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https://www.readbyqxmd.com/read/30310764/an-open-source-software-ecosystem-for-the-interactive-exploration-of-ultrafast-electron-scattering-data
#1
Laurent P René de Cotret, Martin R Otto, Mark J Stern, Bradley J Siwick
This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, iris , is graphical user-interface program and library for interactive exploration of UES data. Under the hood, iris makes use of npstreams , an extensions of numpy to streaming array-processing, for high-throughput parallel data reduction. Finally, we present scikit-ued , a library of reusable routines and data structures for analysis of UES data, including specialized image processing algorithms, simulation routines, and crystal structure manipulation operations...
2018: Advanced Structural and Chemical Imaging
https://www.readbyqxmd.com/read/30306936/modular-knowledge-based-decision-support-system-dedicated-to-a-cooperative-decision-to-prevent-cardiovascular-diseases
#2
Adrien Ugon, Emmanuel Jobez, Hector Falcoff, Marie-Christine Jaulent, Pierre Meneton, Madeleine Favre, Rosy Tsopra
Despite the success of artificial intelligence solutions in the recent years, physicians are still reticent to use integrated functionalities to support their decision. Methods used to create these functionalities can be divided into two groups, each being associated to different questions. Data-based methods are seen as black boxes for which it is impossible to understand how the decision is taken; knowledge-based methods need to rely on formalized knowledge sources on the basis of evidence, which can be discussed and criticized by physicians for their use in real life...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/30304367/metaomics-analysis-pipeline-and-browser-based-software-suite-for-transcriptomic-meta-analysis
#3
Tianzhou Ma, Zhiguang Huo, Anche Kuo, Li Zhu, Zhou Fang, Xiangrui Zeng, Chien-Wei Lin, Silvia Liu, Lin Wang, Peng Liu, Tanbin Rahman, Lun-Ching Chang, Sunghwan Kim, Jia Li, Yongseok Park, Chi Song, Steffi Oesterreich, Etienne Sibille, George C Tseng
Summary: The rapid advances of omics technologies have generated abundant genomic data in public repositories and effective analytical approaches are critical to fully decipher biological knowledge inside these data. Meta-analysis combines multiple studies of a related hypothesis to improve statistical power, accuracy and reproducibility beyond individual study analysis. To date, many transcriptomic meta-analysis methods have been developed, yet few thoughtful guidelines exist. Here, we introduce a comprehensive analytical pipeline and browser-based software suite, called MetaOmics, to meta-analyze multiple transcriptomic studies for various biological purposes, including quality control, differential expression analysis, pathway enrichment analysis, differential co-expression network analysis, prediction, clustering and dimension reduction...
October 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/30301090/evaluating-the-impact-of-sewage-discharges-on-the-marine-environment-with-a-lightweight-auv
#4
Francisco Bonin-Font, Jordi Lalucat, Gabriel Oliver-Codina, Miquel Massot-Campos, Eric Guerrero Font, Pep Lluis Negre Carrasco
Environmental studies that use small Autonomous Underwater Vehicles (AUVs) can survey wider and deeper areas, compared to traditional methods, at a reasonable cost. Thanks to the precise vehicle navigation systems, the data collected can be accurately geolocalized. Besides, lightweight vehicles can be deployed from the shore or from small boats and programmed by means of user-friendly graphical interfaces, thus reducing and simplifying the need of human resources and infrastructures. Based on such a technology, this paper presents a framework to assess the environmental impact of a marine sewage outfall set in the Bay of Palma (Mallorca, Spain)...
October 2018: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/30300393/quantitative-optical-coherence-tomography-angiography-biomarkers-for-neovascular-age-related-macular-degeneration-in-remission
#5
Florence Coscas, Diogo Cabral, Telmo Pereira, Carlos Geraldes, Hemaxi Narotamo, Alexandra Miere, Marco Lupidi, Alexandre Sellam, Ana Papoila, Gabriel Coscas, Eric Souied
PURPOSE: To characterize quantitative optical coherence tomography angiography (OCT-A) parameters in active neovascular age-related macular degeneration (nAMD) patients under treatment and remission nAMD patients. DESIGN: Retrospective, cross-sectional study. PARTICIPANTS: One hundred and four patients of whom 72 were in Group 1 (active nAMD) and 32 in Group 2 (remission nAMD) based on SD-OCT (Spectral Domain OCT) qualitative morphology. METHODS: This study was conducted at the Centre Ophtalmologique de l'Odeon between June 2016 and December 2017...
2018: PloS One
https://www.readbyqxmd.com/read/30291716/peptic-ulcer-is-the-most-common-cause-of-non-variceal-upper-gastrointestinal-bleeding-nvugib-in-china
#6
Mingliang Lu, Gang Sun, Xiao-Mei Zhang, You-Qing Xv, Shi-Yao Chen, Ying Song, Xue-Liang Li, Bin Lv, Jian-Lin Ren, Xue-Qing Chen, Hui Zhang, Chen Mo, Yan-Zhi Wang, Yun-Sheng Yang
BACKGROUND This study aimed to discover the common cause of non-variceal upper-gastrointestinal bleeding (NVUGIB) by conducting a multi-center retrospective study from 2008 to 2012. MATERIAL AND METHODS Hospitalized patients ages ≥18 years old, from 8 hospitals in China, diagnosed with NVUGIB by endoscopy from 1 January 2008 to 31 December 2012 were enrolled. Questionnaires were developed and a data-entry graphical user interface was designed by using EpiData software. RESULTS Total of 2977 hospitalized patients from 8 medical centers were included...
October 6, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/30289930/design-and-validation-of-an-open-source-modular-microplate-photoirradiation-system-for-high-throughput-photobiology-experiments
#7
Suzanna Katz, Peter Backeris, Christopher Merck, Maria Suprun, Sunita D'Souza, David F Bishop, Robert J Desnick, Kateri Moore, Iban Ubarretxena-Belandia, Ihor R Lemischka
Research in photobiology is currently limited by a lack of devices capable of delivering precise and tunable irradiation to cells in a high-throughput format. This limits researchers to using expensive commercially available or custom-built light sources which make it difficult to replicate, standardize, optimize, and scale experiments. Here we present an open-source Microplate Photoirradiation System (MPS) developed to enable high-throughput light experiments in standard 96 and 24-well microplates for a variety of applications in photobiology research...
2018: PloS One
https://www.readbyqxmd.com/read/30289549/cellmarker-a-manually-curated-resource-of-cell-markers-in-human-and-mouse
#8
Xinxin Zhang, Yujia Lan, Jinyuan Xu, Fei Quan, Erjie Zhao, Chunyu Deng, Tao Luo, Liwen Xu, Gaoming Liao, Min Yan, Yanyan Ping, Feng Li, Aiai Shi, Jing Bai, Tingting Zhao, Xia Li, Yun Xiao
One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substantial cell markers for distinguishing different cell types in tissues. Here, we developed the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/), aiming to provide a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse...
October 5, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30287396/a-graphic-user-interface-for-the-evaluation-of-knee-osteoarthritis-geko-an-open-source-tool-for-histological-grading
#9
Heidi E Kloefkorn, Brittany Y Jacobs, Danny F Xie, Kyle D Allen
OBJECTIVE: In osteoarthritis (OA) models, histology is commonly used to evaluate the severity of joint damage. Unfortunately, semi-quantitative histological grading systems include some level of subjectivity, and quantitative grading systems can be tedious to implement. The objective of this work is to introduce an open source, graphic user interface (GUI) for quantitative grading of knee OA. METHODS: Inspired by the 2010 OARSI histopathology recommendations for the rat, our laboratory has developed a GUI for the evaluation of knee OA, nicknamed GEKO...
October 1, 2018: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/30284311/pydef-2-0-an-easy-to-use-post-treatment-software-for-publishable-charts-featuring-a-graphical-user-interface
#10
Adrien Stoliaroff, Stéphane Jobic, Camille Latouche
Herein we present an open-source program automating the post-treatment of solid-state ab initio calculations performed with VASP, the most used solid-state simulation package. The program plots Density of States (DOS) and Band Diagrams, enabling the user to conduct efficiently a detailed study of electronic properties of a material. Our tool includes a complete module dedicated to point defects studies, proposing various corrections which can be activated at will and innovative property calculations such as defect concentrations...
October 3, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/30280999/intravital-imaging-for-tracking-of-angiogenesis-and-cellular-events-around-surgical-bone-implants
#11
Niloufar Khosravi, Vanessa V Mendes, Ghata Nirmal, Safa Majeed, Ralph S DaCosta, John E Davies
Peri-implant endosseous wound healing involves cascades of cellular and molecular events that lead to the integration of the implant to the recipient bone. Currently, tools are lacking to track peri-implant healing events at high spatiotemporal resolution in vivo. A cranial window chamber model (CIWC), which is compatible with confocal and multiphoton intravital microscopic imaging systems, has been developed for spatiotemporal tracking of angiogenesis, and cellular dynamics in the peri-implant wound site. In this study, we describe a step-by-step procedure for implantation of the CIWC in the calvaria of fluorescent reporter mice with endogenously labeled mesenchymal progenitor cells...
October 3, 2018: Tissue Engineering. Part C, Methods
https://www.readbyqxmd.com/read/30277515/psichomics-graphical-application-for-alternative-splicing-quantification-and-analysis
#12
Nuno Saraiva-Agostinho, Nuno L Barbosa-Morais
Alternative pre-mRNA splicing generates functionally distinct transcripts from the same gene and is involved in the control of multiple cellular processes, with its dysregulation being associated with a variety of pathologies. The advent of next-generation sequencing has enabled global studies of alternative splicing in different physiological and disease contexts. However, current bioinformatics tools for alternative splicing analysis from RNA-seq data are not user-friendly, disregard available exon-exon junction quantification or have limited downstream analysis features...
October 2, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30273404/blaunet-an-r-based-graphical-user-interface-package-to-analyze-blau-space
#13
Michael Genkin, Cheng Wang, George Berry, Matthew E Brashears
McPherson's Blau space and affiliation ecology model is a powerful tool for analyzing the ecological competition among social entities, such as organizations, along a combination of sociodemographic characteristics of their members. In this paper we introduce the R-based Graphical User Interface (GUI) package Blaunet, an integrated set of tools to calculate, visualize, and analyze the statuses of individuals and social entities in Blau space, parameterized by multiple sociodemographic traits as dimensions. The package is able to calculate the Blau statuses at the nodal, dyadic, and meso levels based on three types of information: sociodemographic characteristics, group affiliations (e...
2018: PloS One
https://www.readbyqxmd.com/read/30270947/randomization-based-statistical-inference-a-resampling-and-simulation-infrastructure
#14
Ivo D Dinov, Selvam Palanimalai, Ashwini Khare, Nicolas Christou
Statistical inference involves drawing scientifically-based conclusions describing natural processes or observable phenomena from datasets with intrinsic random variation. There are parametric and non-parametric approaches for studying the data or sampling distributions, yet few resources are available to provide integrated views of data (observed or simulated), theoretical concepts, computational mechanisms and hands-on utilization via flexible graphical user interfaces. We designed, implemented and validated a new portable randomization-based statistical inference infrastructure (http://socr...
2018: Teaching Statistics
https://www.readbyqxmd.com/read/30266410/hccdb-a-database-of-hepatocellular-carcinoma-expression-atlas
#15
Qiuyu Lian, Shicheng Wang, Guchao Zhang, Dongfang Wang, Guijuan Luo, Jing Tang, Lei Chen, Jin Gu
Hepatocellular carcinoma (HCC) is highly heterogeneous in nature and has been one of the most common cancer types worldwide. To ensure repeatability of identified gene expression patterns and comprehensively annotate the transcriptomes of HCC, we carefully curated 15 public HCC expression datasets that cover around 4000 clinical samples and developed the database HCCDB to serve as a one-stop online resource for exploring HCC gene expression with user-friendly interfaces. The global differential gene expression landscape of HCC was established by analyzing the consistently differentially expressed genes across multiple datasets...
September 25, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30256983/bacdive-in-2019-bacterial-phenotypic-data-for-high-throughput-biodiversity-analysis
#16
Lorenz Christian Reimer, Anna Vetcininova, Joaquim Sardà Carbasse, Carola Söhngen, Dorothea Gleim, Christian Ebeling, Jörg Overmann
The bacterial metadatabase BacDive (http://bacdive.dsmz.de) has become a comprehensive resource for structured data on the taxonomy, morphology, physiology, cultivation, isolation and molecular data of prokaryotes. With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains. During recent developments of BacDive, the enrichment of information on existing strains was prioritized. This has resulted in a 146% increase of database content over the past three years...
September 26, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30256496/a-matlab-toolbox-for-multivariate-analysis-of-brain-networks
#17
Mohsen Bahrami, Paul J Laurienti, Sean L Simpson
Complex brain networks formed via structural and functional interactions among brain regions are believed to underlie information processing and cognitive function. A growing number of studies indicate that altered brain network topology is associated with physiological, behavioral, and cognitive abnormalities. Graph theory is showing promise as a method for evaluating and explaining brain networks. However, multivariate frameworks that provide statistical inferences about how such networks relate to covariates of interest, such as disease phenotypes, in different study populations are yet to be developed...
September 5, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/30253838/stattarget-a-streamlined-tool-for-signal-drift-correction-and-interpretations-of-quantitative-mass-spectrometry-based-omics-data
#18
Hemi Luan, Fenfen Ji, Yu Chen, Zongwei Cai
Large-scale quantitative mass spectrometry-based metabolomics and proteomics study requires the long-term analysis of multiple batches of biological samples, which often accompanied with significant signal drift and various inter- and intra-batch variations. The unwanted variations can lead to poor inter- and intra-day reproducibility, which is a hindrance to discover real significance. The use of quality control samples and data treatment strategies in the quality assurance procedure provides a mechanism to evaluate the quality and remove the analytical variance of the data...
December 7, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/30243013/a-thermometry-software-tool-for-monitoring-laser-induced-interstitial-thermotherapy
#19
Babak Bazrafshan, Ahmad Koujan, Frank Hübner, Christian Leithäuser, Norbert Siedow, Thomas J Vogl
The purpose of this study was to develop a thermometry software tool for temperature monitoring during laser-induced interstitial thermotherapy (LITT). C++ programming language and several libraries including DICOM Toolkit, Grassroots DICOM library, Insight Segmentation and Registration Toolkit, Visualization Toolkit and Quasar Toolkit were used. The software's graphical user interface creates windows displaying the temperature map and the coagulation extent in the tissue, determined by the magnetic resonance imaging (MRI) thermometry with the echo planar imaging sequence and a numerical simulation based on the radiation and heat transfer in biological tissues, respectively...
September 22, 2018: Biomedizinische Technik. Biomedical Engineering
https://www.readbyqxmd.com/read/30241474/astigmatic-an-automatic-tool-for-standard-astigmatism-vector-analysis
#20
Mathieu Gauvin, Avi Wallerstein
BACKGROUND: Standardization for reporting medical outcomes facilitates clinical study comparisons and has a fundamental role on research reproducibility. In this context, we present AstigMATIC, a free standalone application for automated standardized astigmatism vector analyses in corneal and intraocular refractive surgeries. AstigMATIC uses a simple graphical user interface (GUI) and allows the simultaneous display and analysis of astigmatism magnitude and axis. RESULTS: The software produces the four following standard graphs according to the standards of the Alpins Method; 1-Target-Induced Astigmatism Vector, 2- Surgically-Induced Astigmatism Vector, 3-Difference Vector and 4-Correction Index...
September 21, 2018: BMC Ophthalmology
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