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Mohamad Ahtisham Wani, Wasim Ahmad Bhat
Since B-tree file system (Btrfs) is set to become de facto standard file system on Linux (and Linux based) operating systems, Btrfs dataset for forensic analysis is of great interest and immense value to forensic community. This article presents a novel dataset for forensic analysis of Btrfs that was collected using a proposed data-recovery procedure. The dataset identifies various generalized and common file system layouts and operations, specific node-balancing mechanisms triggered, logical addresses of various data structures, on-disk records, recovered-data as directory entries and extent data from leaf and internal nodes, and percentage of data recovered...
June 2018: Data in Brief
Anthony Nash, Thomas Sewell, Rhys A Farrer, Alireza Abdolrasouli, Jennifer M G Shelton, Matthew C Fisher, Johanna Rhodes
Summary: The increase of antifungal drug resistance is a major global human health concern and threatens agriculture and food security; in order to tackle these concerns, it is important to understand the mechanisms that cause antifungal resistance. The curated Mycology Antifungal Resistance Database (MARDy) is a web-service of antifungal drug resistance mechanisms, including amino acid substitutions, tandem repeat sequences and genome ploidy. MARDy is implemented on a Linux, Apache, MySQL and PHP web development platform and includes a local installation of BLASTn of the database of curated genes...
April 20, 2018: Bioinformatics
Kuo-Yao Hsu, Yun-Fang Tsai, Chu-Ching Huang, Wen-Ling Yeh, Kai-Ping Chang, Chen-Chun Lin, Ching-Yen Chen, Hsiu-Lan Lee
BACKGROUND: Smoking tobacco, drinking alcohol, and chewing betel quid are health-risk behaviors for several diseases, such as cancer, cardiovascular disease, and diabetes, with severe impacts on health. However, health care providers often have limited time to assess clients' behaviors regarding smoking tobacco, drinking alcohol, and chewing betel quid and intervene, if needed. OBJECTIVE: The objective of this study was to develop a Web-based survey system; determine the rates of tobacco-smoking, alcohol-drinking, and betel-quid-chewing behaviors; and estimate the efficiency of the system (time to complete the survey)...
June 11, 2018: JMIR MHealth and UHealth
V P Nagraj, Neal E Magee, Nathan C Sheffield
The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb...
June 6, 2018: Nucleic Acids Research
Daniel Franke, Cy M Jeffries, Dmitri I Svergun
Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (Dmax ) as well as molecular mass directly from experimental scattering data...
June 5, 2018: Biophysical Journal
Kevin D Murray, Justin O Borevitz
Summary: We describe a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial indexing, indices of differing length, and several mismatches per index sequence. Availability and Implementation: Axe is implemented in C, and is used as a command-line program on Unix-like systems. Axe is available online at https://github...
June 1, 2018: Bioinformatics
Sebastian F Wirtz, Adauto P A Cunha, Marc Labusch, Galina Marzun, Stephan Barcikowski, Dirk Söffker
Today, the demand for continuous monitoring of valuable or safety critical equipment is increasing in many industrial applications due to safety and economical requirements. Therefore, reliable in-situ measurement techniques are required for instance in Structural Health Monitoring (SHM) as well as process monitoring and control. Here, current challenges are related to the processing of sensor data with a high data rate and low latency. In particular, measurement and analyses of Acoustic Emission (AE) are widely used for passive, in-situ inspection...
June 1, 2018: Sensors
John M Hoffman, Frédéric Noo, Stefano Young, Scott S Hsieh, Michael McNitt-Gray
PURPOSE: To facilitate investigations into the impacts of acquisition and reconstruction parameters on quantitative imaging, radiomics and CAD using CT imaging, we previously released an open source implementation of a conventional weighted filtered backprojection reconstruction called FreeCT_wFBP. Our purpose was to extend that work by providing an open-source implementation of a model-based iterative reconstruction method using coordinate descent optimization, called FreeCT_ICD. METHODS: Model-based iterative reconstruction offers the potential for substantial radiation dose reduction, but can impose substantial computational processing and storage requirements...
June 1, 2018: Medical Physics
J J Moreno, A Martínez-Sánchez, J A Martínez, E M Garzón, J J Fernández
Summary: TomoEED is an optimized software tool for fast feature-preserving noise filtering of large 3D tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers. Availability and implementation: TomoEED has been developed in C...
May 29, 2018: Bioinformatics
Tao Ma, Zhenqing Ye, Liguo Wang
BACKGROUND: Transcription factors are DNA-binding proteins that play key roles in many fundamental biological processes. Unraveling their interactions with DNA is essential to identify their target genes and understand the regulatory network. Genome-wide identification of their binding sites became feasible thanks to recent progress in experimental and computational approaches. ChIP-chip, ChIP-seq, and ChIP-exo are three widely used techniques to demarcate genome-wide transcription factor binding sites...
May 29, 2018: Current Medicinal Chemistry
Yupeng Cun, Tsun-Po Yang, Viktor Achter, Ulrich Lang, Martin Peifer
The genomes of cancer cells constantly change during pathogenesis. This evolutionary process can lead to the emergence of drug-resistant mutations in subclonal populations, which can hinder therapeutic intervention in patients. Data derived from massively parallel sequencing can be used to infer these subclonal populations using tumor-specific point mutations. The accurate determination of copy-number changes and tumor impurity is necessary to reliably infer subclonal populations by mutational clustering. This protocol describes how to use Sclust, a copy-number analysis method with a recently developed mutational clustering approach...
June 2018: Nature Protocols
David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P C Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel
CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems...
May 22, 2018: Nucleic Acids Research
Pablo Vinuesa, Luz E Ochoa-Sánchez, Bruno Contreras-Moreira
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES...
2018: Frontiers in Microbiology
Michael L Richardson, Behrang Amini
RATIONALE AND OBJECTIVES: The goal of this study is to demonstrate how the teaching of radiology physics can be enhanced with the use of interactive scientific notebook software. METHODS: We used the scientific notebook software known as Project Jupyter, which is free, open-source, and available for the Macintosh, Windows, and Linux operating systems. RESULTS: We have created a scientific notebook that demonstrates multiple interactive teaching modules we have written for our residents using the Jupyter notebook system...
June 2018: Academic Radiology
Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin
BACKGROUND: A new emerged cancer treatment utilizes intrinsic immune surveillance mechanism that is silenced by those malicious cells. Hence, studies of tumor infiltrating lymphocyte populations (TILs) are key to the success of advanced treatments. In addition to laboratory methods such as immunohistochemistry and flow cytometry, in silico gene expression deconvolution methods are available for analyses of relative proportions of immune cell types. RESULTS: Herein, we used microarray data from the public domain to profile gene expression pattern of twenty-two immune cell types...
May 8, 2018: BMC Bioinformatics
Jordan Matelsky, Gregory Kiar, Erik Johnson, Corban Rivera, Michael Toma, William Gray-Roncal
Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis...
May 8, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
Trunil S Desai, Shireesh Srivastava
13 C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13 C-MFA data analysis...
2018: PeerJ
Jia-Xing Yue, Gianni Liti
Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process...
June 2018: Nature Protocols
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura
The molecular evolutionary genetics analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www...
May 2, 2018: Molecular Biology and Evolution
Julien Dorier, Dimos Goundaroulis, Fabrizio Benedetti, Andrzej Stasiak
Summary: The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves...
May 2, 2018: Bioinformatics
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