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Visualization and Diagrams

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https://www.readbyqxmd.com/read/29280419/a-preliminary-analysis-of-incident-investigation-reports-of-an-integrated-steel-plant-some-reflection
#1
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
https://www.readbyqxmd.com/read/29258680/conditional-inference-tree-for-multiple-gene-environment-interactions-on-myocardial-infarction-among-chinese-men
#2
Zhijun Wu, Xiuxiu Su, Haihui Sheng, Yanjia Chen, Xiang Gao, Le Bao, Wei Jin
BACKGROUND AND AIMS: Identifying gene-environment interaction in the context of multiple environmental factors has been a challenging task. We aimed to use conditional inference tree (CTREE) to strata myocardial infarction (MI) risk synthesizing information from both genetic and environmental factors. METHODS: We conducted a case-control study including 1440 Chinese men (730 MI patients and 710 controls). We first calculated a weighted genetic risk score (GRS) by combining 25 single nucleotide polymorphisms (SNPs) that had been identified to be associated with coronary artery diseases in previous genome wide association studies...
December 16, 2017: Archives of Medical Research
https://www.readbyqxmd.com/read/29240126/analysis-of-long-term-visual-quality-with-numerical-3d-ray-tracing-after-corneal-crosslinking-treatment
#3
Staffan Schedin, Per Hallberg, Anders Behndig
A numerical 3D ray tracing model was used to evaluate the long-term visual effects of two regimens of corneal crosslinking (CXL) treatment of 48 patients with the corneal degeneration keratoconus. The 3D ray tracing analyses were based on corneal elevation data measured by Scheimpflug photography. Twenty-two patients were treated with standard CXL applied uniformly across the corneal surface, whereas 26 patients underwent a customized, refined treatment only at local zones on the cornea (photorefractive intrastromal CXL; PiXL)...
December 10, 2017: Applied Optics
https://www.readbyqxmd.com/read/29236906/auditory-perceptual-and-acoustic-analysis-of-voices-of-hiv-infected-children
#4
Eliane Cristina Pereira, Cristina de Oliveira Rodrigues, Kelly Cristina Alves Silvério, Glaucya Madazio, Mara Behlau
PURPOSE: To compare vocal and acoustic parameters of HIV-infected children and non-HIV-infected children. METHODS: Vocal samples were submitted to auditory-perceptual and acoustic analysis. Samples of the sustained vowel /ε/ and continuous speech of 74 children between 6 and incomplete 12 years old were analyzed, divided into two groups: 37 HIV-infected children (GHIV) and 37 non-HIV-infected children, the control group (CG), age and gender-matched and without previous vocal evaluation; they were all prepubescent by the Tanner Stages (MS, 2014)...
December 11, 2017: CoDAS
https://www.readbyqxmd.com/read/29233133/user-testing-of-an-adaptation-of-fishbone-diagrams-to-depict-results-of-systematic-reviews
#5
Gerald Gartlehner, Marie-Therese Schultes, Viktoria Titscher, Laura C Morgan, Georgiy V Bobashev, Peyton Williams, Suzanne L West
BACKGROUND: Summary of findings tables in systematic reviews are highly informative but require epidemiological training to be interpreted correctly. The usage of fishbone diagrams as graphical displays could offer researchers an effective approach to simplify content for readers with limited epidemiological training. In this paper we demonstrate how fishbone diagrams can be applied to systematic reviews and present the results of an initial user testing. METHODS: Findings from two systematic reviews were graphically depicted in the form of the fishbone diagram...
December 12, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/29216553/mathematical-quantification-of-the-induced-stress-resistance-of-microbial-populations-during-non-isothermal-stresses
#6
Alberto Garre, Juan Pablo Huertas, Gerardo A González-Tejedor, Pablo S Fernández, Jose A Egea, Alfredo Palop, Arturo Esnoz
This contribution presents a mathematical model to describe non-isothermal microbial inactivation processes taking into account the acclimation of the microbial cell to thermal stress. The model extends the log-linear inactivation model including a variable and model parameters quantifying the induced thermal resistance. The model has been tested on cells of Escherichia coli against two families of non-isothermal profiles with different constant heating rates. One of the families was composed of monophasic profiles, consisting of a non-isothermal heating stage from 35 to 70°C; the other family was composed of biphasic profiles, consisting of a non-isothermal heating stage followed by a holding period at constant temperature of 57...
November 27, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29211828/asar-visual-analysis-of-metagenomes-in-r
#7
Askarbek Orakov, Nazgul Sakenova, Anatoly Sorokin, Igor Goryanin
Motivation: Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome. Results: An interactive data analysis tool for selection, aggregation, and visualization of metagenomic data is presented...
December 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29207334/peptidenavigator-an-interactive-tool-for-exploring-large-and-complex-data-sets-generated-during-peptide-based-drug-design-projects
#8
Kyle I Diller, Alexander S Bayden, Joseph Audie, David J Diller
There is growing interest in peptide-based drug design and discovery. Due to their relatively large size, polymeric nature, and chemical complexity, the design of peptide-based drugs presents an interesting "big data" challenge. Here, we describe an interactive computational environment, PeptideNavigator, for naturally exploring the tremendous amount of information generated during a peptide drug design project. The purpose of PeptideNavigator is the presentation of large and complex experimental and computational data sets, particularly 3D data, so as to enable multidisciplinary scientists to make optimal decisions during a peptide drug discovery project...
November 24, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29194206/predictive-factors-for-visual-field-conversion-comparison-of-scanning-laser-polarimetry-and-optical-coherence-tomography
#9
Theresa Diekmann, Laura M Schrems-Hoesl, Christian Y Mardin, Robert Laemmer, Folkert K Horn, Friedrich E Kruse, Wolfgang A Schrems
PURPOSE: The purpose of this study was to compare the ability of scanning laser polarimetry (SLP) and spectral-domain optical coherence tomography (SD-OCT) to predict future visual field conversion of subjects with ocular hypertension and early glaucoma. METHODS: All patients were recruited from the Erlangen glaucoma registry and examined using standard automated perimetry, 24-hour intraocular pressure profile, and optic disc photography. Peripapillary retinal nerve fiber layer thickness (RNFL) measurements were obtained by SLP (GDx-VCC) and SD-OCT (Spectralis OCT)...
November 30, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/29166145/effect-of-background-luminance-level-on-the-assessment-of-color-visual-acuity-using-colored-landolt-rings-in-young-healthy-subjects
#10
Yoshiki Tanaka, Sho Yokoyama, Rie Horai, Takashi Kojima, Sato Hiroyuki, Yukihito Kato, Mari Takagi, Hideki Nakamura, Kiyoshi Tanaka, Kazuo Ichikawa, Shoko Tanabe
PURPOSE: To evaluate the color visual acuity (CVA) of young healthy subjects using colored Landolt rings and the effect of background luminance level on the CVA. MATERIALS AND METHODS: We measured the CVA of 20 young healthy subjects (age: 23.8 ± 3.8 years) with different colors using a computer and a liquid crystal display, with 15 Landolt ring colors (30 cd/m(2)) with a background luminance of 30 cd/m(2), and then 100 cd/m(2). We then used different background luminance levels (15-50 cd/m(2)) using four Landolt ring colors (red, green-yellow, green, and blue-green) to evaluate the effect of the background luminance level on CVA...
November 22, 2017: Current Eye Research
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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