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https://www.readbyqxmd.com/read/29329361/pyhvis3d-visualising-molecular-simulation-deduced-h-bond-networks-in-3d-application-to-t-cell-receptor-interactions
#1
Bernhard Knapp, Marta Alcala, Hao Zhang, Clare West, P Anton van der Merwe, Charlotte M Deane
Motivation: Hydrogen bonds (H-bonds) play an essential role for many molecular interactions but are also often transient, making visualizing them in a flexible system challenging. Results: We provide pyHVis3D which allows for an easy to interpret 3D visualisation of H-bonds resulting from molecular simulations. We demonstrate the power of pyHVis3D by using it to explain the changes in experimentally measured binding affinities for three T-cell receptor/peptide/MHC complexes and mutants of each of these complexes...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29329151/gadolinium-retention-brain-t1-hyperintensity-and-endogenous-metals-a-comparative-study-of-macrocyclic-versus-linear-gadolinium-chelates-in-renally-sensitized-rats
#2
Marlène Rasschaert, Andréa Emerit, Nathalie Fretellier, Cécile Factor, Philippe Robert, Jean-Marc Idée, Claire Corot
OBJECTIVES: This preclinical study was designed to compare gadolinium (Gd) brain uptake after repeated injections of a macrocyclic Gd-based contrast agent (GBCA) (gadoterate meglumine) or 2 linear GBCAs (L-GBCAs) (gadobenate dimeglumine or gadodiamide) on a translational model of moderate renal impairment in rats. METHODS: The study was carried out in subtotally nephrectomized rats. Animals received 4 intravenous injections per week of GBCA (gadoterate meglumine, gadobenate dimeglumine, or gadodiamide) for 5 weeks, resulting in a cumulative dose of 12 mmol/kg, followed by a 1-month injection-free period...
January 12, 2018: Investigative Radiology
https://www.readbyqxmd.com/read/29298731/spontaneous-rhythms-in-a-harbor-seal-pup-calls
#3
Andrea Ravignani
OBJECTIVES: Timing and rhythm (i.e. temporal structure) are crucial, though historically neglected, dimensions of animal communication. When investigating these in non-human animals, it is often difficult to balance experimental control and ecological validity. Here I present the first step of an attempt to balance the two, focusing on the timing of vocal rhythms in a harbor seal pup (Phoca vitulina). Collection of this data had a clear aim: To find spontaneous vocal rhythms in this individual in order to design individually-adapted and ecologically-relevant stimuli for a later playback experiment...
January 3, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29280991/r2dgc-threshold-free-peak-alignment-and-identification-for-2d-gas-chromatography-mass-spectrometry-in-r
#4
Ryne C Ramaker, Emily Gordon, Sara J Cooper
Summary: Comprehensive two dimensional gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds, but produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. Very few existing tools address this aspect of analysis and those that do have shortfalls in usability or performance...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29276003/-i-just-want-to-do-everything-right-primiparous-women-s-accounts-of-early-breastfeeding-via-an-app-based-diary
#5
Jill Demirci, Erin Caplan, Nora Murray, Susan Cohen
INTRODUCTION: Our objective was to describe the early breastfeeding experience of primiparous women. METHODS: Healthy, primiparous women intending to exclusively breastfeed downloaded a commercial infant feeding mobile application (app) during their postpartum hospitalization. Women free-texted breastfeeding thoughts and experiences through 8 weeks postpartum in the app's diary. Diary content was qualitatively coded. RESULTS: Thirty-five participants completed diaries and were included in analyses...
December 21, 2017: Journal of Pediatric Health Care
https://www.readbyqxmd.com/read/29233308/evaluation-of-students-perceptions-of-the-socrative-application-versus-a-traditional-student-response-system-and-its-impact-on-classroom-engagement
#6
Anthony J Guarascio, Branden D Nemecek, David E Zimmerman
BACKGROUND AND PURPOSE: Student response systems (SRSs) or "clickers" are common tools that lecturers can implement into didactic lectures. Socrative is a convenient and free SRS application that can be downloaded on personal handheld devices and used by faculty and students. It is unknown if students prefer using this application and what advantages or disadvantages can be seen with Socrative's use. PURPOSE: To measure student preference of standard SRS methods compared to Socrative as well as the impact of Socrative use on student engagement during delivery of clinical pharmacy instruction EDUCATIONAL ACTIVITY AND SETTING: Standard SRS and Socrative incorporated lectures were presented to students during an infectious disease module...
September 2017: Currents in Pharmacy Teaching & Learning
https://www.readbyqxmd.com/read/29228185/dncon2-improved-protein-contact-prediction-using-two-level-deep-convolutional-neural-networks
#7
Badri Adhikari, Jie Hou, Jianlin Cheng
Motivation: Significant improvements in the prediction of protein residue-residue contacts are observed in the recent years. These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in the recent CASP experiments. Continuing the development of new methods to reliably predict contact maps is essential to further improve ab initio structure prediction...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29215372/efficacy-and-safety-of-apatinib-as-second-line-therapy-for-advanced-gastric-cancer-a-single-center-observational-study
#8
Yong Zhang, Miaomiao Gou, Chun Han, Juan Li, Lijie Wang, Qian Qiao, Yi Hu, Li Bai, Zhefeng Liu
Apatinib has been proven to be effective and safe among patients in the third-line treatment of advanced gastric cancer in phase II and III trials. We aimed to evaluate its efficacy and safety in second-line practice, and to explore the factors associated with efficacy. Between April 2015 and May 2017, a total of 23 patients with advanced gastric adenocarcinoma or adenocarcinoma of gastroesophageal junction were enrolled and followed up retrospectively after failing the first line of systemic therapy. The median progression-free survival was 4...
December 5, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/29212627/how-do-infant-feeding-apps-in-china-measure-up-a-content-quality-assessment
#9
Jing Zhao, Becky Freeman, Mu Li
BACKGROUND: Globally, with the popularization of mobile phones, the number of health-related mobile phone apps has skyrocketed to 259,000 in 2016. In the digital era, people are accessing health information through their fingertips. In China, there are several apps that claim to provide infant feeding and nutrition guidance. However, the quality of information in those apps has not been extensively assessed. OBJECTIVE: We aimed to assess the quality of Chinese infant feeding apps using comprehensive quality assessment criteria and to explore Chinese mothers' perceptions on apps' quality and usability...
December 6, 2017: JMIR MHealth and UHealth
https://www.readbyqxmd.com/read/29212269/low-neighbor-of-brca1-gene-expression-predicts-poor-clinical-outcome-and-resistance-of-sunitinib-in-clear-cell-renal-cell-carcinoma
#10
Wen Xiao, Zhiyong Xiong, Changfei Yuan, Lin Bao, Di Liu, Xiong Yang, Wencheng Li, Junwei Tong, Yan Qu, Lei Liu, Haibing Xiao, Hongmei Yang, Xiaoping Zhang, Ke Chen
Objective: To study the expression of Neighbor of Brca1 gene (NBR1) in clear cell renal cell carcinoma (ccRCC), renal cancer cells and the chemoresistance cells and to elucidate its clinical prognostic and chemoresistance value. Materials and Methods: We screened the NBR1 mRNA in ccRCC from The Cancer Genome Atlas (TCGA) database and examined expression levels of NBR1 mRNA in 48 cases of ccRCC tissues, renal cancer cell lines and chemoresistance cells by qRT-PCR...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29207508/preparation-of-a-spaceflight-apoptosis-search-in-sutured-wound-healing-models
#11
Stefan Riwaldt, Monica Monici, Asbjørn Graver Petersen, Uffe Birk Jensen, Katja Evert, Desiré Pantalone, Kirsten Utpatel, Matthias Evert, Markus Wehland, Marcus Krüger, Sascha Kopp, Sofie Frandsen, Thomas Corydon, Jayashree Sahana, Johann Bauer, Ronald Lützenberg, Manfred Infanger, Daniela Grimm
To prepare the ESA (European Space Agency) spaceflight project "Wound healing and Sutures in Unloading Conditions", we studied mechanisms of apoptosis in wound healing models based on ex vivo skin tissue cultures, kept for 10 days alive in serum-free DMEM/F12 medium supplemented with bovine serum albumin, hydrocortisone, insulin, ascorbic acid and antibiotics at 32 °C. The overall goal is to test: (i) the viability of tissue specimens; (ii) the gene expression of activators and inhibitors of apoptosis and extracellular matrix components in wound and suture models; and (iii) to design analytical protocols for future tissue specimens after post-spaceflight download...
December 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29202721/portable-acuity-screening-for-any-school-validation-of-patched-hotv-with-amblyopic-patients-and-bangerter-normals
#12
Maya Tsao Wu, M Diane Armitage, Claire Trujillo, Anna Trujillo, Laura E Arnold, Lauren Tsao Wu, Robert W Arnold
BACKGROUND: We needed to validate and calibrate our portable acuity screening tools so amblyopia could be detected quickly and effectively at school entry. METHODS: Spiral-bound flip cards and download pdf surround HOTV acuity test box with critical lines were combined with a matching card. Amblyopic patients performed critical line, then threshold acuity which was then compared to patched E-ETDRS acuity. 5 normal subjects wore Bangerter foil goggles to simulate blur for comparative validation...
December 4, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/29181613/simpleitk-image-analysis-notebooks-a-collaborative-environment-for-education-and-reproducible-research
#13
Ziv Yaniv, Bradley C Lowekamp, Hans J Johnson, Richard Beare
Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit...
November 27, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29172307/the-paradoxes-of-phantom-bite-syndrome-or-occlusal-dysaesthesia-%C3%A2-dysesthesia%C3%A2
#14
Martin G Kelleher, Lakshmi Rasaratnam, Serpil Djemal
Phantom bite syndrome was first described by Marbach over 40 years ago as a mono-symptomatic hypochondriacal psychosis. He used the term to describe a prolonged syndrome in which patients report that their ‘bite is wrong’ or that ‘their dental occlusion is abnormal’ with this causing them great difficulties. This strong belief about ‘their bite’ being the source of their problems leads to them demanding, and subsequently getting, various types of dentistry carried out by multiple dentists and ‘specialists’...
January 2017: Dental Update
https://www.readbyqxmd.com/read/29121561/flip-an-assisting-software-in-structure-based-drug-design-using-fingerprint-of-protein-ligand-interaction-profiles
#15
Ali Hajiebrahimi, Younes Ghasemi, Amirhossein Sakhteman
With the growing number of labor-intensive data in the pharmaceutical industries and public domain for protein-ligand complexes, a significant challenge is still remaining in managing and leveraging this vast information. Here, a standalone application is presented for analysis, organization, and illustration of structural data and molecular interactions for exploiting 3D-structures into simple 1D fingerprints. The utility of the approach was shown in unraveling a feasible solution for post-processing of docking results in parallel with providing fruitful analysis for users in order to investigate molecular interactions...
November 1, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29111991/multiple-chemical-sensitivity-review-of-the-state-of-the-art-in-epidemiology-diagnosis-and-future-perspectives
#16
Sabrina Rossi, Alessio Pitidis
OBJECTIVE: Systematic bibliography analysis of about the last 17 years on multiple chemical sensitivity (MCS) was carried out in order to detect new diagnostic and epidemiological evidence. The MCS is a complex syndrome that manifests as a result of exposure to a low level of various common contaminants. The etiology, diagnosis, and treatment are still debated among researchers. METHOD: Querying PubMed, Web of Science, Scopus, Cochrane library, both using some specific MESH terms combined with MESH subheadings and through free search, even by Google...
November 3, 2017: Journal of Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/29101091/recruiting-women-to-a-mobile-health-smoking-cessation-trial-low-and-no-cost-strategies
#17
Kristopher J Abbate, Melanie D Hingle, Julie Armin, Peter Giacobbi, Judith S Gordon
BACKGROUND: Successful recruitment of participants to mobile health (mHealth) studies presents unique challenges over in-person studies. It is important to identify recruitment strategies that maximize the limited recruitment resources available to researchers. OBJECTIVE: The objective of this study was to describe a case study of a unique recruitment process used in a recent mHealth software app designed to increase smoking cessation among weight-concerned women smokers...
November 3, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/29098485/idac-dose-2-1-an-internal-dosimetry-program-for-diagnostic-nuclear-medicine-based-on-the-icrp-adult-reference-voxel-phantoms
#18
Martin Andersson, Lennart Johansson, Keith Eckerman, Sören Mattsson
BACKGROUND: To date, the estimated radiation-absorbed dose to organs and tissues in patients undergoing diagnostic examinations in nuclear medicine is derived via calculations based on models of the human body and the biokinetic behaviour of the radiopharmaceutical. An internal dosimetry computer program, IDAC-Dose2.1, was developed based on the International Commission on Radiological Protection (ICRP)-specific absorbed fractions and computational framework of internal dose assessment given for reference adults in ICRP Publication 133...
November 3, 2017: EJNMMI Research
https://www.readbyqxmd.com/read/29077811/reactome-enhanced-pathway-visualization
#19
Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steve Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews, Heeyeon Song, Lincoln Stein, Robin Haw, Peter D'Eustachio, Peipei Ping, Henning Hermjakob, Antonio Fabregat
Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications...
November 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29076961/six-sessions-of-sprint-interval-training-improves-running-performance-in-trained-athletes
#20
Jerome Koral, Dustin J Oranchuk, Roberto Herrera, Guillaume Y Millet
Sprint interval training (SIT) is gaining popularity with endurance athletes. Various studies have shown that SIT allows similar or greater endurance, strength, and power performance improvements than traditional endurance training, but demands less time and volume. One of the main limitations in SIT research is that most studies were performed in a laboratory using expensive treadmills or ergometers. The aim of this study was to assess the performance effects of a novel short term and highly accessible training protocol based on maximal shuttle runs in the field (SIT-F)...
October 20, 2017: Journal of Strength and Conditioning Research
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