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Visualization and System Diagrams

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https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#1
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P Telles, Gabriela Vaz Meirelles, Rosane Minghim
BACKGROUND: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28910932/-downscaling-research-of-spatial-distribution-of-incidence-of-hand-foot-and-mouth-disease-based-on-area-to-area-poisson-kriging-method
#2
J X Wang, M G Hu, S C Yu, G X Xiao
Objective: To understand the spatial distribution of incidence of hand foot and mouth disease (HFMD) at scale of township and provide evidence for the better prevention and control of HFMD and allocation of medical resources. Methods: The incidence data of HFMD in 108 counties (district) in Shandong province in 2010 were collected. Downscaling interpolation was conducted by using area-to-area Poisson Kriging method. The interpolation results were visualized by using geographic information system (GIS). The county (district) incidence was interpolated into township incidence to get the distribution of spatial distribution of incidence of township...
September 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28866561/graphiti-interactive-specification-of-attribute-based-edges-for-network-modeling-and-visualization
#3
Arjun Srinivasan, Hyunwoo Park, Alex Endert, Rahul C Basole
Network visualizations, often in the form of node-link diagrams, are an effective means to understand relationships between entities, discover entities with interesting characteristics, and to identify clusters. While several existing tools allow users to visualize pre-defined networks, creating these networks from raw data remains a challenging task, often requiring users to program custom scripts or write complex SQL commands. Some existing tools also allow users to both visualize and model networks. Interaction techniques adopted by these tools often assume users know the exact conditions for defining edges in the resulting networks...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28866520/a-virtual-reality-visualization-tool-for-neuron-tracing
#4
Will Usher, Pavol Klacansky, Frederick Federer, Peer-Timo Bremer, Aaron Knoll, Alessandra Angelucci, Valerio Pascucci
Tracing neurons in large-scale microscopy data is crucial to establishing a wiring diagram of the brain, which is needed to understand how neural circuits in the brain process information and generate behavior. Automatic techniques often fail for large and complex datasets, and connectomics researchers may spend weeks or months manually tracing neurons using 2D image stacks. We present a design study of a new virtual reality (VR) system, developed in collaboration with trained neuroanatomists, to trace neurons in microscope scans of the visual cortex of primates...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28866503/the-topology-toolkit
#5
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/28738824/visibiome-an-efficient-microbiome-search-engine-based-on-a-scalable-distributed-architecture
#6
Syafiq Kamarul Azman, Muhammad Zohaib Anwar, Andreas Henschel
BACKGROUND: Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel samples. This process facilitates the identification of similar compositional features in microbiota elsewhere and therefore can help to understand driving factors for microbial community assembly. RESULTS: We present Visibiome, a microbiome search engine that can perform exhaustive, phylogeny based similarity search and contextualization of user-provided samples against a comprehensive dataset of 16S rRNA profiles environments, while tackling several computational challenges...
July 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28718788/implementation-of-an-imu-aided-image-stacking-algorithm-in-a-digital-camera-for-unmanned-aerial-vehicles
#7
Ahmad Audi, Marc Pierrot-Deseilligny, Christophe Meynard, Christian Thom
Images acquired with a long exposure time using a camera embedded on UAVs (Unmanned Aerial Vehicles) exhibit motion blur due to the erratic movements of the UAV. The aim of the present work is to be able to acquire several images with a short exposure time and use an image processing algorithm to produce a stacked image with an equivalent long exposure time. Our method is based on the feature point image registration technique. The algorithm is implemented on the light-weight IGN (Institut national de l'information géographique) camera, which has an IMU (Inertial Measurement Unit) sensor and an SoC (System on Chip)/FPGA (Field-Programmable Gate Array)...
July 18, 2017: Sensors
https://www.readbyqxmd.com/read/28685035/initiating-a-participatory-action-research-process-in-the-agincourt-health-and-socio-demographic-surveillance-site
#8
Oghenebrume Wariri, Lucia D'Ambruoso, Rhian Twine, Sizzy Ngobeni, Maria van der Merwe, Barry Spies, Kathleen Kahn, Stephen Tollman, Ryan G Wagner, Peter Byass
BACKGROUND: Despite progressive health policy, disease burdens in South Africa remain patterned by deeply entrenched social inequalities. Accounting for the relationships between context, health and risk can provide important information for equitable service delivery. The aims of the research were to initiate a participatory research process with communities in a low income setting and produce evidence of practical relevance. METHODS: We initiated a participatory action research (PAR) process in the Agincourt health and socio-demographic surveillance site (HDSS) in rural north-east South Africa...
June 2017: Journal of Global Health
https://www.readbyqxmd.com/read/28630034/fall-prevention-self-assessments-via-mobile-3d-visualization-technologies-community-dwelling-older-adults-perceptions-of-opportunities-and-challenges
#9
Julian Hamm, Arthur Money, Anita Atwal
BACKGROUND: In the field of occupational therapy, the assistive equipment provision process (AEPP) is a prominent preventive strategy used to promote independent living and to identify and alleviate fall risk factors via the provision of assistive equipment within the home environment. Current practice involves the use of paper-based forms that include 2D measurement guidance diagrams that aim to communicate the precise points and dimensions that must be measured in order to make AEPP assessments...
June 19, 2017: JMIR Human Factors
https://www.readbyqxmd.com/read/28533467/the-current-and-future-state-of-animal-coloration-research
#10
REVIEW
John A Endler, Johanna Mappes
Animal colour patterns are a model system for understanding evolution because they are unusually accessible for study and experimental manipulation. This is possible because their functions are readily identifiable. In this final paper of the symposium we provide a diagram of the processes affecting colour patterns and use this to summarize their functions and put the other papers in a broad context. This allows us to identify significant 'holes' in the field that only become obvious when we see the processes affecting colour patterns, and their interactions, as a whole...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28412452/enhancement-of-dissolution-rate-through-eutectic-mixture-and-solid-solution-of-posaconazole-and-benznidazole
#11
Camila Bezerra Melo Figueirêdo, Daniela Nadvorny, Amanda Carla Quintas de Medeiros Vieira, José Lamartine Soares Sobrinho, Pedro José Rolim Neto, Ping I Lee, Monica Felts de La Roca Soares
Benznidazole (BNZ), the only commercialized antichagasic drug, and the antifungal compound posaconazole (PCZ) have shown synergistic action in the therapy of Chagas disease, however both active pharmaceutical ingredients (APIs) exhibit low aqueous solubility potentially limiting their bioavailability and therapeutic efficacy. In this paper, we report for the first time the formation of a eutectic mixture as well as an amorphous solid solution of PCZ and BNZ (at the same characteristic ratio of 80:20wt%), which provided enhanced solubility and dissolution rate for both APIs...
April 12, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28287524/a-web-tool-for-generating-high-quality-machine-readable-biological-pathways
#12
Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, Jason Grant, Anthony Wu, David S Wishart
PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events...
February 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28250343/evaluating-the-properties-of-poly-lactic-co-glycolic-acid-nanoparticle-formulations-encapsulating-a-hydrophobic-drug-by-using-the-quality-by-design-approach
#13
Masato Kozaki, Shin-Ichiro Kobayashi, Yukihiro Goda, Haruhiro Okuda, Kumiko Sakai-Kato
We applied the Quality by Design (QbD) approach to the development of poly(lactic-co-glycolic acid) (PLGA) nanoparticle formulations encapsulating triamcinolone acetonide, and the critical process parameters (CPPs) were identified to clarify the correlations between critical quality attributes and CPPs. Quality risk management was performed by using an Ishikawa diagram and experiments with a fractional factorial design (ANOVA). The CPPs for particle size were PLGA concentration and rotation speed, and the CPP for relative drug loading efficiency was the poor solvent to good solvent volume ratio...
2017: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28196576/care-coordination-from-a-strengths-perspective-a-practice-based-evidence-evaluation-of-evidence-based-practice
#14
Karen A Monsen, Catherine E Vanderboom, Kirstie S Olson, Mary E Larson, Diane E Holland
BACKGROUND AND PURPOSE: It is critical to accurately represent strengths interventions to improve data and enable intervention effectiveness research from a strengths perspective. However, it is challenging to understand strengths interventions from the multiple perspectives of computerized knowledge representation, evidence-based practice guidelines, and practice-based evidence narratives. Intervention phrases abstracted from nurse care coordinator practice narratives described strengths interventions with community-dwelling elders...
February 1, 2017: Research and Theory for Nursing Practice
https://www.readbyqxmd.com/read/28186915/a-novel-variable-precision-reduction-approach-to-comprehensive-knowledge-systems
#15
Chao Yang, Hongbo Liu, Sean McLoone, C L Philip Chen, Xindong Wu
A comprehensive knowledge system reveals the intangible insights hidden in an information system by integrating information from multiple data sources in a synthetical manner. In this paper, we present a variable precision reduction theory, underpinned by two new concepts: 1) distribution tables and 2) genealogical binary trees. Sufficient and necessary conditions to extract comprehensive knowledge from a given information system are also presented and proven. A complete variable precision reduction algorithm is proposed, in which we introduce four important strategies, namely, distribution table abstracting, attribute rank dynamic updating, hierarchical binary classifying, and genealogical tree pruning...
February 8, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28152841/evaluating-data-driven-breast-surgery-treatment-path-visualizations-from-registry-and-administrative-data
#16
Alexander S Taylor, Mia Alyce Levy
195 Background: Breast cancer patients face difficult decisions about their surgical care without a full understanding of their options. The learning health system goal is to use information from the care of prior patients to inform the care of future patients. We aim to apply this concept to generate data-driven surgical paths, develop interactive path visualizations to inform patients, and evaluate their impact. METHODS: We used cancer registry and administrative CPT codes for women diagnosed with stage 0-III breast cancer between FY2010-14 at a comprehensive cancer center...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28035814/sbml-diff-a-tool-for-visually-comparing-sbml-models-in-synthetic-biology
#17
James Scott-Brown, Antonis Papachristodoulou
We present sbml-diff, a tool that is able to read a model of a biochemical reaction network in SBML format and produce a range of diagrams showing different levels of detail. Each diagram type can be used to visualize a single model or to visually compare two or more models. The default view depicts species as ellipses, reactions as rectangles, rules as parallelograms, and events as diamonds. A cartoon view replaces the symbols used for reactions on the basis of the associated Systems Biology Ontology terms...
January 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27956095/real-time-visualization-of-the-precipitation-and-phase-behavior-of-octaethylporphyrin-in-lipid-microparticles
#18
Elisa Parra, Pablo Hervella, David Needham
The material properties of micro- and nanoparticles are fundamental for their bulk properties in suspension, like their stability and encapsulation efficiency. A particularly interesting system with potential biomedical applications is the encapsulation of hydrophobic porphyrins into lipid particles and their use as metal atom chelators, where retention and stability are keys for the design process. The overall goal here was to study the solubility, phase behavior, and mixing of octaethylporphyrin (OEP) and OEP-Cu chelates with 2 core materials, triolein (TO) and cholesteryl acetate, as single microparticles...
December 9, 2016: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27893370/network-visualization-as-a-higher-order-visual-analysis-tool
#19
Tim Dwyer
The transformation of data into visuals that are as effective and engaging as possible for compelling presentation is an emerging topic in information visualization research. With this goal in mind, several data-analysis system approaches offer a higher-order network visualization that map insights rather than raw data. Knowledge visualization or externalization in the form of small, focused diagrams can communicate insights as well as help analysts structure their reasoning process.
November 2016: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/27878315/a-plasmonic-elisa-for-the-naked-eye-detection-of-chromium-ions-in-water-samples
#20
Cuize Yao, Shiting Yu, Xiuqing Li, Ze Wu, Jiajie Liang, Qiangqiang Fu, Wei Xiao, Tianjiu Jiang, Yong Tang
Here, we describe the development of a triangular silver nanoprism (AgNPR) etching-based plasmonic ELISA for the colorimetric determination of Cr(III) levels in environmental water samples. This involved the creation of a novel signal generation system (substrate reaction solution) for a competitive ELISA in which hydrogen peroxide (H2O2) is used to etch triangular AgNPRs, inducing a change in color. This is achieved by controlling the H2O2 concentration that remains after degradation by catalase, which is conjugated to the secondary antibody of the ELISA...
November 22, 2016: Analytical and Bioanalytical Chemistry
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