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https://www.readbyqxmd.com/read/28918707/wdnfinder-a-method-for-minimum-driver-node-set-detection-and-analysis-in-directed-and-weighted-biological-network
#1
Chu Yanshuo, Wang Zhenxing, Wang Rongjie, Zhang Ningyi, Li Jie, Hu Yang, Teng Mingxiang, Wang Yadong
Structural controllability is the generalization of traditional controllability for dynamical systems. During the last decade, interesting biological discoveries have been inferred by applied structural controllability analysis to biological networks. However, false positive/negative information (i.e. nodes and edges) widely exists in biological networks that documented in public data sources, which can hinder accurate analysis of structural controllability. In this study, we propose WDNfinder, a comprehensive analysis package that provides structural controllability with consideration of node connection strength in biological networks...
September 4, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28918078/assessment-of-environmental-impacts-and-operational-costs-of-the-implementation-of-an-innovative-source-separated-urine-treatment
#2
Elorri Igos, Mathilde Besson, Tomás Navarrete Gutiérrez, Ana Barbara Bisinella de Faria, Enrico Benetto, Ligia Barna, Aras Ahmadi, Mathieu Spérandio
Innovative treatment technologies and management methods are necessary to valorise the constituents of wastewater, in particular nutrients from urine (highly concentrated and can have significant impacts related to artificial fertilizer production). The FP7 project, ValuefromUrine, proposed a new two-step process (called VFU) based on struvite precipitation and microbial electrolysis cell (MEC) to recover ammonia, which is further transformed into ammonium sulphate. The environmental and economic impacts of its prospective implementation in the Netherlands were evaluated based on life cycle assessment (LCA) methodology and operational costs...
September 8, 2017: Water Research
https://www.readbyqxmd.com/read/28916961/practical-computational-toolkits-for-dendrimers-and-dendrons-structure-design
#3
Nuno Martinho, Liana C Silva, Helena F Florindo, Steve Brocchini, Teresa Barata, Mire Zloh
Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures...
September 15, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28901669/automating-tasks-in-protein-structure-determination-with-the-clipper-python-module
#4
Stuart McNicholas, Tristan Croll, Tom Burnley, Colin M Palmer, Soon Wen Hoh, Huw T Jenkins, Eleanor Dodson, Kevin Cowtan, Jon Agirre
Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalised for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language...
September 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28890720/porcine-b-cell-subset-responses-to-toll-like-receptor-ligands
#5
Roman Othmar Braun, Sylvie Python, Artur Summerfield
Toll-like receptors (TLR) triggering of B cells are known to promote B cell expansion, differentiation of B cells into antibody-producing and memory cells, but the TLR responses of porcine B cells is poorly characterized. Therefore, this study investigated the response pattern of porcine B cell subsets to a large collection of TLR ligands and demonstrates that the TLR2 ligand Pam3Cys-SK4 and the TLR7/8 ligands gardiquimod and resiquimod are particularly efficient at inducing proliferation, CD25 and CCR7. This activation was also determined in B-cell subpopulations including a CD21(+)IgM(+) subset, an IgG(+) subset and two putative B1-like subsets, defined as CD21(-)IgM(high)CD11R1(+)CD11c(+)CD14(+) and CD21(-)IgM(high) CD11R1(-)CD11c(+)CD14(-) B cells...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28886064/sexcmd-development-and-validation-of-sex-marker-sequences-for-whole-exome-genome-and-rna-sequencing
#6
Seongmun Jeong, Jiwoong Kim, Won Park, Hongmin Jeon, Namshin Kim
Over the last decade, a large number of nucleotide sequences have been generated by next-generation sequencing technologies and deposited to public databases. However, most of these datasets do not specify the sex of individuals sampled because researchers typically ignore or hide this information. Male and female genomes in many species have distinctive sex chromosomes, XX/XY and ZW/ZZ, and expression levels of many sex-related genes differ between the sexes. Herein, we describe how to develop sex marker sequences from syntenic regions of sex chromosomes and use them to quickly identify the sex of individuals being analyzed...
2017: PloS One
https://www.readbyqxmd.com/read/28882003/minimds-3d-structural-inference-from-high-resolution-hi-c-data
#7
Lila Rieber, Shaun Mahony
Motivation: Recent experiments have provided Hi-C data at resolution as high as 1 kbp. However, 3D structural inference from high-resolution Hi-C datasets is often computationally unfeasible using existing methods. Results: We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and then reassembles the partitions using low-resolution MDS. miniMDS is faster, more accurate, and uses less memory than existing methods for inferring the human genome at high resolution (10 kbp)...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28875074/atropos-specific-sensitive-and-speedy-trimming-of-sequencing-reads
#8
John P Didion, Marcel Martin, Francis S Collins
A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments...
2017: PeerJ
https://www.readbyqxmd.com/read/28873961/transcriptome-analysis-of-the-response-of-burmese-python-to-digestion
#9
Jinjie Duan, Kristian Wejse Sanggaard, Leif Schauser, Sanne Enok Lauridsen, Jan J Enghild, Mikkel Heide Schierup, Tobias Wang
Exceptional and extreme feeding behaviour makes the Burmese python (Python bivittatus) an interesting model to study physiological remodelling and metabolic adaptation in response to refeeding after prolonged starvation. In this study, we used transcriptome sequencing of 5 visceral organs during fasting as well as 24 hours and 48 hours after ingestion of a large meal to unravel the postprandial changes in Burmese pythons. We first used the pooled data to perform a de novo assembly of the transcriptome and supplemented this with a proteomic survey of enzymes in the plasma and gastric fluid...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28873498/a-python-script-to-compute-isochrones-for-modflow
#10
Alessandra Feo, Andrea Zanini, Emma Petrella, Fulvio Celico
MODFLOW constitutes today the most popular modeling tool in the study of water flow in aquifers and in modeling aquifers. To simplify the interface to MODFLOW various GUI have been developed for the creation of model definition files and for the visualization and interpretation of results. Recently Bakker et al. (2016) developed the FloPy interface to MODFLOW that allows to import and use the produced simulation data using Python. This allows to construct model input files, run the models, read and plot simulations results through Python scripts...
September 5, 2017: Ground Water
https://www.readbyqxmd.com/read/28872698/a-multivariate-distance-based-analytic-framework-for-microbial-interdependence-association-test-in-longitudinal-study
#11
Yilong Zhang, Sung Won Han, Laura M Cox, Huilin Li
Human microbiome is the collection of microbes living in and on the various parts of our body. The microbes living on our body in nature do not live alone. They act as integrated microbial community with massive competing and cooperating and contribute to our human health in a very important way. Most current analyses focus on examining microbial differences at a single time point, which do not adequately capture the dynamic nature of the microbiome data. With the advent of high-throughput sequencing and analytical tools, we are able to probe the interdependent relationship among microbial species through longitudinal study...
September 5, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28868107/a-simple-and-reusable-bilayer-membrane-based-microfluidic-device-for-the-study-of-gradient-mediated-bacterial-behaviors
#12
Wu Shang, Chen-Yu Tsao, Xiaolong Luo, Mairan Teodoro, Ryan McKay, David N Quan, Hsuan-Chen Wu, Gregory F Payne, William E Bentley
We have developed a user-friendly microfluidic device for the study of gradient-mediated bacterial behaviors, including chemotaxis. This device rapidly establishes linear concentration gradients by exploiting solute diffusion through porous membranes in the absence of convective flows. As such, the gradients are created rapidly and can be sustained for long time periods (e.g., hours), sufficient to evaluate cell phenotype. The device exploits a unique simple bilayer configuration that enables rapid setup and quick reproducible introduction of cells...
July 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28866503/the-topology-toolkit
#13
Julien Tierny, Guillaume Favelier, Joshua A Levine, Charles Gueunet, Michael Michaux
This system paper presents the Topology ToolKit (TTK), a software platform designed for the topological analysis of scalar data in scientific visualization. While topological data analysis has gained in popularity over the last two decades, it has not yet been widely adopted as a standard data analysis tool for end users or developers. TTK aims at addressing this problem by providing a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28857244/rhorix-an-interface-between-quantum-chemical-topology-and-the-3d-graphics-program-blender
#14
Matthew J L Mills, Kenneth L Sale, Blake A Simmons, Paul L A Popelier
Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available...
August 31, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28842816/single-center-experience-implementing-the-loinc-rsna-radiology-playbook-for-adult-abdomen-pelvis-ct-and-mr-procedures-using-a-semi-automated-method
#15
Ranjit S Sandhu, James Shin, Kenneth C Wang, George Shih
The LOINC-RSNA Radiology Playbook represents the future direction of standardization for radiology procedure names. We developed a software solution ("RadMatch") utilizing Python 2.7 and FuzzyWuzzy, an open-source fuzzy string matching algorithm created by SeatGeek, to implement the LOINC-RSNA Radiology Playbook for adult abdomen and pelvis CT and MR procedures performed at our institution. Execution of this semi-automated method resulted in the assignment of appropriate LOINC numbers to 86% of local CT procedures...
August 25, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28836000/antcaller-an-accurate-variant-caller-incorporating-ancient-dna-damage
#16
Boyan Zhou, Shaoqing Wen, Lingxiang Wang, Li Jin, Hui Li, Hong Zhang
Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule...
August 23, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28834713/paramap-standardized-parameterization-of-sinoatrial-node-myocyte-action-potentials
#17
Christian Rickert, Catherine Proenza
Sinoatrial node myocytes act as cardiac pacemaker cells by generating spontaneous action potentials (APs). Much information is encoded in sinoatrial AP waveforms, but both the analysis and the comparison of AP parameters between studies is hindered by the lack of standardized parameter definitions and the absence of automated analysis tools. Here we introduce ParamAP, a standalone cross-platform computational tool that uses a template-free detection algorithm to automatically identify and parameterize APs from text input files...
August 22, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28829965/evolution-a-paradigm-shift-in-snake-sex-chromosome-genetics
#18
J J Emerson
The belief that all snakes possess ZW sex chromosomes has prevailed for decades, despite no evidence of this in boas, pythons, and their relatives. A recent discovery of male-specific genetic markers reveals that these snakes instead possess XY sex chromosomes.
August 21, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28818520/owlready-ontology-oriented-programming-in-python-with-automatic-classification-and-high-level-constructs-for-biomedical-ontologies
#19
Jean-Baptiste Lamy
OBJECTIVE: Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies...
July 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28817630/pet-snakes-illegally-marketed-in-brazil-climatic-viability-and-establishment-risk
#20
Érica Fonseca, Mirco Solé, Dennis Rödder, Paulo de Marco
Invasive species are one among many threats to biodiversity. Brazil has been spared, generically, of several destructive invasive species. Reports of invasive snakes' populations are nonexistent, but the illegal pet trade might change this scenario. Despite the Brazilian laws forbid to import most animals, illegal trade is frequently observed and propagules are found in the wild. The high species richness within Brazilian biomes and accelerated fragmentation of natural reserves are a critical factors facilitating successful invasion...
2017: PloS One
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