Read by QxMD icon Read

Visualization and System Diagrams

Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Xuewen Ni, Kai Wang, Kao Wu, Harold Corke, Katsuyoshi Nishinari, Fatang Jiang
This study aims to investigate the stability, microstructure and rheological properties of konjac glucomannan (KGM)/zein mixed systems in different mixing ratios. A phase diagram was established by centrifugation and visual observation. KGM/zein could form a stable homogeneous dispersion with appropriate mixing formula, and the particle size in mixed systems increased with increasing zein content. During storage, zein particles increased in size but were homogeneously distributed in the continuous phase of KGM without flocculation as observed by confocal light scanning microscopy...
May 15, 2018: Carbohydrate Polymers
A Verma, J Maiti, V N Gaikwad
Large integrated steel plants employ an effective safety management system and gather a significant amount of safety-related data. This research intends to explore and visualize the rich database to find out the key factors responsible for the occurrences of incidents. The study was carried out on the data in the form of investigation reports collected from a steel plant in India. The data were processed and analysed using some of the quality management tools like Pareto chart, control chart, Ishikawa diagram, etc...
December 27, 2017: International Journal of Injury Control and Safety Promotion
Luis Henrique Lira, Flávio E Hirai, Marivaldo Oliveira, Waldir Portellinha, Eliane Mayumi Nakano
PURPOSE: To identify the causes of a diffuse lamellar keratitis (DLK) outbreak using a systematic search tool in a case-control analysis. METHODS: An Ishikawa diagram was used to guide physicians to determine the potential risk factors involved in this outbreak. Coherence between the occurrences and each possible cause listed in the diagram was verified, and the total number of eyes at risk was used to calculate the proportion of affected eyes. Multivariate analysis was performed using logistic regression to determine the independent effect of the risk factors, after controlling for confounders and test interactions...
September 2017: Arquivos Brasileiros de Oftalmologia
Katherine Icay, Chengyu Liu, Sampsa Hautaniemi
BACKGROUND AND OBJECTIVE: High-throughput measurement technologies have triggered a rise in large-scale cancer studies containing multiple levels of molecular data. While there are a number of efficient methods to analyze individual data types, there are far less that enhance data interpretation after analysis. We present the R package Director, a dynamic visualization approach to linking and interrogating multiple levels of molecular data after analysis for clinically meaningful, actionable insights...
January 2018: Computer Methods and Programs in Biomedicine
Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steve Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews, Heeyeon Song, Lincoln Stein, Robin Haw, Peter D'Eustachio, Peipei Ping, Henning Hermjakob, Antonio Fabregat
Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications...
November 1, 2017: Bioinformatics
Bobin Mi, Guohui Liu, Wu Zhou, Huijuan Lv, Kun Zha, Yi Liu, Qipeng Wu, Jing Liu
The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF‑β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co‑expressed DEGs were selected using Venn Diagram. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool...
December 2017: Molecular Medicine Reports
Zhiguang Zhou, Zhifei Ye, Yanan Liu, Fang Liu, Yubo Tao, Weihua Su
With the rapid development of industrial society, air pollution has become a major issue in the modern world. The development and widespread deployment of sensors has enabled the collection of air-quality datasets with detailed spatial and temporal scales. Analyses of these spatiotemporal air-quality datasets can help decision makers explore the major causes of air pollution and find efficient solutions. The authors designed a visual analytics system that uses multidimensional scaling (MDS) to transform the air-quality data from monitor stations into 2D plots and uses hierarchical clustering, Voronoi diagrams, and storyline visualizations to help experts explore various attributes and time scales in the data...
2017: IEEE Computer Graphics and Applications
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
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
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...
January 2018: IEEE Transactions on Visualization and Computer Graphics
Will Usher, Pavol Klacansky, Frederick Federer, Peer-Timo Bremer, Aaron Knoll, Jeff Yarch, 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...
January 2018: IEEE Transactions on Visualization and Computer Graphics
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
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
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
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
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
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
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
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
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"