Life Sciences Commons^™

Predicting Drug-Induced Liver Injury With Artificial Intelligence, Ting Li

Theses and Dissertations

Drug-induced liver injury (DILI) is an undesirable side effect to the liver caused by the common use of drugs, which is of great concern to the patients, physicians, the pharmaceutical industry, and government regulators. The current animal testing models do not present reliable results on the human DILI risk prediction during the preclinical phase. Therefore, there is an urgent need to find alternative methods to improve the human DILI risk prediction during the early stage of development. Utilizing the accumulated high-throughput transcriptomics profiles from L1000, we constructed an 8-layer deep neural network for human DILI prediction based on the largest …

A Tale Of Three Resources: The Influence Of Multiple Resources On Plant-Herbivore Interactions, Neha Mohan Babu

Dissertations - ALL

Although studies indicate that plant growth can be co-limited by multiple resources, particularly water, nitrogen (N), and phosphorus (P), the role of co-limiting resources in driving plant-herbivore interactions remains poorly understood. Evidence indicates that the resources that limit plant and herbivore growth may differ which likely influences trophic interactions. In this dissertation, I explored how multiple resource limitation of plants affects herbivore abundance, herbivore impact on plant biomass, and plant traits, using both theoretical and empirical methods. As none of the existing hypotheses account for the effects of multiple resource limitation, I developed a novel theoretical model to predict the …

The Phase Behavior Of Ubqln Proteins And Implications For Protein Quality Control, Yiran Yang

Dissertations - ALL

The ubiquitin-proteasome system (UPS) and autophagy are essential pathways for maintaining protein quality control (PQC) in cells. Misfolded proteins and large aggregates are cleared by UPS and autophagy signaled by ubiquitin (Ub) or polyubiquitin (polyUb) chains. Shuttle proteins facilitate cargo transporting by interacting with both ubiquitin and degradation machineries. Previously, our lab discovered that the shuttle protein Ubiquilin-2 (UBQLN2) is recruited to stress granules in cells and undergoes liquid-liquid phase separation (LLPS) in vitro. LLPS is a biophysical process by which proteins separate themselves from the surrounding aqueous solution by forming protein-rich droplets. The overarching goals of this work are …

Direct Single Molecule Imaging Of Enhanced Diffusion For Enzymes And Enzyme-Conjugated Dna Origami, Mengqi Xu

Dissertations - ALL

Enzymes have been shown to diffuse faster in the presence of their substrates. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF) microscopy. We found that the mobility of individual enzymes was enhanced three-fold in the presence of the substrate, and the motion remained Brownian. We showed that the relative increase in diffusion is independent of the total enzyme concentrations; and the oligomerization state of enzymes did not change during the catalytic turnover. These experiments ruled out the possibility that the enhanced enzyme diffusion was caused by the …

Developing An Air Pollutant Emissions Database For Global Economic Analysis, Maksym Chepeliev

Department of Agricultural Economics Faculty Publications

According to the Global Burden of Disease study (Cohen et al., 2017), in 2015 ambient air pollutant emissions caused 4.2 million deaths and a loss of 103.1 million disability-adjusted life-years, making it the fifth-ranked global risk factor. In terms of the welfare costs of mortality and illnesses associated with outdoor air pollutant emissions, global estimates for 2015 range between $2.7-3.2 trillion (Coady et al., 2015; OECD, 2016). Still, while greenhouse gas emissions are usually well represented in many global economic databases and models, air pollutant emission accounts in most cases are not included. In particular, this is the case for …

Bactericidal Effects And Stability Of Ll-37 And Cama In The Presence Of Human Lung Epithelial Cells, Regina Geitani, Carole Ayoub Moubareck, Floriane Costes, Léa Marti, Gabrielle Dupuis, Dolla Karam Sarkis, Lhousseine Touqui

All Works

Cationic antimicrobial peptides (CAMPs) are important actors in host innate immunity and represent a promising alternative to combat antibiotic resistance. Here, the bactericidal activity of two CAMPs (LL-37, and CAMA) was evaluated against Pseudomonas aeruginosa (PA) in the presence of IB3-1 cells, a cell line derived from patients with cystic fibrosis. The two CAMPs exerted different effects on PA survival depending on the timing of their administration. We observed a greater bactericidal effect when IB3-1 cells were pretreated with sub-minimum bactericidal concentrations (Sub-MBCs) of the CAMPs prior to infection. These findings suggest that CAMPs induce the production of factors by …

Investigating The Behavioral And Social Context Of Sound In The Surface Foraging Strategies Of Humpback Whales (Megaptera Novaeangliae), Sarah Weiss

Theses - ALL

Humpback whales are known for the plastic and variable nature of their acoustic communication, social interactions, and foraging behaviors. Distinct foraging strategies are used to capture different prey types at the surface and on the seafloor. Sounds produced during foraging are thought to facilitate intraspecific social communication. Previous studies have identified specific sound types produced by humpbacks associated exclusively with benthic foraging strategies, suggesting functions related to foraging behavior. In this study, we use suction cup acoustic tags (DTAGs) deployed on humpbacks in the western North Atlantic from 2006-2009 to investigate the social sound production associated with surface foraging ecology, …

Fine Scales, Broad Consequences: Drivers And Effects Of Microclimatic Variation In Great Smoky Mountains National Park, Jordan Rebecca Stark

Theses - ALL

Climate is highly variable at scales that are not captured by most weather and climate models due to local effects of topography and living systems. This variation in microclimate has been noted for many decades but has been difficult to incorporate into quantitative understanding of ecological systems and processes due to the large amount of data and complex models required to adequately describe fine-scale patterns across complex landscapes. In recent years, models of thermal microclimate variation have been developed using low-cost temperature sensors, but few of these models have been used to predict the effects of microclimatic variation on ecological …

Intralocus Sexual Conflict Over Optimal Nutrient Intake And The Evolution Of Sex Differences In Life Span And Reproduction, Michael Hawkes, Sarah M. Lane, Scott K. Sakaluk, John Hunt, Clarissa M. House, Kim Jensen, James Rapkin

Faculty Publications – Biological Sciences

1. Despite widespread variation in life span across species, three clear patterns exist: sex differences in life span are ubiquitous, life span is commonly traded against reproduction, and nutrition has a major influence on these traits and how they trade-off. One process that potentially unites these patterns is intralocus sexual conflict over the optimal intake of nutrients for life span and reproduction. If nutrient intake has sex-specific effects on life span and reproduction but nutrient choice is genetically linked across the sexes, intralocus sexual conflict will occur and may prevent one or both sexes from feeding to their nutritional optima.
2. Here …

Effects Of Nitrogen Fertilization On The Production Of Panicum Maximum Cv. Ipr 86 Under Grazing, S. M. B. Lugão, L. R. De A. Rodrigues, E. B. Malheiros, J. J. Dos S. Abrahão, A. De Morais

IGC Proceedings (1977-2023)

The experiment was conducted at the Experimental Station of Paranavaí/IAPAR-PR-Brazil, from October 1998 to May 1999, to evaluate the effects of N fertilization on Panicum maximum cv. IPR 86 pastures. Four doses of N (0; 150; 300; and 450 kg.ha^-1.year^-1) were applied to pastures under rotational grazing with grazing cycles (GCs) of 40 days (5 days-grazing and 35 days-rest). It was used a randomized complete block design, with split-plots, and two replications per treatment, being the N-doses studied in the main plots and the GCs in the sub-plots. In all GCs the variables dry matter of …

Effects Of Management Strategies On Seed Production And Seedling Recruitment In Birdsfoot Trefoil-White Clover Mixtures, W. Ayalá, M. Carámbula, D. F. Risso, J. Hodgson, Peter D. Kemp

IGC Proceedings (1977-2023)

The effects of grazing management on seed production, seed bank size and seedling emergence patterns of Trifolium repens cv. Zapicán (WC) and Lotus corniculatus cv. San Gabriel (BFT) oversown swards were evaluated. A complete randomized block design with 4 replicate blocks was used, in which 4 grazing strategies (grazing all year (SI), summer spelling for seed production (S2), winter rest plus summer spelling (S3) and autumn rest plus summer spelling (S4)), were combined with two defoliation severalties (4 and 10 cm height post-grazing residuals). Plots of 110 m² were grazed monthly by sheep. Seed production, soil seed bank and …

Agricultural Support For The Old Colony Mennonites Of Belize: A Collaborative Effort Between North American Old Order Mennonites And A Cornell Extension Educator, Judson Reid

Journal of Amish and Plain Anabaptist Studies

The Old Colony Mennonites of Belize practice a conservative form of Anabaptism where technology, dress and lifestyle choices are informed by church standards. Members live in a spatially contiguous Colony, which creates land pressure over time as population increases. The development of new Colonies is necessary for the Mennonites to participate in agricultural livelihoods. The Indian Creek Colony of Belize has experienced agricultural and economic hardships since its inception in the 1989 due to land costs, crop failures and debt structure. Old Order Mennonites of North America developed an outreach effort to assist with on-farm production of vegetable crops to …

Penn State Extension Services And Plain People: An Inside Perspective On A Trust-Based Relationship, Phillip Martin

Journal of Amish and Plain Anabaptist Studies

This perspective on Penn State Extension Services and plain people is based on my personal experiences as a plain person, in which I interacted with Extension Services first as a farmer, and then (while working on a doctorate) as a part of the Extension system. Penn State Extension started over a century ago and was deliberate in reaching out to plain (conservative Anabaptist) farmers since the beginning, which led to a history of trust-based cooperation. For all these successes there remain challenges to effective cooperation with certain plain individuals and subgroups. I suggest these challenges are broadly similar to those …

Hotline Number To Reach And Offer Agricultural Information To Plain Anabaptists During The Covid-19 Workplace Closures, Emily Shoop, Carly Becker, Nathan Glenn Briggs, Danielle Smarsh

Journal of Amish and Plain Anabaptist Studies

The Penn State Extension Animal Systems Team developed a toll-free hotline phone number to convey short educational messages to maintain contact and outreach to Pennsylvania’s animal producing Amish, Mennonite, and other plain Anabaptist populations. During the COVID-19 pandemic, Penn State Extension’s programming went largely online via webinars, online courses, and emails. This change in programming excluded a large sector of Pennsylvania farmers who do not use or have access to the internet and, as such, were liable to miss important best management practice reviews and timely updates in animal agriculture. The Animal Systems Hotline offered callers the choice to listen …

Providing Agricultural Information To Amish And Mennonite Farmers: Creative Adaptations To Wisconsin Extension Programs And Communications, Richard Halopka

Journal of Amish and Plain Anabaptist Studies

This service provider report taps into the experience of a longtime Extension Educator in Wisconsin. Pulling from his work in Clark County, WI, where Amish and Old Order Mennonites have been particularly important to the local agricultural economy, he provides examples of how Extension can modify programming to meet the needs of plain producers. Topics of interest to Amish and Mennonite farmers include nutrient management, forage quality, and farm safety. Areas of program modification include approaches to communication, training, and support in ways that are culturally sensitive to church restrictions. In-person training and informational voicemail recordings have been particularly useful …

Effective Communication And Programming When Working With Amish Farmers: Reflections From A Wisconsin Agriculture Educator, Vance Haugen

Journal of Amish and Plain Anabaptist Studies

The author, an agricultural educator who worked with the Amish in Wisconsin for over 30 years, discusses his outreach efforts, which have been focused on managed grazing, a method well suited to Amish producers. Managed grazing offers agronomic, economic, and ecological benefits. A key educational tool for communicating managed grazing practices is the pasture walk, and the author relates lessons learned from these events. The communal nature and focus on farmer-to-farmer information exchange is well received by Amish producers. It is helpful if pasture walk scheduling is done well in advance and is focused on farmer-based problems with farmer-based solutions …

Ohio’S Amish And Mennonite Produce Growers: Farm Trends, Information Needs, And Agricultural Communication Preferences, Brad Bergefurd

Journal of Amish and Plain Anabaptist Studies

This study (1) describes the characteristics of Ohio Amish and Mennonite produce farmers and their operations; (2) determines awareness of and participation in OSU Extension programs by Amish and Mennonite produce farmers; (3) determines the methods used by Amish and Mennonite produce farmers to acquire farming information; and (4) identifies subject matter needs of Amish and Mennonite produce farmers for future Extension programming. In order to provide effective future Extension programming efforts for this particular clientele, a mail survey was used to collect data from 345 Ohio Amish and Mennonite farmers who participate at Ohio produce auctions. They were asked …

The Success Of Plain People’S Produce Auctions And Partnership With Missouri Extension, James Quinn, John Kruse, Londa Nwadike, James C. Piñero, David Trinklein

Journal of Amish and Plain Anabaptist Studies

The number of produce auctions led by plain Anabaptist producers has surged since the mid-1990s. Typically grower-owned, these businesses are centralized facilities providing a wholesale market to area growers for a diverse group of buyers. For growers seeking an adequate living from growing produce, these facilities help reduce marketing time and product transportation, and provide frequent sales events that guarantee payment. As such, they have developed into a solid and long-standing market for local produce. However, plain growers have experienced challenges trying new crops or scaling up production. This article details how Missouri Extension assisted plain farmers with their challenges …

Farm Food Safety Training For Amish Produce Growers Covered Under The Food Safety Modernization Act (Fsma), Luke Laborde, Jeffrey Stoltzfus, Kaila Thorn

Journal of Amish and Plain Anabaptist Studies

Commercial production of fruits and vegetables on Amish farms provides significant amounts of fresh produce that are regionally distributed through wholesale markets. In response to several multi-state foodborne disease outbreaks linked to contamination of fresh produce, the U.S. Food and Drug Administration (FDA) mandated farm food safety standards that most commercial produce growers must implement. Although there have been no foodborne disease outbreaks attributed to fresh produce grown on Amish farms, this regulation poses regulatory challenges for those who sell produce at wholesale produce auctions, cooperatives, and distribution warehouses. This article describes recent farm food safety standards issued by the …

Guest Editor’S Introduction: Outreach And Applied Agriculture Research With Plain Anabaptists: Lessons Learned And Future Directions, Caroline Brock

Journal of Amish and Plain Anabaptist Studies

This issue of the Journal of Amish and Plain Anabaptist Studies (JAPAS) contributes to a dearth of literature on ways to understand how plain Anabaptist culture influences agri-environmental beliefs and practices and how it informs outreach and research. Only a few studies currently focus on outreach with plain Anabaptist growers (e.g., Brock, Ulrich-Schad, and Prokopy 2018; Bergefurd 2011; Jepsen and Mann 2015; Stoltzfus 2019; Hoorman and Spencer 2001/2002). This issue of JAPAS is the first comprehensive publication to include research articles and service provider reports focusing on plain people and agriculture. This issue addresses the history of Anabaptist …

Assessment Of Virus-Induced Myocarditis In Human Heart Tissue Samples, Gabriel Galeotos

Honors Theses

The heart is a major organ whose function is to transport nutrients and waste throughout the body. This organ can become infected by pathogens, such as viruses, bacteria, or parasites. Infection of the middle heart layer, or myocardium, is often caused by a viral agent. This disease has three stages: viral infiltration, adaptive immune system activation, and finally either viral clearance or cardiac cell remodeling. During this process the immune system will begin to secrete cytokines, which are signaling molecules that alert other members of the immune pathways, and also participate in cardiac remodeling. Evaluating the correlation between the cytokine …

Genetic Contributors Of Incident Stroke In 10,700 African Americans With Hypertension: A Meta-Analysis From The Genetics Of Hypertension Associated Treatments And Reasons For Geographic And Racial Differences In Stroke Studies, Nicole D. Armstrong, Vinodh Srinivasasainagendra, Amit Patki, Rikki M. Tanner, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Ethan M. Lange, Leslie A. Lange, Donna K. Arnett, Marguerite R. Irvin

Epidemiology and Environmental Health Faculty Publications

Background: African Americans (AAs) suffer a higher stroke burden due to hypertension. Identifying genetic contributors to stroke among AAs with hypertension is critical to understanding the genetic basis of the disease, as well as detecting at-risk individuals.

Methods: In a population comprising over 10,700 AAs treated for hypertension from the Genetics of Hypertension Associated Treatments (GenHAT) and Reasons for Geographic and Racial Differences in Stroke (REGARDS) studies, we performed an inverse variance-weighted meta-analysis of incident stroke. Additionally, we tested the predictive accuracy of a polygenic risk score (PRS) derived from a European ancestral population in both GenHAT and REGARDS AAs …

Nondestructive Detection Of Codling Moth Infestation In Apples Using Pixel-Based Nir Hyperspectral Imaging With Machine Learning And Feature Selection, Nader Ekramirad, Alfadhl Y. Khaled, Lauren E. Doyle, Julia R. Loeb, Kevin D. Donohue, Raul T. Villanueva, Akinbode A. Adedeji

Electrical and Computer Engineering Faculty Publications

Codling moth (CM) (Cydia pomonella L.), a devastating pest, creates a serious issue for apple production and marketing in apple-producing countries. Therefore, effective nondestructive early detection of external and internal defects in CM-infested apples could remarkably prevent postharvest losses and improve the quality of the final product. In this study, near-infrared (NIR) hyperspectral reflectance imaging in the wavelength range of 900–1700 nm was applied to detect CM infestation at the pixel level for three organic apple cultivars, namely Gala, Fuji and Granny Smith. An effective region of interest (ROI) acquisition procedure along with different machine learning and data processing …

Studying The Behavioral Role Of The Kcnn2 Gene In Zebrafish Embryos, Gina Dragonette

Honors Theses

Introduction: Mutations in the KCNN2 gene have been linked to phenotypes of movement disorders and autism. The goal of this experiment was to use the CIUSPR-Cas9 system to create a deletion within the KCNN2 gene and to observe the effect on the expression of movement in zebra fish embryos.

Methods: Linearized Cas9 DNA and guide DNA underwent in vitm transcription (IVT) reactions to produce RNA to be injected into zebrafish embryos at the one cell stage. KCNN guide RNAs were produced for the KCNN2 and KCNN3 genes (to prevent KCNN3 protein function from compensating for loss ofKCNN2's protein function), and …

Late-Life Exercise Mitigates Skeletal Muscle Epigenetic Aging, Kevin A. Murach, Andrea L. Dimet-Wiley, Yuan Wen, Camille R. Brightwell, Christine M. Latham, Cory M. Dungan, Christopher S. Fry, Stanley J. Watowich

Center for Muscle Biology Faculty Publications

There are functional benefits to exercise in muscle, even when performed late in life, but the contributions of epigenetic factors to late-life exercise adaptation are poorly defined. Using reduced representation bisulfite sequencing (RRBS), ribosomal DNA (rDNA) and mitochondrial-specific examination of methylation, targeted high-resolution methylation analysis, and DNAge™ epigenetic aging clock analysis with a translatable model of voluntary murine endurance/resistance exercise training (progressive weighted wheel running, PoWeR), we provide evidence that exercise may mitigate epigenetic aging in skeletal muscle. Late-life PoWeR from 22–24 months of age modestly but significantly attenuates an age-associated shift toward promoter hypermethylation. The epigenetic age of muscle …

Sap Beetles, Nick Volesky, Zachery R. Schrumm, Kalen Taylor

All Current Publications

Sap beetles are typically considered a secondary pest of corn and overripe fruits and vegetables. They are broadly identified by their small and ovular bodies and club-shaped antennae. Adult sap beetles often feed on corn silk, pollen, and tassels. Larvae feed on kernels inside the husk. This fact sheet reviews how to identify sap beetles and their hosts and damage. It also provides ideas on how to monitor for sap beetles and outlines the options for managing them.

Adipose-Specific Pparα Knockout Mice Have Increased Lipogenesis By Pask–Srebp1 Signaling And A Polarity Shift To Inflammatory Macrophages In White Adipose Tissue, Terry D. Hinds, Jr., Zachary A. Kipp, Mei Xu, Frederique B. Yiannikouris, Andrew J. Morris, Donald F. Stec, Walter Wahli, David E. Stec

Pharmacology and Nutritional Sciences Faculty Publications

The nuclear receptor PPARα is associated with reducing adiposity, especially in the liver, where it transactivates genes for β-oxidation. Contrarily, the function of PPARα in extrahepatic tissues is less known. Therefore, we established the first adipose-specific PPARα knockout (Ppara^FatKO) mice to determine the signaling position of PPARα in adipose tissue expansion that occurs during the development of obesity. To assess the function of PPARα in adiposity, female and male mice were placed on a high-fat diet (HFD) or normal chow for 30 weeks. Only the male Ppara^FatKO animals had significantly more adiposity in the inguinal white …

The Effects Of Boric Acid Sugar Bait On Wolbachia Trans-Infected Male Aedes Albopictus (Zap Males®) In Laboratory Conditions, Vindhya S. Aryaprema, Whitney A. Qualls, Karen L. Dobson, Stephen L. Dobson, Rui-De Xue

Entomology Faculty Publications

The field release of Wolbachia trans-infected male mosquitoes, as well as the use of toxic sugar baits, is a novel and promising candidate technique for integrated mosquito management programs. However, the methods of action of the two techniques may not be complementary, because the Wolbachia method releases mosquitoes into the environment expecting a wild population reduction in subsequent generations while the toxic baits are intended to reduce the wild population by killing mosquitoes. This laboratory study was conducted to evaluate the effectiveness of boric acid toxic sugar baits on Wolbachia trans-infected male Aedes albopictus, relative to wild-type Ae. albopictus …

Linking Migration To Community Resilience In The Receiving Basin Of A Large-Scale Water Transfer Project, Anna Erwin, Zhao Ma, Ruxandra Popovici, Emma Patricia Salas O’Brien, Laura Zanotti, Chelsea A. Silva, Eliseo Zeballos Zeballos, Jonathan Bauchet, Nelly Ramírez Calderón, Glenn Roberto Arce Larrea

Department of Agricultural Economics Faculty Publications

Large-scale water transfer projects (LWTPs) transfer water to urban and agricultural areas. The Majes-Siguas canal, established in 1983, is an LWTP that created a thriving agricultural area through irrigating the Majes district in the Atacama Desert of Peru. Like other LWTP receiving basins, the project has attracted an influx of migrants who work on the farms. At the same time, the Majes LWTP is the district’s only source of water and has an aging infrastructure which presents significant risks. While many studies critically analyze the consequences of LWTPs in water supply basins, few evaluate the resilience of communities living in …

Induction Of Il19 Expression Through Jnk And Cgas-Sting Modulates Dna Damage–Induced Cytokine Production, Sara H. Small, E. Jessica Tang, Ryan L. Ragland, Yaroslava Ruzankina, David W. Schoppy, Rahul S. Mandal, M. Rebecca Glineburg, Zgjim Ustelenca, Daniel J. Powell, Fiona Simpkins, F. Bradley Johnson, Eric J. Brown

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Cytokine production is a critical component of cell-extrinsic responses to DNA damage and cellular senescence. Here, we demonstrated that expression of the gene encoding interleukin-19 (IL-19) was enhanced by DNA damage through pathways mediated by c-Jun amino-terminal kinase (JNK) and cGAS-STING and that IL19 expression was required for the subsequent production of the cytokines IL-1, IL-6, and IL-8. IL19 expression was stimulated by diverse cellular stresses, including inhibition of the DNA replication checkpoint kinase ATR (ataxia telangiectasia and Rad3-related protein), oncogene expression, replicative exhaustion, oxidative stress, and DNA double-strand breaks. Unlike the production of IL-6 and IL-8, IL19 expression was …