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Visualization and Diagrams

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https://www.readbyqxmd.com/read/28922427/knowledge-evolution-in-physics-research-an-analysis-of-bibliographic-coupling-networks
#1
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
#2
REVIEW
Kristin Mmari, Robert W Blum, Rebkha Atnafou, Elisa Chilet, Sara de Meyer, Omaima El-Gibaly, Sharmista 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
#3
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
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
#4
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/28901452/screening-critical-genes-associated-with-malignant-glioma-using-bioinformatics-analysis
#5
Yonggang Xu, Jie Wang, Yanbin Xu, Hong Xiao, Jianhua Li, Zhi Wang
Malignant gliomas are high‑grade gliomas, which are derived from glial cells in the spine or brain. To examine the mechanisms underlying malignant gliomas in the present study, the expression profile of GSE54004, which included 12 grade II astrocytomas, 33 grade III astrocytomas and 98 grade IV astrocytomas, was downloaded from the Gene Expression Omnibus. Using the Limma package in R, the differentially expressed genes (DEGs) in grade III, vs. grade II astrocytoma, grade IV, vs. grade II astrocytoma, and grade IV, vs...
September 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28866584/dynamic-influence-networks-for-rule-based-models
#6
Angus G Forbes, Andrew Burks, Kristine Lee, Xing Li, Pierre Boutillier, Jean Krivine, Walter Fontana
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rulebased models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28866562/visualizing-dataflow-graphs-of-deep-learning-models-in-tensorflow
#7
Kanit Wongsuphasawat, Daniel Smilkov, James Wexler, Jimbo Wilson, Dandelion Mane, Doug Fritz, Dilip Krishnan, Fernanda B Viegas, Martin Wattenberg
We present a design study of the TensorFlow Graph Visualizer, part of the TensorFlow machine intelligence platform. This tool helps users understand complex machine learning architectures by visualizing their underlying dataflow graphs. The tool works by applying a series of graph transformations that enable standard layout techniques to produce a legible interactive diagram. To declutter the graph, we decouple non-critical nodes from the layout. To provide an overview, we build a clustered graph using the hierarchical structure annotated in the source code...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28866561/graphiti-interactive-specification-of-attribute-based-edges-for-network-modeling-and-visualization
#8
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/28866521/how-do-ancestral-traits-shape-family-trees-over-generations
#9
Siwei Fu, Hao Dong, Weiwei Cui, Jian Zhao, Huamin Qu
Whether and how does the structure of family trees differ by ancestral traits over generations? This is a fundamental question regarding the structural heterogeneity of family trees for the multi-generational transmission research. However, previous work mostly focuses on parent-child scenarios due to the lack of proper tools to handle the complexity of extending the research to multi-generational processes. Through an iterative design study with social scientists and historians, we develop TreeEvo that assists users to generate and test empirical hypotheses for multi-generational research...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28866520/a-virtual-reality-visualization-tool-for-neuron-tracing
#10
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/28866506/bubble-treemaps-for-uncertainty-visualization
#11
Jochen Gortler, Christoph Schulz, Daniel Weiskopf, Oliver Deussen
We present a novel type of circular treemap, where we intentionally allocate extra space for additional visual variables. With this extended visual design space, we encode hierarchically structured data along with their uncertainties in a combined diagram. We introduce a hierarchical and force-based circle-packing algorithm to compute Bubble Treemaps, where each node is visualized using nested contour arcs. Bubble Treemaps do not require any color or shading, which offers additional design choices. We explore uncertainty visualization as an application of our treemaps using standard error and Monte Carlo-based statistical models...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28866503/the-topology-toolkit
#12
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/28829333/phase-current-absorbance-and-photoluminescence-of-double-and-triple-metal-ion-doped-synthetic-and-salmon-dna-thin-films
#13
Prathamesh Chopade, Sreekantha Reddy Dugasani, Mallikarjuna Reddy Kesama, Sanghyun Yoo, Bramaramba Gnapareddy, Yun Woo Lee, Sohee Jeon, Jun-Ho Jeong, Sung Ha Park
We fabricated synthetic double-crossover (DX) DNA lattices and natural salmon DNA (SDNA) thin films, doped with 3 combinations of double divalent metal ions (M(2+))-doped groups (Co(2+)-Ni(2+), Cu(2+)-Co(2+), and Cu(2+)-Ni(2+)) and single combination of a triple M(2+)-doped group (Cu(2+)-Ni(2+)-Co(2+)) at various concentrations of M(2+) ([M(2+)]). We evaluated the optimum concentration of M(2+) ([M(2+)]O) (the phase of M(2+)-doped DX DNA lattices changed from crystalline (up to ([M(2+)]O) to amorphous (above [M(2+)]O)) and measured the current, absorbance, and photoluminescent characteristics of multiple M(2+)-doped SDNA thin films...
August 22, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28815488/exploring-vaccine-hesitancy-through-an-artist-scientist-collaboration-visualizing-vaccine-critical-parents-health-beliefs
#14
Kaisu Koski, Johan Holst
This project explores vaccine hesitancy through an artist-scientist collaboration. It aims to create better understanding of vaccine hesitant parents' health beliefs and how these influence their vaccine-critical decisions. The project interviews vaccine-hesitant parents in the Netherlands and Finland and develops experimental visual-narrative means to analyse the interview data. Vaccine-hesitant parents' health beliefs are, in this study, expressed through stories, and they are paralleled with so-called illness narratives...
August 16, 2017: Journal of Bioethical Inquiry
https://www.readbyqxmd.com/read/28796770/what-is-the-relationship-between-visual-impairment-and-cognitive-function-in-octogenarians
#15
COMPARATIVE STUDY
Denise S de Kok, Ruth O Teh, Avinesh Pillai, Martin J Connolly, Tim J Wilkinson, Simon A Moyes, Robert Jacobs, Marama Muru-Lanning, Anna Rolleston, Dieuwke Schiphof, Ngaire Kerse
AIMS: To examine direct and indirect pathways between visual and cognitive function in advanced age. METHODS: We analysed cross-sectional baseline data from Life and Living in Advanced Age: A Cohort Study in New Zealand, which recruited equal sample sizes of Māori (n=421) and non-Māori (n=516) octogenarians. The Modified Mini-Mental State Examination assessed cognitive function. Vision was assessed with self-report and measured distance visual acuity. Associations between visual and cognitive function were explored using general linear models and structural equation modelling...
August 11, 2017: New Zealand Medical Journal
https://www.readbyqxmd.com/read/28789690/first-year-medical-students-learning-style-preferences-and-their-correlation-with-performance-in-different-subjects-within-the-medical-course
#16
Daniel Hernández-Torrano, Syed Ali, Chee-Kai Chan
BACKGROUND: Students commencing their medical training arrive with different educational backgrounds and a diverse range of learning experiences. Consequently, students would have developed preferred approaches to acquiring and processing information or learning style preferences. Understanding first-year students' learning style preferences is important to success in learning. However, little is understood about how learning styles impact learning and performance across different subjects within the medical curriculum...
August 8, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/28783447/topological-relations-between-objects-are-categorically-coded
#17
Andrew Lovett, Steven L Franconeri
How do individuals compare images-for example, two graphs or diagrams-to identify differences between them? We argue that categorical relations between objects play a critical role. These relations divide continuous space into discrete categories, such as "above" and "below," or "containing" and "overlapping," which are remembered and compared more easily than precise metric values. These relations should lead to categorical perception, such that viewers find it easier to notice a change that crosses a category boundary (one object is now above, rather than below, another, or now contains, rather than overlaps with, another) than a change of equal magnitude that does not cross a boundary...
August 1, 2017: Psychological Science
https://www.readbyqxmd.com/read/28759655/synthesis-and-thermodynamic-properties-of-arsenate-and-sulfate-arsenate-ettringite-structure-phases
#18
Weixing Wang, Yan Shao, Haobo Hou, Min Zhou
Arsenic is a toxic and carcinogenic contaminant of potential concern. Ettringite [Ca6Al2(SO4)3(OH)12·26H2O] has the ability to incorporate oxyanions as a solid solution with SO42-, which could lower the soluble oxyanion concentrations. Therefore, ettringite containing SO42- and AsO43- has been synthesized. Results indicated that AsO43- could substitute for SO42- inside the channels of ettringite in the form of HAsO42-, and a linear correlation existed between Xinitial solution and Xsolid. The thermodynamic characterization of the solid samples was investigated by means of Visual MINTEQ, a freeware chemical equilibrium model, and the solubility product logK of -48...
2017: PloS One
https://www.readbyqxmd.com/read/28738824/visibiome-an-efficient-microbiome-search-engine-based-on-a-scalable-distributed-architecture
#19
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/28732642/performance-of-the-phonatory-deviation-diagram-in-the-evaluation-of-rough-and-breathy-synthesized-voices
#20
Leonardo Wanderley Lopes, Jonas Almeida de Freitas, Anna Alice Almeida, Priscila Oliveira Costa Silva, Giorvan Ânderson Dos Santos Alves
INTRODUCTION: Voice disorders alter the sound signal in several ways, combining several types of vocal emission disturbances and noise. The Phonatory Deviation Diagram (PDD) is a two-dimensional chart that allows the evaluation of the vocal signal based on the combination of periodicity (jitter, shimmer, and correlation coefficient) and noise (Glottal to Noise Excitation - GNE) measurements. The use of synthesized signals, where one has a greater control and knowledge of the production conditions, may allow a better understanding of the physiological and acoustic mechanisms underlying the vocal emission and its main perceptual-auditory correlates regarding the intensity of the deviation and types of vocal quality...
July 5, 2017: Brazilian Journal of Otorhinolaryngology
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