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TOPAC: ALIGNMENT OF GENE REGULATORY NETWORKS USING TOPOLOGY-AWARE colorING

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2012年第1期10卷 1240001-1240001页

作者： Guelsoy, Guenhan Gandhi, Bhavik Kahveci, Tamer Univ Florida Comp & Informat Sci & Engn Dept Bioinformat Lab Gainesville FL 32611 USA

We consider the problem of finding a subnetwork in a given biological network (i.e. target network) that is most similar to a given small query network. We aim to find the optimal solution (i.e. the subnetwork with the largest alignment score) with a provable confidence bound. There is no known polynomial time solution to this problem in the literature. Alon et al. has developed a state-of-the-art coloring method that reduces the cost of this problem. This method randomly colors the target network prior to alignment for many iterations until a user-supplied confidence is reached. Here we develop a novel coloring method, named k-hop coloring (k is a positive integer), that achieves a provable confidence value in a small number of iterations without sacrificing the optimality. Our method considers the color assignments already made in the neighborhood of each target network node while assigning a color to a node. This way, it preemptively avoids many color assignments that are guaranteed to fail to produce the optimal alignment. We also develop a filtering method that eliminates the nodes that cannot be aligned without reducing the alignment score after each coloring instance. We demonstrate both theoretically and experimentally that our coloring method outperforms that of Alon et al., which is also used by a number network alignment methods, including QPath and QNet, by a factor of three without reducing the confidence in the optimality of the result. Our experiments also suggest that the resulting alignment method is capable of identifying functionally enriched regions in the target network successfully.

关键词： Gene regulatory networks network alignment color coding

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Three Dimension Measurement Method and its Simulation by Red-blue color Coded Structured Light

Three Dimension Measurement Method and its Simulation by Red...

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2nd International Conference on Instrumentation and Measurement, Computer, Communication and Control (IMCCC)

作者： Yu, Shuang Zhang, Jing Ren, Bin Wang, Yang Wu, Haibin Yu, Xiaoyang Harbin Engn Univ Coll Comp Sci & Technol Harbin 150001 Peoples R China

ISBN: (纸本)9780769549354

Coded structured light method was proposed for surface three dimension measurement, where two primary colors of red and blue were used to generate Gray code projecting patterns, with advantages of one unit Hamming distance and avoiding influence from the bright stripe to the dark one in grey coding. System mathematical model was established and simulation system was designed, then method and system in this paper were evaluated by simulation measurement experiments of plane and sphere. Experimental results of plane show that the maximal measuring error is less than 10mm and the maximal relative error is less than 0.8% in depth range 1200mm. Experimental results of sphere show that the maximal measuring error is less than 12mm and the maximal relative error is less than 1.0% for sphere with 170mm radius, at difference spheric center depth in range 1200mm.

关键词： three dimension measurement structured light color coding simulation

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An Algorithm for Generating color Scales for Both Categorical and Ordinal coding

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color RESEARCH AND APPLICATION 2010年第1期35卷 18-28页

作者： Breslow, Leonard A. Trafton, J. Gregory McCurry, J. Malcolm Ratwani, Raj M. USN Res Lab Washington DC 20375 USA George Mason Univ Fairfax VA 22030 USA

Previous research has shown multihue scales to be well-suited to code categorical features and shown lightness scales to be well-suited to code ordinal quanti. ties. We introduce an algorithm, Motley, that produces color scales varying in both hue and lightness, intended to be effective for both categorical and ordinal coding, allowing users to determine both absolute and relative quantities efficiently and accurately. The algorithm first determines the lightnesses of scale colors to maximize perceived lightness differences and establish the lightness ordering, generating separate search spaces for each scale position. It then selects hues by heuristic search to maximize the discriminability of the scale. It produces scales that are ordered with respect to lightness but unordered with respect to hue and thus more discriminable than typical multihue lightness scales. In an experimental evaluation on human subjects, Motley's scales enabled accurate judgments of relative quantity, with response times superior to unordered multihue scales and comparable to ordered lightness scales, and enabled accuracy and speed of judgments of absolute quantity superior to lightness scales and comparable to multihue scales. (dagger)Published 2009 Wiley Periodicals, Inc. Col Res Appl, 35, 18-28, 2010;Published online 17 November 2009 in Wiley InterScience (***). DOI 10.1002/col.20559

关键词： color coding color order systems color categorization visualizations displays computer graphics

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Bipolar cell pathways for color vision in non-primate dichromats

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VISUAL NEUROSCIENCE 2011年第1期28卷 51-60页

作者： Puller, Christian Haverkamp, Silke Max Planck Inst Brain Res Dept Neuroanat D-60528 Frankfurt Germany

color vision in mammals is based on the expression of at least two cone opsins that are sensitive to different wavelengths of light. Furthermore, retinal pathways conveying color-opponent signals are required for color discrimination. Most of the primates are trichromats, and "color-coded channels" of their retinas are unveiled to a large extent. In contrast, knowledge of cone-selective pathways in nonprimate dichromats is only slowly emerging, although retinas of dichromats like mice or rats are extensively studied as model systems for retinal information processing. Here, we review recent progress of research on color-coded pathways in nonprimate dichromats to identify differences or similarities between di- and trichromatic mammals. In addition, we applied immunohistochemical methods and confocal microscopy to retinas of different species and present data on their neuronal properties, which are expected to contribute to color vision. Basic neuronal features such as the "blue cone bipolar cell" exist in every species investigated so far. Moreover, there is increasing evidence for chromatic OFF channels in dichromats and retinal ganglion cells that relay color-opponent signals to the brain. In conclusion, di- and trichromats share similar retinal pathways for color transmission and processing.

关键词： color coding Parallel pathways Blue cone bipolar cells Horizontal cells Glutamate receptors

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Mining Protein Interactions and Gene Expression Data to Gain Insights into Drug-induced Toxicity Mechanisms

Mining Protein Interactions and Gene Expression Data to Gain...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Desai, Kaushal Brott, David Hu, Xiaohua Christianson, Anastasia Drexel Univ Coll Info Sci & Tech Philadelphia PA 19104 USA AstraZeneca Wilmington DE USA AstraZeneca Wilmington DE USA AstraZeneca Pharm Wilmington DE USA

ISBN: (纸本)9780769545745

In silico approaches for drug-induced toxicity evaluation are likely to enable improved screening of new chemical entities during drug discovery and development. Analysis of protein-protein interaction (PPI) networks using an edge centrality-based measure has previously been shown to reveal protein modules that may be associated with drug-induced toxicity. Here, we extend the algorithm by integrating protein interaction information with in vitro gene expression data from tissue treated with drugs known to be associated with the toxicity. We evaluate the new measure for its ability to detect nonimmune neutropenia related proteins and propose a biomarker panel that may be valuable for screening future drug candidates.

关键词： systems biology protein Interaction networks color coding neutropenia hotspots toxicity

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A new color coding scheme for easy polyp visualization in CT-Based virtual colonoscopy

A new color coding scheme for easy polyp visualization in CT...

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Medical Imaging 2007 Conference

作者： Chen, Dongqing Hassouna, M. Sabry Farag, Aly A. Falk, Robert Univ Louisville Dept Elect & Comp Engn Comp Vis & Image Proc Lab Louisville KY 40292 USA Vital Images Inc Minneapolis MN 55343 USA Jewish Hosp Dept Med Imaging Louisville KY 40202 USA

ISBN: (纸本)9780819466327

In this paper, we first introduce three different geometric features including shape index, curvedness and sphericity ratio, for colonic polyp detection. A new color coding scheme is designed to highlight the detected polyps, and help radiologists to distinguish them from other tissues more easily. The key idea is to place the detected polyp candidates at the same locations in a newly created polygonal dataset with exactly the same topological and geometrical properties as the triangulated mesh surface of real colon dataset, and assign different colors to the two separated datasets to highlight the polyps. Finally, we validate the proposed polyp detection framework and color coding scheme by computer simulated and real colon datasets. For sixteen synthetic polyps with different shapes and different sizes, the sensitivity is 100%, and false positive is 0.

关键词： colorectal cancer curvature-based geometric features virtual colonoscopy color coding topological and geometrical property

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Ultra-Large color Difference and Small Subtense

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color RESEARCH AND APPLICATION 2010年第1期35卷 4-17页

作者： Carter, Robert Huertas, Rafael Univ Granada Fac Ciencias Dept Opt E-18071 Granada Spain

color difference calculations are usually applied to match or tolerance of small differences between large (>2 degrees) visual fields. In contrast, we examine here the application of ultra-large color differences to enhance conspicuousness and discriminability of small (1 degrees subtense or smaller) visual targets, e.g., in visual information displays. We show that CIEDE2000, and color difference metrics based on the OSA Uniform color Space and CIECAM02 are superior to CIELAB and CIELUV. Considering gray scale only, we show that Whittle's JND metric of achromatic contrast is as good as L* for this purpose, while also modeling contrast polarity and "crispening." Furthermore, using this JND metric, we replicate Highnote's finding that elongation of small targets affects their apparent contrast. We discuss the perceived fading of color differences when targets become smaller, and suggest practical methods to mitigate the adverse effect on color conspicuousness and discriminability. (C) 2009 Wiley Periodicals, Inc. Cot Res Appl, 35, 4-17, 2010;Published online 17 November 2009 in Wiley InterScience (***). DOI 10.1002/col.20557

关键词： color difference color coding conspicuousness discriminability visual search aspect ratio contrast

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BENEFITS ANALYSIS OF A ROUTING AID FOR NEW YORK AREA DEPARTURES

BENEFITS ANALYSIS OF A ROUTING AID FOR NEW YORK AREA DEPARTU...

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29th Digital Avionics Systems Conference on Improving Our Environment through Green Avionics and ATM Solutions

作者： DeArmon, James Jackson, Claude Bateman, Hilton Song, Lixia Brown, Philip Mitre Corp Ctr Adv Aviat Syst Dev Mclean VA USA

ISBN: (纸本)9781424466177

The New York area is well-known to have some of the most congested airspace and airports in the U. S. National Airspace System (NAS). The challenge to air traffic management results from high demand, proximity of busy airports, and occasional disruptive weather events. A prototype capability called Integrated Departure Route Planning (IDRP) is being tested this year (2010), in its "Phase 1" version. It will be an adjunct capability to the Route Availability Planning Tool (RAPT), developed by the Massachusetts Institute of Technology/Lincoln Laboratory (MIT/LL), which has been used successfully in a prototype mode for several years. The IDRP display windows will be output onto the RAPT terminal device, which is now installed at the New York approach control, several en route centers, multiple towers, and several air carrier operations desks. IDRP provides a forecast horizon of fix- and route-specific loading for New York departures, with color-coding to alert traffic managers about fix congestion and possible weather impacts. Whereas the RAPT display shows route blockage/availability and is useful only in situations of convective weather, IDRP should have benefits during both good weather and convective activity. A benefits estimation process was undertaken to approximate the total annual dollar benefit that might be expected from the full deployment of IDRP (which is some years away) to deal with non-weather-related congestion. Analysis of archived data found cases where fix congestion, and the associated taxi-out delays could have been ameliorated by reassigning affected flights to uncongested alternate fixes, subject to airline acceptance.

关键词： IDRP display Massachusetts Institute of Technology-Lincoln Laboratory New York area departures RAPT display RAPT terminal device US national airspace system air traffic air traffic management aircraft displays airports airports alert traffic managers color coding integrated departure route planning nonweather related congestion route availability planning tool

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Racial Prejudice and Spending on Drug Rehabilitation: The Role of Attitudes Toward Blacks and Latinos

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Race and Social Problems 2010年第3-4期2卷 149-163页

作者： Nielsen, Amie L. Bonn, Scott Wilson, George Department of Sociology University of Miami Coral Gables FL 33124 P.O. Box 248162 United States Department of Sociology Drew University Madison NJ United States

We enhance understanding of the prejudice-induced "color coding" phenomenon among whites by determining whether racial and ethnic prejudices are associated with a previously unexplored policy outcome, spending on drug rehabilitation. We examine attitudes toward both blacks and Latinos;the latter is a group largely ignored in previous research. We assess the impact of several types of racial/ethnic views, including those that manifest modern/indirect prejudice (e. g., stereotypes about violence, individualistic causal attributions) and those that reflect social-distance-based traditional prejudice (opposition to residential proximity and to interracial marriage). These relationships are examined using data from the General Social Survey. Bivariate results support the linkage between both traditional and modern prejudice and rehabilitation spending. Logistic regression analyses also indicate that support for rehabilitation is racialized: Attributing race differences in socioeconomic outcomes to "structural" factors, namely discrimination and lack of chance for education, is associated with believing rehabilitation spending is inadequate, controlling for the effects of other racial/ethnic attitudes and background factors. The relationship between this measure of modern prejudice and the outcome is consistent with color coding. The implications of the findings are discussed, and suggestions for future research that further examine the scope of color coding are offered. © 2010 Springer Science+Business Media, LLC.

关键词： color coding Drug rehabilitation Drugs Prejudice Racism

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Comment on "Do different body colors and labels of insulin pens enhance a patient's ability to correctly identify pens for injecting long acting versus short-acting insulins?"

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Journal of diabetes science and technology 2011年第6期5卷 1627-8页

作者： Andreas Pfützner IKFE Institute for Clinical Research and Development Mainz Germany

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