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Visualization and Diagrams

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https://www.readbyqxmd.com/read/29160536/use-of-the-ishikawa-diagram-in-a-case-control-analysis-to-assess-the-causes-of-a-diffuse-lamellar-keratitis-outbreak
#1
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
https://www.readbyqxmd.com/read/29157999/chromaticity-separation-and-the-alpha-response
#2
S M Haigh, N R Cooper, A J Wilkins
Chromatic gratings can be uncomfortable to view and can evoke a large haemodynamic response. Both the discomfort and the amplitude of the haemodynamic response increase monotonically with the perceptual difference in the colour of the component bars of the grating, as registered by the separation in their chromaticity in the CIE 1976 UCS diagram. Individuals with photosensitive epilepsy exhibit epileptiform EEG activity in response to flickering light of alternate colours. The probability of the epileptiform response again increases monotonically with the separation of the colours in the CIE UCS diagram...
November 17, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/29157446/dynamic-visualization-of-multi-level-molecular-data-the-director-package-in-r
#3
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
https://www.readbyqxmd.com/read/29134600/visualization-of-phage-genomic-data-comparative-genomics-and-publication-quality-diagrams
#4
Dann Turner, J Mark Sutton, Darren M Reynolds, Eby M Sim, Nicola K Petty
The presentation of bacteriophage genomes as diagrams allows the location and organization of features to be communicated in a clear and effective manner. A wide range of software applications are available for the clear and accurate visualization of genomic data. Several of these applications incorporate comparative analysis tools, allowing for insertions, deletions, rearrangements and variations in syntenic regions to be visualized. In this chapter, freely available software and resources for the generation of high-quality graphical maps of bacteriophage genomes are listed and discussed...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29131816/automated-visualization-of-rule-based-models
#5
John Arul Prakash Sekar, Jose-Juan Tapia, James R Faeder
Frameworks such as BioNetGen, Kappa and Simmune use "reaction rules" to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions between rules scale poorly with model size...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29117849/seeking-ways-to-inform-the-uninformed-improving-the-informed-consent-process-in-online-social-science-research
#6
Evan K Perrault, David M Keating
Participants often do not read consent forms in social science research. This is not surprising, especially for online studies, given they do not typically offer greater risk than what is encountered in daily life. However, if no one is reading, are participants really informed? This study used previous research to craft experimentally manipulated consent forms utilizing different visual presentations (e.g., greater use of line spacing, bullets, bolding, diagrams). Participants ( n = 547) were randomly exposed to one of seven form variations...
November 1, 2017: Journal of Empirical Research on Human Research Ethics: JERHRE
https://www.readbyqxmd.com/read/29077811/reactome-enhanced-pathway-visualization
#7
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
https://www.readbyqxmd.com/read/29073314/the-sdm-3-circle-model-a-literature-synthesis-and-adaptation-for-shared-decision-making-in-the-hospital
#8
Stephanie Rennke, Patrick Yuan, Brad Monash, Rebecca Blankenburg, Ian Chua, Stephanie Harman, Debbie S Sakai, Adeena Khan, Joan F Hilton, Lisa Shieh, Jason Satterfield
Patient engagement through shared decision-making (SDM) is increasingly seen as a key component for patient safety, patient satisfaction, and quality of care. Current SDM models do not adequately account for medical and environmental contexts, which may influence medical decisions in the hospital. We identified leading SDM models and reviews to inductively construct a novel SDM model appropriate for the inpatient setting. A team of medicine and pediatric hospitalists reviewed the literature to integrate core SDM concepts and processes and iteratively constructed a synthesized draft model...
October 18, 2017: Journal of Hospital Medicine: An Official Publication of the Society of Hospital Medicine
https://www.readbyqxmd.com/read/29065629/exploring-space-management-goals-in-institutional-care-facilities-in-china
#9
Lingzhi Li, Jingfeng Yuan, Yan Ning, Qiuhu Shao, Jiankun Zhang
Space management has been widely examined in commercial facilities, educational facilities, and hospitals but not in China's institutional care facilities. Poor spatial arrangements, such as wasted space, dysfunctionality, and environment mismanagement, are increasing; in turn, the occupancy rate is decreasing due to residential dissatisfaction. To address these problems, this paper's objective is to explore the space management goals (SMGs) in institutional care facilities in China. Systematic literature analysis was adopted to set SMGs' principles, to identify nine theoretical SMGs, and to develop the conceptual model of SMGs for institutional care facilities...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29051701/mgupgma-a-fast-upgma-algorithm-with-multiple-graphics-processing-units-using-nccl
#10
REVIEW
Guan-Jie Hua, Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, Yu-Wei Chan, Chuan Yi Tang
A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28984353/care-maps-for-children-with-medical-complexity
#11
Sherri Adams, David Nicholas, Sanjay Mahant, Natalie Weiser, Ronik Kanani, Katherine Boydell, Eyal Cohen
AIM: Children with medical complexity require multiple providers and services to keep them well and at home. A care map is a patient/family-created diagram that pictorially maps out this complex web of services. This study explored what care maps mean for families and healthcare providers to inform potential for clinical use. METHOD: Parents (n=15) created care maps (hand drawn n=10 and computer-generated n=5) and participated in semi-structured interviews about the process of developing care maps and their perceived impact...
October 6, 2017: Developmental Medicine and Child Neurology
https://www.readbyqxmd.com/read/28983581/bioinformatics-analysis-of-fibroblasts-exposed-to-tgf%C3%A2-%C3%AE-at-the-early-proliferation-phase-of-wound-repair
#12
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
https://www.readbyqxmd.com/read/28975713/pepsweetener-a-web-based-tool-to-support-manual-annotation-of-intact-glycopeptide-ms-spectra
#13
Marcin Jakub Domagalski, Davide Alocci, Andreia Almeida, Daniel Kolarich, Frédérique Lisacek
PURPOSE: PepSweetener is a web-based visualization tool designed to facilitate the manual annotation of intact glycopeptides from mass spectrometry (MS) data regardless of the instrument that produced this data. EXPERIMENTAL DESIGN: This exploratory tool uses a theoretical glycopeptide dataset to visualize all peptide-glycan combinations that fall within the error range of the query precursor ion. PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass...
October 3, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28956822/the-formation-of-self-organized-domain-structures-at-non-polar-cuts-of-lithium-niobate-as-a-result-of-local-switching-by-an-spm-tip
#14
Anton Turygin, Denis Alikin, Yury Alikin, Vladimir Shur
We have studied experimentally the interaction of isolated needle-like domains created in an array via local switching using a biased scanning probe microscope (SPM) tip and visualized via piezoelectric force microscopy (PFM) at the non-polar cuts of MgO-doped lithium niobate (MgOLN) crystals. It has been found that the domain interaction leads to the intermittent quasiperiodic and chaotic behavior of the domain length in the array in a manner similar to that of polar cuts, but with greater spacing between the points of bias application and voltage amplitudes...
September 28, 2017: Materials
https://www.readbyqxmd.com/read/28955277/the-time-course-of-inhibition-of-return-evidence-from-steady-state-visual-evoked-potentials
#15
Ai-Su Li, Gong-Liang Zhang, Cheng-Guo Miao, Shuang Wang, Ming Zhang, Yang Zhang
Inhibition of return (IOR) refers to slower responses to targets at a previously cued location than that at an uncued location. The time course of IOR has long been a topic of interest in the field. Investigations into the time course of IOR are typically performed by examining the magnitude of IOR under various cue-target onset asynchrony (CTOA) conditions. Therefore, the results are vulnerable to influence of factors that could affect the target processes (e.g., the frequency of the target type). In the present study, steady-state visual evoked potentials (SSVEPs) were implemented to directly take a continuous measurement of the degree to which cued location is processed, eliminating the influence mentioned above...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28945584/visual-analytics-for-spatial-clusters-of-air-quality-data
#16
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
https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#17
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/28922427/knowledge-evolution-in-physics-research-an-analysis-of-bibliographic-coupling-networks
#18
Wenyuan Liu, Andrea Nanetti, Siew Ann Cheong
Even as we advance the frontiers of physics knowledge, our understanding of how this knowledge evolves remains at the descriptive levels of Popper and Kuhn. Using the American Physical Society (APS) publications data sets, we ask in this paper how new knowledge is built upon old knowledge. We do so by constructing year-to-year bibliographic coupling networks, and identify in them validated communities that represent different research fields. We then visualize their evolutionary relationships in the form of alluvial diagrams, and show how they remain intact through APS journal splits...
2017: PloS One
https://www.readbyqxmd.com/read/28915986/exploration-of-gender-norms-and-socialization-among-early-adolescents-the-use-of-qualitative-methods-for-the-global-early-adolescent-study
#19
REVIEW
Kristin Mmari, Robert W Blum, Rebkha Atnafou, Elisa Chilet, Sara de Meyer, Omaima El-Gibaly, Sharmistha Basu, Bamidele Bello, Beatrice Maina, Xiayun Zuo
PURPOSE: The Global Early Adolescent Study (GEAS) was launched in 2014 with the primary goal of understanding the factors in early adolescence that predispose young people to subsequent sexual risks, and conversely, those that promote healthy sexuality across different cultural contexts. The present article describes the methodology that was used for the first phase of GEAS, which consisted of conducting qualitative research to understand the gendered transitions into adolescence and the role that gender norms play within the key relationships of adolescents...
October 2017: Journal of Adolescent Health: Official Publication of the Society for Adolescent Medicine
https://www.readbyqxmd.com/read/28914494/sketching-biological-phenomena-and-mechanisms
#20
Benjamin Sheredos, William Bechtel
In many fields of biology, both the phenomena to be explained and the mechanisms proposed to explain them are commonly presented in diagrams. Our interest is in how scientists construct such diagrams. Researchers begin with evidence, typically developed experimentally and presented in data graphs. To arrive at a robust diagram of the phenomenon or the mechanism, they must integrate a variety of data to construct a single, coherent representation. This process often begins as the researchers create a first sketch, and it continues over an extended period as they revise the sketch until they arrive at a diagram they find acceptable...
September 15, 2017: Topics in Cognitive Science
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