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https://www.readbyqxmd.com/read/28804525/mdts-automatic-complex-materials-design-using-monte-carlo-tree-search
#1
Thaer M Dieb, Shenghong Ju, Kazuki Yoshizoe, Zhufeng Hou, Junichiro Shiomi, Koji Tsuda
Complex materials design is often represented as a black-box combinatorial optimization problem. In this paper, we present a novel python library called MDTS (Materials Design using Tree Search). Our algorithm employs a Monte Carlo tree search approach, which has shown exceptional performance in computer Go game. Unlike evolutionary algorithms that require user intervention to set parameters appropriately, MDTS has no tuning parameters and works autonomously in various problems. In comparison to a Bayesian optimization package, our algorithm showed competitive search efficiency and superior scalability...
2017: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/28803195/a-gis-based-atmospheric-dispersion-model-for-pollutants-emitted-by-complex-source-areas
#2
Sergio Teggi, Sofia Costanzini, Grazia Ghermandi, Carlotta Malagoli, Marco Vinceti
Gaussian dispersion models are widely used to simulate the concentrations and deposition fluxes of pollutants emitted by source areas. Very often, the calculation time limits the number of sources and receptors and the geometry of the sources must be simple and without holes. This paper presents CAREA, a new GIS-based Gaussian model for complex source areas. CAREA was coded in the Python language, and is largely based on a simplified formulation of the very popular and recognized AERMOD model. The model allows users to define in a GIS environment thousands of gridded or scattered receptors and thousands of complex sources with hundreds of vertices and holes...
August 10, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28795112/real-time-fmri-data-for-testing-opennft-functionality
#3
Yury Koush, John Ashburner, Evgeny Prilepin, Ronald Sladky, Peter Zeidman, Sergei Bibikov, Frank Scharnowski, Artem Nikonorov, Dimitri Van De Ville
Here, we briefly describe the real-time fMRI data that is provided for testing the functionality of the open-source Python/Matlab framework for neurofeedback, termed Open NeuroFeedback Training (OpenNFT, Koush et al. [1]). The data set contains real-time fMRI runs from three anonymized participants (i.e., one neurofeedback run per participant), their structural scans and pre-selected ROIs/masks/weights. The data allows for simulating the neurofeedback experiment without an MR scanner, exploring the software functionality, and measuring data processing times on the local hardware...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28794044/nidovirus-associated-proliferative-pneumonia-in-the-green-tree-python-morelia-viridis
#4
Eva Dervas, Jussi Hepojoki, Andrea Laimbacher, Fernando Romero-Palomo, Christine Jelinek, Saskia Keller, Teemu Smura, Satu Hepojoki, Anja Kipar, Udo Hetzel
In 2014 we observed a noticeable increase in sudden deaths of green tree pythons (Morelia viridis). Pathological examination revealed accumulation of mucoid material within airways and lung, associated with enlargement of the entire lung. We performed full necropsy and histological examination on 12 affected green tree pythons from 7 different breeders to characterise the pathogenesis of this "mucinous" pneumonia. By histology we could show a marked hyperplasia of the airway epithelium and of faveolar type II pneumocytes...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28782629/normcorre-an-online-algorithm-for-piecewise-rigid-motion-correction-of-calcium-imaging-data
#5
Eftychios A Pnevmatikakis, Andrea Giovannucci
BACKGROUND: Motion correction is a challenging pre-processing problem that arises early in the analysis pipeline of calcium imaging data sequences. The motion artifacts in two-photon microscopy recordings can be non-rigid, arising from the finite time of raster scanning and non-uniform deformations of the brain medium. NEW METHOD: We introduce an algorithm for fast Non-Rigid Motion Correction (NoRMCorre) based on template matching. NoRMCorre operates by splitting the field of view (FOV) into overlapping spatial patches along all directions...
August 3, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28776963/structure_threader-an-improved-method-for-automation-parallelization-of-programs-structure-faststructure-and-maverick-on-multi-core-cpu-systems
#6
Francisco Pina-Martins, Diogo N Silva, Joana Fino, Octávio S Paulo
Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multi-threading technology (structure, fastStructure and MavericK) on multi-core computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task - ParallelStructure and StrAuto, and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios...
August 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28770487/integrating-the-allen-brain-institute-cell-types-database-into-automated-neuroscience-workflow
#7
David B Stockton, Fidel Santamaria
We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features...
August 2, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/28766794/an-open-source-framework-for-analyzing-n-electron-dynamics-ii-hybrid-density-functional-theory-configuration-interaction-methodology
#8
Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay
In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al...
August 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28763045/mzstudio-a-dynamic-digital-canvas-for-user-driven-interrogation-of-mass-spectrometry-data
#9
Scott B Ficarro, William M Alexander, Jarrod A Marto
Although not yet truly 'comprehensive', modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed...
August 1, 2017: Proteomes
https://www.readbyqxmd.com/read/28756314/incorporating-twitter-based-human-activity-information-in-spatial-analysis-of-crashes-in-urban-areas
#10
Jie Bao, Pan Liu, Hao Yu, Chengcheng Xu
The primary objective of this study was to investigate how to incorporate human activity information in spatial analysis of crashes in urban areas using Twitter check-in data. This study used the data collected from the City of Los Angeles in the United States to illustrate the procedure. The following five types of data were collected: crash data, human activity data, traditional traffic exposure variables, road network attributes and social-demographic data. A web crawler by Python was developed to collect the venue type information from the Twitter check-in data automatically...
July 27, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28751678/morpho-functional-characterization-of-the-systemic-venous-pole-of-the-reptile-heart
#11
Bjarke Jensen, Signe Vesterskov, Bastiaan J Boukens, Jan M Nielsen, Antoon F M Moorman, Vincent M Christoffels, Tobias Wang
Mammals evolved from reptile-like ancestors, and while the mammalian heart is driven by a distinct sinus node, a sinus node is not apparent in reptiles. We characterized the myocardial systemic venous pole, the sinus venosus, in reptiles to identify the dominant pacemaker and to assess whether the sinus venosus remodels and adopts an atrium-like phenotype as observed in mammals. Anolis lizards had an extensive sinus venosus of myocardium expressing Tbx18. A small sub-population of cells encircling the sinuatrial junction expressed Isl1, Bmp2, Tbx3, and Hcn4, homologues of genes marking the mammalian sinus node...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28749600/pyretis-a-well-done-medium-sized-python-library-for-rare-events
#12
Anders Lervik, Enrico Riccardi, Titus S van Erp
Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics...
July 27, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28729343/flowtrace-simple-visualization-of-coherent-structures-in-biological-fluid-flows
#13
William Gilpin, Vivek N Prakash, Manu Prakash
We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results to more experimentally-difficult and mathematically-sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential "middle ground" allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques...
July 20, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28724111/agricultural-conservation-planning-framework-3-land-use-and-field-boundary-database-development-and-structure
#14
Mark D Tomer, David E James, Claudette M J Sandoval-Green
Conservation planning information is important for identifying options for watershed water quality improvement and can be developed for use at field, farm, and watershed scales. Translation across scales is a key issue impeding progress at watershed scales because watershed improvement goals must be connected with implementation of farm- and field-level conservation practices to demonstrate success. This is particularly true when examining alternatives for "trap and treat" practices implemented at agricultural-field edges to control (or influence) water flows through fields, landscapes, and riparian corridors within agricultural watersheds...
May 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28723960/a-validation-of-11-body-condition-indices-in-a-giant-snake-species-that-exhibits-positive-allometry
#15
Bryan G Falk, Ray W Snow, Robert N Reed
Body condition is a gauge of the energy stores of an animal, and though it has important implications for fitness, survival, competition, and disease, it is difficult to measure directly. Instead, body condition is frequently estimated as a body condition index (BCI) using length and mass measurements. A desirable BCI should accurately reflect true body condition and be unbiased with respect to size (i.e., mean BCI estimates should not change across different length or mass ranges), and choosing the most-appropriate BCI is not straightforward...
2017: PloS One
https://www.readbyqxmd.com/read/28723908/sorting-cells-by-their-density
#16
Nazila Norouzi, Heran C Bhakta, William H Grover
Sorting cells by their type is an important capability in biological research and medical diagnostics. However, most cell sorting techniques rely on labels or tags, which may have limited availability and specificity. Sorting different cell types by their different physical properties is an attractive alternative to labels because all cells intrinsically have these physical properties. But some physical properties, like cell size, vary significantly from cell to cell within a cell type; this makes it difficult to identify and sort cells based on their sizes alone...
2017: PloS One
https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#17
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28716000/quantiprot-a-python-package-for-quantitative-analysis-of-protein-sequences
#18
Bogumił M Konopka, Marta Marciniak, Witold Dyrka
BACKGROUND: The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. RESULTS: Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28715209/comparison-of-the-predictive-performance-and-interpretability-of-random-forest-and-linear-models-on-benchmark-data-sets
#19
Richard L Marchese Robinson, Anna Palczewska, Jan Palczewski, Nathan Kidley
The ability to interpret the predictions made by quantitative structure-activity relationships (QSARs) offers a number of advantages. While QSARs built using nonlinear modeling approaches, such as the popular Random Forest algorithm, might sometimes be more predictive than those built using linear modeling approaches, their predictions have been perceived as difficult to interpret. However, a growing number of approaches have been proposed for interpreting nonlinear QSAR models in general and Random Forest in particular...
August 2, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28706482/samuroi-a-python-based-software-tool-for-visualization-and-analysis-of-dynamic-time-series-imaging-at-multiple-spatial-scales
#20
Martin Rueckl, Stephen C Lenzi, Laura Moreno-Velasquez, Daniel Parthier, Dietmar Schmitz, Sten Ruediger, Friedrich W Johenning
The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data...
2017: Frontiers in Neuroinformatics
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