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Safa Naraghi, Tinashe Mutsvangwa, René Goliath, Molebogeng X Rangaka, Tania S Douglas
BACKGROUND: The tuberculin skin test is the most widely used method for detecting latent tuberculosis infection in adults and active tuberculosis in children. We present the development of a mobile-phone based screening tool for measuring the tuberculin skin test induration. METHOD: The tool makes use of a mobile application developed on the Android platform to capture images of an induration, and photogrammetric reconstruction using Agisoft PhotoScan to reconstruct the induration in 3D, followed by 3D measurement of the induration with the aid of functions from the Python programming language...
May 8, 2018: Computers in Biology and Medicine
Edoardo Balzani, Matteo Falappa, Fuat Balcà, Valter Tucci
Genetically modified mice are used as models for a variety of human behavioral conditions. However, behavioral phenotyping can be a major bottleneck in mouse genetics because many of the classic protocols are too long and/or are vulnerable to unaccountable sources of variance, leading to inconsistent results between centers. We developed a home-cage approach using a Chora feeder that is controlled by-and sends data to-software. In this approach, mice are tested in the standard cages in which they are held for husbandry, which removes confounding variables such as the stress induced by out-of-cage testing...
June 2018: Nature Protocols
Milad Hobbi Mobarhan, Geir Halnes, Pablo Martínez-Cañada, Torkel Hafting, Marianne Fyhn, Gaute T Einevoll
Visually evoked signals in the retina pass through the dorsal geniculate nucleus (dLGN) on the way to the visual cortex. This is however not a simple feedforward flow of information: there is a significant feedback from cortical cells back to both relay cells and interneurons in the dLGN. Despite four decades of experimental and theoretical studies, the functional role of this feedback is still debated. Here we use a firing-rate model, the extended difference-of-Gaussians (eDOG) model, to explore cortical feedback effects on visual responses of dLGN relay cells...
May 17, 2018: PLoS Computational Biology
Vikram Krishnasamy, Lauren Stevenson, Lia Koski, Marilee Kellis, Betsy Schroeder, Madhura Sundararajan, Stephen Ladd-Wilson, Ashley Sampsel, Mike Mannell, Andrew Classon, Darlene Wagner, Kelley Hise, Heather Carleton, Eija Trees, Linda Schlater, Kristina Lantz, Megin Nichols
No abstract text is available yet for this article.
May 19, 2018: MMWR. Morbidity and Mortality Weekly Report
Daniel G A Smith, Lori A Burns, Dominic A Sirianni, Daniel R Nascimento, Ashutosh Kumar, Andrew M James, Jeffrey B Schriber, Tianyuan Zhang, Boyi Zhang, Adam S Abbott, Eric J Berquist, Marvin H Lechner, Leonardo A Cunha, Alexander G Heide, Jonathan M Waldrop, Tyler Y Takeshita, Asem Alenaizan, Daniel Neuhauser, Rollin A King, Andrew C Simmonett, Justin M Turney, Henry F Schaefer, Francesco A Evangelista, A Eugene DePrince, T Daniel Crawford, Konrad Patkowski, C David Sherrill
Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory...
May 17, 2018: Journal of Chemical Theory and Computation
Louis-Marie Bobay, Brian Shin-Hua Ellis, Howard Ochman
Summary: Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. Availability and implementation: ConSpeciFix's webserver is freely available at
May 16, 2018: Bioinformatics
Andrew Dalke, Jérôme Hert, Christian Kramer
Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit...
May 17, 2018: Journal of Chemical Information and Modeling
Anshul Aggarwal, Sunita Garhwal, Ajay Kumar
Objectives: One of the most important functions for a medical practitioner while treating a patient is to study the patient's complete medical history by going through all records, from test results to doctor's notes. With the increasing use of technology in medicine, these records are mostly digital, alleviating the problem of looking through a stack of papers, which are easily misplaced, but some of these are in an unstructured form. Large parts of clinical reports are in written text form and are tedious to use directly without appropriate pre-processing...
April 2018: Healthcare Informatics Research
Jae-Hong Lee, Do-Hyung Kim, Seong-Nyum Jeong, Seong-Ho Choi
Purpose: The aim of the current study was to develop a computer-assisted detection system based on a deep convolutional neural network (CNN) algorithm and to evaluate the potential usefulness and accuracy of this system for the diagnosis and prediction of periodontally compromised teeth (PCT). Methods: Combining pretrained deep CNN architecture and a self-trained network, periapical radiographic images were used to determine the optimal CNN algorithm and weights...
April 2018: Journal of Periodontal & Implant Science
Jinha Yu, Antonella Ciancetta, Steven Dudas, Sierra Duca, Justine Lottermoser, Kenneth A Jacobson
The P2Y14 receptor (P2Y14 R) mediates inflammatory activity by activating neutrophil motility, but few classes of antagonists are known. We have explored the structure-activity relationship of a 3-(4-phenyl-1 H-1,2,3-triazol-1-yl)-5-(aryl)benzoic acid antagonist scaffold, assisted by docking and molecular dynamics (MD) simulation at a P2Y14 R homology model. A computational pipeline using the High Throughput MD Python environment guided the analogue design. Selection of candidates was based upon ligand-protein shape and complementarity and the persistence of ligand-protein interactions over time...
May 16, 2018: Journal of Medicinal Chemistry
Carmen Moret-Tatay, Daniel Gamermann, Esperanza Navarro-Pardo, Pedro Fernández de Córdoba Castellá
The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density...
2018: Frontiers in Psychology
Emmanuel Klinger, Dennis Rickert, Jan Hasenauer
Summary: Likelihood-free methods are often required for inference in systems biology. While Approximate Bayesian Computation (ABC) provides a theoretical solution, its practical application has often been challenging due to its high computational demands. To scale likelihood-free inference to computationally demanding stochastic models we developed pyABC: a distributed and scalable ABC-Sequential Monte Carlo (ABC-SMC) framework. It implements a scalable, runtime-minimizing parallelization strategy for multi-core and distributed environments scaling to thousands of cores...
May 14, 2018: Bioinformatics
Kathrin M Seibt, Thomas Schmidt, Tony Heitkam
Summary: FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of ambiguities and substitutions. Our shading modules facilitate dotplot interpretation and motif identification by adding information on sequence annotations and sequence similarities. Combined with collage-like outputs, FlexiDot supports simultaneous visual screening of large sequence sets, enabling dotplot use for routine analyses...
May 14, 2018: Bioinformatics
Carmen Moret-Tatay, Daniel Gamermann, Michael Murphy, Anezka Kuzmičová
Word frequency is one of the most robust factors in the literature on word processing, based on the lexical corpus of a language. However, different sources might be used in order to determine the actual frequency of each word. Recent research has determined frequencies based on movie subtitles, Twitter, blog posts, or newspapers. In this paper, we examine a determination of these frequencies based on the World Wide Web. For this purpose, a Python script was developed to obtain frequencies of a word through online search results...
April 2018: Journal of General Psychology
Sergey V Kovalchuk, Anastasia A Funkner, Oleg G Metsker, Aleksey N Yakovlev
INTRODUCTION: An approach to building a hybrid simulation of patient flow is introduced with a combination of data-driven methods for automation of model identification. The approach is described with a conceptual framework and basic methods for combination of different techniques. The implementation of the proposed approach for simulation of the acute coronary syndrome (ACS) was developed and used in an experimental study. METHODS: A combination of data, text, process mining techniques, and machine learning approaches for the analysis of electronic health records (EHRs) with discrete-event simulation (DES) and queueing theory for the simulation of patient flow was proposed...
May 10, 2018: Journal of Biomedical Informatics
João M C Teixeira, Simon P Skinner, Miguel Arbesú, Alexander L Breeze, Miquel Pons
We present Farseer-NMR ( ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution...
May 11, 2018: Journal of Biomolecular NMR
Nadine Schneider, Richard A Lewis, Nikolas Fechner, Peter Ertl
Chirality is understood by many as a binary concept: a molecule is either chiral or it is not. In terms of the action of a structure on polarized light, this is indeed true. When examined through the prism of molecular recognition, the answer becomes more nuanced. In this work, we investigated chiral behavior on protein-ligand binding: when does chirality make a difference in binding activity? Chirality is a property of the 3D structure, so recognition also requires an appreciation of the conformation. In many situations, the bioactive conformation is undefined...
May 11, 2018: ChemMedChem
R Biczok, P Bozsoky, P Eisenmann, J Ernst, T Ribizel, F Scholz, A Trefzer, F Weber, M Hamann, A Stamatakis
Motivation: The presence of terraces in phylogenetic tree space, that is, a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. (2011). However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace, and (iii) enumerate all trees on a terrace...
May 8, 2018: Bioinformatics
Vita Rozman, Tanja Kunej
Harnessing the genomics big data requires innovation in how we extract and interpret biologically relevant variants. Currently, there is no established catalog of prioritized missense variants associated with deleterious protein function phenotypes. We report in this study, to the best of our knowledge, the first genome-wide prioritization of sequence variants with the most deleterious effect on protein function (potentially deleterious variants [pDelVars]) in nine vertebrate species: human, cattle, horse, sheep, pig, dog, rat, mouse, and zebrafish...
May 10, 2018: Omics: a Journal of Integrative Biology
Akash Parvatikar, Gabriel S Vacaliuc, Arvind Ramanathan, S Chakra Chennubhotla
Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA)...
May 8, 2018: Biophysical Journal
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