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Diagrams and Visualization

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https://www.readbyqxmd.com/read/27913586/local-circuits-of-v1-layer-4b-neurons-projecting-to-v2-thick-stripes-define-distinct-cell-classes-and-avoid-cytochrome-oxidase-blobs
#1
Jeff Yarch, Frederick Federer, Alessandra Angelucci
: Decades of anatomical studies on the primate primary visual cortex (V1) have led to a detailed diagram of V1 intrinsic circuitry, but this diagram lacks information about the output targets of V1 cells. Understanding how V1 local processing relates to downstream processing requires identification of neuronal populations defined by their output targets. In primates, V1 layers (L)2/3 and 4B send segregated projections to distinct cytochrome oxidase (CO) stripes in area V2: neurons in CO blob-columns project to thin stripes, and those outside blob columns to thick and pale stripes, suggesting functional specialization of V1-to-V2 CO streams...
December 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27899612/ymdb-2-0-a-significantly-expanded-version-of-the-yeast-metabolome-database
#2
Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, An Chi Guo, Tanvir Sajed, Noah A Wishart, Naama Karu, Yannick Djoumbou Feunang, David Arndt, David S Wishart
YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896435/course-of-pelvic-lift-during-total-hip-arthroplasty
#3
Steffen Brodt, Dimitri Nowack, Linda Krakow, Christoph Windisch, Georg Matziolis
INTRODUCTION: The position of the cup makes a major contribution to the success of total hip arthroplasty (THA). In conventional implantation of the prosthesis without navigation, the surgeon relies on the spatial position of the pelvis. However, iatrogenic manipulation of the pelvis during different surgical steps constantly changes the position of the pelvis during the operation. The position of the pelvis is substantial for the correct placement of the cup. The objective of this study was to investigate and visualize the course of this pelvic lift and correlate it to certain surgical steps...
November 28, 2016: Archives of Orthopaedic and Trauma Surgery
https://www.readbyqxmd.com/read/27893370/network-visualization-as-a-higher-order-visual-analysis-tool
#4
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/27886450/comprehending-3d-diagrams-sketching-to-support-spatial-reasoning
#5
Kristin M Gagnier, Kinnari Atit, Carol J Ormand, Thomas F Shipley
Science, technology, engineering, and mathematics (STEM) disciplines commonly illustrate 3D relationships in diagrams, yet these are often challenging for students. Failing to understand diagrams can hinder success in STEM because scientific practice requires understanding and creating diagrammatic representations. We explore a new approach to improving student understanding of diagrams that convey 3D relations that is based on students generating their own predictive diagrams. Participants' comprehension of 3D spatial diagrams was measured in a pre- and post-design where students selected the correct 2D slice through 3D geologic block diagrams...
November 25, 2016: Topics in Cognitive Science
https://www.readbyqxmd.com/read/27878315/a-plasmonic-elisa-for-the-naked-eye-detection-of-chromium-ions-in-water-samples
#6
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
https://www.readbyqxmd.com/read/27875178/optimizing-hierarchical-visualizations-with-the-minimum-description-length-principle
#7
Rafael Veras, Christopher Collins
In this paper we examine how the Minimum Description Length (MDL) principle can be used to efficiently select aggregated views of hierarchical datasets that feature a good balance between clutter and information. We present MDL formulae for generating uneven tree cuts tailored to treemap and sunburst diagrams, taking into account the available display space and information content of the data. We present the results of a proof-of-concept implementation. In addition, we demonstrate how such tree cuts can be used to enhance drill-down interaction in hierarchical visualizations by implementing our approach in an existing visualization tool...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27875177/visualizing-social-media-content-with-sententree
#8
Mengdie Hu, Krist Wongsuphasawat, John Stasko
We introduce SentenTree, a novel technique for visualizing the content of unstructured social media text. SentenTree displays frequent sentence patterns abstracted from a corpus of social media posts. The technique employs design ideas from word clouds and the Word Tree, but overcomes a number of limitations of both those visualizations. SentenTree displays a node-link diagram where nodes are words and links indicate word co-occurrence within the same sentence. The spatial arrangement of nodes gives cues to the syntactic ordering of words while the size of nodes gives cues to their frequency of occurrence...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27875170/towards-unambiguous-edge-bundling-investigating-confluent-drawings-for-network-visualization
#9
Benjamin Bach, Nathalie Henry Riche, Christophe Hurter, Kim Marriott, Tim Dwyer
In this paper, we investigate Confluent Drawings (CD), a technique for bundling edges in node-link diagrams based on network connectivity. Edge-bundling techniques are designed to reduce edge clutter in node-link diagrams by coalescing lines into common paths or bundles. Unfortunately, traditional bundling techniques introduce ambiguity since edges are only bundled by spatial proximity, rather than network connectivity; following an edge from its source to its target can lead to the perception of incorrect connectivity if edges are not clearly separated within the bundles...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27875169/probabilistic-graph-layout-for-uncertain-network-visualization
#10
Christoph Schulz, Arlind Nocaj, Jochen Goertler, Oliver Deussen, Ulrik Brandes, Daniel Weiskopf
We present a novel uncertain network visualization technique based on node-link diagrams. Nodes expand spatially in our probabilistic graph layout, depending on the underlying probability distributions of edges. The visualization is created by computing a two-dimensional graph embedding that combines samples from the probabilistic graph. A Monte Carlo process is used to decompose a probabilistic graph into its possible instances and to continue with our graph layout technique. Splatting and edge bundling are used to visualize point clouds and network topology...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27875156/evaluation-of-graph-sampling-a-visualization-perspective
#11
Yanhong Wu, Nan Cao, Daniel Archambault, Qiaomu Shen, Huamin Qu, Weiwei Cui
Graph sampling is frequently used to address scalability issues when analyzing large graphs. Many algorithms have been proposed to sample graphs, and the performance of these algorithms has been quantified through metrics based on graph structural properties preserved by the sampling: degree distribution, clustering coefficient, and others. However, a perspective that is missing is the impact of these sampling strategies on the resultant visualizations. In this paper, we present the results of three user studies that investigate how sampling strategies influence node-link visualizations of graphs...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27875142/visflow-web-based-visualization-framework-for-tabular-data-with-a-subset-flow-model
#12
Bowen Yu, Claudio T Silva
Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27872857/visual-and-quantitative-analysis-methods-of-respiratory-patterns-for-respiratory-gated-pet-ct
#13
Hye Joo Son, Young Jin Jeong, Hyun Jin Yoon, Jong-Hwan Park, Do-Young Kang
We integrated visual and quantitative methods for analyzing the stability of respiration using four methods: phase space diagrams, Fourier spectra, Poincaré maps, and Lyapunov exponents. Respiratory patterns of 139 patients were grouped based on the combination of the regularity of amplitude, period, and baseline positions. Visual grading was done by inspecting the shape of diagram and classified into two states: regular and irregular. Quantitation was done by measuring standard deviation of x and v coordinates of Poincaré map (SD x , SD v ) or the height of the fundamental peak (A1) in Fourier spectrum or calculating the difference between maximal upward and downward drift...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27849543/a-benchmark-dataset-for-ssvep-based-brain-computer-interfaces
#14
Yijun Wang, Xiaogang Chen, Xiaorong Gao, Shangkai Gao
This paper presents a benchmark steady-state visual evoked potential (SSVEP) dataset acquired with a 40-target brain-computer interface (BCI) speller. The dataset consists of 64-channel Electroencephalogram (EEG) data from 35 healthy subjects (8 experienced and 27 naïve) while they performed a cue-guided target selecting task. The virtual keyboard of the speller was composed of 40 visual flickers, which were coded using a joint frequency and phase modulation (JFPM) approach. The stimulation frequencies ranged from 8Hz to 15...
November 10, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/27810865/graphical-displays-for-meta-analysis
#15
REVIEW
Amit Kiran, Abel Pérez Crespillo, Kazem Rahimi
Graphical displays play a pivotal role in understanding data sets and disseminating results. For meta-analysis, they are instrumental in presenting findings from multiple studies. This report presents guidance to authors wishing to submit graphical displays as part of their meta-analysis to a clinical cardiology journal, such as HeartWhen using graphical displays for meta-analysis, we recommend the following:▸ Use a flow diagram to describe the number of studies returned from the initial search, the inclusion/exclusion criteria applied and the final number of studies used in the meta-analysis...
November 3, 2016: Heart: Official Journal of the British Cardiac Society
https://www.readbyqxmd.com/read/27791157/commensurate-4a0-period-charge-density-modulations-throughout-the-bi2sr2cacu2o8-x-pseudogap-regime
#16
Andrej Mesaros, Kazuhiro Fujita, Stephen D Edkins, Mohammad H Hamidian, Hiroshi Eisaki, Shin-Ichi Uchida, J C Séamus Davis, Michael J Lawler, Eun-Ah Kim
Theories based upon strong real space (r-space) electron-electron interactions have long predicted that unidirectional charge density modulations (CDMs) with four-unit-cell (4a0) periodicity should occur in the hole-doped cuprate Mott insulator (MI). Experimentally, however, increasing the hole density p is reported to cause the conventionally defined wavevector QA of the CDM to evolve continuously as if driven primarily by momentum-space (k-space) effects. Here we introduce phase-resolved electronic structure visualization for determination of the cuprate CDM wavevector...
October 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27788224/quantifying-a-systems-map-network-analysis-of-a-childhood-obesity-causal-loop-diagram
#17
Jaimie McGlashan, Michael Johnstone, Doug Creighton, Kayla de la Haye, Steven Allender
Causal loop diagrams developed by groups capture a shared understanding of complex problems and provide a visual tool to guide interventions. This paper explores the application of network analytic methods as a new way to gain quantitative insight into the structure of an obesity causal loop diagram to inform intervention design. Identification of the structural features of causal loop diagrams is likely to provide new insights into the emergent properties of complex systems and analysing central drivers has the potential to identify leverage points...
2016: PloS One
https://www.readbyqxmd.com/read/27769890/concept-and-implementation-of-a-study-dashboard-module-for-a-continuous-monitoring-of-trial-recruitment-and-documentation
#18
Dennis Toddenroth, Janakan Sivagnanasundaram, Hans-Ulrich Prokosch, Thomas Ganslandt
BACKGROUND: The difficulty of managing patient recruitment and documentation for clinical trials prompts a demand for instruments for closely monitoring these critical but unpredictable processes. Increasingly adopted Electronic Data Capture (EDC) applications provide novel opportunities to reutilize stored information for an efficient management of traceable trial workflows. In related clinical and administrative settings, so-called digital dashboards that continuously visualize time-dependent parameters have recently met a growing acceptance...
October 18, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27757231/emergency-department-crowding-in-singapore-insights-from-a-systems-thinking-approach
#19
Lukas K Schoenenberger, Steffen Bayer, John P Ansah, David B Matchar, Rajagopal L Mohanavalli, Sean Sw Lam, Marcus Eh Ong
OBJECTIVES: Emergency Department crowding is a serious and international health care problem that seems to be resistant to most well intended but often reductionist policy approaches. In this study, we examine Emergency Department crowding in Singapore from a systems thinking perspective using causal loop diagramming to visualize the systemic structure underlying this complex phenomenon. Furthermore, we evaluate the relative impact of three different policies in reducing Emergency Department crowding in Singapore: introduction of geriatric emergency medicine, expansion of emergency medicine training, and implementation of enhanced primary care...
2016: SAGE Open Medicine
https://www.readbyqxmd.com/read/27752914/chemical-diversity-and-complexity-of-scotch-whisky-as-revealed-by-high-resolution-mass-spectrometry
#20
Will Kew, Ian Goodall, David Clarke, Dušan Uhrín
Scotch Whisky is an important product, both culturally and economically. Chemically, Scotch Whisky is a complex mixture, which comprises thousands of compounds, the nature of which are largely unknown. Here, we present a thorough overview of the chemistry of Scotch Whisky as observed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Eighty-five whiskies, representing the majority of Scotch Whisky produced and sold, were analyzed by untargeted high-resolution mass spectrometry. Thousands of chemical formulae were assigned for each sample based on parts-per-billion mass accuracy of FT-ICR MS spectra...
October 17, 2016: Journal of the American Society for Mass Spectrometry
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