Digital Commons Network^™

Minerals Matter: Science, Technology, And Society, Barbara L. Dutrow

Faculty Publications

The expertise of earth scientists is crucial for solving some of today's most pressing challenges, including global warming and the climate crises, natural hazard reduction, water and soil quality, exploration for critical elements for our technological society, and many others.

The Small Rna Universe Of Capitella Teleta, Sweta Khanal, Beatriz Schueng Zancanela, Jacob Oche Peter, Alex Sutton Flynt

Faculty Publications

RNAi is an evolutionarily fluid mechanism with dramatically different activities across animal phyla. One major group where there has been little investigation is annelid worms. Here, the small RNAs of the polychaete developmental model Capitella teleta are profiled across development. As is seen with nearly all animals, nearly 200 microRNAs were found with 58 high-confidence novel species. Greater miRNA diversity was associated with later stages consistent with differentiation of tissues. Outside miRNA, a distinct composition of other small RNA pathways was found. Unlike many invertebrates, an endogenous siRNA pathway was not observed, indicating pathway loss relative to basal planarians. No …

Exploring Pre-Service Teachers’ Perspectives: Gender And Gender Representation Across Human Protagonists In Picture Books, Taraneh Matloob Haghanikar, Shan Jiang, Sara Tomek, Lisa M. Hooper

Faculty Publications

Gender is ever present in education preparation, school materials, curriculum, and school systems. To improve our knowledge about different facets of gender and the extent to which the depiction of gender has changed over time in picture books, there is a need to dig beneath the surface of questions about gender representation in picture books. Given that in-service teachers have proximity to approximately 75 million K-12 students, how in-service teachers think about gender, gender representation, and their own experiences with gender socialization have important implications on how K-12 students think, act, and feel about gender. In this study, we focused …

Disclaiming Disability, Nicole Buonocore Porter

Faculty Publications

In the Americans with Disabilities Act (“ADA”) Amendments Act of 2008, Congress ordered the courts to broadly interpret the definition of disability under the ADA. For the most part, courts have followed that instruction, but there are still too many instances in which they have not. One particularly pernicious error made by courts is relying on a plaintiff’s statement “disclaiming” her disability — that is, testifying that she does not consider herself “disabled” — to hold that she does not meet the statutory definition of disability, and therefore loses her claim. This Article addresses this error. Specifically, after cataloguing this …

Transcriptional Coactivators: Driving Force Of Plant Immunity, Muhammad Saad Shoaib Khan, Faisal Islam, Huan Chen, Ming Chang, Daowen Wang, Fengquan Liu, Zhengqing Fu, Jian Chen

Faculty Publications

Salicylic acid (SA) is a plant defense signal that mediates local and systemic immune responses against pathogen invasion. However, the underlying mechanism of SA-mediated defense is very complex due to the involvement of various positive and negative regulators to fine-tune its signaling in diverse pathosystems. Upon pathogen infections, elevated level of SA promotes massive transcriptional reprogramming in which Non-expresser of PR genes 1 (NPR1) acts as a central hub and transcriptional coactivator in defense responses. Recent findings show that Enhanced Disease Susceptibility 1 (EDS1) also functions as a transcriptional coactivator and stimulates the expression of PR1 in the presence of …

Dispersed Crude Oil Induces Dysbiosis In The Red Snapper Lutjanus Campechanus External Microbiota, Andrew M. Tarnecki, Christelle Miller, Tracy A. Sherwood, Robert J. Griffitt, Ryan W. Schloesser, Dana L. Wetzel

Faculty Publications

The fish external microbiota competitively excludes primary pathogens and prevents the proliferation of opportunists. A shift from healthy microbiota composition, known as dysbiosis, may be triggered by environmental stressors and increases host susceptibility to disease. The Deepwater Horizon (DWH) oil spill was a significant stressor event in the Gulf of Mexico. Despite anecdotal reports of skin lesions on fishes following the oil spill, little information is available on the impact of dispersed oil on the fish external microbiota. In this study, juvenile red snapper (Lutjanus campechanus) were exposed to a chemically enhanced water-accommodated fraction (CEWAF) of Corexit 9500/DWH …

Reassessing The Role Of Anthropogenic Climate Change In The Extinction Of Silphium, Paul Pollaro, Paul Robertson

Faculty Publications

The famed ancient herb, known to the Romans as silphium (Greeksilphion), is widely regarded as the first recorded instance of human-induced species extinction. Modern scholars have largely credited direct exploitation (e.g., over-harvesting; over-grazing) as the primary cause of silphium's extinction, due to an overwhelming demand for the plant in ancient times. Recent research has revealed strict cold-stratification requirements for the germination of silphium's closest living relatives, revealing the likelihood that silphium shared these same germination requirements. Documented environmental changes in ancient Cyrenaica (e.g., widespread deforestation; cropland expansion) likely resulted in accelerated rates of desertification throughout the region as well as …

Future Of Winter In Northeastern North America: Climate Indicators Portray Warming And Snow Loss That Will Impact Ecosystems And Communities, Elizabeth Burakowski, Alix Contosta, Danielle Grogan, Sarah Nelson, Sarah Garlick, Nora Casson

Faculty Publications

Winters in northeastern North America have warmed faster than summers, with impacts on ecosystems and society. Global climate models (GCMs) indicate that winters will continue to warm and lose snow in the future, but uncertainty remains regarding the magnitude of warming. Here, we project future trends in winter indicators under lower and higher climate-warming scenarios based on emission levels across northeastern North America at a fine spatial scale (1/16°) relevant to climate-related decision making. Under both climate scenarios, winters continue to warm with coincident increases in days above freezing, decreases in days with snow cover, and fewer nights below freezing. …

An Exploratory Study On The Microbiome Of Northern And Southern Populations Of Ixodes Scapularis Ticks Predicts Changes And Unique Bacterial Interactions, Deepak Kumar, Latoyia P. Downs, Abdulsalam Adegoke, Erika Machtinger, Kelly Oggenfuss, Richard S. Ostfeld, Monica Embers, Shahid Karim

Faculty Publications

The black-legged tick (Ixodes scapularis) is the primary vector of Borrelia burgdorferi, the causative agent of Lyme disease in North America. However, the prevalence of Lyme borreliosis is clustered around the Northern States of the United States of America. This study utilized a metagenomic sequencing approach to compare the microbial communities residing within Ix. scapularis populations from northern and southern geographic locations in the USA. Using a SparCC network construction model, we performed potential interactions between members of the microbial communities from Borrelia burgdorferi–infected tissues of unfed and blood-fed ticks. A significant difference in bacterial composition …

Ultrafast High-Energy Micro-Supercapacitors Based On Open-Shell Polymer-Graphene Composites, Lulu Yao, Naresh Eedugurala, Paramasivam Mahalingavelar, Daniel J. Adams, Kaiping Wang, Kevin S. Mayer, Jason D. Azoulay, Tse Nga Ng

Faculty Publications

Micro-supercapacitors are poised to serve as on-chip power sources for electronics. However, the challenge to simultaneously increase their power, energy, and lifetime demands new material combinations beyond current carbon-based systems. Here, we demonstrate that electro-deposition of an open-shell conjugated polymer with reduced graphene oxide achieves electrodes with capacitance up to 186 mF cm⁻² (372 F cm⁻³). The extended delocalization within the open-shell polymer stabilizes redox states and facilitates a 3 V wide potential window, while the hierarchical electrode structure promotes ultrafast kinetics. The micro-supercapacitor shows a high power density of 227 mW cm⁻² with an energy …

Reef Sediments Can Act As A Stony Coral Tissue Loss Disease Vector, Michael S. Studivan, Ashley M. Rossin, Ewelina Rubin, Nash Soderberg, Daniel M. Holstein, Ian C. Enochs

Faculty Publications

Stony coral tissue loss disease (SCTLD) was first observed in 2014 near Virginia Key in Miami-Dade County, Florida. Field sampling, lab experiments, and modeling approaches have suggested that reef sediments may play a role in SCTLD transmission, though a positive link has not been tested experimentally. We conducted an ex situ transmission assay using a statistically-independent disease apparatus to test whether reef sediments can transmit SCTLD in the absence of direct contact between diseased and healthy coral tissue. We evaluated two methods of sediment inoculation: batch inoculation of sediments collected from southeast Florida using whole colonies of diseased Montastraea cavernosa, …

Improved Chromosome-Level Genome Assembly Of The Glanville Fritillary Butterfly (Melitaea Cinxia) Integrating Pacific Biosciences Long Reads And A High-Density Linkage Map, Olli-Pekka Smolander, Daniel Blande, Virpi Ahola, Pasi Rastas, Jaakko Tanskanen, Juhana Kammonen, Vicencio Oostra, Lorenzo Pellegrini, Suvi Ikonen, Tad Dallas, Michelle F. Dileo, Anne Duplouy, Iihan Cem Duru, Pauliina Halimaa, Aapo Kahilainen, Suyog S. Kuwar, Sirpa O. Kärenlampi, Elvira Lafuente, Shiqi Luo, Jenny Makkonen, Abhilash Nair, Narua De La Paz Celorio-Mancera, Ville Pennanen, Annukka Ruokolainen, Tarja Sundell, Arja I. Tervahauta, Victoria Twort, Erik Van Bergen, Janina Österman-Udd, Lars Paulin, Mikko J. Frilander, Petri Auvinen, Marjo Saastamoinen

Faculty Publications

Background

The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses.

Results

The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and …

Current Methods And Future Directions In Avian Diet Analysis, Brandon D. Hoenig, Allison M. Snider, Anna M. Forsman, Keith A. Hobson, Steven C. Latta, Eliot T. Miller, Michael J. Polito, Luke L. Powell, Samantha L. Rogers, Thomas W. Sherry, David P.L. Toews, Andreanna J. Welch, Sabrina S. Taylor, Brady A. Porter

Faculty Publications

Identifying the composition of avian diets is a critical step in characterizing the roles of birds within ecosystems. However, because birds are a diverse taxonomic group with equally diverse dietary habits, gaining an accurate and thorough understanding of avian diet can be difficult. In addition to overcoming the inherent difficulties of studying birds, the field is advancing rapidly, and researchers are challenged with a myriad of methods to study avian diet, a task that has only become more difficult with the introduction of laboratory techniques to dietary studies. Because methodology drives inference, it is important that researchers are aware of …

The Isocaloric Substitution Of Plant-Based And Animal-Based Protein In Relation To Aging-Related Health Outcomes: A Systematic Review, Jiali Zheng, Tianren Zhu, Guanghuan Yang, Longgang Zhao, Fangyu Li, Yong-Moon Park, Fred K. Tabung, Susan E. Steck Phd, Mph, Rd, Xiaoguang Li, Hui Wang

Faculty Publications

Plant-based and animal-based protein intake have differential effects on various aging-related health outcomes, but less is known about the health effect of isocaloric substitution of plant-based and animal-based protein. This systematic review summarized current evidence of the isocaloric substitutional effect of plant-based and animal-based protein on aging-related health outcomes. PubMed and Embase databases were searched for epidemiologic observational studies published in English up to 15 March 2021. Studies that included adults ≥18 years old; use of a nutritional substitution model to define isocaloric substitution of plant protein and animal protein; health outcomes covering mortality, aging-related diseases or indices; and reported …

Evolutionary Analyses Of Visual Opsin Genes In Frogs And Toads: Diversity, Duplication, And Positive Selection, Ryan K. Schott, Leah Perez, Matthew Kwiatkowski, Vance Imhoff, Jennifer M. Gumm

Faculty Publications

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found …

Chronic Background Radiation Correlates With Sperm Swimming Endurance In Bank Voles From Chernobyl, Kati Kivisaari, Sara Calhim, Zbyszek Boratyríski, Timothy Mousseau, Anders P. Møller, Tapio Mappes

Faculty Publications

Sperm quantity and quality are key features explaining intra- and interspecific variation in male reproductive success. Spermatogenesis is sensitive to ionizing radiation and laboratory studies investigating acute effects of ionizing radiation have indeed found negative effects of radiation on sperm quantity and quality. In nature, levels of natural background radiation vary dramatically, and chronic effects of low-level background radiation exposure on spermatogenesis are poorly understood. The Chernobyl region offers a unique research opportunity for investigating effects of chronic low-level ionizing radiation on reproductive properties of wild organisms. We captured male bank voles (Myodes glareolus) from 24 locations in the Chernobyl …

Assessing Reproducibility Of Inherited Variants Detected With Short-Read Whole Genome Sequencing, Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan, Rebecca Kusko, Steve Bruinsma, Len Trigg, Andreas Scherer, Baitang Ning, Chaoyang Zhang, Christine Glidewell-Kenney, Chunlin Xiao, Eric Donaldson, Fritz J. Sedlazeck, Gary Schroth, Gokhan Yavas, Haiying Grunenwald, Haodong Chen, Heather Meinholz, Joe Meehan, Jing Wang, Jingcheng Yang, Jonathan Foox, Jun Shang, Kelci Miclaus, Lianhua Dong, Leming Shi, Marghoob Mohiyuddin, Mehdi Pirooznia, Ping Gong, Rooz Golshani, Russ Wolfinger, Samir Lababidi, Sayed Mohammed Ebrahim Sahraeian, Steve Sherry, Tao Han, Tieliu Shi, Wanwan Hou, Weigong Ge, Wen Zou, Wenjing Guo, Wenjun Bao, Wenzhong Xiao, Xiaohui Fan, Yoichi Gondo, Ying Yu, Yongmei Zhao, Zhenqiang Su, Zhichao Liu, Weida Tong, Wenming Xiao, Justin M. Zook, Yuanting Zeng, Huixiao Hong

Faculty Publications

Background: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS.

Results: To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and …

Electrophysiological Responses To Conspecific Odorants In Xenopus Laevis Show Potential For Chemical Signaling, Heather J. Rhodes, Melanie Amo

Faculty Publications

No abstract provided.

Overview Of Multi-Factor Prediction Using Deep Neural Networks, Machine Learning, And Their Open-Source Software, Richard S. Segall

Faculty Publications

This chapter first provides an overview with examples of what neural networks (NN), machine learning (ML), and artificial intelligence (AI) are and their applications in biomedical and business situations. The characteristics of 29 types of neural networks are provided including their distinctive graphical illustrations. A survey of current open-source software (OSS) for neural networks, neural network software available for free trail download for limited time use, and open-source software (OSS) for machine learning (ML) are provided. Characteristics of artificial intelligence (AI) technologies for machine learning available as open source are discussed. Illustrations of applications of neural networks, machine learning, and …

In God’S House, There Are Many Rooms: A University Minister Reflects Upon Fratelli Tutti., Melanie-Prejean Sullivan

Faculty Publications

For over fifty years, Roman Catholics who are interreligious leaders have been guided by the Second Vatican Council document, Nostra Aetate. The author, a retired university lay minister in the United States, was one such interreligious leader who worked with students, faculty, and staff of all faiths and none on a small Catholic campus to create an atmosphere open to diversity, inclusion, and respect for all. Her office facilitated campus programs that encouraged service, dialogue, and spiritual growth. In twenty years, campus ministry involvement grew from three dozen primarily Catholic students to over 400 students of many different faiths. …

Kinetics And Connectivity Properties Of Parvalbumin- And Somatostatin-Positive Inhibition In Layer 2/3 Medial Entorhinal Cortex, Fernando R. Fernandez, Guillem Via, Carmen C. Canavier, John A. White

Faculty Publications

No abstract provided.

The Havoc Death Wreaks: Civil Rights Challenges To Capital Punishment, Bailey D. Barnes

Faculty Publications

Following a per curium opinion that banned the imposition of capital punishment because it violated the Eighth Amendment, as made applicable to the states through the Fourteenth Amendment, United States Supreme Court Justice Thurgood Marshall offered a unique criticism of capital punishment. Justice Marshall, an iconic civil rights litigator prior to his confirmation to the Court, stated, "[T]he death penalty wreaks havoc with our entire criminal justice system." Similarly, sometime in the late 1950s, Associate Justice Robert H. Jackson reportedly said that capital punishment "completely bitches up the criminal law." In essence, both Justices were asserting that the death penalty …

Solving The Procedural Puzzles Of The Texas Heartbeat Act And Its Imitators: The Limits And Opportunities For Offensive Litigation, Charles W. "Rocky" Rhodes, Howard M. Wasserman

Faculty Publications

Texas' Fetal Heartbeat Act, enacted in 2021 as Senate Bill 8, prohibits abortions following detection of a fetal heartbeat, a constitutionally invalid ban under current Supreme Court precedent. But the method of enforcement in the Texas law is unique—it prohibits enforcement by government officials in favor of private civil actions brought by “any person,” regardless of injury. Texas sought to burden reproductive-health providers and rights advocates with costly litigation and potentially crippling liability.

In a series of articles, we explore how SB8's exclusive reliance on private enforcement creates procedural and jurisdictional hurdles to challenging the law's constitutional validity and obtaining …

Solving The Procedural Puzzles Of Texas’ Fetal-Heartbeat Law And Its Imitators: The Potential For Defensive Litigation, Charles W. "Rocky" Rhodes, Howard M. Wasserman

Faculty Publications

Texas' Fetal Heartbeat Act, enacted in 2021 as Senate Bill 8, prohibits abortions following detection of a fetal heartbeat, a constitutionally invalid ban under current Supreme Court precedent. But the method of enforcement in the Texas law is unique—it prohibits enforcement by government officials in favor of private civil actions brought by “any person,” regardless of injury. Texas sought to burden reproductive-health providers and rights advocates with costly litigation and potentially crippling liability.

In a series of articles, we explore how SB8's exclusive reliance on private enforcement creates procedural and jurisdictional hurdles to challenging the law's constitutional validity and obtaining …

Constitutional Authority, Common Resources, And The Climate, Anthony L. Moffa

Faculty Publications

This work sets out to re-examine and challenge the history of the property clause with an eye towards increased congressional reliance on it in the face of daunting threats to our natural environment. No one could seriously question the primary motivations of the Framers, but that does not foreclose the importance of searching for secondary motivations that deepen our understanding of arguably the Constitution’s most explicitly environmental provision. Eugene Gaetke’s work in the 1980’s and Peter Appel’s work twenty years later laid the groundwork for the argument here by pushing back on the originalist argument for a narrow interpretation of …

Factors Related To Species Richness, Endemism, And Conservation Status Of The Herpetofauna (Amphibia And Reptilia) Of Mexican States, Geoffrey R. Smith, Julio A. Lemos-Espinal

Faculty Publications

No abstract provided.

Clouded Precedent: Tandon V. Newsom And Its Implications For The Shadow Docket, Alexander Gouzoules

Faculty Publications

The Supreme Court’s “shadow docket”—the decisions issued outside its procedures for deciding cases on the merits—has drawn increasing attention and criticism from scholars, commentators, and elected representatives. Shadow docket decisions have been criticized on the grounds that they are made without the benefit of full briefing and argument, and because their abbreviated, per curiam opinions can be difficult for lower courts to interpret.

A spate of shadow docket decisions in the context of free-exercise challenges to COVID-19 public health orders culminated in Tandon v. Newsom, a potentially groundbreaking decision that may upend longstanding doctrines governing claims brought under the Free …

Food, Freedom, Fairness, And The Family Farm, Robin M. Rotman, Sophie Mendelson

Faculty Publications

The concept of the “family farm” holds powerful sway within the American narrative, embodying both nostalgia for an imagined past and anxiety for a future perceived to be under threat. Since the founding of the United States, this cultural ideal has been invoked in support of a rosy vision of agrarian democracy while obscuring the ways in which the U.S. Department of Agriculture’s codified definition of “family farm” has unfairly aggregated advantages for the benefit of a particular kind of family (nuclear) and farmer (white, male, straight). At the same time, consumers are misled by an under-interrogated conflation of family …

The Contributions Of Immediate Retrieval And Spaced Retrieval To Word Learning In Preschoolers With Developmental Language Disorder, Laurence B. Leonard, Justin B. Kueser, Patricia Deevy, Eileen Haebig, Jeffrey D. Karpicke, Christine Weber

Faculty Publications

Background and Aims: Children with developmental language disorder (DLD) benefit from word learning procedures that include a mix of immediate retrieval and spaced retrieval trials. In this study, we examine the relative contribution of these two types of retrieval.

Methods: We examine data from Haebig et al. (2019) in their study that compared an immediate retrieval condition and a condition of spaced retrieval that also included immediate retrieval trials. Participants were 4- and 5-year old children with DLD and same-age peers with typical language development. Each child learned novel (made-up) words referring to unusual plants and animals in both conditions. …

The Contributions Of Immediate Retrieval And Spaced Retrieval To Word Learning In Preschoolers With Developmental Language Disorder, L B. Leonard, J B. Kueser, P Deevy, E Haebig, L B. Leonard, C Weber

Faculty Publications

Background and Aims: Children with developmental language disorder (DLD) benefit from word learning procedures that include a mix of immediate retrieval and spaced retrieval trials. In this study, we examine the relative contribution of these two types of retrieval. Methods: We examine data from Haebig et al. (2019) in their study that compared an immediate retrieval condition and a condition of spaced retrieval that also included immediate retrieval trials. Participants were 4- and 5-year old children with DLD and same-age peers with typical language development. Each child learned novel (made-up) words referring to unusual plants and animals in both conditions. …