Digital Commons Network^™

Experimental Evaluation Of Ecological Principles To Understand And Modulate The Outcome Of Bacterial Strain Competition In Gut Microbiomes, Rafael R. Segura Munoz, Sara Mantz, Ines Martinez, Fuyong Li, Robert J. Schmaltz, Nicholas A. Pudlo, Karthik Urs, Eric C. Martens, Jens Walter, Amanda Ramer-Tait

Department of Food Science and Technology: Faculty Publications

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus …

Recent Advances In Biosensors For Detection Of Covid-19 And Other Viruses, Shobhit K. Patel, Jaymit Surve, Juveriya Parmar, Kawsar Ahmed, Francis M. Bui, Fahad Ahmed Al-Zahrani

Department of Mechanical and Materials Engineering: Faculty Publications

This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and …

A Robot-Assisted Acoustofluidic End Effector, Jan Durrer, Prajwal Agrawal, Ali Ozgul, Stephen C.F. Neuhauss, Nitesh Nama, Daniel Ahmed

Department of Mechanical and Materials Engineering: Faculty Publications

Liquid manipulation is the foundation of most laboratory processes. For macroscale liquid handling, both do-it-yourself and commercial robotic systems are available; however, for microscale, reagents are expensive and sample preparation is difficult. Over the last decade, lab-on-a-chip (LOC) systems have come to serve for microscale liquid manipulation; however, lacking automation andmulti-functionality. Despite their potential synergies, each has grown separately and no suitable interface yet exists to link macro-level robotics with micro-level LOC or microfluidic devices. Here, we present a robot-assisted acoustofluidic end effector (RAEE) system, comprising a robotic arm and an acoustofluidic end effector, that combines robotics and microfluidic functionalities.We …

A Prototype Evaluation Tool For Museum Exhibition Design: Aligning Display Techniques With Learning Identities, Khloud Khalid Eldamshiry, Rania Rushdy Moussa

Architectural Engineering

Museums have been forced by the pressure of change to switch practices and outlooks to transform museum visitors from passive consumers in a collection-focused ‘static exhibition’ to active participants in a visitor- centred ‘interactive technology exhibition’. This paper aims to model a framework for museum exhibition design that can be used as a prototype evaluation tool. It is achieved throughout analysing the interrelationships between museum visitors learning identities and their museum experiences and what are the display techniques that can be used to increase museum visitors’ social interaction with the museum environment and how each technique will affect the visitor’s …

Open Air Natural History Museums Transformation: From Static To Interactive, Khloud Khalid Eldamshiry

Architectural Engineering

Open air natural history museums act as a distinct type of museum that exhibits its collections out of doors aiming to record earlier life forms, ways of life, cultural customs and habits. Nowadays, museums including the Natural History Museums, look forward to increase the number of visitors and revisited visitors, throughout transforming museum visitors from passive consumers in a collection focused ‘static exhibition’ to active participants in a visitor centered ‘interactive technology exhibition’ by making the museum collection easier for the general public to use, more technically and technologically displayed. Therefore, display techniques became a main key within the visitors …

An Examination Of Ethical Attitudes Towards Wild Pig (Sus Scrofa) Toxicants In The United States, Keith Carlisle, Erin E. Harper, Stephanie A. Shwiff

United States Department of Agriculture Wildlife Services: Staff Publications

This research aims to understand ethical attitudes of the U.S. public towards the use of a toxicant to control wild pigs (Sus scrofa), a destructive invasive species whose population growth is proving difficult to control through conventional management methods. Using a nationwide self-administered survey with 2,186 completed and returned questionnaires, we found that among six different lethal control methods, toxicant usage was the only method that a majority of respondents (51%) found to be unethical, with no significant differences between rural and urban respondents or between respondents from counties with wild pigs and counties where the species is absent. The …

Celecoxib As An Adjuvant To Chemotherapy For Patients With Metastatic Colorectal Cancer: A Randomized Controlled Clinical Study, Tarek M. Mostafa, Amira R. Rashdan

Saudi Medical Journal

Abstract Objectives: To investigate the anti-tumor activity and tolerability of celecoxib as an adjuvant therapy for patients with metastatic colorectal cancer (CRC). Methods: In this randomized controlled study, 54 patients with metastatic CRC were randomized into 2 groups; the control group (n=28) which received 6 cycles of folinic acid, fluorouracil and irinotecan (FOLFIRI) regimen (5-flourouracil, leucovorin, irinotecan), and the celecoxib group (n=26) which received 6 cycles of FOLFIRI regimen plus celecoxib 200 mg twice daily. The study duration was 3 months. Patients were assessed at baseline and at the end of intervention through the Response Evaluation Criteria in Solid Tumors …

The Third International Hackathon For Applying Insights Into Large-Scale Genomic Composition To Use Cases In A Wide Range Of Organisms, Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, Fritz J. Sedlazeck, Ben Busby, Chia-Sin Liew, Et Al.

Nebraska Center for Biotechnology: Faculty and Staff Publications

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Improving Taxonomic Delimitation Of Fungal Species In The Age Of Genomics And Phenomics, Ashley Stengel, Kimberly M. Stanke, Amanda C. Quattrone, Joshua R. Herr

Department of Plant Pathology: Faculty Publications

Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss …

Dynamic Causal Modeling Of Neural Responses To An Orofacial Pneumotactile Velocity Array, Yingying Wang, Rebecca Custead, Hyuntaek Oh, Steven M. Barlow

Department of Special Education and Communication Disorders: Faculty Publications

The effective connectivity of neuronal networks during orofacial pneumotactile stimulation with different velocities is still unknown. The present study aims to characterize the effectivity connectivity elicited by three different saltatory velocities (5, 25, and 65 cm/s) over the lower face using dynamic causal modeling on functional magnetic resonance imaging data of twenty neurotypical adults. Our results revealed the contralateral SI and SII as the most likely sources of the driving inputs within the sensorimotor network for the pneumotactile stimuli, suggesting parallel processing of the orofacial pneumotactile stimuli. The 25 cm/s pneumotactile stimuli modulated forward interhemispheric connection from the contralateral SII …

Ankrd24 Organizes Triobp To Reinforce Stereocilia Insertion Points, Jocelyn F. Krey, Chang Liu, Inna A. Belyantseva, Michael Bateschell, Rachel A. Dumont, Jennifer Goldsmith, Paroma Chatterjee, Rachel S. Morrill, Lev M. Fedorov, Sarah Foster, Jinkyung Kim, Alfred L. Nuttal, Sherri M. Jones, Dongseok Choi, Thomas B. Friedman, Anthony J. Ricci, Bo Zhao, Peter G. Barr-Gillespie

Department of Special Education and Communication Disorders: Faculty Publications

The stereocilia rootlet is a key structure in vertebrate hair cells, anchoring stereocilia firmly into the cell’s cuticular plate and protecting them from overstimulation. Using superresolution microscopy, we show that the ankyrin-repeat protein ANKRD24 concentrates at the stereocilia insertion point, forming a ring at the junction between the lower and upper rootlets. Annular ANKRD24 continues into the lower rootlet, where it surrounds and binds TRIOBP-5, which itself bundles rootlet F-actin. TRIOBP-5 is mislocalized in Ankrd24^KO/KO hair cells, and ANKRD24 no longer localizes with rootlets in mice lacking TRIOBP-5; exogenous DsRed–TRIOBP-5 restores endogenous ANKRD24 to rootlets in these mice. Ankrd24 …

Relationship Between Reproductive Hormones And Migration Distance In A Polygynous Songbird, The Red‑Winged Blackbird (Agelaius Phoeniceus), Michelle A. Eshleman, Page E. Klug, Esther Morales‑Vega, Björn Wissel, Timothy J. Grelves

United States Department of Agriculture Wildlife Services: Staff Publications

Many bird species migrate to southern overwintering locations to avoid harsh conditions at their breeding grounds, but at the cost of an energetically demanding migration that may delay their spring reproductive development. Previous work on the relationship between migration distance and reproductive readiness has primarily focused on early season baseline testosterone in both males and females. However, for females, testosterone alone may not be the appropriate measurement of reproductive development. Estradiol, a metabolite of testosterone that is essential for breeding behaviors and reproduction, should also be measured. Furthermore, baseline testosterone varies throughout the day and may change due to social …

A Systematic Map Of Human-Carnivore Coexistence, Cassandre C. Venumière-Lefebvre, Stewart W. Breck, Kevin R. Crooks

United States Department of Agriculture Wildlife Services: Staff Publications

Carnivore populations globally have largely declined, and coexistence, where humans and carnivores share landscapes, plays a crucial role in carnivore conservation. However, the term “coexistence” is often used in scientific and popular literature without being clearly defined. Herein, we provide a global perspective on what coexistence is and how it is studied. We conducted a systematic map of 366 articles published between 1987 and 2020 to characterize human-carnivore coexistence literature according to coexistence definitions, temporal trends, geographic and taxonomic focus, and four thematic aspects of coexistence: carnivore ecology, human endeavors, social conflict and human-carnivore conflict. We used chi-squared tests and …

Frugivory And Seed Dispersal By Carnivorans, John P. Draper, Julie K. Young, Eugene W. Schupp, Noelle G. Beckman, Trisha B. Atwood

United States Department of Agriculture Wildlife Services: Staff Publications

Seed dispersal is critical to the ecological performance of sexually reproducing plant species and the communities that they form. The Mammalian order Carnivora provide valuable and effective seed dispersal services but tend to be overlooked in much of the seed dispersal literature. Here we review the literature on the role of Carnivorans in seed dispersal, with a literature search in the Scopus reference database. Overall, we found that Carnivorans are prolific seed dispersers. Carnivorans’ diverse and plastic diets allow them to consume large volumes of over a hundred families of fruit and disperse large quantities of seeds across landscapes. Gut …

Aboveground Carbon Responses To Experimental And Natural Hurricane Impacts In A Subtropical Wet Forest In Puerto Rico, Hervé Chevalier, Nicholas V.L. Brokaw, Sheila E. Ward, Jess K. Zimmerman, Aaron B. Shiels, John Bithorn, Samuel Matta Carmona

United States Department of Agriculture Wildlife Services: Staff Publications

Climate change and disturbance make it difficult to project long-term patterns of carbon sequestration in tropical forests, but large ecosystem experiments in these forests can inform predictions. The Canopy Trimming Experiment (CTE) manipulates two key components of hurricane disturbance, canopy openness and detritus deposition, in a tropical forest in Puerto Rico. We documented how the CTE and a real hurricane affected tree recruitment, biomass, and aboveground carbon storage over 15 years. In the CTE treatments, we trimmed branches, but we did not fell trees. We expected that during the 14-year period after initial canopy trimming, regrowth of branches and stems …

Behavioral States In Space And Time: Understanding Landscape Use By An Invasive Mammal, Steven M. Gray, John M. Humphreys, Robert A. Montgomery, Dwayne R. Etter, Kurt C. Vercauteren, Daniel B. Kramer, Gary J. Roloff

United States Department of Agriculture Wildlife Services: Staff Publications

Animal movement models can be used to understand species behavior and assist with implementation of management activities. We explored behavioral states of an invasive wild pig (Sus scrofa) population that recently colonized central Michigan, USA, 2014–2018. To quantify environmental factors related to wild pig movement ecology and spatio‐temporal landscape use, we predicted wild pig behavioral states relative to land cover type, landscape structure (i.e., edge and patch cohesion), and weather conditions. We used global positioning system (GPS)‐collars and monitored 8 wild pigs from 2014–2018. We fit local convex hulls and calculated movement metrics revealing 3 wild pig behavioral states (resting, …

Concentration-Response Of An Anthraquinone-Based Repellent For Raccoons (Procyon Lotor), Shylo Johnson, Shelagh T. Deliberto, Kathleen Urchek, Amy T. Gilbert, Scott J. Werner

United States Department of Agriculture Wildlife Services: Staff Publications

Wildlife repellents can be part of non-lethal management strategies to reduce the negative impacts of wildlife to property, agricultural production, and human health and safety. Raccoons (Procyon lotor) are associated with negative impacts in all three of these areas. Anthraquinone is a useful avian repellent and its utility as a mammalian repellent is still being explored. Our objective was to evaluate laboratory efficacy of an anthraquinone-based repellent for raccoons using different concentrations. We fed captive raccoons whole corn treated at 0.5%, 1%, 1.5% and 2% anthraquinone and examined their behavioral response related to feeding repellency including consumption and change in …

Accounting For Animal Movement Improves Vaccination Strategies Against Wildlife Disease In Heterogeneous Landscapes, Katherine M. Mcclure, Guillaume Bastille-Rousseau, Amy J. Davis, Carolyn A. Stengel, Kathleen M. Nelson, Richard B. Chipman, George Wittemyer, Zaid Abdo, Amy Gilbert, Kim M. Pepin

United States Department of Agriculture Wildlife Services: Staff Publications

Oral baiting is used to deliver vaccines to wildlife to prevent, control, and eliminate infectious diseases. A central challenge is how to spatially distribute baits to maximize encounters by target animal populations, particularly in urban and suburban areas where wildlife such as raccoons (Procyon lotor) are abundant and baits are delivered along roads. Methods from movement ecology that quantify movement and habitat selection could help to optimize baiting strategies by more effectively targeting wildlife populations across space. We developed a spatially explicit, individual-based model of raccoon movement and oral rabies vaccine seroconversion to examine whether and when baiting …

Using Noninvasive Genetics For Estimating Density And Assessing Diet Of Urban And Rural Coyotes In Florida, Usa, Bryan M. Kluever, Martin B. Main, Stewart W. Breck, Robert C. Lonsinger, John H. Humphrey, Justin W. Fischer, Michael P. Milleson Usda Aphis Wildlife Services, Gainesville, Antionette J. Piaggio

United States Department of Agriculture Wildlife Services: Staff Publications

Coyotes (Canis latrans) are expanding their range and due to conflicts with the public and concerns of Coyotes affecting natural resources such as game or sensitive species, there is interest and often a demand to monitor Coyote populations. A challenge to monitoring is that traditional invasive methods involving live-capture of individual animals are costly and can be controversial. Natural resource management agencies can benefit from contemporary noninvasive genetic sampling approaches aimed at determining key aspects of Coyote ecology (e.g., population density and food habits). However, the efficacy of such approaches under different environmental conditions is poorly understood. Our …

Invasive Predators Affect Community-Wide Pollinator Visitation, Christina T. Liang, Aaron B. Shiels, William P. Haines, Manette E. Sandor, Clare E. Aslan

United States Department of Agriculture Wildlife Services: Staff Publications

Disruption of plant–pollinator interactions by invasive predators is poorly understood but may pose a critical threat for native ecosystems. In a multiyear field experiment in Hawai’i, we suppressed abundances of globally invasive predators and then observed insect visitation to flowers of six native plant species. Three plant species are federally endangered (Haplostachys haplostachya, Silene lanceolata, Tetramolopium arenarium) and three are common throughout their range (Bidens menziesii, Dubautia linearis, Sida fallax). Insect visitors were primarily generalist pollinators, including taxa that occur worldwide such as solitary bees (e.g., Lasioglossum impavidum), social bees (e.g., …

Spatial Risk Modeling Of Cattle Depredation By Black Vultures In The Midwestern United States, Brandon M. Quinby, Bryan M. Kluever, Grant N. Burcham, Lee Humberg, Landon R. Jones, Marian L. Wahl, Patrick A. Zollner

United States Department of Agriculture Wildlife Services: Staff Publications

ock operations through depredation of stock are a cause of human‐wildlife conflict. Management of such conflict requires identifying environmental and non‐environmental factors specific to a wildlife species' biology and ecology that influence the potential for livestock depredation to occur. Identification of such factors can improve understanding of the conditions placing livestock at risk. Black vultures (Coragyps atratus) have expanded their historical range northward into the midwestern United States. Concomitantly, an increase in concern among agricultural producers regarding potential black vulture attacks on livestock has occurred. We estimated area with greater or lesser potential for depredation of domestic cattle by black …

Capture-Recapture Reveals Heterogeneity In Habitat-Specific Mongoose Densities And Spatiotemporal Variability In Trapping Success In St. Kitts, West Indies, Caroline C. Sauvé, Are R. Berentsen, Amy Gilbert, Anne Conan, Luis Cruz-Martinez, Patrick A. Leighton

United States Department of Agriculture Wildlife Services: Staff Publications

The small Indian mongoose (Urva auropunctata) is a non-native invasive species across the Caribbean and a rabies reservoir on at least four islands in the region. Although previous studies reported mongoose density estimates in their non-native range, the variability in trapping designs, study seasonality, and analytical methods among studies precludes direct comparisons. This study is the first to report mongoose densities for the island of St. Kitts, West Indies. Our objective was to quantify mongoose densities across four habitats characteristic for the island. High capture and recapture rates in this study resulted in detailed estimates of spatial heterogeneity …

Rodents In Agriculture: A Broad Perspective, Gary Witmer

United States Department of Agriculture Wildlife Services: Staff Publications

The largest taxonomic group of mammals is rodents, with over 2200 species known around the world [1]. More recently, it was stated that over 2500 species exist [2]. Many species exist on all continents, with the exception of Antarctica. Rodents have adapted to all ecosystems of the world, including tundra, alpine, temperate forests, grasslands, arid regions, and aquatic systems. They provide many ecosystem functions, including soil aeration and mixing, seed and spore dispersal, vegetation succession, and being an important food source for predatory animals. Some species of rodents are even consumed by people in some parts of the world. Most …

Transmission Of Antibiotic Resistance At The Wildlife-Livestock Interface, Shinyoung Lee, Peixin Fan, Ting Liu, Anni Yang, Raoul K. Boughton, Kim M. Pepin, Ryan S. Miller, Kwangcheol Casey Jeong

United States Department of Agriculture Wildlife Services: Staff Publications

Antibiotic-resistant microorganisms (ARMs) are widespread in natural environments, animals (wildlife and livestock), and humans, which has reduced our capacity to control life threatening infectious disease. Yet, little is known about their transmission pathways, especially at the wildlife-livestock interface. This study investigated the potential transmission of ARMs and antibiotic resistance genes (ARGs) between cattle and wildlife by comparing gut microbiota and ARG profiles of feral swine (Sus scrofa), coyotes (Canis latrans), cattle (Bos taurus), and environmental microbiota. Unexpectedly, wild animals harbored more abundant ARMs and ARGs compared to grazing cattle. Gut microbiota of cattle was …

Dammed Water Quality—Longitudinal Stream Responses Below Beaver Ponds In The Umpqua River Basin, Oregon, John R. Stevenson, Jason B. Dunham, Steven M. Wondzell, Jimmy Taylor

United States Department of Agriculture Wildlife Services: Staff Publications

Beaver-related restoration (BRR) has gained popularity as a means of improving stream ecosystems, but the effects are not fully understood. Studies of dissolved oxygen (DO) and water temperature, key water quality metrics for salmonids, have demonstrated improved conditions in some cases, but warming and decreased DO have been more commonly reported in meta-analyses. These results point to the contingencies that can influence outcomes from BRR. We examined water quality related to beaver ponds in a diverse coastal watershed (Umpqua River Basin, OR, USA). We monitored water temperature 0–400m above and below beaver ponds and at pond surfaces and bottoms across …

Economic Damages Of Wild Pigs In Non-Traditional Areas: From The Fairway To The After Life, Sophie Mckee, Julie Elser, Maryfrances Miller, Lirong Liu, Ryan Miller, Steven S. Shwiff, Stephanie A. Shwiff

United States Department of Agriculture Wildlife Services: Staff Publications

Invasive wild pigs are widely known to cause damage to agricultural properties and commodities, but less has been reported about damages to other types of property. A survey was distributed to golf courses and cemeteries across Texas to explore the extent of damage these properties experience. While both property types reported significant damages, golf courses were found to experience more damage than cemeteries. Using average reported costs and predicted county-level damage, total costs for all golf courses and cemeteries across the state were estimated to exceed $1.6 million USD per year.

Sars-Cov-2 In Wildlife: Q & A With Alan B. Franklin, Alan B. Franklin

United States Department of Agriculture Wildlife Services: Staff Publications

Welcome Dr Franklin and thank you for joining us to help social workers increase their knowledge about the interconnectedness of humans, other mammals, and the environment. Let's begin with zoonosis.

Viruses can be transferred from wild and domestic animals to humans in a process called zoonosis.

Strength In Numbers: Avian Influenza A Virus Transmission To Poultry From A Flocking Passerine, J. Jeffrey Root, Jeremy W. Ellis, Susan A. Shriner

United States Department of Agriculture Wildlife Services: Staff Publications

The effects of flock size of European starlings (Sturnus vulgaris) was experimentally manipulated to assess the potential of influenza A virus (IAV; H4N6) transmission from a flocking passerine to bobwhite quail (Colinus virginianus) through shared food and water resources to mimic starling intrusions into free-range and backyard poultry operations. Of the three starling flock sizes tested (n = 30, n = 20 and n = 10), all successfully transmitted the virus to all or most of the quail in each animal room (6/6, 6/6 and 5/6) by the end of the experimental period, as determined by seroconversion and/or viral RNAshedding. …

Social Learning Of Avoidance Behaviors: Trap Aversion In Captive Coyotes, Julie Young, Jeffrey T. Schultz, Buck Jolley, Nekol Basili, John P. Draper

United States Department of Agriculture Wildlife Services: Staff Publications

Social learning can help animals gain knowledge rapidly and may enhance survival. In species that are subjected to capture in foothold traps and then lethally removed, such as the coyote (Canis latrans), learning to avoid traps is critical to survival. Here, we tested social learning of trap avoidance behavior in three experimental scenarios with captive coyotes. In the first experiment, coyotes observed an unfamiliar coyote get captured in a foothold trap (i.e., demonstrator) or did not observe a demonstrator and were therefore naïve to traps. The coyotes that observed a demonstrator showed similar latencies to approach the trap …

Predicting Consistent Foraging Ecologies Of Migrating Waterbirds: Using Stable Isotope And Parasite Measurements As Indicators Of Landscape Use, Kate L. Sheehan, Brian S. Dorr, Stephen A. Clements, Terrel W. Christie, Katie Hanson-Dorr, Scott A. Rush, J. Brian Davis

United States Department of Agriculture Wildlife Services: Staff Publications

The emergence of novel human pathogens is frequently linked with zoonotic events and human-wildlife interactions that promote disease transmission. Consequently, surveillance of wildlife populations for candidate diseases that could spread to humans is beneficial, but requires widespread collections of numerous samples. A legitimate means to acquire large sample sizes of waterfowl is through cooperation between researchers and hunters, who also work in concert with natural resource managers, landowners, and agricultural entities -e.g., aquaculture facilities. In addition to understanding the occurrence and spread of parasites and pathogens by birds, these samples can be used to answer questions about the ecology of …