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https://www.readbyqxmd.com/read/28431175/minepath-org-a-free-interactive-pathway-analysis-web-server
#1
Lefteris Koumakis, Panos Roussos, George Potamias
Minepath (www.minepath.org) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28419128/cytoskeletal-stability-and-metabolic-alterations-in-primary-human-macrophages-in-long-term-microgravity
#2
Svantje Tauber, Beatrice A Lauber, Katrin Paulsen, Liliana E Layer, Martin Lehmann, Swantje Hauschild, Naomi R Shepherd, Jennifer Polzer, Jürgen Segerer, Cora S Thiel, Oliver Ullrich
The immune system is one of the most affected systems of the human body during space flight. The cells of the immune system are exceptionally sensitive to microgravity. Thus, serious concerns arise, whether space flight associated weakening of the immune system ultimately precludes the expansion of human presence beyond the Earth's orbit. For human space flight, it is an urgent need to understand the cellular and molecular mechanisms by which altered gravity influences and changes the functions of immune cells...
2017: PloS One
https://www.readbyqxmd.com/read/28409507/fasparser-a-package-for-manipulating-sequence-data
#3
Yan-Bo Sun
A computer software package called 'FasParser' was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file...
March 18, 2017: Zoological Research
https://www.readbyqxmd.com/read/28394535/-metaphylaxis-of-urolithiasis-new-look-modern-approach-implementation-in-a-mobile-application
#4
N K Gadzhiev, S S Brovkin, V E Grigorev, V V Dmitriev, V A Malkhasyan, D D Shkarupa, A V Pisarev, D V Mazurenko, V M Obidnyak, I N Orlov, S V Popov, N S Tagirov, S V Petrov
AIM: To analyze the sub-segment of mHealth devoted to assessing of the risk of recurrent stone formation and metaphylaxis of stone formation. To design a smartphone application (app.) in Russian language for urolithiasis patients. MATERIALS AND METHODS: Three working groups of urologists from three St. Petersburg clinics searched for downloadable medical applications relevant to the above requirements. After searching and analyzing existing medical applications, the most acceptable design and structure of our own application were identified...
April 2017: Urologii︠a︡
https://www.readbyqxmd.com/read/28386672/malignancy-in-pheochromocytoma-or-paraganglioma-integrative-analysis-of-176-cases-in-tcga
#5
Yong Joon Suh, Ji-Young Choe, Hyo Jin Park
Methods of diagnosing malignant pheochromocytoma (PCC) or paraganglioma (PGL) are needed. However, there are no reliable histopathologic criteria to distinguish malignant PCC/PGLs. The recent genomic analysis of The Cancer Genome Atlas (TCGA) provides in-depth information enabling more accurate diagnosis of disease entities. Therefore, we investigated genomic expression differences and mutational differences of malignant PCC/PGLs with TCGA. As of December 2014, TCGA had acquired multigenomic analysis of 176 PCC/PGL samples...
April 6, 2017: Endocrine Pathology
https://www.readbyqxmd.com/read/28381259/halc-high-throughput-algorithm-for-long-read-error-correction
#6
Ergude Bao, Lingxiao Lan
BACKGROUND: The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS: Here, we introduce HALC, a high throughput algorithm for long read error correction...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28378517/the-creation-and-dissemination-of-downloadable-information-on-dementia-and-driving-from-a-social-health-perspective
#7
Yumiko Arai, Asuna Arai, Yoko Mizuno, Naoto Kamimura, Manabu Ikeda
BACKGROUND: Driving cessation is a likely consequence of progressive dementia. Patients and families can benefit from support through this transition, both to safeguard the patient and public and to help preserve healthy social activity of the patient. METHODS: To provide appropriate supportive information, we developed a 35-page manual ('Supporting family caregivers of older drivers with dementia') available as a free download from our department website. We then informed municipal governments of its availability, tracked website access metrics, and followed up 7 months later with a postal survey to the heads of each municipal government's department of welfare for older citizens...
April 4, 2017: Psychogeriatrics: the Official Journal of the Japanese Psychogeriatric Society
https://www.readbyqxmd.com/read/28375006/fragment-database-fdb-17
#8
Ricardo Visini, Mahendra Awale, Jean-Louis Reymond
To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragmentlike molecules evenly covering a broad value range for molecular size, polarity, and stereochemical complexity...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28374117/virtual-screening-for-potential-inhibitors-of-ctx-m-15-protein-of-klebsiella-pneumoniae
#9
Tayebeh Farhadi, Atefeh Fakharian, Roman S Ovchinnikov
The Gram-negative bacterium Klebsiella pneumoniae, responsible for a wide variety of nosocomial infections in immuno-deficient patients, involves the respiratory, urinary and gastrointestinal tract infections and septicemia. Extended spectrum β-lactamases (ESBL) belong to β-lactamases capable of conferring antibiotic resistance in Gram-negative bacteria. CTX-M-15, a prevalent ESBL reported from Enterobacteriaceae including K. pneumoniae, was selected as a potent anti-bacterial target. To identify the novel drug-like compounds, structure-based screening procedure was employed against downloaded drug-like compounds from ZINC database...
April 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28371377/validation-of-a-gpu-based-3d-dose-calculator-for-modulated-beams
#10
Saeed Ahmed, Dylan Hunt, Jeff Kapatoes, Robert Hayward, Geoffrey Zhang, Eduardo G Moros, Vladimir Feygelman
A superposition/convolution GPU-accelerated dose computation algorithm (the Calculator) has been recently incorporated into commercial software. The algorithm requires validation prior to clinical use. Three photon energies were examined: conventional 6 MV and 15 MV, and 10 MV flattening filter free (10 MVFFF). For a set of IMRT and VMAT plans based on four of the five AAPM Practice Guideline 5a downloadable datasets, ion chamber (IC) measurements were performed on the water-equivalent phantoms. The average difference between the Calculator and IC was -0...
March 29, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28369462/drvm-a-new-tool-for-efficient-genome-assembly-of-known-eukaryotic-viruses-from-metagenomes
#11
Hsin-Hung Lin, Yu-Chieh Liao
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data...
February 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28365396/use-of-the-3d-surgical-modelling-technique-with-open-source-software-for-mandibular-fibula-free-flap-reconstruction-and-its-surgical-guides
#12
L Ganry, B Hersant, J Quilichini, P Leyder, J P Meningaud
INTRODUCTION: Tridimensional (3D) surgical modelling is a necessary step to create 3D-printed surgical tools, and expensive professional software is generally needed. Open-source software are functional, reliable, updated, may be downloaded for free and used to produce 3D models. Few surgical teams have used free solutions for mastering 3D surgical modelling for reconstructive surgery with osseous free flaps. We described an Open-source software 3D surgical modelling protocol to perform a fast and nearly free mandibular reconstruction with microvascular fibula free flap and its surgical guides, with no need for engineering support...
March 29, 2017: Journal of Stomatology, Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/28360928/a-new-kymogram-based-method-reveals-unexpected-effects-of-marker-protein-expression-and-spatial-anisotropy-of-cytoskeletal-dynamics-in-plant-cell-cortex
#13
Fatima Cvrčková, Denisa Oulehlová
BACKGROUND: Cytoskeleton can be observed in live plant cells in situ with high spatial and temporal resolution using a combination of specific fluorescent protein tag expression and advanced microscopy methods such as spinning disc confocal microscopy (SDCM) or variable angle epifluorescence microscopy (VAEM). Existing methods for quantifying cytoskeletal dynamics are often either based on laborious manual structure tracking, or depend on costly commercial software. Current automated methods also do not readily allow separate measurements of structure lifetime, lateral mobility, and spatial anisotropy of these parameters...
2017: Plant Methods
https://www.readbyqxmd.com/read/28358862/comprehensive-framework-for-visualizing-and-analyzing-spatio-temporal-dynamics-of-racial-diversity-in-the-entire-united-states
#14
Anna Dmowska, Tomasz F Stepinski, Pawel Netzel
The United States is increasingly becoming a multi-racial society. To understand multiple consequences of this overall trend to our neighborhoods we need a methodology capable of spatio-temporal analysis of racial diversity at the local level but also across the entire U.S. Furthermore, such methodology should be accessible to stakeholders ranging from analysts to decision makers. In this paper we present a comprehensive framework for visualizing and analyzing diversity data that fulfills such requirements...
2017: PloS One
https://www.readbyqxmd.com/read/28345762/short-term-effects-of-low-carbohydrate-diet-on-glycaemic-parameters-and-cardiovascular-risk-markers-in-patients-with-type-1-diabetes-a-randomised-open-label-cross-over-trial
#15
A Ranjan, S Schmidt, C Damm-Frydenberg, J Holst, S Madsbad, K Nørgaard
The objective was to compare effects of high carbohydrate diet (HCD) versus low carbohydrate diet (LCD) on glycaemic parameters and cardiovascular risk markers in patients with type 1 diabetes. Ten patients (4 women, insulin pump-treated, median±SD age: 48 ± 10 years, HbA1c: 53 ± 6 mmol/mol (7.0 ± 0.6%)) followed one week of isocaloric HCD (≥250 g/day) and one week of isocaloric LCD (≤50 g/day) in random order. After each week, we downloaded pump and sensor data and collected fasting blood and urine samples...
March 27, 2017: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/28343097/strait-razor-v2s-advancing-sequence-based-str-allele-reporting-and-beyond-to-other-marker-systems
#16
Jonathan L King, Frank R Wendt, Jie Sun, Bruce Budowle
STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and "early access" panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#17
Ramesh Menon, Namrata V Patel, Amitbikram Mohapatra, Chaitanya G Joshi
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328654/outcomes-for-children-receiving-noninvasive-ventilation-as-the-first-line-mode-of-mechanical-ventilation-at-intensive-care-admission-a-propensity-score-matched-cohort-study
#18
Jenny V Morris, Padmanabhan Ramnarayan, Roger C Parslow, Sarah J Fleming
OBJECTIVES: To compare outcomes of children receiving noninvasive ventilation with those receiving invasive ventilation as first-line mode of mechanical ventilation following unplanned intensive care admission. DESIGN: Propensity score-matched cohort study analyzing data prospectively collected by the Pediatric Intensive Care Audit Network over 8 years (2007-2014). SETTING: Thirty-one PICUs in the United Kingdom and Ireland; twenty-one of whom submitted Pediatric Critical Care Minimum Dataset data for the entire study period...
March 21, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28316907/sleep-apps-and-behavioral-constructs-a-content-analysis
#19
Diana S Grigsby-Toussaint, Jong Cheol Shin, Dayanna M Reeves, Ariana Beattie, Evan Auguste, Girardin Jean-Louis
Although sleep apps are among the most popular commercially available health apps, little is known about how well these apps are grounded in behavioral theory. Three-hundred and sixty-nine apps were initially identified using the term "sleep" from the Google play store and Apple iTunes in September 2015. The final sample consisted of 35 apps that met the following inclusion criteria: 1) Stand-alone functionality; 2) Sleep tracker or monitor apps ranked by 100 + users; 3) Sleep Alarm apps ranked by 1000 + users; and 4) English language...
June 2017: Preventive Medicine Reports
https://www.readbyqxmd.com/read/28314164/calculation-spreadsheet-for-uncertainty-estimation-of-measurement-results-in-gamma-ray-spectrometry-and-its-validation-for-quality-assurance-purpose
#20
Alessia Ceccatelli, Ashild Dybdal, Ales Fajgelj, Aurelien Pitois
An Excel calculation spreadsheet has been developed to estimate the uncertainty of measurement results in γ-ray spectrometry. It considers all relevant uncertainty components and calculates the combined standard uncertainty of the measurement result. The calculation spreadsheet has been validated using two independent open access software and is available for download free of charge at: https://nucleus.iaea.org/rpst/ReferenceProducts/Analytical_Methods/index.htm. It provides a simple and easy-to-use template for estimating the uncertainty of γ-ray spectrometry measurement results and supports the radioanalytical laboratories seeking accreditation for their measurements using γ-ray spectrometry...
March 3, 2017: Applied Radiation and Isotopes
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