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Mora And Ensembletfpredictor: An Ensemble Approach To Reveal Functional Transcription Factor Regulatory Networks, Kevin Boyer, Louis Li, Tiandao Li, Bo Zhang, Guoyan Zhao

2020-Current year OA Pubs

MOTIVATION: Our study aimed to identify biologically relevant transcription factors (TFs) that control the expression of a set of co-expressed or co-regulated genes.

RESULTS: We developed a fully automated pipeline, Motif Over Representation Analysis (MORA), to detect enrichment of known TF binding motifs in any query sequences. MORA performed better than or comparable to five other TF-prediction tools as evaluated using hundreds of differentially expressed gene sets and ChIP-seq datasets derived from known TFs. Additionally, we developed EnsembleTFpredictor to harness the power of multiple TF-prediction tools to provide a list of functional TFs ranked by prediction confidence. When applied to …

Rev-Erb Activation As A Novel Pharmacological Approach For Treating Inflammatory Pain, Sangeet Makhija, Joshua D Griffett, Giri Babu Veerakanellore, Thomas P Burris, Bahaa Elgendy, Kristine Griffett

2020-Current year OA Pubs

Pain is a complex problem affecting millions of people worldwide. The current therapies to reduce pain are limited as many treatment options inadequately address the causes of pain, lead to tolerance of the drug, or have adverse effects including abuse potential. While there are many causes of pain, one underlying mechanism to the pathogenesis and maintenance of pain conditions is chronic inflammation driven by the NLRP3 inflammasome. Several inflammasome inhibitors are currently under investigation however have the potential to suppress the functioning of the innate immune system, which may cause unwanted affects in patients. Here, we show that the nuclear …

Sleep Deprivation, Sleep Fragmentation, And Social Jet Lag Increase Temperature Preference In Drosophila, S Tanner Roach, Melanie C Ford, Vikram Simhambhatla, Vasilios Loutrianakis, Hamza Farah, Zhaoyi Li, Erica M Periandri, Dina Abdalla, Irene Huang, Arjan Kalra, Paul J Shaw

2020-Current year OA Pubs

Despite the fact that sleep deprivation substantially affects the way animals regulate their body temperature, the specific mechanisms behind this phenomenon are not well understood. In both mammals and flies, neural circuits regulating sleep and thermoregulation overlap, suggesting an interdependence that may be relevant for sleep function. To investigate this relationship further, we exposed flies to 12 h of sleep deprivation, or 48 h of sleep fragmentation and evaluated temperature preference in a thermal gradient. Flies exposed to 12 h of sleep deprivation chose warmer temperatures after sleep deprivation. Importantly, sleep fragmentation, which prevents flies from entering deeper stages of …

Vigorous-Intensity Exercise As A Modulator Of Cardiac Adipose Tissue In Women With Obesity: A Cross-Sectional And Randomized Pilot Study, Sumsen Thapa, Bharath S Selvaraj, Paige N Davis, Bryan Smith, Amy H Givan, Jose A Perez-Rivera, Pamela K Woodard, Jon D Klingensmith, Maria Fernandez-Del-Valle

2020-Current year OA Pubs

Cardiac adipose tissue (CAT) has become an important target for the reduction of disease risk. Supervised exercise programs have shown potential to "significantly" reduce CAT; however, the impact of different exercise modalities is not clear, and the relationships between CAT, physical activity (PA) levels and fitness (PFit) remain unknown. Therefore, the purpose of this study was to analyze the relationships between CAT, PA and PFit, and to explore the effects of different exercise modalities in a group of women with obesity. A total of 26 women (age: 23.41 ± 5.78 years-old) were enrolled in the cross-sectional study. PA, cardiorespiratory fitness, …

Nrg/Rtog 0837: Randomized, Phase Ii, Double-Blind, Placebo-Controlled Trial Of Chemoradiation With Or Without Cediranib In Newly Diagnosed Glioblastoma, Tracy T Batchelor, Clifford G Robinson, Et Al.

2020-Current year OA Pubs

BACKGROUND: A randomized, phase II, placebo-controlled, and blinded clinical trial (NCT01062425) was conducted to determine the efficacy of cediranib, an oral pan-vascular endothelial growth factor receptor tyrosine kinase inhibitor, versus placebo in combination with radiation and temozolomide in newly diagnosed glioblastoma.

METHODS: Patients with newly diagnosed glioblastoma were randomly assigned 2:1 to receive (1) cediranib (20 mg) in combination with radiation and temozolomide; (2) placebo in combination with radiation and temozolomide. The primary endpoint was 6-month progression-free survival (PFS) based on blinded, independent radiographic assessment of postcontrast T1-weighted and noncontrast T2-weighted MRI brain scans and was tested using a 1-sided …

Enhancing The Therapeutic Activity Of Hyperimmune Igg Against Chikungunya Virus Using Fcγriiia Affinity Chromatography, Julie M Fox, Vicky Roy, Bronwyn M Gunn, Glen R Bolton, Daved H Fremont, Galit Alter, Michael S Diamond, Austin W Boesch

2020-Current year OA Pubs

INTRODUCTION: Chikungunya virus (CHIKV) is a re-emerging mosquito transmitted alphavirus of global concern. Neutralizing antibodies and antibody Fc-effector functions have been shown to reduce CHIKV disease and infection in animals. However, the ability to improve the therapeutic activity of CHIKV-specific polyclonal IgG by enhancing Fc-effector functions through modulation of IgG subclass and glycoforms remains unknown. Here, we evaluated the protective efficacy of CHIKV-immune IgG enriched for binding to Fc-gamma receptor IIIa (FcγRIIIa) to select for IgG with enhanced Fc effector functions.

METHODS: Total IgG was isolated from CHIKV-immune convalescent donors with and without additional purification by FcγRIIIa affinity chromatography. The …

Whole-Brain Imaging Of Freely-Moving Zebrafish, Hamid Hasani, Jipeng Sun, Shuyu I Zhu, Qiangzhou Rong, Florian Willomitzer, Rumelo Amor, Gail Mcconnell, Oliver Cossairt, Geoffrey J Goodhill

2020-Current year OA Pubs

One of the holy grails of neuroscience is to record the activity of every neuron in the brain while an animal moves freely and performs complex behavioral tasks. While important steps forward have been taken recently in large-scale neural recording in rodent models, single neuron resolution across the entire mammalian brain remains elusive. In contrast the larval zebrafish offers great promise in this regard. Zebrafish are a vertebrate model with substantial homology to the mammalian brain, but their transparency allows whole-brain recordings of genetically-encoded fluorescent indicators at single-neuron resolution using optical microscopy techniques. Furthermore zebrafish begin to show a complex …

Designing Home-Based Physical Activity Programs For Rural Cancer Survivors: A Survey Of Technology Access And Preferences, Elizabeth A Salerno, Rohana Gao, Jason Fanning, Neha P Gothe, Lindsay L Peterson, Allison B Anbari, Maura M Kepper, Jingqin Luo, Aimee S James, Edward Mcauley, Graham A Colditz

2020-Current year OA Pubs

BACKGROUND: While technology advances have increased the popularity of remote interventions in underserved and rural cancer communities, less is understood about technology access and preferences for home-based physical activity programs in this cancer survivor population.

PURPOSE: To determine access, preferences, and needs, for a home-based physical activity program in rural cancer survivors.

METHODS: A Qualtrics Research Panel was recruited to survey adults with cancer across the United States. Participants self-reported demographics, cancer characteristics, technology access and usage, and preferences for a home-based physical activity program. The Godin Leisure Time Exercise Questionnaire (GLTEQ) assessed current levels of physical activity. Descriptive statistics …

A Framework For Assessing Environmental Incidents In Coastal Areas: A Case Study In The Southeastern Coastal Area Of Vietnam, Cuong Le Tan, Phuoc Nguyen Van, Quan Nguyen Hong, Loan Tran Thi Diem, Minh Tran Thanh

Applied Environmental Research

As developing dynamic regions, coastal areas have a high potential for environmental incidents, especially chemical spills, which may permanently threaten livelihoods and coastal ecosystems. Establishing an appropriate methodological framework for assessing environmental incidents in coastal areas, ensuring increased predictability and minimising potential consequences is a trend of interest to scientists. In this study, the environmental risk assessment model was applied to develop a framework for assessing environmental incidents in coastal areas due to chemical spills from the mainland based on hazard, exposure and vulnerability factors (i.e., sensitivity and adaptability). Using the multiple criteria decision-making (MCDM) method approach, suitable criteria, their …

Microplastic Contamination In The Coastal Environment: A Case Study From The Mae Klong River, Samut Songkhram, Pattraporn Chaisanguansuk, Suphak Ploenbuppa, Thitiphan Assawincharoenkij, Sumet Phantuwongraj, Akkaneewut Jiraphinyakul

Applied Environmental Research

To investigate the microplastic contamination in the coastal area in Samut Songkhram, we collected sediment samples from six locations in mangrove forests along the Mae Klong River estuary (MK) and the nearby Khlong Khon canal (KK). The microplastics were extracted by ZnCl2 density separation and subsequently H2O2 digestion. The microplastic abundance and physical properties, including their size, color, and shape, were determined under the binocular microscope. The selected microplastic samples were analyzed by µ-FTIR spectroscopy to identify their polymer types. Microplastic concentrations were c. 580 and 1690 items kg-1 d.w. in the samples from MK and KK. The lower microplastic …

Assessment Of Heavy Metal Cd And Pb Concentrations And The Ecological Risk From Seawater, Sediments, And Perna Viridis In Semarang Bay, Indonesia, Max Rudolf Muskananfola, Agus Hartoko, Nurul Latifah

Applied Environmental Research

Semarang Bay is a multiple water source from some rivers located at the forefront of the most populated city in Central Java. These waters are polluted by wastes from various sources. Previous studies conducted were limited to specific areas and were mainly focused on one or two media only. This research aims to analyse the heavy metal Cd and Pb concentrations in seawater, sediments, and green mussels and the ecological risks. Field data were collected from 18 sites from three locations: Semarang, Demak and Kendal during the dry season of 2020. Environmental variables were measured in situ, and the heavy …

Health Impacts From Pm2.5 Exposure Using Environmental Epidemiology And Health Risk Assessment: A Review, Thanakon Sukuman, Kayo Ueda, Sarunya Sujaritpong, Hirunwut Praekunatham, Kornwipa Punnasiri, Tuangsit Wimuktayon, Trakarn Prapaspongsa

Applied Environmental Research

Exposure to PM2.5 has been known to cause a variety of serious health consequences. Quantifying and investigating the health effects of PM2.5 pollution are imperative to understand and collect scientific evidence for supporting policies and associated actions. In this paper, we reviewed published environ-mental epidemiological studies and health risk assessments evaluating the health impacts of PM2.5 exposure in the PubMed database to identify the attributes of each method and aggregate the health impact results to perform analyses and summaries. Forty-two studies were identified after applying our search strategy, inclusion, and exclusion criteria. The epidemiological studies found an increased risk of …

Banana Stem (Musa Balbisiana Colla) As Potential Biosorbent To Remove Methylene Blue Dye In Wastewater: Isotherm, Kinetic, Thermodynamic Studies And Its Application, Rahmiana Zein, Clalitya Akmal, Safni Safni, Syiffa Fauzia, Putri Ramadhani

Applied Environmental Research

Textile industries discharge various waste including dye waste to the environment. Dye waste such as methylene blue taints both aquatic and land ecosystem. Thus, the recent study employs banana stem (Musa balbisiana Colla), as an economical and environmentally friendly biosorbent for methylene blue removal. The chemically activated banana stem indicates the significant methylene blue uptake at pH 5, initial concentration of 800 mg L-1, contact time of 60 min, temperature at 25 °C with adsorption capacity of 71.5470 mg g-1. The adsorption process follows the Langmuir isotherm model (R2 = 0.9965) and pseudo order model which involve monolayer …

Potential Factors Of Landslide Recurrence In Uttaradit, Thailand: A Case Study In Laplae, Mueang Uttaradit, And Tha Pla Districts, Panithan Sawatdikomon, Watit Khokthong, Nipada Santha

Applied Environmental Research

Laplae, Mueang Uttaradit, and Tha Pla district, Uttaradit province, Thailand are considered as high potential landslide areas. Still, this disaster is difficult to address because of complex factors controlling its occurrence. Therefore, the prediction of the potential landslide area using a landslide susceptibility map has been able to accomplish as a great strategy for the disaster.  A landslide susceptibility map was produced by the geographic information system (GIS) data. The methods were initially conducted by the selection of potential factors related to landslides, which were lithology, slope, aspect, plan curvature, profile curvature, distance to stream, land use, and rainfall. All …

Application Of Fe3o4/Thiamine Magnetic Particles In The Removal Of Methylene Blue, Lan Tran-Nguyen, Suong Mai-Thi-Thu, Thanh-Ty Nguyen, Kim-Phung Ly, Luu-Ngoc-Hanh Cao, Tran Thi Bich Quyen, Shella Permatasari Santoso, Nguyen-Phuong-Dung Tran, Nguyen Minh Nhut

Applied Environmental Research

Fe3O4/thiamine particles were prepared in this work via precipitation method. The synthesis method is based on the principle of precipitation of Fe3O4 particles in the presence of thiamine coating agent. Also, the potential application of Fe3O4/ thiamine in the removal of methylene blue (MB) was investigated. Several factors that affect the synthesis of Fe3O4/thiamine such as base concentration, mass ratio of FeCl2 to thiamine, reaction temperature, and reaction time were determined. Optimal conditions for preparing Fe3O4/thiamine are NH4OH concentration = 10%, mass ratio of FeCl2:thiamine = 5:1 (g g-1), reaction temperature = 30 °C, reaction time = 120 min. The …

The Effect Of Incubation Time And Drainage Ph On The Immobilization Of Copper In Post Coal Mine Soil Using Sumatera Brown Coal Char, Muhammad Haviz, Damris Muhammad, Maria Vabylita, Miftahul Djana, Rizka Mayasari, Ashruri -, Sandri Erfani, Yuli Darni, Opik Taufik Purwadi, Simparmin Ginting

Applied Environmental Research

Post coal mine (PCM) activities pose significant environmental challenges. Soils affected by PCM often exhibit increased acidity and elevated levels of heavy metals. In the case of Sungai Buluh PCM in the Jambi Province, Indonesia, copper (Cu) levels in the soil reach 94.79 mg kg-1, surpassing the Indonesian standard of 40 mg kg-1. Sumatera brown coal (SBC), typically is not considered as fuel due to its properties, offers a cost-effective solution for Cu immobilization in such soils. In this study, SBC was subjected to pyrolysis at 400°C for 1 h, sieved through a 10-mesh sieve, and characterized using SEM and …

Distribution Of Exchangeable Magnesium In Lowland Rice-Cultivated Soils Of Sri Lanka As Affected By The Differences In Climate, Soil, And Water Source, Indeera Hetti Arachchige, Buddhi Marambe, Mohomad Nijamudeen, Harsha Kadupitiya, Dinaratne Sirisena, Rohana Chandrajith, Lalith Suriyagoda

Applied Environmental Research

Magnesium (Mg) is an essential macronutrient for plants. Even though Sri Lankans consume rice as the staple food, the Mg status in Sri Lankan paddy soils as affected by its climate, soils, and water sources used are not well understood. This study was conducted to (i) determine the distribution of exchangeable Mg (ex-Mg) concentration, and (ii) examine the interactive effects of agro-climatic zones (ACZs), soil order, and water source in determining the ex-Mg concentra-tion in lowland paddy fields of Sri Lanka. A total of 9,038 soil samples representing six ACZs, six soil orders, and three water sources were collected using …

The Effect Of Irrigation Techniques On Sustainable Water Management For Rice Cultivation System - A Review, Bittawat Wichaidist, Amornrat Intrman, Songsak Puttrawutichai, Chawakorn Rewtragulpaibul, Supatchaya Chuanpongpanich, Chaisri Suksaroj

Applied Environmental Research

Rice serves as a fundamental sustenance for approximately half of the global population, particularly in Asia. Nevertheless, the cultivation of rice demands a substantial water supply, and the challenges associated with water deficits have been exacerbated by irregular rainfall patterns induced by global warming. Consequently, there is a critical need to reassess irrigation techniques to effectively tackle these issues. In this comprehensive review, the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) method was employed to systematically explore literature on irrigation techniques aimed at fostering sustainable water management in rice cultivation systems. The primary components of the framework encompass …

Und Leads: A Strategic Vision For The University Of North Dakota, University Of North Dakota

LEADS Implementation Documents

Official UND LEADS strategic plan for the University of North Dakota. The plan presents UND’s mission and vision, introduces the five LEADS core values of Learning, Equity, Affinity, Discovery, and Service, and outlines the strategic priorities guiding UND’s implementation work.