Life Sciences Commons^™

Monitoring Fine-Scale Forest Health Using Unmanned Aerial Systems (Uas) Multispectral Models, Benjamin T. Fraser, Russell G. Congalton

Faculty Publications

Forest disturbances—driven by pests, pathogens, and discrete events—have led to billions of dollars in lost ecosystem services and management costs. To understand the patterns and severity of these stressors across complex landscapes, there must be an increase in reliable data at scales compatible with management actions. Unmanned aerial systems (UAS or UAV) offer a capable platform for collecting local scale (e.g., individual tree) forestry data. In this study, we evaluate the capability of UAS multispectral imagery and freely available National Agricultural Imagery Program (NAIP) imagery for differentiating coniferous healthy, coniferous stressed, deciduous healthy, deciduous stressed, and degraded individual trees throughout …

Evaluation Of Deep Neural Network Prospr For Accurate Protein Distance Predictions On Casp14 Targets, Jacob A. Stern, Bryce Eric Hedelius, Olivia Fisher, Wendy M. Billings, Dennis Della Corte

Faculty Publications

The field of protein structure prediction has recently been revolutionized through the introduction of deep learning. The current state-of-the-art tool AlphaFold2 can predict highly accurate structures; however, it has a prohibitively long inference time for applications that require the folding of hundreds of sequences. The prediction of protein structure annotations, such as amino acid distances, can be achieved at a higher speed with existing tools, such as the ProSPr network. Here, we report on important updates to the ProSPr network, its performance in the recent Critical Assessment of Techniques for Protein Structure Prediction (CASP14) competition, and an evaluation of its …

Examination Of Athlete Triad Symptoms Among Endurance-Trained Male Athletes: A Field Study, Erin M. Moore, Clemens Drenowatz, David F. Stodden, Kelly Pritchett, Thaddus C. Brodick, Brittany T. Williams, Justin M. Goins, Toni Torres-Mcgehee Phd, Lat, Atc

Faculty Publications

Background: Studies examining the physiological consequences associated with deficits in energy availability (EA) for male athletes are sparse.

Purpose: To examine male athlete triad components; low energy availability (LEA) with or without an eating disorder risk (ED), reproductive hormone [testosterone (T)], and bone mineral density (BMD) in endurance-trained male athletes during different training periods.

Methods: A cross-sectional design with 14 participants (age: 26.4 ± 4.2 years; weight: 70.6 ± 6.4 kg; height: 179.5 ± 4.3 cm; BMI: 21.9 ± 1.8 kg/m2) were recruited from the local community. Two separate training weeks [low (LV) and high (HV) training volumes] were used …

Triophaser: Using Mendelian Inheritance Logic To Improve Genomic Phasing Of Trios, Dustin B. Miller, Stephen R. Piccolo

Faculty Publications

Background: When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be benefcial when trying to identify certain types of DNA variants. Mendelian inheritance logic can be used to accurately phase (haplotype) the majority (67–83%) of an individual’s heterozygous nucleotide positions when genotypes are available for both parents (trio). However, when all members of a trio are heterozygous at a position, Mendelian inheritance logic cannot be used to phase. For such positions, a computational phasing algorithm can be used. Existing phasing algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes …

Panoramic Spatial Vision In The Bay Scallop Argopecten Irradians, Daniel R. Chappell, Tyler M. Horan, Daniel Isaac Speiser

Faculty Publications

We have a growing understanding of the light-sensing organs and light-influenced behaviours of animals with distributed visual systems, but we have yet to learn how these animals convert visual input into behavioural output. It has been suggested they consolidate visual information early in their sensory-motor pathways, resulting in them being able to detect visual cues (spatial resolution) without being able to locate them (spatial vision). To explore how an animal with dozens of eyes processes visual information, we analysed the responses of the bay scallop Argopecten irradians to both static and rotating visual stimuli. We found A. irradians distinguish between …

Examining Eating Attitudes And Behaviors In Collegiate Athletes, The Association Between Orthorexia Nervosa And Eating Disorders, Nancy A. Uriegas, Zachary K. Winkelmann Phd, Lat, Atc, Kelly Pritchett, Toni Torres-Mcgehee Phd, Lat, Atc

Faculty Publications

Purpose: Orthorexia nervosa (Orthorexia) is an eating attitude and behavior associated with a fixation on healthy eating, while eating disorders (EDs) are clinically diagnosed psychiatric disorders associated with marked disturbances in eating that may cause impairment to psychosocial and physical health. The purpose of this study was to examine risk for Orthorexia and EDs in student-athletes across sex and sport type and determine the association between the two.

Methods: Student-athletes (n = 1,090; age: 19.6 ± 1.4 years; females = 756; males = 334) completed a survey including demographics, the ORTO-15 test (values), the Eating Attitudes Test-26 (EAT-26; >20 …

Collegiate Student-Athletes' Perceptions Of Patient-Centered Care Delivered By Athletic Trainers, Ansley Smallen Redinger, Zachary K. Winkelmann, Lindsey Eberman

Faculty Publications

Context

The health care core competencies indicate that all medical professionals should provide patient-centered care (PCC), which is defined as care that is respectful and responsive to the patient's values and preferences, during each encounter.

Objective

To identify collegiate student-athletes' definitions of PCC and measure their perceived level of PCC from an athletic trainer (AT).

Design

Cross-sectional study.

Setting

Mixed-methods survey.

Patients or Other Participants

A total of 610 (age = 19 ± 1 year) National Collegiate Athletic Association student-athletes completed the survey.

Main Outcome Measure(s)

The survey consisted of 1 open-ended question that prompted the participant to define PCC …

Differences By School Location In Summer And School Monthly Weight Change: Findings From A Nationally Representative Sample, Ethan T. Hunt, Bridget Armstrong Ph.D., Gabrielle Turner-Mcgrievy Ph.D., Rd, Michael Beets Med, Mph, Phd, Robert Weaver Med, Phd

Faculty Publications

Objectives: To examine changes in accelerations of Body Mass Index (BMI), age-and-sex specific body mass index (zBMI), and 95th percentile of BMI (%BMIp95) during the summer months and school year by school location designation (i.e., urban, suburban, exurban). This study utilized the Early Childhood Longitudinal Study Kindergarten Class of 2010-2011.

Methods: Of the 18,174 children in the ECLS-K:2011 dataset, I restricted participants to those with at least two consecutive measures that occurred August/September or April/May. Mixed-effect regression analyses estimated differences in monthly change in BMI, zBMI, and %BMIp95 between the summer and school year while accounting for the ECLS-K complex …

Cetacean Acousticwelfare In Wild And Managed-Care Settings: Gaps And Opportunities, Paige E. Stevens, Heather Hill, Jason N. Bruck

Faculty Publications

Cetaceans are potentially at risk of poor welfare due to the animals’ natural reliance on sound and the persistent nature of anthropogenic noise, especially in the wild. Industrial, commercial, and recreational human activity has expanded across the seas, resulting in a propagation of sound with varying frequency characteristics. In many countries, current regulations are based on the potential to induce hearing loss; however, a more nuanced approach is needed when shaping regulations, due to other non-hearing loss effects including activation of the stress response, acoustic masking, frequency shifts, alterations in behavior, and decreased foraging. Cetaceans in managedcare settings share the …

Murine Trophoblast Stem Cells And Their Differentiated Cells Attenuate Zika Virus In Vitro By Reducing Glycosylation Of The Viral Envelope Protein, Biswas Neupane, Mona Fendereski, Farzana Nazneen, Yanlin Guo, Fengwei Bai

Faculty Publications

Zika virus (ZIKV) infection during pregnancy can cause devastating fetal neuropathological abnormalities, including microcephaly. Most studies of ZIKV infection in pregnancy have focused on post-implantation stage embryos. Currently, we have limited knowledge about how a pre-implantation stage embryo deals with a viral infection. This study investigates ZIKV infection on mouse trophoblast stem cells (TSCs) and their in vitro differentiated TSCs (DTSCs), which resemble the cellular components of the trophectoderm layer of the blastocyst that later develops into the placenta. We demonstrate that TSCs and DTSCs are permissive to ZIKV infection; however, ZIKV propagated in TSCs and DTSCs exhibit substantially lower …

Low Light Intensity Delays Vegetative Phase Change, Mingli Xu, Tieqiang Hu, R Scott Poethig

Faculty Publications

Plants that develop under low light (LL) intensity often display a phenotype known as the “shade tolerance syndrome (STS)”. This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master …

Editorial: Fresh Faces, A New Look, And A Bright Future For Lajam, Miriam Marmontel, Daniel Gonzalez-Socoloske

Faculty Publications

No abstract provided.

Implications Of Community-Based Management Of Marine Reserves In The Philippines For Reef Fish Communities And Biodiversity, Sara E. Marriott, Courtney Cox, Rizaller C. Amolo, Dean Apistar, Roquelito H. Mancao, Kim De Mutsert

Faculty Publications

Overfishing and destructive fishing practices are major threats to marine biodiversity in the Philippines, where over 1.9 million small-scale fishers are supported by these biodiverse marine communities. Nearly 50% of all marine fish capture in the Philippines is from artisanal fisheries, with much of it not reported or under-reported. Marine reserves, where fishing is prohibited have been created in many local government units to help restore and preserve this biodiversity. The success of these marine reserves is still under serious debate with effective management still representing a significant challenge. The lack of a governance system to centrally managed marine reserves …

Transcriptomic Analysis Reveals That Municipal Wastewater Effluent Enhances Vibrio Vulnificus Growth And Virulence Potential, Karlen Enid Correa Velez, Robert Sean Norman

Faculty Publications

Vibrio vulnificusis an opportunistic pathogen indigenous to estuarine and marine environments and associated with aquatic organisms. Vibrio vulnificusis of utmost importance because it causes 95% of the seafood-related deaths in the United States due to rapid progression of septicemia. Changes in environmental parameters associated with climate change and coastal population expansion are altering geographical constraints, resulting in increased Vibrio spread, exposure, and rates of infection. In addition, coastal population expansion is resulting in increased input of treated municipal sewage into areas that are also experiencing increased Vibrio proliferation. This study aimed to better understand the influence of treated …

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

Toward A Methodology For Evaluating Dna Variants In Nuclear Families, Dustin B. Miller, Reid Robison, Stephen Piccolo

Faculty Publications

The genetic underpinnings of most pediatric-cancer cases are unknown. Population-based studies use large sample sizes but have accounted for only a small proportion of the estimated heritability of pediatric cancers. Pedigree-based studies are infeasible for most human populations. One alternative is to collect genetic data from a single nuclear family and use inheritance patterns within the family to filter candidate variants. This approach can be applied to common and rare variants, including those that are private to a given family or to an affected individual. We evaluated this approach using genetic data from three nuclear families with 5, 4, and …

Sperm Repository For A Breeding Program Of The Eastern Oyster Crassostrea Virginica: Sample Collection, Processing, Cryopreservation, And Data Management Plan, Huiping Yang, Yuanzi Huo, Jayme C. Yee, Scott Rikard, William C. Walton, Eric A. Saillant

Faculty Publications

The Eastern oyster Crassostrea virginica (Family Ostreidae) is one of the most important fishery and aquaculture species in the U.S. and is a keystone species for coastal reefs. A breeding program was initiated in 2019 to support the fast-growing aquaculture industry culturing this species in the Gulf of Mexico. Oysters from 17 wild populations in embayment along the U.S. Gulf of Mexico coast from southwest Florida to the Matagorda Bay, Texas were used as broodstock for the program to maximize genetic diversity in the base population. A sperm repository of the broodstock was established to support the breeding project. The …

Enhanced Detection Of Desmoplasia By Targeted Delivery Of Iron Oxide Nanoparticles To The Tumour-Specific Extracellular Matrix, Meenu Chopra, Jiansha Wu, Yen Ling Yeow, Louise Winteringham, Tristan D. Clemons, Martin Saunders, Venkata Ramana Kotamraju, Ruth Ganss, Kirk W. Feindel, Juliana Hamzah

Faculty Publications

Diagnostic imaging of aggressive cancer with a high stroma content may benefit from the use of imaging contrast agents targeted with peptides that have high binding affinity to the extracellular matrix (ECM). In this study, we report the use of superparamagnetic iron-oxide nanoparticles (IO-NP) conjugated to a nonapeptide, CSGRRSSKC (CSG), which specifically binds to the laminin-nidogen-1 complex in tumours. We show that CSG-IO-NP accumulate in tumours, predominantly in the tumour ECM, following intravenous injection into a murine model of pancreatic neuroendocrine tumour (PNET). In contrast, a control untargeted IO-NP consistently show poor tumour uptake, and IO-NP conjugated to a pentapeptide. …

Fe-Catalyzed Sulfide Oxidation In Hydrothermal Plumes Is A Source Of Reactive Oxygen Species To The Ocean, Timothy J. Shaw, George W. Luther Iii, Richard Rosas, Véronique E. Oldham, Nicole R. Coffey, John L. Ferry, Dewamunnage M. C. Dias, Mustafa Yücel, Aubin Thibault De Chanvalon

Faculty Publications

Historically, the production of reactive oxygen species (ROS) in the ocean has been attributed to photochemical and biochemical reactions. However, hydrothermal vents emit globally significant inventories of reduced Fe and S species that should react rapidly with oxygen in bottom water and serve as a heretofore unmeasured source of ROS. Here, we show that the Fe-catalyzed oxidation of reduced sulfur species in hydrothermal vent plumes in the deep oceans supported the abiotic formation of ROS at concentrations 20 to 100 times higher than the average for photoproduced ROS in surface waters. ROS (measured as hydrogen peroxide) were determined in hydrothermal …

Analysis Of Body Condition Indices Reveals Different Ecotypes Of The Antillean Manatee, D. N. Castelblanco-Martínez, D. H. Slone, S. S. Landeo-Yauri, E. A. Ramos, A. Alvarez-Alemán, F. L. N. Attademo, C. A. Beck, R. K. Bonde, S. M. Butler, L. J. Cabrias-Contreras, D. Caicedo-Herrera, J. Galves, I. V. Gómez-Camelo, Daniel Gonzalez-Socoloske, J. Jiménez-Domínguez, F. O. Luna, Y. Mona-Sanabria, J. B. Morales-Vela, L. D. Olivera-Gómez, J. A. Padilla-Saldívar, J. Powell, J. P. Reid, G. Rieucau, A. A. Mignucci-Giannoni

Faculty Publications

Assessing the body condition of wild animals is necessary to monitor the health of the population and is critical to defining a framework for conservation actions. Body condition indices (BCIs) are a non-invasive and relatively simple means to assess the health of individual animals, useful for addressing a wide variety of ecological, behavioral, and management questions. The Antillean manatee (Trichechus manatus manatus) is an endangered subspecies of the West Indian manatee, facing a wide variety of threats from mostly human-related origins. Our objective was to define specific BCIs for the subspecies that, coupled with additional health, genetic and …

Editorial: Unraveling Mechanisms Underlying Annual Plankton Blooms In The North Atlantic And Their Implications For Biogenic Aerosol Properties And Cloud Formation, Michael Behrenfeld, Sarah D. Brooks, Peter Gaube, Kristina D.A. Mojica

Faculty Publications

No abstract provided.

Concussion History And Heart Rate Variability During Bouts Of Acute Stress, Adam Harrison, Abbi Lane-Cordova, Michael F. La Fountaine, Robert Davis Moore Ms, Ph.D.

Faculty Publications

Context

After a sport-related concussion, many athletes experience persisting neurophysiological alterations. These alterations may be absent at rest but emerge during moments of physiological stress. Unnoticed and untreated neurophysiological dysfunction may negatively affect long-term neurologic health in adolescent athletes, as they are at a critical point in development. Objective

To assess cardio-autonomic functioning in athletes with and those without a history of concussion by quantifying measures of heart rate variability (HRV) during times of physical and mental exertion. Design

Case-control study. Setting

Research laboratory. Patients or Other Participants

Thirty-four male Hockey Quebec Midget-AAA hockey players were separated into those with …

The Ghost Of Hosts Past: Impacts Of Host Extinction On Parasite Specificity, Maxwell J. Farrell, Andrew W. Park, Clayton E. Cressler, Tad Dallas, Shan Huang, Nicole Mideo, Ignacio Morales-Castilla, T. Jonathan Davies, Patrick Stephens

Faculty Publications

A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may …

The Future Of Zoonotic Risk Prediction, Colin J. Carlson, Maxwell J. Farrell, Zoe Grange, Barbara A. Han, Nardus Mollentze, Alexandra L. Phelan, Angela L. Rasmussen, Gregory F. Albery, Bernard Bett, David M. Brett-Major, Lily E. Cohen, Tad Dallas, Evan A. Eskew, Anna C. Fagre, Kristian M. Forbes, Rory Gibb, Sam Halabi, Charlotte C. Hammer, Rebecca Katz, Jason Kindrachuk, Renata L. Muylaert, Felicia B. Nutter, Joseph Ogola, Kevin J. Olival, Michelle Rourke, Sadie J. Ryan, Noam Ross, Stephanie N. Seifert, Tarja Sironen, Claire J. Standley, Kishana Taylor, Marietjie Venter, Paul W. Webala

Faculty Publications

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open …

Physical Activity In Out Of School Hours Care: An Observational Study, Ruth K. Crowe, Yasmine C. Probst, Rebecca M. Stanley, Sarah T. Ryan, Robert Glenn Weaver Med, Phd, Michael W. Beets Med, Mph, Phd, Jennifer A. Norman, Susan E. Furber, Ceco;Oa Vuong, Megan L. Hammersley, Karen Wardle, Lisa Franco, Marc Davies, Christine Innes-Hughes, Anthony D. Okely

Faculty Publications

Background

Opportunities for physical activity within out of school hours care (OSHC) are not well documented in Australia. This study explored factors associated with children (5–12 years) meeting 30 min of moderate to vigorous physical activity (MVPA) while attending OSHC in the afternoon period.

Methods

A cross-sectional study, conducted in 89 OSHC services in New South Wales, Australia, serving 4,408 children. Each service was visited twice between 2018–2019. Physical activity promotion practices were captured via short interviews and System for Observing Staff Promotion of Physical Activity and Nutrition (SOSPAN). Physical activity spaces was measured (m2) and physical activity of 3,614 …

Identifying Effective Intervention Strategies To Reduce Children’S Screen Time: A Systematic Review And Meta-Analysis, Alexis Jones, Bridget Armstrong Ph.D., Robert Glenn Weaver M.Ed., Phd, Hannah Parker, Lauren Von Klinggraeff, Michael W. Beets Ph.D.

Faculty Publications

Background

Excessive screen time (≥ 2 h per day) is associated with childhood overweight and obesity, physical inactivity, increased sedentary time, unfavorable dietary behaviors, and disrupted sleep. Previous reviews suggest intervening on screen time is associated with reductions in screen time and improvements in other obesogenic behaviors. However, it is unclear what study characteristics and behavior change techniques are potential mechanisms underlying the effectiveness of behavioral interventions. The purpose of this meta-analysis was to identify the behavior change techniques and study characteristics associated with effectiveness in behavioral interventions to reduce children’s (0–18 years) screen time.

Methods

A literature search of …

Small Studies, Big Decisions: The Role Of Pilot/Feasibility Studies In Incremental Science And Premature Scale-Up Of Behavioral Interventions, Michael William Beets, Lauren Von Klinggraeff, Robert G. Weaver, Bridget Ryan Armstrong, Sarah Burkart

Faculty Publications

Background: Careful consideration and planning are required to establish “sufficient” evidence to ensure an investment in a larger, more well-powered behavioral intervention trial is worthwhile. In the behavioral sciences, this process typically occurs where smaller-scale studies inform larger-scale trials. Believing that one can do the same things and expect the same outcomes in a larger-scale trial that were done in a smaller-scale preliminary study (i.e., pilot/feasibility) is wishful thinking, yet common practice. Starting small makes sense, but small studies come with big decisions that can influence the usefulness of the evidence designed to inform decisions about moving forward with a …

Predicting Drug Sensitivity Of Cancer Cells Based On Dna Methylation Levels, Sofia P. Miranda, Fernanda A. Baião, Julia L. Fleck, Stephen R. Piccolo

Faculty Publications

Cancer cell lines, which are cell cultures derived from tumor samples, represent one of the least expensive and most studied preclinical models for drug development. Accurately predicting drug responses for a given cell line based on molecular features may help to optimize drug-development pipelines and explain mechanisms behind treatment responses. In this study, we focus on DNA methylation profiles as one type of molecular feature that is known to drive tumorigenesis and modulate treatment responses. Using genome-wide, DNA methylation profiles from 987 cell lines in the Genomics of Drug Sensitivity in Cancer database, we used machine-learning algorithms to evaluate the …

Urban Bat Pups Take After Their Mothers And Are Bolder And Faster Learners Than Rural Pups., Lee Harten, Nesim Gonceer, Michal Handel, Orit Dash, H. Bobby Fokidis, Yossi Yovel

Faculty Publications

Background: Urbanization is rapidly changing our planet and animals that live in urban environments must quickly adjust their behavior. One of the most prevalent behavioral characteristics of urban dwelling animals is an increased level of risk-taking. Here, we aimed to reveal how urban fruitbats become risk-takers, and how they differ behaviorally from rural bats, studying both genetic and non-genetic factors that might play a role in the process. We assessed the personality of newborn pups from both rural and urban colonies before they acquired experience outdoors, examining risk-taking, exploration, and learning rates.

Results: Urban pups exhibited significantly higher risk-taking levels, …

Leaf Form Diversification In An Ornamental Heirloom Tomato Results From Alterations In Two Different Homeobox Genes, Hokuto Nakayama, Steven D. Rowland, Zizhang Cheng, Kristina Zumstein, Julie Kang, Yohei Kondo, Neelima R. Sinha

Faculty Publications

Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo …