, M. B. Hanson, P. D. Alderman, T. J. Butler, A. Caldeira Rocateli

IGC Proceedings (1977-2023)

While models for predicting forage production are available to aid management decisions for some forage crops, there is limited research for a yield model designed specifically for tall fescue (Schedonorus arundinaceus). Therefore, our objective was to adapt an existing perennial forage model, the Decision Support System for Agrotechnology Transfer Cropping Systems Model (DSSAT-CSM) for predicting forage biomass of tall fescue in the southern Great Plains. To evaluate model performance, there must first be a high level of data manipulation and cleaning. In this project, a cohesive dataset combining biomass, weather, soil, and management data were structured into DSSAT …

Nitrogen Behavior In A No-Tillage Agroecosystem Located In The Inner Bluegrass Of Kentucky, Alec William Besinger Mr.

Theses and Dissertations--Plant and Soil Sciences

Nitrogen (N) is a crucial element, often limiting productivity in ecosystems. This limitation is relieved N fertilizer additions. No-tillage (NT) agroecosystems are prone to lower N availability translating to lower crop yields. The default explanation for lower N availability in NT is microbial immobilization of added N fertilizer. Historically, N availability is often assessed using chemical extractions such as KCl to evaluate levels of inorganic N in the soil. The possibility of this abiotic clay mineral fixation as mechanism in well-drained NT soils has been overlooked. The objectives of this study are to quantify N availability using KCl, NaCl, and …

Histidine Enhances The Anticancer Effect Of Gemcitabine Against Pancreatic Cancer Via Disruption Of Amino Acid Homeostasis And Oxidant—Antioxidant Balance, Narendra Kumar, Satyanarayana Rachagani, Gopalakrishnan Natarajan, Alexandra Crook, Thiyagarajan Gopal, Vinothkumar Rajamanickam, Jyoti B. Kaushal, Sirpu N. Nagabhishek, Robert Powers, Surinder K. Batra, Viswanathan Saraswathi

Robert Powers Publications

Simple Summary: Amino acid metabolism is aberrantly altered in pancreatic cancer (PC). Evidence suggests that circulating histidine (His) levels are low in PC. However, the role of His in modulating the progression of PC remains unknown. We determined the role of His in altering the therapeutic effectiveness of gemcitabine (Gem) against PC. We provide evidence that the expression of histidine ammonia lyase (HAL), an enzyme involved in His catabolism, is greatly increased in mouse and human pancreatic tumors. We show that combining His with Gem led to enhanced cytotoxic effects against aggressive PC cell lines. Our metabolomics analysis revealed that …

Multiplatform Untargeted Metabolomics, Micah J. Jeppesen, Robert Powers

Robert Powers Publications

Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation …

Illegal Unreported And Unregulated Fishing And Overfishing Policymaking In A Caribbean Island Country, Anya J. Moses

Walden Dissertations and Doctoral Studies

Small island developing states, especially those within the Caribbean community, are faced with the challenges of overfishing and illegal, unregulated, and unreported (IUU) fishing activities. Despite global legal reforms, enforcement continues to be ineffective. In the policymaking process, the perspectives of those critically impacted are rarely taken into consideration The purpose of this qualitative study was to explore the issues leading to the lack of inclusion of fisherfolk knowledge in the policymaking process and policies that promote SDG 14. The goal was to explore the importance of fisherfolk involvement in the policymaking process. The research question focused on identifying the …

Comparison Of An Antioxidant Source And Antioxidant Plus Bcaa On Athletic Performance And Post Exercise Recovery Of Horses, Emily Kent, Stephen J. Coloman, Jason E. Bruemmer, Renan Regatieri Casagrande, Christine Levihn, Grace Romo, Kevin Herkelman, Tanja Hess

United States Department of Agriculture Wildlife Services: Staff Publications

Antioxidant supplementation decreases postexercise oxidative stress but could also decrease muscle pro- tein synthesis. This study compared the effects of three diets: low antioxidant (control, CON), high an- tioxidant (AO), and branched-chain amino acid high antioxidant (BCAO) supplementation on postexercise protein synthesis and oxidative stress. We hypothesized that supplementing antioxidants with branched- chain amino acids(BCAA) would reduce oxidative stress without hindering muscle protein synthesis. Eigh- teen mixed-breed polo horses (11 mares and 7 geldings, with age range between 5 and 18 years, were on CON diet for 30 days (from day -45 until day 0) and then were assigned to …

Variance In Offspring Sex Ratio And Maternal Allocation In A Highly Invasive Mammal, Sarah M. Chinn, Timothy J. Smyser, James C. Beasley

United States Department of Agriculture Wildlife Services: Staff Publications

Skewed sex ratios at birth are widely reported in wild populations, however, the extent to which parents are able to modulate the sex ratio of offspring to maximize their own fitness remains unclear. This is particularly true for highly polytocous species as maximizing fitness may include trade-offs between sex ratio and the size and number of offspring in litters. In such cases, it may be adaptive for mothers to adjust both the number of offspring per litter and offspring sex to maximize individual fitness. Investigating maternal sex allocation in wild pigs (Sus scrofa) under stochastic environmental conditions, we predicted that …

The Past, Present, And Future Of Equine Science, Sarah H. White-Springer, Jason E. Bruemmer, Robert J. Coleman

United States Department of Agriculture Wildlife Services: Staff Publications

A core group of 27 equine nutritionists and physiologists joined together in the late 1960s to formally address and enhance the direction of equine research, creating the Equine Nutrition and Physiology Soci- ety. In 2003, that growing society transformed into the Equine Science Society, which now serves as the preeminent, internationally recognized scientific equine organization. In recent years, it has been appre- ciated that equine science encompasses a wide range of focus areas, including exercise science, nutrition, genetics, reproductive physiology, teaching and extension, production and management, and mix of other specialties, qualified as biosciences. Additionally, trainees are highly valued in …

Invasive Frogs Show Persistent Physiological Differences To Elevation And Acclimate To Colder Temperatures, Jack R. Marchetti, Karen H. Beard, Emily E. Virgin, Erin L. Lewis, Steven C. Hess, Kwanho C. Ki, Layne O. Sermersheim, Adriana P. Furtado, Susannah S. French

United States Department of Agriculture Wildlife Services: Staff Publications

The coqui frog (Eleutherodactylus coqui) was introduced to the island of Hawai’i in the 1980s and has spread across much of the island. Concern remains that this frog will continue to expand its range and invade higher elevation habitats where much of the island’s endemic species are found. We determined whether coqui thermal tolerance and physiology change along Hawai’i’s elevational gradients. We measured physiological responses using a short-term experiment to determine baseline tolerance and physiology by elevation, and a long-term experiment to determine the coqui’s ability to acclimate to different temperatures. We collected frogs from low, medium, and …

Alternatives To Corn For Baiting Wild Pigs, Justin A. Foster, Lee H. Williamson, John C. Kinsey, Ryan L. Reitz, Kurt C. Vercauteren, Nathan P. Snow

United States Department of Agriculture Wildlife Services: Staff Publications

We examined dietary preferences of wild pigs to discern possible bait alternatives to corn. Captive trials were conducted during spring and fall 2021 in the Wild Pig Research Facility at Kerr Wildlife Management Area, Hunt, Texas, USA. We conducted 2‐choice tests by allowing wild pigs to feed ad libitum on soybeans, split peas, mealworms, and peanuts (spring 2021), and oats, acorns, earthworms, and peanuts (fall 2021), always with corn available as a second choice for reference. In each trial, we used proportion of test bait eaten versus total bait eaten, and relative access to both food sources as indices of …

Outbreak Of Epizootic Hemorrhagic Disease In Captive Reindeer (Rangifer Tarandus), Emma H. Torii, Arno Wünschmann, Mia Kim Torchetti, Leo Koster, Albert Van Geelen, Randy Atchison, Anne Rivas

United States Department of Agriculture Wildlife Services: Staff Publications

In September 2020, an outbreak of epizootic hemorrhagic disease occurred in captive reindeer (Rangifer tarandus) and was associated with neurological signs and mortality. Four reindeer died or were euthanized after acute illness over a 12-day period. Affected reindeer displayed abnormal behavior, neurologic signs, lethargy, and/or lameness. The most consistent gross finding was dark red streaks throughout the adrenal gland cortices (4/4). One animal had acute hemorrhage involving the subcutis and skeletal muscles over the ventrolateral body wall and back, and abomasal serosa. Histologically, the most common lesions were adrenal gland cortical hemorrhage (4/4) with necrosis (3/4) and lymphoplasmacytic meningoencephalitis with …

Prediction Of Kinase-Substrate Associations Using The Functional Landscape Of Kinases And Phosphorylation Sites, Marzieh Ayati, Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Mark R. Chance, Mehmet Koyutürk

Computer Science Faculty Publications

Protein phosphorylation is a key post-translational modification that plays a central role in many cellular processes. With recent advances in biotechnology, thousands of phosphorylated sites can be identified and quantified in a given sample, enabling proteome-wide screening of cellular signaling. However, for most (> 90%) of the phosphorylation sites that are identified in these experiments, the kinase(s) that target these sites are unknown. To broadly utilize available structural, functional, evolutionary, and contextual information in predicting kinase-substrate associations (KSAs), we develop a network-based machine learning framework. Our framework integrates a multitude of data sources to characterize the landscape of functional relationships …

Optimization Of Optical Nanosensor Response For The Detection Of Anthracyclines Using A Binary Machine Learning Classifier, Myesha Thahsin

Dissertations and Theses

Pharmacokinetic variables such as interindividual variation in metabolizing and eliminating drugs makes dose selection of chemotherapeutic anthracyclines difficult. One potential solution to determining dosing levels of an anthracycline is the development of non-invasive sensors to monitor their pharmacology in vivo. Single-walled carbon nanotubes (SWCNT) have substantial potential for in vivo sensor development, as they exhibit near-infrared fluorescence in the tissue-transparent window and a robust response to their local environment. An emerging method for evaluating and optimizing SWCNT sensor response is through machine learning. In this study, anthracyclines Daunorubicin, Doxorubicin, Epirubicin, Mitoxantrone and Idarubicin, were used to interrogate 12 SWCNT preparations …

Discovery Of Acetyl Coa Synthetase And Sars-Cov-2 Protease Inhibitors, Taiwo Elijah Esan

Graduate Research Theses & Dissertations

There is an urgent need for new antifungal drugs. Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. This body of work focuses on the inhibition of the Acetyl CoA synthetase enzyme in fungal species. This work has involved designing and synthesizing compounds that are potential fungal ACS1 …

Using Machine Learning To Predict Student Outcomes, Saba Fatima

Graduate Research Theses & Dissertations

Predicting students’ performance to identify which students are at risk of receiving aD/Fail/Withdraw (DFW) grade and ensuring their timely graduation is not just desirable but also necessary in most educational entities. In the US, not only is the Science, Technology, Engineering, and Mathematics (STEM) major becoming less popular among students, the graduation rate of STEM students is steadily declining. The lack of STEM graduates in the US is a serious problem that will place this country at a disadvantage as a competitor in international technological advancement. In order to secure its status as a technological leader internationally, the US institutions …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Addressing Soil Carbon Sequestration Response From Multispecies Dairy Forage Systems And Modeling Rangeland Beef Cow Dry Matter Intake Using Precision Enteric Emissions Measurements, Lillian J. Mcfadden

Electronic Theses and Dissertations

Regenerative agriculture is a pressing matter for the dairy industry to address cropland sustainability and carbon sequestration. One regenerative management practice that has been identified to help with row crop sustainability for key metrics like soil organic carbon (SOC) is complex covers. When producers use complex covers one of the main challenges is that it takes time to detect a change in SOC. However, simulation models are a tool that can be used to help determine if a regenerative practice is a strategy that gives the best results (i.e., increased SOC) while aligning with long-term production goals. Therefore, our objectives …

The Role Of Bacteria And Factors Affecting The Decomposition Of Pollutants In The Biofilter Reactor: A Review, Muliyadi Muliyadi, Purwanto Purwanto, Sri Sumiyati, Sudarno Sudarno, Budiyono Budiyono, Budi Warsito, Hadiyanto Hadiyanto

Applied Environmental Research

The findings showed that several types of bacteria can help biodegrade organic pollutants, such as Comamonadacea, which can biodegrade volatile fatty acids and aromatic compounds. Proteobacteria, Bacteroidetes, and Actinobacteria can biodegrade ammonium. Burkholderiales can biodegrade ferric ions and hydrogen. Comamonas testosteroni is able to biodegrade nitrates. Pseudomonas taiwanensis, Acinetobacter guillouiae, and Klebsiella pneumoniae can reduce copper, chromium and zinc levels. Azolla biomass reduces strontium. Rhodospirillum sp. can biodegrade cadmium, mercury, lead, and nickel. Gallionella ferruginea and Leptothrix sp. can biodegrade arsenic and manganese. Gracilaria sp. can biodegrade aluminum, chromium, and zinc. Desulfovibrio sp. can …

Distribution Of Exchangeable Magnesium In Lowland Rice-Cultivated Soils Of Sri Lanka As Affected By The Differences In Climate, Soil, And Water Source, Indeera Hetti Arachchige, Buddhi Marambe, Mohomad Nijamudeen, Harsha Kadupitiya, Dinaratne Sirisena, Rohana Chandrajith, Lalith Suriyagoda

Applied Environmental Research

Magnesium (Mg) is an essential macronutrient for plants. Even though Sri Lankans consume rice as the staple food, the Mg status in Sri Lankan paddy soils as affected by its climate, soils, and water sources used are not well understood. This study was conducted to (i) determine the distribution of exchangeable Mg (ex-Mg) concentration, and (ii) examine the interactive effects of agro-climatic zones (ACZs), soil order, and water source in determining the ex-Mg concentra-tion in lowland paddy fields of Sri Lanka. A total of 9,038 soil samples representing six ACZs, six soil orders, and three water sources were collected using …

The Effect Of Irrigation Techniques On Sustainable Water Management For Rice Cultivation System - A Review, Bittawat Wichaidist, Amornrat Intrman, Songsak Puttrawutichai, Chawakorn Rewtragulpaibul, Supatchaya Chuanpongpanich, Chaisri Suksaroj

Applied Environmental Research

Rice serves as a fundamental sustenance for approximately half of the global population, particularly in Asia. Nevertheless, the cultivation of rice demands a substantial water supply, and the challenges associated with water deficits have been exacerbated by irregular rainfall patterns induced by global warming. Consequently, there is a critical need to reassess irrigation techniques to effectively tackle these issues. In this comprehensive review, the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) method was employed to systematically explore literature on irrigation techniques aimed at fostering sustainable water management in rice cultivation systems. The primary components of the framework encompass …

Microbial Community And Genome Structure In Coastal Seawater From A Commercial Port And Nearby Offshore Island In Northern Taiwan, Chi-Yu Shih, Ching-Hsiang Chin, Shiow-Yi Chen, Chun-Ru Hsu, Lee-Kuo Kan, Wen-Shyong Tzou

Journal of Marine Science and Technology–Taiwan

The pollution stemming from the use of petroleum by boats, the presence of deceased marine life, hazardous chemicals, and wastewater is a major issue in human-made commercial ports. This pollution poses a considerable challenge to the diverse organisms inhabiting the seawater. To comprehend the impact of this pollution on the microbiome, we conducted a study in which we collected surface water samples from a commercial port called Keelung Port, as well as a nearby offshore island known as Keelung Islet. These locations are situated in northern Taiwan, along the Northwestern Pacific Ocean. Through the use of whole-metagenome shotgun sequencing, we …

Ecuadorian Gravel Pack Spring Water Intakes, Derek Ten Pas, Julie Wildschut, Robert Hoeksema, Bruce Rydbeck, Chris Visscher

University Faculty Publications and Creative Works

This paper describes the basic design concept to design and build a type of spring water intake. The spring protection method bears similarity to a gravel pack well albeit constructed horizontally rather than the vertical construction of a gravel pack well. The design approach includes:

• collection of spring water subterranean using the aquifer and surrounding soil to filter the water supply,
• use of gravel pack to retain the surrounding aquifer materials and soil structure in place while providing an easy flow path for water to enter a slotted collector pipe and flow to a receiving tank without impounding spring water, …

Eating Change: A Critical Autoethnography Of Community Gardening And Social Identity, Jessica Gerrior

Antioch University Dissertations & Theses

Community gardening efforts often carry a social purpose, such as building climate resilience, alleviating hunger, or promoting food justice. Meanwhile, the identities and motivations of community gardeners reflect both personal stories and broader social narratives. The involvement of universities in community gardening projects introduces an additional dimension of power and privilege that is underexplored in scholarly literature. This research uses critical autoethnography to explore the relationship of community gardening and social identity. Guided by Chang (2008) and Anderson and Glass-Coffin (2013), a systematic, reflexive process of meaning-making was used to compose three autoethnographic accounts. Each autoethnography draws on the author’s …