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Computer use

Arjun Sethi, Valerie Voon, Hugo D Critchley, Mara Cercignani, Neil A Harrison
Computational models of reinforcement learning have helped dissect discrete components of reward-related function and characterize neurocognitive deficits in psychiatric illnesses. Stimulus novelty biases decision-making, even when unrelated to choice outcome, acting as if possessing intrinsic reward value to guide decisions toward uncertain options. Heightened novelty seeking is characteristic of attention deficit hyperactivity disorder, yet how this influences reward-related decision-making is computationally encoded, or is altered by stimulant medication, is currently uncertain...
March 13, 2018: Brain: a Journal of Neurology
Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Luca Häfliger, Jonas Behr, Hesam Montazeri, Michael N Hall, Niko Beerenwinkel
Motivation: Several molecular events are known to be cancer-related, including genomic aberrations, hypermethylation of gene promoter regions, and differential expression of microRNAs. These aberration events are very heterogeneous across tumors and it is poorly understood how they affect the molecular makeup of the cell, including the transcriptome and proteome. Protein interaction networks can help decode the functional relationship between aberration events and changes in gene and protein expression...
March 14, 2018: Bioinformatics
Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Zhang Yanju, Tatsuya Akutsu, Kuo-Chen Chou, Richard A Strugnell, Jiangning Song, Trevor Lithgow
Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data...
March 14, 2018: Bioinformatics
Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
Motivation: Large scale genome-wide association studies (GWAS) are tools of choice for discovering associations between genotypes and phenotypes. To date, many studies rely on univariate statistical tests for association between the phenotype and each assayed single nucleotide polymorphism (SNP). However, interaction between SNPs, namely epistasis, must be considered when tackling the complexity of underlying biological mechanisms. Epistasis analysis at large scale entails a prohibitive computational burden when addressing the detection of more than two interacting SNPs...
March 14, 2018: Bioinformatics
Klemen Pavlic, Maja Pohar Perme
A common goal in the analysis of the long-term survival related to a specific disease is to estimate a measure that is comparable between populations with different general population mortality. When cause of death is unavailable or unreliable, as for example in cancer registry studies, relative survival methodology is used-in addition to the mortality data of the patients, we use the data on the mortality of the general population. In this article, we focus on the marginal relative survival measure that summarizes the information about the disease-specific hazard...
March 13, 2018: Biostatistics
Ivan Yu Chernyshov, Philip V Toukach
Motivation: Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. Results: The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule...
March 14, 2018: Bioinformatics
Priti Sengupta, Aniruddha Ganguly, Adity Bose
The crucial role of chemosensor for the immediate recognition of environment pollutant motivates the researchers to develop variety of sensing protocols. Of various chemosensory protocols, the colour change observed by the naked eye is considered to be a conceivable and on-site way to indicate the presence of an analyte. We herein report a colourimetric and commercially available absorption probe, sinapic acid (SA) that is completely ready to use for "on-site" visual determination of copper ions. The molecule, SA is well-known phenolic acid, often utilized for its antibacterial activity...
March 3, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Harsha T Garimella, Reuben H Kraft, Andrzej J Przekwas
Subject-specific computer models (male and female) of the human head were used to investigate the possible axonal deformation resulting from the primary phase blast-induced skull flexures. The corresponding axonal tractography was explicitly incorporated into these finite element models using a recently developed technique based on the embedded finite element method. These models were subjected to extensive verification against experimental studies which examined their pressure and displacement response under a wide range of loading conditions...
2018: PloS One
Zanxia Cao, Yunqiang Bian, Guodong Hu, Liling Zhao, Zhenzhen Kong, Yuedong Yang, Jihua Wang, Yaoqi Zhou
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling...
March 16, 2018: International Journal of Molecular Sciences
Charrise M Ramkissoon, Pau Herrero, Jorge Bondia, Josep Vehi
The artificial pancreas (AP) system is designed to regulate blood glucose in subjects with type 1 diabetes using a continuous glucose monitor informed controller that adjusts insulin infusion via an insulin pump. However, current AP developments are mainly hybrid closed-loop systems that include feed-forward actions triggered by the announcement of meals or exercise. The first step to fully closing the loop in the AP requires removing meal announcement, which is currently the most effective way to alleviate postprandial hyperglycemia due to the delay in insulin action...
March 16, 2018: Sensors
Kurtis H Dekker, Rubin Hazarika, Matheus A Silveira, Kevin J Jordan
Optical cone beam computed tomography (CT) scanning of radiochromic gel dosimeters, using a CCD camera and a low stray light convergent source, provides fast, truly 3D radiation dosimetry with high accuracy. However, a key limiting factor in radiochromic gel dosimetry at large (⩾10 cm diameter) volumes is the initial attenuation of the dosimeters. It is not unusual to observe a 5-10×  difference in signal intensity through the dosimeter center versus through the surrounding medium in pre-irradiation images...
March 16, 2018: Physics in Medicine and Biology
Saikat Chowdhury, Noopur Sinha, Piyali Ganguli, Rupa Bhowmick, Vidhi Singh, Sutanu Nandi, Ram Rup Sarkar
BIOchemical PathwaY DataBase is developed as a manually curated, readily updatable, dynamic resource of human cell specific pathway information along with integrated computational platform to perform various pathway analyses. Presently, it comprises of 46 pathways, 3189 molecules, 5742 reactions and 6897 different types of diseases linked with pathway proteins, which are referred by 520 literatures and 17 other pathway databases. With its repertoire of biochemical pathway data, and computational tools for performing Topological, Logical and Dynamic analyses, BIOPYDB offers both the experimental and computational biologists to acquire a comprehensive understanding of signaling cascades in the cells...
March 16, 2018: Journal of Integrative Bioinformatics
N G Fischer, A Tsujimoto, A G Baruth
OBJECTIVE: Limited information is available on how to polish and finish zirconia surfaces following computer-aided design/computer-aided manufacturing (CAD/CAM), specifically, how differing application forces and reuse of zirconia polishing systems affect zirconia topography. PURPOSE: To determine the effect of differing, clinically relevant, polishing application forces and multiple usages of polishing burs on the surface topography of CAD/CAM zirconia. METHODS: One hundred twenty 220-grit carbide finished zirconia disks were sintered according to manufacturer's directions and divided into two groups for the study of two coarse polishing bur types...
March 16, 2018: Operative Dentistry
Simon Badger, Christian Brønnum-Hansen, Heribertus Bayu Hartanto, Tiziano Peraro
We compute the leading-color contributions to five-gluon scattering at two loops in massless QCD. The integrands of all independent helicity amplitudes are evaluated using d-dimensional generalized unitarity cuts and finite field reconstruction techniques. Numerical evaluation of the integral basis is performed with sector decomposition methods to obtain the first benchmark results for all helicity configurations of a 2→3 scattering process in QCD.
March 2, 2018: Physical Review Letters
Lucia Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trenor, Ferran Sanz, Manuel Pastor, Javier Saiz
Drug-induced proarrhythmicity is a major concern for regulators and pharmaceutical companies. For novel drug candidates, the standard assessment involves the evaluation of the potassium hERG channels block and the in vivo prolongation of the QT interval. However, this method is known to be too restrictive and to stop the development of potentially valuable therapeutic drugs. The aim of this work is to create an in silico tool for early detection of drug-induced proarrhythmic risk. The system is based on simulations of how different compounds affect the action potential duration (APD) of isolated endocardial, midmyocardial, and epicardial cells as well as the QT prolongation in a virtual tissue...
March 16, 2018: Journal of Chemical Information and Modeling
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Binit Sureka, Aliza Mittal, Mahesh K Mittal, Kanhaiya Agarwal, Mukul Sinha, Brij Bhushan Thukral
Background: Accurate and detailed measurements of spinal canal diameter (SCD) and transverse foraminal morphometry are essential for understanding spinal column-related diseases and for surgical planning, especially for transpedicular screw fixation. This is especially because lateral cervical radiographs do not provide accurate measurements. Aim: This study was conducted to measure the dimensions of the transverse foramen sagittal and transverse diameters (SFD, TFD), SCD, and the distance of spinal canal from the transverse foramina (dSC-TF) at C1-C7 level in the Indian population...
March 2018: Neurology India
Vinayak Narayan, Hima Pendharkar, Bhagavatula Indira Devi, Dhananjaya I Bhat, Dhaval P Shukla
Background: The conventional medical management of cerebral vasospasm following aneurysmal subarachnoid hemorrhage (SAH) is associated with uncertainty of outcome and complications. Aims and Objectives: To examine the effect of direct intra-arterial nimodipine therapy on outcome in patients with delayed cerebral ischemia (DCI). Settings and Design: The retrospective observational study was conducted at a single neurosurgical unit and interventional neuroradiolgy suite of a center managing SAH...
March 2018: Neurology India
Raphaël Le Bouc, Mathias Pessiglione
Motivation can be defined as the function that orients and activates the behavior. Motivation deficits such as apathy are pervasive in both neurological and psychiatric diseases, and are currently assessed with clinical scales that do not give any mechanistic insight. Here, we present another approach that consists in phenotyping the behaviour of patients in motivation tests, using computational models. These formal models impose a precise and operational definition of motivation that is embedded in decision theory...
March 2018: Médecine Sciences: M/S
Elizabeth G Mosher, John A Butman, Les R Folio, Nadia M Biassou, Choonsik Lee
OBJECTIVE: Radiation exposure of the lens during neck CT may increase a patient's risk of developing cataracts. Radiologists at the National Institutes of Health worked with technicians to modify the neck CT scanning procedure to include a reduction in the scanning range, a reduction in the tube potential (kilovoltage), and a change in neck positioning using a head tilt. We objectively quantified the organ dose changes after this procedure modification using a computer simulation. MATERIALS AND METHODS: We retrospectively analyzed CT images of 40 patients (20 men and 20 women) scanned before and after the procedure change...
March 16, 2018: AJR. American Journal of Roentgenology
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