Medicine and Health Sciences Commons^™

Sctiger: A Deep-Learning Method For Inferring Gene Regulatory Networks From Case Versus Control Scrna-Seq Datasets., Madison Dautle, Shaoqiang Zhang, Yong Chen

Faculty Scholarship for the College of Science & Mathematics

Inferring gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data is an important computational question to find regulatory mechanisms involved in fundamental cellular processes. Although many computational methods have been designed to predict GRNs from scRNA-seq data, they usually have high false positive rates and none infer GRNs by directly using the paired datasets of case-versus-control experiments. Here we present a novel deep-learning-based method, named scTIGER, for GRN detection by using the co-differential relationships of gene expression profiles in paired scRNA-seq datasets. scTIGER employs cell-type-based pseudotiming, an attention-based convolutional neural network method and permutation-based significance testing for inferring GRNs among …

Voluntary Wheel Running Promotes Resilience To The Behavioral Effects Of Unpredictable Chronic Mild Stress In Male And Female Mice., Elias Elias, Ariel Y Zhang, Abigail G White, Matthew J Pyle, Melissa T Manners

Faculty Scholarship for the College of Science & Mathematics

Besides significant benefits to physical health, exercise promotes mental health, reduces symptoms of mental illness, and enhances psychological development. Exercise can offset the impact of chronic stress, which is a major precursor to the development of mental disorders. The effects of exercise on chronic stress-induced behaviors are contradictory in preclinical studies, primarily due to the lack of data and sex-specific investigations. We sought to evaluate the effects of exercise on chronic stress-induced behavioral changes in both male and female mice. Mice were subjected to an Unpredictable Chronic Mild Stress (UCMS) paradigm with accessibility to running wheels for 2 h daily. …

The Landscape Of Rna Polymerase Ii-Associated Chromatin Interactions In Prostate Cancer, Susmita G Ramanand, Yong Chen, Jiapei Yuan, Kelly Daescu, Maryou Bk Lambros, Kathleen E Houlahan, Suzanne Carreira, Wei Yuan, Guemhee Baek, Adam Sharp, Alec Paschalis, Mohammed Kanchwala, Yunpeng Gao, Adam Aslam, Nida Safdar, Xiaowei Zhan, Ganesh V Raj, Chao Xing, Paul C Boutros, Johann De Bono, Michael Q Zhang, Ram S Mani

Faculty Scholarship for the College of Science & Mathematics

Transcriptional dysregulation is a hallmark of prostate cancer (PCa). We mapped the RNA polymerase II-associated (RNA Pol II-associated) chromatin interactions in normal prostate cells and PCa cells. We discovered thousands of enhancer-promoter, enhancer-enhancer, as well as promoter-promoter chromatin interactions. These transcriptional hubs operate within the framework set by structural proteins - CTCF and cohesins - and are regulated by the cooperative action of master transcription factors, such as the androgen receptor (AR) and FOXA1. By combining analyses from metastatic castration-resistant PCa (mCRPC) specimens, we show that AR locus amplification contributes to the transcriptional upregulation of the AR gene by increasing …

Transcranial Direct Current Stimulation Of Motor Cortex Enhances Running Performance., Seung-Bo Park, Dong Jun Sung, Bokyung Kim, Sojung Kim, Joung-Kyue Han

Faculty Scholarship for the College of Science & Mathematics

Transcranial direct current stimulation (tDCS) is a technique used to modulate neuronal excitability through non-invasive brain stimulation that can enhance exercise performance. We hypothesize that tDCS would improve submaximal running time to exhaustion (TTE) and delay the increase in the rating of perceived exertion (RPE) over time. We also hypothesize that tDCS would not lead to difference in cardiorespiratory responses. We employed a randomized, single-blinded, and counterbalanced design in which 10 trained men participated. After receiving either 20 min of 1.98 mA anodal tDCS applied over the primary motor cortex (M1) or sham-operated control on separate days, participants completed a …

Normative Data For The Neurocom Sensory Organization Test In Us Military Special Operations Forces., Erin R. Pletcher, Valerie J Williams, John P Abt, Paul M Morgan, Jeffrey J Parr, Meleesa F Wohleber, Mita Lovalekar, Timothy C Sell

Faculty Scholarship for the College of Science & Mathematics

CONTEXT: Postural stability is the ability to control the center of mass in relation to a person's base of support and can be affected by both musculoskeletal injury and traumatic brain injury. The NeuroCom Sensory Organization Test (SOT) can be used to objectively quantify impairments to postural stability. The ability of postural stability to predict injury and be used as an acute injury-evaluation tool makes it essential to the screening and rehabilitation process. To our knowledge, no published normative data for the SOT from a healthy, highly active population are available for use as a reference for clinical decision making. …

Examining Multi-Session Brief Intervention For Substance Use In Primary Care: Research Methods Of A Randomized Controlled Trial., Jaclyn E Chambers, Adam C Brooks, Rachel Medvin, David S Metzger, Jennifer Lauby, Carolyn M Carpenedo, Kevin E Favor, Kimberly C Kirby

Faculty Scholarship for the College of Science & Mathematics

BACKGROUND: Brief interventions such as Screening, a single session of Brief Intervention, and Referral to Treatment (SBIRT) have shown mixed effectiveness in primary care. However, there are indications that multi-session brief interventions may demonstrate more consistently positive outcomes, and perhaps a more intensive approach would be of benefit in addressing substance use in primary care. This study compared the effectiveness of SBIRT with a single BI session (BI/RT) to a multi-session brief-treatment intervention (BI/RT+) in primary care. We also developed easy-to-use, evidence-based materials to assist clinicians in delivering these interventions.

METHODS/DESIGN: This study was conducted in three Federally Qualified Healthcare …

Randomized Clinical Trial Examining Duration Of Voucher-Based Reinforcement Therapy For Cocaine Abstinence., Kimberly C Kirby, Carolyn M Carpenedo, Karen L Dugosh, Beth J Rosenwasser, Lois A Benishek, Alicia Janik, Rachel Keashen, Elena Bresani, Kenneth Silverman

Faculty Scholarship for the College of Science & Mathematics

BACKGROUND: This is the first study to systematically manipulate duration of voucher-based reinforcement therapy (VBRT) to see if extending the duration increases abstinence during and following VBRT.

METHODS: We randomized cocaine-dependent methadone-maintained adults to Standard (12 weeks; n=62) or Extended (36 weeks; n=68) VBRT and provided escalating voucher amounts contingent upon urinalysis verification of cocaine abstinence. Urinalysis was scheduled at least every 2 weeks during the 48-week study and more frequently during VBRT (3/week) and 12 weeks of Aftercare (2/week).

RESULTS: Extended VBRT produced longer durations of continuous cocaine abstinence during weeks 1-24 (5.7 vs 2.7 weeks; p=0.003) and proportionally …