Digital Commons Network^™

Gut Microbiome Analyses Of Lone Star, Black-Legged And Dog Ticks, William Bennett, Jeremy Seto

Publications and Research

The focus of much tick research is often on the detrimental effects caused by the pathogens found inside the ticks. However, some focus has been shifted towards researching the natural microbiota already present and trying to determine if host-pathogen interactions are influenced by the gut microbiota. Lone Star, Deer / Black-Legged, and Dog ticks at each life stage (larval, nymph, adult) had their guts collected and analyzed. Larvae were unfed, nymphs had fed once, and the adults have fed at least twice. Three samples of each species adult male and female were collected along with three samples of their nymph …

Facebook As A Social Outreach And Advocacy Tool In Intersex/Dsd Groups, Emelie J. Ali Ms

Publications and Research

My project includes a netnography of a Facebook intersex group called Families and Friends of Intersex People. I observed the group’s forms of communication within the group and which topics they discussed. It appears one of the major concerns the group has is the use of nonconsensual, sex assignment surgery on infants to “correct” their body to match a gender identity. I have also discovered a link between being intersex and affiliated with the LGBT+ community. Since the 20th century, intersex people have been stigmatized due to their assumed ability to engage in sexual, same-sex relations. I have concluded that …

Comparing Microbiome Sampling Methods In A Wild Mammal: Fecal And Intestinal Samples Record Different Signals Of Host Ecology, Evolution, Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A. Speer, Susan L. Perkins

Publications and Research

Processing of multimodal information is essential for an organism to respond to environmental events. However, how multimodal integration in neurons translates into behavior is far from clear. Here, we investigate integration of biologically relevant visual and auditory information in the goldfish startle escape system in which paired Mauthner-cells (M-cells) initiate the behavior. Sound pips and visual looms as well as multimodal combinations of these stimuli were tested for their effectiveness of evoking the startle response. Results showed that adding a low intensity sound early during a visual loom (low visual effectiveness) produced a supralinear increase in startle responsiveness as compared …

Phase Diagram Of Water Confined By Graphene, Zhenghan Gao, Nicolas Giovambattista, Ozgur Sahin

Publications and Research

The behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in …

White Women, U.S. Popular Culture, And Narratives Of Addiction, Jessie Daniels

Publications and Research

The United States war on drugs has, for decades now, systematically targeted communities of color. This sustained attack on people of color is accomplished through the use of whiteness. Recently, mainstream news media and elected officials have called for a “gentler war on drugs” to address the opioid epidemic. While some may see this as a welcome change, we take a more critical view. Specifically, we examine the role of White women in two popular television series that feature narratives of addiction as a gendered instance of “white drug exceptionalism.” To do this, we conducted a systematic analysis of a …

Generating And Repairing Genetically Programmed Dna Breaks During Immunoglobulin Class Switch Recombination, Laura Nicolas, Montserrat Cols, Jee Eun Choi, Jayanta Chaudhuri

Publications and Research

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig …

The Fata Morgana Of Unconscious Perception, Marjan Persuh

Publications and Research

No abstract provided.

Bifurcated Response Of A Regional Forest To Drought, Wei Fang, Chuixiang Yi, Guangwei Mu, George Hendrey, Sergio M. Vicente-Serrano, Tao Zhou, Shan Gao, Peipei Xu

Publications and Research

Several lines of evidence suggest that forest growth in many regions is declining as a consequence of changing climate. To predict the fate of forests in the future, a quantitative understanding of how the key climate variables (insolation, precipitation and temperature) interact with forests to cause the decline is a pressing need. Here we use a regionally-averaged tree-ring width index (RWIr ) to quantify forest growth in the Southwest United States (SWUS). We show that over a period of 100 years, SWUS RWIr bifurcated into forest stands with enhanced (healthy) and reduced (declining) branches when regressed on shortwave-radiation and temperature, …

Multi Institutional Quantitative Phantom Study Of Yttrium-90 Pet In Pet/Mri: The Mr-Quest Study, Nicole M. Maughan, Mootaz Eldib, David Faul, Maurizio Conti, Mattijs Elschot, Karin Knešaurek, Francesca Leek, David Townsend, Frank P. Difilippo, Kimberly Jackson, Stephan G. Nekolla, Mathias Lukas, Michael Tapner, Parag J. Parikh, Richard Laforest

Publications and Research

Background

Yttrium-90 (⁹⁰Y) radioembolization involves the intra-arterial delivery of radioactive microspheres to treat hepatic malignancies. Though this therapy involves careful pre-treatment planning and imaging, little is known about the precise location of the microspheres once they are administered. Recently, there has been growing interest post-radioembolization imaging using positron-emission tomography (PET) for quantitative dosimetry and identifying lesions that may benefit from additional salvage therapy. In this study, we aim to measure the inter-center variability of ⁹⁰Y PET measurements as measured on PET/MRI in preparation for a multi-institutional prospective phase I/II clinical trial.

Eight institutions participated in this study …

Hip Extensor Mechanics And The Evolution Of Walking And Climbing Capabilities In Humans, Apes, And Fossil Hominins, Elaine E. Kozma, Nicole M. Webb, William Harcourt-Smith, David A. Raichlen, Kristiaan D’Août, Mary H. Brown, Emma M. Finestone, Stephen R. Ross, Peter Aerts, Herman Pontzer

Publications and Research

The evolutionary emergence of humans’ remarkably economical walking gait remains a focus of research and debate, but experi- mentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental mea- surements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal–terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by …

Debt's Poetry In Timon Of Athens, Laura Kolb

Publications and Research

No abstract provided.

An Investigation Of Predictors Of Self-Efficacy To Cope With Stress And Implications For Health Education Practice, Asrat G. Amnie

Publications and Research

ABSTRACT

Background: We investigated predictors of self-efficacy to cope with stress in diverse popula- tions with stressful life experiences. We also examined the association between predictors of coping self-efficacy and the different copying strategies adapted by study participants. Purpose: The purpose of this study was to determine the relationship between sociodemo- graphic variables and individuals’ self-efficacy to cope with stress resulting from exposure to adverse life experiences. Methods: A total of 233 adult U.S. residents aged 18 years or above were recruited in a self-administered questionnaire survey study. Results: Regression results showed that male gender, older age, being non-white, not …

Predicting Serious Rare Adverse Reactions Of Novel Chemicals, Aleksandar Poleksic, Lei Xie

Publications and Research

Motivation: Adverse drug reactions (ADRs) are one of the main causes of death and a major financial burden on the world's economy. Due to the limitations of the animal model, computational prediction of serious and rare ADRs is invaluable. However, current state-of-the-art computational methods do not yield significantly better predictions of rare ADRs than random guessing.

Results: We present a novel method, based on the theory of 'compressed sensing' (CS), which can accurately predict serious side-effects of candidate and market drugs. Not only is our method able to infer new chemical-ADR associations using existing noisy, biased and incomplete databases, but …

Maternal Choline Supplementation During Normal Murine Pregnancy Alters The Placental Epigenome: Results Of An Exploratory Study, Sze Ting (Cecilia) Kwan, Julia H. King, Jennifer K. Grenier, Jian Yan, Xinyin Jiang, Mark S. Roberson, Marie A. Caudill

Publications and Research

The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, …

Boundary Spanning At The Science–Policy Interface: The Practitioners’ Perspectives, A. T. Bednarek, C. Wyborn, C. Cvitanovic, R. Meyer, R. M. Colvin, P. F. E. Addison, S. L. Close, K. Curran, M. Farooque, E. Goldman, D. Hart, H. Mannix, B. Mcgreavy, Adam Parris, S. Posner, C. Robinson, M. Ryan, P. Leith

Publications and Research

Cultivating a more dynamic relationship between science and policy is essential for responding to complex social challenges such as sustainability. One approach to doing so is to “span the boundaries” between science and decision making and create a more comprehensive and inclusive knowledge exchange process. The exact definition and role of boundary spanning, however, can be nebulous. Indeed, boundary spanning often gets conflated and confused with other approaches to connecting science and policy, such as science communication, applied science, and advocacy, which can hinder progress in the field of boundary spanning. To help overcome this, in this perspective, we present …

Primordial Origin And Diversification Of Plasmids In Lyme Disease Agent Bacteria, Sherwood R. Casjens, Lia Di, Saymon Akther, Emmanuel F. Mongodin, Benjamin J. Luft, Steven E. Schutzer, Claire M. Fraser, Weigang Qiu

Publications and Research

Abstract

Background: With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparative analysis of plasmids in eleven Borreliella (also known as Borrelia burgdorferi sensu lato) species.

Results: We sequenced the complete genomes of two B. afzelii, two B. garinii, and individual B. spielmanii, B. bissettiae, B. valaisiana and B. finlandensis isolates. These individual isolates carry between seven and sixteen plasmids, and together harbor 99 plasmids. We report here a comparative analysis of these plasmids, along with 70 additional …

Resistance Training-Induced Gains In Muscle Strength, Body Composition, And Functional Capacity Are Attenuated In Elderly Women With Sarcopenic Obesity, Alessandro De Oliveira Silva, Maurílio Tiradentes Dutra, Wilson Max Almeida Monteiro De Moraes, Silvana Schwerz Funghetto, Darlan Lopes De Farias, Paulo Henrique Fernandes Dos Santos, Denis Cesar Leite Vieira, Dahan Da Cunha Nascimento, Vânia Silva Macedo Orsano, Brad J. Schoenfeld, Jonato Prestes

Publications and Research

Objectives: The purpose of this study was to compare the effects of resistance training (RT) on body composition, muscle strength, and functional capacity in elderly women with and without sarcopenic obesity (SO).

Methods: A total of 49 women (aged $60 years) were divided in two groups: without SO (non-SO, n=41) and with SO (n=8). Both groups performed a periodized RT program consisting of two weekly sessions for 16 weeks. All measures were assessed at baseline and postintervention, including anthropometry and body composition (dual-energy X-ray absorptiometry), muscle strength (one repetition maximum) for chest press and 45° leg press, and functional capacity …

Assessment Of A Single Decoupling Alchemical Approach For The Calculation Of The Absolute Binding Free Energies Of Protein-Peptide Complexes, Denise Kilburg, Emilio Gallicchio

Publications and Research

The computational modeling of peptide inhibitors to target protein-protein binding interfaces is growing in interest as these are often too large, too shallow, and too feature-less for conventional small molecule compounds. Here, we present a rare successful application of an alchemical binding free energy method for the calculation of converged absolute binding free energies of a series of protein-peptide complexes. Specifically, we report the binding free energies of a series of cyclic peptides derived from the LEDGF/p75 protein to the integrase receptor of the HIV1 virus. The simulations recapitulate the effect of mutations relative to the wild-type binding motif of …

Bpwrapper: Bioperl-Based Sequence And Tree Utilities For Rapid Prototyping Of Bioinformatics Pipelines, Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William Mccaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Weigang Qiu

Publications and Research

Abstract:

Background: Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl (http://bioperl.org) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users.

Results: Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of …

Influence Of Perceived Stress On Dressing And Eating Behaviors Of Chinese Female University Students Residing In The United States, Kandiah Jayanthi, Diana Saiki, Kiya Dues, Alyssa Dana Adomaitis

Publications and Research

The objective of this research was to evaluate how perceived stressful conditions (PSC) and perceived non-stressful conditions (PNSC) influence eating and dressing behaviors of Chinese females. Chinese female university students (18–30 years) residing in the United States, completed a validated and reliable 45-itemized Chinese Stress Eating and Dressing Survey (CSEDS). The CSEDS included: (i) effort to control making healthy eating choices and dressing, (ii) foods eaten and dress items selected during PSC, (iii) foods eaten and dress items selected during PNSC, and (iv) demographics. Seven comfort food categories and eight appearance categories were used. The CSEDS included multiple choice, yes/no, …

Market Integration Predicts Human Gut Microbiome Attributes Across A Gradient Of Economic Development, Keaton Stagaman, Tara J. Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan

Publications and Research

Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population. Despite relatively modest differences in lifestyle across the population, greater economic development correlated with significantly …

Resveratrol And Pterostilbene Exhibit Anticancer Properties Involving The Downregulation Of Hpv Oncoprotein E6 In Cervical Cancer Cells, Kaushiki Chatterjee, Dina Alsharif, Christina Mazza, Palwasha Syar, Mohamed Al Sharif, Jimmie E. Fata

Publications and Research

Cervical cancer is one of the most common cancers in women living in developing countries. Due to a lack of affordable effective therapy, research into alternative anticancer compounds with low toxicity such as dietary polyphenols has continued. Our aim is to determine whether two structurally similar plant polyphenols, resveratrol and pterostilbene, exhibit anticancer and anti-HPV (Human papillomavirus) activity against cervical cancer cells. To determine anticancer activity, extensive in vitro analyses were performed. Anti-HPV activity, through measuring E6 protein levels, subsequent downstream p53 effects, and caspase-3 activation, were studied to understand a possible mechanism of action. Both polyphenols are effective agents …

Type I Ifns And Tnf Cooperatively Reprogram The Macrophage Epigenome To Promote Inflammatory Activation, Sung Ho Park, Kyuho Kang, Eugenia Giannopoulou, Yu Qiao, Keunsoo Kang, Geonho Kim, Kyung-Hyun Park-Min, Lionel B. Ivashkiv

Publications and Research

Cross-regulation of Toll-like receptor responses by cytokines is essential for effective host defense, avoidance of toxicity, and homeostasis, but the underlying mechanisms are not well understood. A comprehensive epigenomic approach in human macrophages showed that the proinflammatory cytokines TNF and type I IFNs induce transcriptional cascades that alter chromatin states to broadly reprogram TLR4-induced responses. TNF tolerized inflammatory genes to prevent toxicity, while preserving antiviral and metabolic gene induction. Type I IFNs potentiated TNF inflammatory function by priming chromatin to prevent silencing of inflammatory NF-κB target genes. Priming of chromatin enabled robust transcriptional responses to weak upstream signals. Similar chromatin …

Spatial Relationship Between Bone Formation And Mechanical Stimulus Within Cortical Bone: Combining 3d Fluorochrome Mapping And Poroelastic Finite Element Modelling, Alessandra Carriero, A. F. Pereira, A. J. Wilson, S. Castagno, B. Javaheri, A. A. Pitsillides, M. Marenzana, S. J. Shefelbine

Publications and Research

Bone is a dynamic tissue and adapts its architecture in response to biological and mechanical factors. Here we investigate how cortical bone formation is spatially controlled by the local mechanical environment in the murine tibia axial loading model (C57BL/6). We obtained 3D locations of new bone formation by performing ‘slice and view’3D fluorochrome mapping of the entire bone and compared these sites with the regions of high fluid velocity or strain energy density estimated using a finite element model, validated with ex-vivo bone surface strain map acquired ex-vivo using digital image correlation. For the comparison, 2D maps of the average …

The Disruption And Diversification Of Higher Education Funding: Cryptocurrency For Higher Education Wealth Generation, Edward Lehner, John R. Ziegler

Publications and Research

This work conceptualizes a process for cryptocurrency to diversify traditional methods of higher education funding in the United States. Higher education funding has seemingly reached an impasse, and opinions remain divided over both which societal parties should bear the educational costs for the vast majority of Americans and how to remedy the student debt crisis. Cryptocurrency funding augments traditional revenue streams, and shifts the discussion of education costs from expenses to a more robust conversation about innovative avenues to wealth generation as a potential solution to fund the mission of American higher education. Historically, higher education has been rooted in …

Retinal Progenitor Cells Release Extracellular Vesicles Containing Developmental Transcription Factors, Microrna And Membrane Proteins, Jing Zhou, Alberto Benito-Martin, Jason Mighty, Lynne Chang, Shima Ghoroghi, Hao Wu, Madeline Wong, Sara Guariglia, Petr Baranov, Michael Young, Rajendra Ghardbaran, Mark Emerson, Milica Tesic Mark, Henrik Molina, M. Valeria Canto-Solar, Hector Peinado Selgas, Stephen Redenti

Publications and Research

A range of cell types, including embryonic stem cells, neurons and astrocytes have been shown to release extracellular vesicles (EVs) containing molecular cargo. Across cell types, EVs facilitate transfer of mRNA, microRNA and proteins between cells. Here we describe the release kinetics and content of EVs from mouse retinal progenitor cells (mRPCs). Interestingly, mRPC derived EVs contain mRNA, miRNA and proteins associated with multipotency and retinal development. Transcripts enclosed in mRPC EVs, include the transcription factors Pax6, Hes1, and Sox2, a mitotic chromosome stabilizer Ki67, and the neural intermediate filaments Nestin and GFAP. Proteomic analysis of EV content revealed retinogenic …

The Candida Albicans Stress Response Gene Stomatin-Like Protein 3 Is Implicated In Ros-Induced Apoptotic-Like Death Of Yeast Phase Cells, Karen A. Conrad, Ronald Rodriguez, Eugenia C. Salcedo, Jason M. Rauceo

Publications and Research

The ubiquitous presence of SPFH (Stomatin, Prohibitin, Flotillin, HflK/HflC) proteins in all domains of life suggests that their function would be conserved. However, SPFH functions are diverse with organism-specific attributes. SPFH proteins play critical roles in physiological processes such as mechanosensation and respiration. Here, we characterize the stomatin ORF19.7296/SLP3 in the opportunistic human pathogen Candida albicans. Consistent with the localization of stomatin proteins, a Slp3p-Yfp fusion protein formed visible puncta along the plasma membrane. We also visualized Slp3p within the vacuolar lumen. Slp3p primary sequence analyses identified four putative S-palmitoylation sites, which may facilitate membrane localization and are conserved features …

The Candida Albicans Stress Response Gene Stomatin-Like Protein 3 Is Implicated In Ros-Induced Apoptotic-Like Death Of Yeast Phase Cells, Karen A. Conrad, Ronald Rodriguez, Eugenia C. Salcedo, Jason M. Rauceo

Publications and Research

The ubiquitous presence of SPFH (Stomatin, Prohibitin, Flotillin, HflK/HflC) proteins in all domains of life suggests that their function would be conserved. However, SPFH functions are diverse with organism-specific attributes. SPFH proteins play critical roles in physiological processes such as mechanosensation and respiration. Here, we characterize the stomatin ORF19.7296/SLP3 in the opportunistic human pathogen Candida albicans. Consistent with the localization of stomatin proteins, a Slp3p-Yfp fusion protein formed visible puncta along the plasma membrane. We also visualized Slp3p within the vacuolar lumen. Slp3p primary sequence analyses identified four putative S-palmitoylation sites, which may facilitate membrane localization and are conserved features …

Chronic Voluntary Oral Methamphetamine Induces Deficits In Spatial Learning And Hippocampal Protein Kinase Mzeta With Enhanced Astrogliosis And Cyclooxygenase-2 Levels, Jorge A. Avila, Roseanna M. Zanca, Denis Shor, Nicholas Paleologos, Amber A. Alliger, Maria E. Figueiredo-Pereira, Peter A. Serrano

Publications and Research

Methamphetamine (MA) is an addictive drug with neurotoxic effects on the brain producing cognitive impairment and increasing the risk for neurodegenerative disease. Research has focused largely on examining the neurochemical and behavioral deficits induced by injecting relatively high doses of MA [30 mg/kg of body weight (bw)] identifying the upper limits of MA-induced neurotoxicity. Accordingly, we have developed an appetitive mouse model of voluntary oral MA administration (VOMA) based on the consumption of a palatable sweetened oatmeal mash containing a known amount of MA. This VOMA model is useful for determining the lower limits necessary to produce neurotoxicity in the …

Positive Outcomes: Strategies For Assessing The Progress Of Youth Involved In The Justice System, Jeffrey A. Butts, Emily K. Pelletier, Lila Kazemian

Publications and Research

This report examines the shift in U.S. youth justice systems toward using adolescent development science to improve interventions and measure youth success. It emphasizes the adoption of Positive Youth Development (PYD) principles, which focus on fostering positive relationships and skills rather than just preventing recidivism. The report highlights various frameworks—such as the Developmental Assets model and Positive Youth Justice model—that align with PYD principles and research on desistance from crime. These frameworks offer a path for transforming youth justice systems into strengths-based approaches that promote long-term positive outcomes.