Life Sciences Commons^™

Multi-Omics Integrative Analysis For Incomplete Data Using Weighted P-Value Adjustment Approaches, Wenda Zhang, Zichen Ma, Yen Yi Ho, Shuyi Yang, Joshua Habiger, Hsin Hsiung Huang, Yufei Huang

Faculty Publications

The advancements in high-throughput technologies provide exciting opportunities to obtain multi-omics data from the same individuals in a biomedical study, and joint analyses of data from multiple sources offer many benefits. However, the occurrence of missing values is an inevitable issue in multi-omics data because measurements such as mRNA gene expression levels often require invasive tissue sampling from patients. Common approaches for addressing missing measurements include analyses based on observations with complete data or multiple imputation methods. In this paper, we propose a novel integrative multi-omics analytical framework based on p-value weight adjustment in order to incorporate observations with incomplete …

Life Cycle Greenhouse Gas Emissions In Maize No-Till Agroecosystems In Southern Brazil Based On A Long-Term Experiment, Guilherme Rosa Da Silva, Adam J. Liska, Cimelio Bayer

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Brazilian agriculture is constantly questioned concerning its environmental impacts, particularly greenhouse gas (GHG) emissions. This research study used data from a 34-year field experiment to estimate the life cycle GHG emissions intensity of maize production for grain in farming systems under no-tillage (NT) and conventional tillage (CT) combined with Gramineae (oat) and legume (vetch) cover crops in southern Brazil. We applied the Feedstock Carbon Intensity Calculator for modeling the “field-to-farm gate” emissions with measured annual soil N₂O and CH₄ emissions data. For net CO₂ emissions, increases in soil organic C (SOC) were applied as a proxy, …

Conceptualizing Sustainability And Resilience In Value Chains In Times Of Multiple Crises—Notes On Agri-Food Chains, Alexander Follmann, Peter Dannenberg, Nina Baur, Boris Braun, Grit Walther, Amelie Bernzen, Jan Börner, Michael Brüntrup, Martin Franz, Emmanuel Sulle

Arusha Climate and Environmental Research Centre

Global and regional agri-food value chains feed societies and are an income source for hundreds of millions of farmers around the world. They are also target areas for action to achieve a global sustainability transformation. Agri-food chains are highly vulnerable in the context of multiple crises, including the global environmental crisis, geopolitical fragmentation, armed conflicts and wars, and the aftermath of the COVID-19 pandemic. Measures to increase chain resilience are widely discussed; however, some such measures contradict sustainability measures. While there has been considerable research on the sustainability and resilience of agri-food chains, few studies have integrated both perspectives or …

Assessing The Environmental Footprint Of Alternative Green Biorefinery Protein Extraction Techniques From Grasses And Legumes, James Gaffey, Andres Arce Martinez, Thalles Allan Andrade, Morten Ambye-Jensen, George Bishop, Maurice N. Collins, David Styles

Publications

The significant grasslands of Europe and its member states represents a significant feedstock opportunity for circular bioeconomy development. The development of green biorefineries (GBR), to supply protein for the feed industry from grass, could help many European member states to address significant deficits in protein availability and reduce imports. The current study assesses the environmental footprint of alternative GBR protein extraction techniques from grasses and legumes using life cycle assessment. The focus is on comparing feedstock and technology pathways that could displace soya bean imports. The study finds that leaf protein concentrate (LPC) produced from grass had an improved environmental …

Half Of Atlantic Reef-Building Corals At Elevated Risk Of Extinction Due To Climate Change And Other Threats, Luis Gutierrez, Beth Polidoro, David Obura, Francoise Cabada-Blanco, Christi Linardich, Emma Pettersson, Paul Pearce-Kelly, Krista Kemppinen, Juan Jose Alvarado, Lorenzo Alvarez-Filip, Anastazia Banaszak, Pilar Casado De Amezua, James Crabbe, Aldo Croquer, Joshua Feingold, Elizabeth Goergen, Stefano Goffredo, Bert Hoeksema, Danwei Huang, Emma Kennedy, Diego Kersting, Marcelo Kitahara, Petar Kružić, Margaret Miller, Flavia Nunes, Juan Pablo Quimbayo, Andrea Rivera-Sosa, Rosa Rodríguez-Martínez, Nadia Santodomingo, Michael Sweet, Mark Vermeij, Estrella Villamizar, Greta Aeby, Khatija Alliji, Daniel Bayley, Elena Couce, Benjamin Cowburn, C. Isabel Nuñez Lendo, Sean Porter, Kaveh Samimi-Namin, Tom Shlesinger, Bryan Wilson

Biological Sciences Faculty Publications

Atlantic reef-building corals and coral reefs continue to experience extensive decline due to increased stressors related to climate change, disease, pollution, and numerous anthropogenic threats. To understand the impact of ocean warming and reef loss on the estimated extinction risk of shallow water Atlantic reef-building scleractinians and milleporids, all 85 valid species were reassessed under the IUCN Red List Categories and Criteria, updating the previous Red List assessment of Atlantic corals published in 2008. For the present assessment, individual species declines were estimated based on the modeled coral cover loss (1989–2019) and projected onset of annual severe bleaching events (2020–2050) …

Letter From The Dean, Jeff Edwards

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Contents, Discovery Editors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Instructions For Authors, Discovery Editors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

The Joint Effects Of Cognitive Function And Sedentary Time On Mortality Risk In Older Adults: 2011-2014 Nhanes, Sarah A. Wilson

UNF Graduate Theses and Dissertations

Background: Examining the joint effects of cognitive function (CF) and sedentary time (ST) may provide insight into the complex mechanisms underlying mortality risk within older adults. This study examines the joint effects of CF and ST on mortality risk in older adults.

Methods: Sample included 2,230 older adults (≥ 60 years of age) participants in the 2011-2014 National Health and Nutrition Examination Survey. The Digit Symbol Substitution Test (DSST), Consortium to Establish a Registry for Alzheimer's Disease (CERAD) subtests, and Animal Fluency (AF) were used to assess CF. Average daily sitting and television time represented ST. Quartiles of CF and …

Rose Nourish To Flourish Obesity Prevention Program Targeting Children At Risk For Food Insecurity In Jacksonville, Florida, Jamie Marchio

UNF Graduate Theses and Dissertations

The Nourish to Flourish study aimed to decrease the prevalence of obesity among food insecure children in Jacksonville, FL. Specifically, the program focused on nutrition education and access to healthy foods. The study consisted of a 4-week nutrition education series emphasizing the major determinants of healthy weight known as 5-2-1-0! This includes expanding knowledge of fruit and vegetable intake to achieve a target intake of five servings a day, screen time reduction to no more than two hours a day, achieving a physical activity goal of one hour a day outside of school hours, and limiting sugar sweetened beverage consumption …

Turtlegrass (Thalassia Testudinum) Undergoes A Coordinated Hypersensitive Response When Challenged With Pathogenic Labyrinthula Sp., Ava Vasile Larson

UNF Graduate Theses and Dissertations

Infection of the subtropical seagrass Thalassia testudinum Banks ex König by pathogenic Labyrinthula sp. was found to induce lesion progression, alterations to the host’s oxidative metabolism, and production of defense metabolites over the early stages of infection (monitored over a 72-hr time course). By 48-hrs post-infection, host oxygen consumption, internal reactive oxygen concentrations, and caspase-3 proteolytic activity reached their highest levels. The formation of reactive oxygen species (ROS) and nitric oxide (NO) were detected in T. testudinum lesions by use of redox-sensitive probes/substrates and fluorescent imaging. To our knowledge, this work represents the first time NO has been detected in …

Integrating Remote Sensing With Ground-Based Observations To Quantify The Effects Of An Extreme Freeze Event On Black Mangroves (Avicennia Germinans) At The Landscape Scale, Melinda Martinez, Michael J. Osland, James B. Grace, Nicholas M. Enwright, Camille L. Stagg, Camille L. Stagg, Simen Kaalstad, Gordon H. Anderson, Elena A. Flores, Alejandro Fierro-Cabo

School of Earth, Environmental, & Marine Sciences Faculty Publications

Climate change is altering the frequency and intensity of extreme weather events. Quantifying ecosystem responses to extreme events at the landscape scale is critical for understanding and responding to climate-driven change but is constrained by limited data availability. Here, we integrated remote sensing with ground-based observations to quantify landscape-scale vegetation damage from an extreme climatic event. We used ground- and satellite-based black mangrove (Avicennia germinans) leaf damage data from the northern Gulf of Mexico (USA and Mexico) to examine the effects of an extreme freeze in a region where black mangroves are expanding their range. The February 2021 …

Cover, Editorial Staff, Journal Information

Human–Wildlife Interactions

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Table Of Contents

Human–Wildlife Interactions

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New Associate Editors, S. Nicole Frey

Human–Wildlife Interactions

New associate editors include Breanna Martinico, Shannon Skalos, Paula Pebsworth, and Donna J. Perry.

Regular Surveys Rescue Wildlife: What A Lucky And Unlucky Individual Tsukuba Clawed Salamander, Chia-Hsuan Hsu, Jiefeng Kang

Human–Wildlife Interactions

The Tsukuba clawed salamander (Onychodactylus tsukubaensis), native to Japan's Tsukuba mountain areas, faces peril from human activities and climate change. Classified as critically endangered by both the Japanese Ministry of Environment and the IUCN Red List, limited research has been conducted since its identification as a distinct species. Monthly surveys initiated in August 2023 aimed to understand its ecology. During a December 2023 survey, a remarkable encounter unfolded: a trapped individual salamander was discovered, initially assumed dead but miraculously alive. Despite an ulcerated tail wound, the salamander's survival presents a hopeful outcome for this endangered species. Uncertain of …

Grazing Management For Livestock, Free-Roaming Horses And Burros, And Resilience, Sherman R. Swanson

Human–Wildlife Interactions

Grazing management avoids overgrazing by allocating forage for livestock on the basis of animal unit months and managing wild and free-roaming horses (Equus caballus) and burros (E. asinus) to achieve and maintain an appropriate management level (AML) for each herd. Riparian green forage and water attracts cattle (Bos taurus) and equids when upland forage is brown. Key species that focus management for resilience to weather variation, fire, and floods are preferred forage plants for cattle and horses. They include riparian stabilizers such as densely rooted sedges and deep-rooted perennial grasses in sagebrush (Artemisia …

Special Topic: Pest And Beneficial Bird Management, Breanna Martinico, Shannon Skalos

Human–Wildlife Interactions

This is the call for papers for the special issue on Pest and Beneficial Bird Management.

Preparing For Publication: An Inside Look At Production Processes And Recommendations For Authors Of Human–Wildlife Interactions, Rosanna M. Vail

Human–Wildlife Interactions

This segment of The Back Page provides a transparent look at the journal's article production tasks, including pre-production, copyediting, layout, proofs, pre-publication, and publication, as well as recommendations for authors to reduce time to publication.

Cover, Editorial Staff, Journal Information

Human–Wildlife Interactions

This includes the cover caption, editorial staff, and journal information.

Table Of Contents

Human–Wildlife Interactions

This is the table of contents.

New Associate Editors, S. Nicole Frey

Human–Wildlife Interactions

New associate editors include Brian S. Dorr and Jorge Tobajas.

Exploring The Consistency Of Flow Regimes Within And Among Ecoregions Of The Southeastern United States, Frank Paul Braun Iv

College of Graduate Studies: Theses & Dissertations

Human manipulation of river systems has long been a known contributor to the loss of freshwater biodiversity. By accounting for environmental causes of hydrologic variation among rivers, we can better understand how ecoregion mediates flow regimes and forecast species that may be at risk. Presumably, natural variation associated with ecoregion boundaries exerts strong influence on flow regimes, and may mediate relationships between other features (e.g., land use, dam operations) and hydrology. However, such between-ecoregion variation is poorly investigated, particularly at fine spatial and temporal scales. I characterized 10 hydrologic metrics, representing the five key dimensions of the flow regime (magnitude, …

Multi-Year Effectiveness Of Pzp-22 In Free-Roaming Suburban White-Tailed Deer, Allen T. Rutberg, Kali M. Pereira, Kayla A. Grams, John W. Turner Jr.

Human–Wildlife Interactions

To address the challenge that is posed to the use of fertility control to mitigate human–deer (Cervidae) conflicts by the need to regularly re-inoculate free-roaming animals, we captured, ear-tagged, and hand-injected 68 individual adult female white-tailed deer (Odocoileus virginianus) with the PZP-22 immunocontraceptive vaccine from February through April, 2014 to 2017, in the Village of Hastings-on-Hudson, New York, USA. Approximately 2.5 years after initial treatments, we booster-darted 29 of the previously treated females with either PZP-22 or native PZP (ZonaStat-D). We observed fawn production between 2014 and 2021. The combination of initial PZP-22 hand-treatments followed by single dart-delivered PZP …

Spatial Predictors Of Human–Black Bear Interactions In Nova Scotia, Canada, Jason I. Airst, Tricia B. Fleming

Human–Wildlife Interactions

The increased global frequency of human–wildlife conflict with large, wild carnivores and omnivores negatively impacts human, wildlife, and ecosystem health. The goal of this study was to determine what landscape characteristics best predicted where human–black bear (Ursus americanus) interactions occurred in Nova Scotia, Canada, to support management efforts. We compared the location of 3,278 human–bear conflict reports and 867 non-conflict reports collected between 2017 and 2021 to 12,000 randomly generated locations. Data were analyzed using logistic additive mixed models. We found that interactions (conflict and non-conflict reports) occurred near roads and farther from forests and surface water features. …

Screening H3 Histone Acetylation In A Wild Bird, The House Sparrow (Passer Domesticus), Daniella Ray

College of Graduate Studies: Theses & Dissertations

Epigenetic mechanisms are increasingly understood to have major impacts across ecology. However, one molecular epigenetic mechanism, DNA methylation, currently dominates the literature. A second mechanism, histone modification, is likely important to ecologically relevant phenotypes and thus warrants investigation, especially because molecular interplay between methylation and histone acetylation can strongly affect gene expression. There are a limited number of histone acetylation studies on non-model organisms, yet those that exist show that it can impact gene expression and phenotypic plasticity. Wild birds provide an excellent system to investigate histone acetylation, as free-living individuals must rapidly adjust to environmental change. Here, we screen …

Efficacy Of A Laser As A Starling Deterrent And Its Effect On Lactating Dairy Cow Behavior, Callan A. Lichtenwalter, Marcos Marcondes, Kyle R. Taylor, Craig Mcconnel, Amber Adams Progar

Human–Wildlife Interactions

European starlings (Sturnus vulgaris) cause damage (including structural damage) on dairies, eat cattle feed, and can potentially spread disease through their fecal matter. Deterring starlings from dairies without affecting cow (Bos taurus) welfare is vital, and lasers have been effective starling deterrence tools in urban roosts and in some crops. To evaluate if the use of lasers on dairies would affect starling use of freestall barns as night roosts, or lactating cow behavior, 1 laser was installed in each of the 2 freestall barns at the Knott Dairy Center at Washington State University, Pullman, Washington, USA. …

Jack H. Berryman Institute Update, Julie K. Young, Becky Quay

Human–Wildlife Interactions

The Jack H. Berryman Institute at Utah State University, publisher of Human–Wildlife Interactions journal, is under new leadership to forward its mission of resolving human–wildlife conflicts through research, education, and outreach. This Back Page article from the director and the administrative and outreach coordinator of the Berryman Institute focuses on preparing to meet the challenges at the intersection of humans and wildlife.

Forthcoming Hwi Monographs

Human–Wildlife Interactions

The HWI Monograph Series is publishing an open access monograph on urban coyotes.

Cover, Editorial Staff, Journal Information

Human–Wildlife Interactions

This includes the cover caption, editorial staff, and journal information.