Digital Commons Network^™

The Magnetic Couples Study: Protocol For A Mixed Methods Prospective Cohort Study Of Hiv-Serodifferent Heterosexual Couples’ Perspectives And Use Of Pre-Exposure Prophylaxis (Prep), James M. Mcmahon, Janie Simmons, Jessica E. Haberer, Sharon Mannheimer, Natalie M. Leblanc, Leilani Torres, Robert Quiles, Guillermo Aedo, Anabel Javier, Amy Braksmajer, Graham Harriman, Nicole Trabold, Enrique R. Pouget, Ann Kurth, Martez D. R Smith, Judith Brasch, Eric J. Podsiadly, Peter L. Anderson

Publications and Research

Introduction HIV transmission within serodifferent heterosexual couples plays a key role in sustaining the global HIV pandemic. In the USA, transmission within established mixed-status couples accounts for up to half of all new HIV infections among heterosexuals. Oral HIV pre-exposure prophylaxis (PrEP) is a highly effective prevention method, although underutilised among serodifferent couples. Moreover, there is a dearth of research on US HIV-serodifferent couples’ perspectives and use of PrEP, alone or in combination with other prevention methods. In this paper, we describe the study protocol for the Magnetic Couples Study, designed to fill critical knowledge gaps regarding HIV-serodifferent heterosexual couples’ …

The Cost Of Being Black In Social Work Practicum, Nia Johnson, Paul Archibald, Anthony Estreet, Amanda Morgan

Publications and Research

The social work profession is not exempt from fueling institutional racism, which affects the provision of social work practicum education for Black social work students. This article highlights how the historical and current social cost of being Black in the United States presents itself within social work education’s signature pedagogy. Social workers who hold bachelor’s degrees in social work (BSW) are more likely to be Black than those holding master’s degrees in social work (MSW; Salsberg et al., 2017). It takes Black students longer to earn an MSW degree though they are more likely to hold a BSW while also …

Mother Monsters And Monster Mothers From Dracula To Stranger Things, Melissa Dinsman

Publications and Research

Netflix’s hit show Stranger Things is an homage to 1970s and 1980s sci-fi and horror, including Alien and Aliens, Carrie, the Star Wars trilogy, and Poltergeist, as well as buddy adventure films like Goonies and Stand by Me. But it is also, in its obsessive presentation of monsters as mothers and mothers as monsters, a show that takes its 1980s mothering cues straight out of Bram Stoker’s 1890s. Despite its 2016 production date, the Duffer Brother’s Stranger Things presents viewers with very old fashioned ideas of mothering, with Joyce Byers (Wynona Ryder) as the single, but exceedingly pro-active mom from …

Radiologic Contrast-Induced Transmetallation In Mineral Rich Fruits: X-Ray Imaging To Understand Heat Cycling During Climate Change And Map Metal Redistribution In Biological Media For Biomedical Applications, Lin Mousa, Hayley Sanchez, Subhendra Sarkar, Zoya Vinokur

Publications and Research

Heat cycling due to climate change can affect hydrated protein or carbohydrate functions, the latter is not well studied. The project started with involving the study of heat-stressed carbohydrate behavior when bulk water was partly stripped from carbohydrates in model microwaved fruits and vegetables, like apples and sweet potatoes (that are mineral-rich) and was set in mineral exchange competition with toxic metals like Gadolinium and chelating complexes like iodinated EDTA. These are common radiologic contrast medias that strongly absorb x-rays and are currently implicated in man-made environmental toxins. Our goal was to map diffusion of injected heavy atoms as well …

Examining Inequities In Rates Of Undiagnosed Hiv And Rectal Stis In A Large Nationwide Cohort Study Of Sexual Minority Men, H Jonathon Rendina, Ali Talan, K Marie Sizemore, Nicola F. Tavella, Brian Salfas, Ore Shalhav, Drew Westmoreland, Brian Mustanski, Carlos E. Rodríguez- Díaz

Publications and Research

Objective Sexual minority men (SMM) of colour are disproportionately impacted by HIV and bacterial STIs (bSTIs). To better understand within-group heterogeneity and differential risk factors by race and ethnicity, we sought to examine rates of undiagnosed HIV and rectal bSTI at the intersection of racial and ethnic identity with other sociodemographic factors.

Methods We examined data from 8105 SMM conducting home-based self-testing at enrollment in a nationwide cohort study collected from November 2017 to August 2018. We conducted analyses stratified by racial and ethnic groups to examine within- group (ie, subgroup) unadjusted rates of HIV and rectal bSTI infection across …

Telomeric And Sub-Telomeric Structure And Implications In Fungal Opportunistic Pathogens, Raffaella Diotti, Michelle Esposito, Chang Hui Shen

Publications and Research

Telomeres are long non-coding regions found at the ends of eukaryotic linear chromosomes. Although they have traditionally been associated with the protection of linear DNA ends to avoid gene losses during each round of DNA replication, recent studies have demonstrated that the role of these sequences and their adjacent regions go beyond just protecting chromosomal ends. Regions nearby to telomeric sequences have now been identified as having increased variability in the form of duplications and rearrangements that result in new functional abilities and biodiversity. Furthermore, unique fungal telomeric and chromatin structures have now extended clinical capabilities and understanding of pathogenicity …

A Fused Radar–Optical Approach For Mapping Wetlands And Deepwaters Of The Mid–Atlantic And Gulf Coast Regions Of The United States, Brian T. Lamb, Maria A. Tzortziou, Kyle C. Mcdonald

Publications and Research

Tidal wetlands are critically important ecosystems that provide ecosystem services including carbon sequestration, storm surge mitigation, water filtration, and wildlife habitat provision while supporting high levels of biodiversity. Despite their importance, monitoring these systems over large scales remains challenging due to difficulties in obtaining extensive up-to-date ground surveys and the need for high spatial and temporal resolution satellite imagery for effective space-borne monitoring. In this study, we developed methodologies to advance the monitoring of tidal marshes and adjacent deepwaters in the Mid-Atlantic and Gulf Coast United States. We combined Sentinel-1 SAR and Landsat 8 optical imagery to classify marshes and …

Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge, Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, M. R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley

Publications and Research

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pK_a for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pK_a challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was …

The Effect Of Fluid Flow Shear Stress And Substrate Stiffness On Yes-Associated Protein (Yap) Activity And Osteogenesis In Murine Osteosarcoma Cells, Thomas R. Coughlin, Ali Sana, Kevin Voss, Abhilash Gadi, Upal Basu-Roy, Caroline M. Curtin, Alka Mansukhani, Oran D. Kennedy

Publications and Research

Osteosarcoma (OS) is an aggressive bone cancer originating in the mesenchymal lineage. Prognosis for metastatic disease is poor, with a mortality rate of approximately 40%; OS is an aggressive disease for which new treatments are needed. All bone cells are sensitive to their mechanical/ physical surroundings and changes in these surroundings can affect their behavior. However, it is not well understood how OS cells specifically respond to fluid movement, or substrate stiffness—two stimuli of relevance in the tumor microenvironment. We used cells from spontaneous OS tumors in a mouse engineered to have a bone-specific knockout of pRb-1 and p53 in …

Sites Of Circadian Clock Neuron Plasticity Mediate Sensory Integration And Entrainment, Maria P. Fernand, Hannah L. Pettibone, Joseph T. Bogart, Casey J. Roell, Charles E. Davey, Ausra Pranevicius, Khang V. Huynh, Sara M. Lennox, Boyan Kostadinov, Orie T. Shafer

Publications and Research

Networks of circadian timekeeping in the brain display marked daily changes in neuronal morphology. In Drosophila melanogaster, the striking daily structural remodeling of the dorsal medial termini of the small ventral lateral neurons has long been hypothesized to mediate endogenous circadian timekeeping. To test this model, we have specifically abrogated these sites of daily neuronal remodeling through the reprogramming of neural development and assessed the effects on circadian timekeeping and clock outputs. Remarkably, the loss of these sites has no measurable effects on endogenous circadian timekeeping or on any of the major output functions of the small ventral lateral neurons. …

Area Characteristics And Consumer Nutrition Environments In Restaurants: An Examination Of Hispanic Caribbean Restaurants In New York City, Melissa Fuster, Hanish Kodali, Krishnendu Ray, Brian Elbel, Margaret A. Handley, Terry T. Huang, Glen Johnson

Publications and Research

Hispanics in the USA, particularly those of Caribbean descent, experience high levels of diet-related diseases and dietary risk factors. Restaurants are an increasingly important yet understudied source of food and may present opportunities to positively influence urban food environments. We sought to explore food environments further, by examining the association between neighborhood characteristics and restaurant consumer nutrition environments within New York City’s Hispanic Caribbean (HC) restaurant environments. We applied an adapted version of the Nutrition Environment Measurements Survey for Restaurants (NEMS-R) to evaluate a random sample of HC restaurants (n=89). NEMS-HCR scores (continuous and categorized as low, medium, and high …

Remission Of Type 2 Diabetes With Very Low-Calorie Diets —A Narrative Review, Susan Juray, Kathleen V. Axen, Steven Trasino

Publications and Research

Very low-calorie diets (VLCD) are hypocaloric dietary regimens of approximately 400–800 kcal/day that result in 20–30% reductions in body weight, sometimes in just 12–16 weeks. A body of evidence demonstrates that adherence to VLCD in adults with type 2 diabetes (T2D) can result in marked improvements to glycemic control and even full T2D remission, challenging the convention that T2D is a lifelong disease. Although these data are promising, the majority of VLCD studies have focused on weight loss and not T2D remission as a primary endpoint. Moreover, there is a wide range of VLCD protocols and definitions of T2D remission …

Annotated Genome Sequence Of The High-Biomass-Producing Yellow-Green Alga Tribonema Minus, Kristina M. Mahan, Jüergen E.W. Polle, Zaid Mckie-Krisberg, Anna Lipzen, Alan Kuo, Igor V. Grigoriev, Todd W. Lane, Aubrey K. Davis

Publications and Research

Here, we report the annotated genome sequence for a heterokont alga from the class Xanthophyceae. This high-biomass-producing strain, Tribonema minus UTEX B 3156, was isolated from a wastewater treatment plant in California. It is stable in outdoor raceway ponds and is a promising industrial feedstock for biofuels and bioproducts.

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

Covid-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning, Yang Liu, You Wu, Xiaoke Shen, Lei Xie

Publications and Research

The life-threatening disease COVID-19 has inspired significant efforts to discover novel therapeutic agents through repurposing of existing drugs. Although multi-targeted (polypharmacological) therapies are recognized as the most efficient approach to system diseases such as COVID-19, computational multi-targeted compound screening has been limited by the scarcity of high-quality experimental data and difficulties in extracting information from molecules. This study introduces MolGNN , a new deep learning model for molecular property prediction. MolGNN applies a graph neural network to computational learning of chemical molecule embedding. Comparing to state-of-the-art approaches heavily relying on labeled experimental data, our method achieves equivalent or superior prediction …

Fostering Information Literacy: A Call For Collaboration Between Academic Librarians And Msw Instructors., Sarah C. Johnson, Margaret Bausman, Sarah Ward

Publications and Research

Genuine collaboration between academic librarians and social work faculty in which information literacy is embedded in social work education is lacking. Drawing from the results of the authors’ 2016 quantitative study surveying academic social work librarians across the United States, this qualitative follow-up uses data from 27 semi-structured interviews concerning the prevalence and nature of information literacy instruction (ILI) in social work education, how ILI is introduced and sustained in social work curricula, and the alignment between ILI efforts with institutional goals, guidelines from accreditation authorities, and professional social work practice standards. The literature review engages the reader in a …

First Report Of Mummenhoffia Alliacea (Brassicaceae) For New York, Daniel Atha, Eve Levine, John F. Gaskin, César Castillo

Publications and Research

Mummenhoffia alliacea is naturalized in New York. The first documented occurrences are reported from Dutchess, Kings, New York (Manhattan), Onondaga, Queens, and Suffolk counties. Verification is provided by herbarium specimens at NY and photographs uploaded to iNaturalist and cited at the Global Biodiversity Information Facility.

Defining The Basis Of Cyanine Phototruncation Enables A New Approach To Single-Molecule Localization Microscopy, Siddharth S. Matikonda, Dominic A. Helmerich, Mara Meub, Gerti Beliu, Philip Kollmannsberger, Alexander Greer, Markus Sauer, Martin J. Schnermann

Publications and Research

The light-promoted conversion of extensively used cyanine dyes to blue-shifted emissive products has been observed in various contexts. However, both the underlying mechanism and the species involved in this photoconversion reaction have remained elusive. Here we report that irradiation of heptamethine cyanines provides pentamethine cyanines, which, in turn, are photoconverted to trimethine cyanines. We detail an examination of the mechanism and substrate scope of this remarkable twocarbon phototruncation reaction. Supported by computational analysis, we propose that this reaction involves a singlet oxygeninitiated multistep sequence involving a key hydroperoxycyclobutanol intermediate. Building on this mechanistic framework, we identify conditions to improve the …

Draft Genome Sequences Of 13 Vibrio Cholerae Strains From The Rio Grande Delta, Jeffrey W. Turner, Jorge Duran-Gonzalez, David A. Laughlin, Daniel Unterweger, David Silva, Boris Ermolinsky, Stefan Pukatzki, Daniele Provenzano

Publications and Research

Vibrio cholerae is the etiologic agent of cholera, an acute and often fatal diarrheal disease that affects millions globally. We report the draft genome sequences of 13 non-O1/O139 V. cholerae strains isolated from the Rio Grande Delta in Texas. These genomes will aid future analyses of environmental serovars.

Detection Methods And Clinical Applications Of Circulating Tumor Cells In Breast Cancer, Hongyi Zhang, Xiaoyan Lin, Yuan Huang, Minghong Wang, Chunmei Cen, Shasha Tang, Marcia R. Dique, Lu Cai, Manuel A. Luis, Jillian Smollar, Yuan Wan, Fengfeng Cai

Publications and Research

Circulating Tumor Cells (CTCs) are cancer cells that split away from the primary tumor and appear in the circulatory system as singular units or clusters, which was first reported by Dr. Thomas Ashworth in 1869. CTCs migrate and implantation occurs at a new site, in a process commonly known as tumor metastasis. In the case of breast cancer, the tumor cells often migrate into locations such as the lungs, brain, and bones, even during the early stages, and this is a notable characteristic of breast cancer. Survival rates have increased significantly over the past few decades because of progress made …

Dna Barcoding Of The High-Altitude Artemisia And Nepeta Species, Vyacheslav Dushenkov, Csanad Gurdon, Shukhratdzhon Satorov

Publications and Research

DNA barcoding was performed for four medicinal plant species from the mountain region of Tajikistan. The nucleotide sequences for Artemisia sieberi, Artemisia scoparia, Artemisia vulgaris, and Nepeta glutinosa were deposited into the GenBank at the National Center for Biotechnology Information.

Heparan Sulfate Proteoglycan Glypican‑1 And Pecam‑1 Cooperate In Shear‑Induced Endothelial Nitric Oxide Production, Anne Marie W. Bartosch, Rick Mathews, Marwa M. Mahmoud, Limary M. Cancel, Zahin S. Haq, John M. Tarbell

Publications and Research

This study aimed to clarify the role of glypican-1 and PECAM-1 in shear-induced nitric oxide production in endothelial cells. Atomic force microscopy pulling was used to apply force to glypican-1 and PECAM-1 on the surface of human umbilical vein endothelial cells and nitric oxide was measured using a fluorescent reporter dye. Glypican-1 pulling for 30 min stimulated nitric oxide production while PECAM-1 pulling did not. However, PECAM-1 downstream activation was necessary for the glypican-1 force-induced response. Glypican-1 knockout mice exhibited impaired flow-induced phosphorylation of eNOS without changes to PECAM-1 expression. A cooperation mechanism for the mechanotransduction of fluid shear stress …

Deep Learning Predicts Chromosomal Instability From Histopathology Images, Zhuoran Xu, Akanksha Verma, Uska Naveed, Samuel F. Bakhoum, Pegah Khosravi, Olivier Elemento

Publications and Research

Chromosomal instability (CIN) is a hallmark of human cancer yet not readily testable for patients with cancer in routine clinical setting. In this study, we sought to explore whether CIN status can be predicted using ubiquitously available hematoxylin and eosin histology through a deep learning-based model. When applied to a cohort of 1,010 patients with breast cancer (Training set: n = 858, Test set: n = 152) from The Cancer Genome Atlas where 485 patients have high CIN status, our model accurately classified CIN status, achieving an area under the curve of 0.822 with 81.2% sensitivity and 68.7% specificity in …

Analysis Of Gaps In Feline Ectoparasiticide Purchases From Veterinary Clinics In The United States, Robert Lavan, Dorothy Normile, Imran Husain, Amita Singh, Kathleen Heaney

Publications and Research

Background: The study objective was to examine cat owner ectoparasiticide purchases in the United States and estimate the impact of purchase gaps on timely ectoparasite protection administration. These purchase gaps lead to periods of time when cats are unprotected from ectoparasites.

Methods: Ectoparasiticide purchase transactions for individual cats from 671 U.S. veterinary clinics from January 1, 2017 through June 30, 2019 were evaluated to determine time “gaps” between doses of ectoparasiticides purchased in a defined 12-month period. Ectoparasiticides examined were topically applied products that contained fluralaner, fipronil/(S)-methoprene/pyriproxyfen, imidacloprid/pyriproxyfen or selamectin as active ingredients. The duration of protection following administration of …

The Paradox Of Retained Genetic Diversity Of Hippocampus Guttulatus In The Face Of Demographic Decline, Rupert Stacy, Jorge Palma, Miguel Correia, Anthony B. Wilson, José Pedro Andrade, Rita Castilho

Publications and Research

Genetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has …

A Lexical And Syntactic Study Of Research Article Titles In Library Science And Scientometrics, Junli Diao

Publications and Research

Title of a research article is an abstract of the abstract. Titles play a decisive role in convincing readers at first sight whether articles are worth reading or not. Not only do research article titles show how carefully words are chosen by authors, but also reflect disciplinary differences in terms of title words and structure between hard sciences and soft sciences. This study examined the lexical density and syntactic structure of 690 research article titles chosen from five Library Science and Scientometrics journals, aiming to reveal disciplinary differences. The result suggested both Library Science and Scientometrics have almost the same …

Dom Degradation By Light And Microbes Along The Yukon River‑Coastal Ocean Continuum, Brice K. Grunert, Maria Tzortziou, Patrick Neale, Alana Menendez, Peter Hernes

Publications and Research

The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure …

Neurophysiological Changes After Paired Brain And Spinal Cord Stimulation Coupled With Locomotor Training In Human Spinal Cord Injury, Timothy S. Pulverenti, Morad Zaaya, Monika Grabowski, Ewelina Grabowski Grabowski, Md. Anamul Islam, Jeffrey Li, Lynda M. Murray, Maria Knikou

Publications and Research

Neurophysiological changes that involve activity-dependent neuroplasticity mechanisms via repeated stimulation and locomotor training are not commonly employed in research even though combination of interventions is a common clinical practice. In this randomized clinical trial, we established neurophysiological changes when transcranial magnetic stimulation (TMS) of the motor cortex was paired with transcutaneous thoracolumbar spinal (transspinal) stimulation in human spinal cord injury (SCI) delivered during locomotor training. We hypothesized that TMS delivered before transspinal (TMS-transspinal) stimulation promotes functional reorganization of spinal networks during stepping. In this protocol, TMS-induced corticospinal volleys arrive at the spinal cord at a sufficient time to interact with …

Intangible Cultural Heritage: A Benefit To Climate-Displaced And Host Communities, Gül Aktürk, Martha B. Lerski

Publications and Research

Climate change is borderless, and its impacts are not shared equally by all communities. It causes an imbalance between people by creating a more desirable living environment for some societies while erasing settlements and shelters of some others. Due to floods, sea level rise, destructive storms, drought, and slow-onset factors such as salinization of water and soil, people lose their lands, homes, and natural resources. Catastrophic events force people to move voluntarily or involuntarily. The relocation of communities is a debatable climate adaptation measure which requires utmost care with human rights, ethics, and psychological well-being of individuals upon the issues …

Interfacial Dynamics And Ionic Transport Of Radiologic Contrast Media In Carbohydrate Matrix: Utility And Limits Of X-Ray Imaging, Lin Mousa, Hayley Sanchez, Subhendra Sarkar, Zoya Vinokur

Publications and Research

Hello, our names are Lin Mousa and Hayley Sanchez, this semester we participated in a research project dedicated to analyzing the interactions of contrast media with the molecular components of fruits to compare how they would react with the human brain. This project involved the injection of fruits with varying contrasts and the imaging of the diffusion and interactions of the contrast within the fruits with X-rays. With setup technical parameters on the x-ray equipment images were taken with identical setups at an hourly rate for several days. The final results of this experiment indicated that contrasts such as Gadolinium …