Digital Commons Network^™

Ad Fontes: Divergence-Time Estimation And The Age Of Angiosperms, Stephen A. Smith, Jeremy M. Beaulieu

Biological Sciences Faculty Publications and Presentations

Accurate divergence times are essential for interpreting and understanding the context in which lineages have evolved. Over the past several decades, debates have surrounded the discrepancies between the inferred molecular ages of crown angiosperms, often estimated from the Late Jurassic into the Permian, and the fossil record, placing angiosperms in the Early Cretaceous. That crown angiosperms could have emerged as early as the Permian or even the Triassic would have major implications for the paleoecological context of the origin of one of the most consequential clades in the tree of life. Here, we argue, and demonstrate through simulations, that the …

Multiomics Of Yaks Reveals Significant Contribution Of Microbiome Into Host Metabolism, Shuli Yang, Jeiyi Zheng, Huaming Mao, Paramintra Vinitchaikul, Dongwang Wu, Jianmin Chai

Animal Science Faculty Publications and Presentations

An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, …

Editorial: Predicting, Managing, And Minimizing Mycotoxicosis In Farm Animals, Jesus Adonai Maguey-Gonzalez, Juan D. Latorre, Sergio Gomez-Rosales, Abraham Mendez-Albores

Poultry Science Faculty Publications and Presentations

Editorial on the Research Topic: Predicting, managing, and minimizing mycotoxicosis in farm animals

A Comparison Of Inversion Test Holding Methods For Broilers, A. Perretti, S. Weimer

Poultry Science Faculty Publications and Presentations

Objective, robust, and repeatable assessments of fear responses of poultry can lead to improvements in research techniques, the validity of test results, and ultimately bird welfare. The objective of this study was to examine the effect of 2 different holding methods on broiler fear responses during the inversion test, a standardized method of assessing fear in poultry. On D15 and D34 mixed-sex broilers (N = 80) were inverted and held either by their shanks (N = 40) or feet (N = 40) at arm's length away from the experimenter for 30 s. The frequency of wing flapping, head movement, attempts …

A Liquid Crystal-Based Biomaterial Platform For Rapid Sensing Of Heat Stress Using Machine Learning, Prateek Verma, Elizabeth Adeogun, Elizabeth S. Greene, Sami Dridi, Ukash Nakarmi, Karthik Nayani

Poultry Science Faculty Publications and Presentations

Novel biomaterials that bridge the knowledge gap in coupling molecular/protein signatures of disease/stress with rapid readouts are a critical need of society. One such scenario is an imbalance between bodily heat production and heat dissipation which leads to heat stress in organisms. In addition to diminished animal well-being, heat stress is detrimental to the poultry industry as poultry entails fast growth and high yields, resulting in greater metabolic activity and higher body heat production. When stressed, cells overexpress heat shock proteins (such as HSP70, a well-established intracellular stress indicator) and may undergo changes in their mechanical properties. Liquid crystals (LCs, …

Geosciences Affiliated Publications: Snapshot Of The Research Publications 2018-2023, Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report provides a snapshot of the research publications for authors affiliated with the Geosciences department at the University of Arkansas, Fayetteville, for the period 2018-2023. It includes publications by material type; co-author characteristics; ranking of journals according to journal citation reports.

Electron-Beam-Killed Staphylococcus Vaccine Reduced Lameness In Broiler Chickens, Anna L.F.V. Assumpcao, Komala Arsi, Andi Asnayanti, Khawla Alharbi, Anh Dang Trieu Do, Quentin D. Read, Ruvindu Perera, Abdulkarim Shwani, Amer Abdullah Hasan, Suresh D. Pillai, Robin C. Anderson, Annie M. Donoghue, Douglas D. Rhoads, Palmy R.R. Jesudhasan, Adnan A. Alrubaye

Poultry Science Faculty Publications and Presentations

Broiler chicken lameness caused by bacterial chondronecrosis with osteomyelitis (BCO) is presently amongst the most important economic and animal welfare issues faced by the poultry industry, and the estimated economic loss is around USD 150 million. BCO lameness is associated with multiple opportunistic bacterial pathogens inhabiting the respiratory and gastrointestinal tracts. In cases of immune deficiency resulting from stress, injury, or inflammation of the tissue, opportunistic pathogens, mainly Staphylococcus spp., can infiltrate the respiratory or gastrointestinal mucosa and migrate through the bloodstream to eventually colonize the growth plates of long bones, causing necrosis that leads to lameness. This is the …

Advancing Crispr-Based Solutions For Covid-19 Diagnosis And Therapeutics, Roaa Hadi, Abhishek Poddar, Shivakuma Sonnaila, Venkata Suryanarayana Murthy Bhavaraju, Shilpi Agrawal

Chemistry & Biochemistry Faculty Publications and Presentations

Since the onset of the COVID-19 pandemic, a variety of diagnostic approaches, including RT-qPCR, RAPID, and LFA, have been adopted, with RT-qPCR emerging as the gold standard. However, a significant challenge in COVID-19 diagnostics is the wide range of symptoms presented by patients, necessitating early and accurate diagnosis for effective management. Although RT-qPCR is a precise molecular technique, it is not immune to false-negative results. In contrast, CRISPR-based detection methods for SARS-CoV-2 offer several advantages: they are cost-effective, time-efficient, highly sensitive, and specific, and they do not require sophisticated instruments. These methods also show promise for scalability, enabling diagnostic tests. …

Natural Panola Mountain Ehrlichia Infections In Cattle In A Longitudinal Study Of Angus Beef Calves, Cierra Briggs, Drew Casey, Anna Grace Deakins, Jeremy G. Powell, Kelly Loftin, Emily G. Mcdermott

Entomology and Plant Pathology Faculty Publications and Presentations

Panola Mountain Ehrlichia (PME) is an emerging zoonotic pathogen, transmitted by Amblyomma americanum ticks in the southeastern United States. It is closely related to Ehrlichia ruminantium, the causative agent of heartwater disease. Heartwater disease is an often-fatal illness of ruminant livestock present in Africa and the Caribbean. The taxonomic relationship between PME and E. ruminantium has raised concerns about the pathogenicity of PME in livestock. To determine whether cattle could be naturally infected with PME in an endemic area, we conducted a one-year longitudinal study of Angus-breed beef calves in Fayetteville, Arkansas. One hundred seventy-seven calves born between September …

Shell Translucency: A Novel Eggshell Quality Parameter In Broiler Breeders, Duarte Neves, Austin Jasek, Colwayne Morris, Raquel Burin, Kevin Stephens, Marco Rebollo

Proceedings of the Arkansas Nutrition Conference

In the United States, nearly 240 million commercial broiler breeder eggs are incubated weekly with an average hatchability of 79.1% (Third Party Reporting). Between 160 eggs/hen and 125 chicks/hen the loss is considerable. In 2007, an estimated 1% improvement in hatchability would escalate profits by over $25 million to hatcheries and markedly increase profitability in broiler operations (Schaal and Gherian, 2007). In order to tap into top hatchability performances, egg management in commercial hatcheries such as egg storage time and conditions, incubation temperature and humidity, as well as turning frequency are of utmost importance (Vick et al., 1993; Reis et …

Sexual Dimorphism And Divergent Evolutionary Pathways In Primate Cranial Biomechanics: Insights From A Theoretical Morphology Framework, Z. Jack Tseng, Claire E. Terhune

Anthropology Faculty Publications and Presentations

he mammalian order Primates is known for widespread sexual dimorphism in size and phenotype. Despite repeated speculation that primate sexual size dimorphism either facilitates or is in part driven by functional differences in how males and females interact with their environments, few studies have directly assessed the influence of sexual dimorphism on performance traits. Here, we use a theoretical morphology framework to show that sexual dimorphism in primate crania is associated with divergent biomechanical performance traits. The degree of dimorphism is a significant covariate in biomechanical trait divergence between sexes. Males exhibit less efficient but stiffer cranial shapes and significant …

Ontogenetic Biomechanics Of Tufted (Sapajus) And Untufted (Cebus) Capuchin Mandibles, Taylor A. Polvadore, Caitlin B. Yoakum, Parker M. Taylor, Megan A. Holmes, Myra F. Laird, Janine Chalk-Wilayto, Claudia Misue Kanno, Jose Americano De Oliveira, Claire E. Terhune

Anthropology Faculty Publications and Presentations

Objectives

Cortical bone geometry is commonly used to investigate biomechanical properties of primate mandibles. However, the ontogeny of these properties is less understood. Here we investigate changes in cortical bone cross-sectional properties throughout capuchin ontogeny and compare captive versus wild, semi-provisioned groups. Tufted capuchins (Sapajus spp.) are known to consume relatively hard/tough foods, while untufted capuchins (Cebus spp.) exploit less mechanically challenging foods. Previous research indicates dietary differences are present early in development and adult Sapajus mandibles can resist higher bending/shear/torsional loads.

Materials and methods

This study utilized microCT scans of 22 Cebus and 45 Sapajus from early …

Effect Of Heat Stress On The Expression Of Circulating Cyto(Chemo)Kine And Inflammatory Markers In Broiler Chickens Selected For High- Or Low-Water Efficiency, Elizabeth S. Greene, Travis Tabler, Walter G. Bottje, Sara Orlowski, Sami Dridi

Poultry Science Faculty Publications and Presentations

Background:

Water scarcity is a current, significant global concern that will only increase under the pressure of climate change. Improving water efficiency of poultry is a new and promising area to help temper agriculture's future impact on fresh water availability. Here, we explored the effects of acute heat stress (HS) on circulating stress and inflammatory markers in 2 lines of broilers divergently selected for water efficiency. Methods:

Male chicks from low (LWE) and high water efficient (HWE) lines were raised in 12 environmental chambers (2 pens/chamber, 6 chambers/line, 20 birds/pen) under normal conditions until day 28. On day 29, birds …

Investigating In Vivo Tumor Biomolecular Changes Following Radiation Therapy Using Raman Spectroscopy, Varsha Karunakaran, Sina Dadgar, Santosh K. Paidi, April Mordi, Whitney A. Lowe, Umme Marium Mim, Jesse D. Ivers, Joel Rodriguez Troncoso, Jared A. Mcpeake, Alric Fernandes, Sanidhya D. Tripathi, Ishan Barman, Narasimhan Rajaram

Biomedical Engineering Faculty Publications and Presentations

Treatment resistance is a major bottleneck in the success of cancer therapy. Early identification of the treatment response or lack thereof in patients can enable an earlier switch to alternative treatment strategies that can enhance response rates. Here, Raman spectroscopy was applied to monitor early tumor biomolecular changes in sensitive (UM-SCC-22B) and resistant (UM-SCC-47) head and neck tumor xenografts for the first time in in vivo murine tumor models in response to radiation therapy. We used a validated multivariate curve resolution-alternating least-squares (MCR-ALS) model to resolve complex multicomponent Raman spectra into individual pure spectra and their respective contributions. We observed …

Food Science Affiliated Publications, University Of Arkansas, Fayetteville: Snapshot Of The Research Publications, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report provides a snapshot of the research publications for authors affiliated with the Food Science department at the University of Arkansas, Fayetteville, for the period 2018-2023. It includes publications by material type; co-author characteristics; ranking of journals according to journal citation reports.

Leveraging Imitation Learning In Agricultural Robotics: A Comprehensive Survey And Comparative Analysis, Siavash Mahmoudi, Amirreza Davar, Pouya Sohrabipour, Ramesh Bahadur Bist, Yang Tao, Dongyi Wang

Biological and Agricultural Engineering Faculty Publications and Presentations

Imitation learning (IL), a burgeoning frontier in machine learning, holds immense promise across diverse domains. In recent years, its integration into robotics has sparked significant interest, offering substantial advancements in autonomous control processes. This paper presents an exhaustive insight focusing on the implementation of imitation learning techniques in agricultural robotics. The survey rigorously examines varied research endeavors utilizing imitation learning to address pivotal agricultural challenges. Methodologically, this survey comprehensively investigates multifaceted aspects of imitation learning applications in agricultural robotics. The survey encompasses the identification of agricultural tasks that can potentially be addressed through imitation learning, detailed analysis of specific models …

Blend Feeding Broilers To Daily Nutrient Requirements, J.T. Pope

Proceedings of the Arkansas Nutrition Conference

Broiler producers and nutritionists have used phase feeding as a practical means to define broiler feeding programs. Each feed phase has discreet nutrient definitions intended to be fed for a defined number of days based on a feed mass delivered per broiler. A typical broiler feeding program would consist of three to five feed phases over the production cycle that intend to address the changing nutrient requirements as broilers age. Phase feeding programs are easily defined, practical to manage, and provide a predictable cost structure for broiler producers. Despite the practicality of phase feeding, there are inherent flaws that will …

Current Trends And Experiences From A Contract Research Organization Perspective, Dan Moore

Proceedings of the Arkansas Nutrition Conference

The primary goal of this presentation is to provide an update on the trends of research observed at a contract research organization (CRO) in recent years as it relates to species, study design type and products tested, as well as, challenge models used and products that have shown benefits in various study designs. The information in the presentation is based off of studies conducted from 2014-2024 at one CRO, Colorado Quality Research (CQR), and represents the experiences at CQR. Many of the parameters discussed will be from 2014-2019 and 2020-2024 to observe trends from over 5 years ago and more …

Importance Of A Rooster Feed In Broiler Breeder Production, Alex Corzo, Marcelo Silva

Proceedings of the Arkansas Nutrition Conference

Of all feed phases in poultry production, rooster feeding is arguably the least studied. During the rear phase, there is general agreement that male and female broiler breeders can be provided a common feed program, only differing on feed amounts provided, that results in growth targets reached for each sex. It is during the production phase that there is some disagreement on the best way to support the nutritional needs of the adult rooster. A considerable segment of the world does employ a rooster feed as a way to better support the nutritional needs of working males. Other poultry operations …

Vitamin Update And Sustainability, Edgar Orlando Oviedo-Rondón

Proceedings of the Arkansas Nutrition Conference

This presentation addressed the status of research on vitamin nutrition in poultry species and current recommended levels. The economic, environmental, and socio-political aspects of sustainability are addressed. Most of the information presented is described in detail in the book Optimum Vitamin Nutrition for More Sustainable Poultry Farming (Oviedo-Rondon et al., 2023). However, this presentation also used more recent publications and news of the latest events related to scientific recommendations and the worldwide vitamin market. The objective is to provide a brief overview of scientific findings to aid nutritionists in the decision-making process when selecting optimum levels for poultry nutrition. …

Every Day Feeding Of Broiler Breeder Pullets, David Brandt

Proceedings of the Arkansas Nutrition Conference

Broiler breeders are characterized by their fast growth and sensitivity to light stimuli. Unlike commercial layers, they have a lower egg production rate and are kept on the floor during rearing and laying periods. Fertile eggs are the primary objective, necessitating careful management of their egg-laying properties, while controlling their body weights. Unrestricted feeding leads to early laying with poor peak and persistency in egg production. Therefore, nutrient intake must be restricted to achieve target body weights at light stimulation (22 weeks). This involves both quantitative and qualitative feed restrictions. Quantitative feed restriction can lead to issues such as poor …

Integration Of Commercial Broiler Data Into A Broiler Growth Model, David Brandt

Proceedings of the Arkansas Nutrition Conference

This study explores the alignment of theoretical broiler growth models with practical farm conditions, emphasizing the value of integrating commercial data into simulation models. The EFG Broiler Growth Model, developed by Emmens, Fisher and Gous, is highlighted for its mechanistic approach, predicting growth based on feed intake. While empirical models are useful, they are limited by changes in genetics. Both mechanistic and empirical models struggle to predict how broilers will respond to feed under the challenging conditions typically experienced in commercial operations. The study also discusses the development of empirical models to determine broiler responses to balanced protein and energy, …

Expanded Gene And Taxon Sampling Of Diplomonads Shows Multiple Switches To Parasitic And Free-Living Lifestyle, Monika Wiśniewska, Erik Salomaki, Jeffrey D. Silberman, Kristina Terpis, Eva Mazancová, Petr Táborský, Vasana Jinathama, Eleni Gentekaki, Ivan Čepička, Martin Kolisko

Biological Sciences Faculty Publications and Presentations

Background

Diplomonads are anaerobic flagellates classified within Metamonada. They contain both host-associated commensals and parasites that reside in the intestinal tracts of animals, including humans (e.g., Giardia intestinalis), as well as free-living representatives that inhabit freshwater and marine anoxic sediments (e.g., Hexamita inflata). The evolutionary trajectories within this group are particularly unusual as the free-living taxa appear to be nested within a clade of host-associated species, suggesting a reversal from host-dependence to a secondarily free-living lifestyle. This is thought to be an exceedingly rare event as parasites often lose genes for metabolic pathways that are essential to a …

Predicting Spatiotemporal Patterns Of Productivity And Grazing From Multispectral Data Using Neural Network Analysis Based On System Complexity, Amanda J. Ashworth, A. Avila, H. Smith, T. E. Winzeler, P. Owens, C. Flynn, P. O'Brien, D. Philipp, J. Su

Environmental Dynamics Faculty Publications and Presentations

Remote sensing tools, along with Global Navigation Satellite System cattle collars and digital soil maps, may help elucidate spatiotemporal relationships among soils, terrain, forages, and animals. However, standard computational procedures preclude systems-level evaluations across this continuum due to data inoperability and processing limitations. Deep learning, a subset of neural network, may elucidate efficiency of livestock production and linkages within the livestock-grazing environment. Consequently, we applied deep learning to environmental remote sensing data to (1) develop predictive models for yield and forage nutrition based on vegetation indices and (2) at a pixel-level (per 55 m²), identify how grazing is …

Is The Local Environment More Important Than Within-Host Interactions In Determining Coinfection?, Adam Zvanut Hasik, Jason T. Bried, Daniel I. Bolnick, Adam M. Siepielski

Biological Sciences Faculty Publications and Presentations

• Host populations often vary in the magnitude of coinfection they experience across environmental gradients. Furthermore, coinfection often occurs sequentially, with a second parasite infecting the host after the first has established a primary infection. Because the local environment and interactions between coinfecting parasites can both drive patterns of coinfection, it is important to disentangle the relative contributions of environmental factors and within-host interactions to patterns of coinfection.
• Here, we develop a conceptual framework and present an empirical case study to disentangle these facets of coinfection. Across multiple lakes, we surveyed populations of five damselfly (host) species and quantified primary parasitism …

The Wisdom Of Cultural Mapping In Reparative Planning — City In The Woods: Mapping Of Cherokee Village, Arkansas, Stephen Luoni

Community Design Center Faculty Publications and Presentations

As communities and design professionals confront complex cultural issues in planning, new tools are needed to introduce interdisciplinary cultural inquiry into urban design/planning. Reparative planning is premised on a reckoning with socio-economic and environmental decline through design of the built environment. Cultural mapping is necessary to both visibilize suppressed narratives behind decline and inequity, as well as underwrite new policy and development approaches. City in the Woods is a cultural mapping project that supports planning for Cherokee Village. Moving beyond the map as object to mapping as a process, we employed the deep map to sketch a memoir of place …

Noise Leads To The Perceived Increase In Evolutionary Rates Over Short Time Scales, Brian C. O'Meara, Jeremy M. Beaulieu

Biological Sciences Faculty Publications and Presentations

Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show …

Diverse Origins Of Near-Identical Antifreeze Proteins In Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms Of New Gene Birth And Protein Sequence Convergence, Nathan Rives, Vinita Lamba, C.H. Christina Cheng, Xuan Zhuang

Biological Sciences Faculty Publications and Presentations

Determining the origins of novel genes and the mechanisms driving the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. Recently evolved fish antifreeze proteins (AFPs) offer a unique opportunity to explore these processes, particularly the near-identical type I AFP (AFPI) found in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages. Through comprehensive comparative analyses of newly sequenced genomes of winter flounder and grubby sculpin, along with available high-quality genomes of cunner and 14 other related species, the study revealed that near-identical …

Assessment Of Novel Protein Ingredient Arthrospira Platensis And Soybean Genotype Amino Acid And Oil Selection Improvements On Broiler Performance For A 28-42 D Feeding Period, Savannah C. Wells-Crofton, Kenneth B. Nelson, Garrett J. Mullenix, Craig W. Maynard, Michael T. Kidd

Poultry Science Faculty Publications and Presentations

Two experiments were conducted to assess the efficiency of including the novel protein ingredient Arthrospira platensis or improved soybean meal in a broiler diet. The first experiment aimed to determine the feeding value of soybean meal produced from varieties of soybeans bred for increased amino acid content (SBAA) and improved oil content (SBO) compared to a conventional soybean variety in an ANOVA design fed to Cobb 500 female broilers for 28–42 d. The SBAA and SBO soybeans contained overall higher amino acid content and lower oligosaccharide content compared to the conventional soybean variety in addition to improved oil quality. The …

Research Note: Carcass Yield And Meat Quality In High- And Low-Water Efficient Broiler Lines Exposed To Heat Stress, Sara Orlowski, Elizabeth Greene, Kentu Lassiter, Travis Tabler, Walter Bottje, Sami Dridi

Poultry Science Faculty Publications and Presentations

Heat stress (HS) and water scarcity are significant challenges to sustainable poultry production worldwide. It is, therefore, critical to identify effective strategies to prevent, withstand, or adapt to these challenges. After four generations of divergent selection for water efficiency, the present study was undertaken to determine the effect of HS on meat quality and muscle myopathy incidences in high (HWE)- and low (LWE)-water efficient broilers. Day-old male chicks (240 chicks/line) were allotted randomly by line and body weight-matched groups to 12 controlled-environmental chambers (2 pens/chamber). At d29, birds were exposed to 2 environmental conditions …