WorldWideScience

Sample records for profile plot integrating

  1. Reaction Order Ambiguity in Integrated Rate Plots

    Science.gov (United States)

    Lee, Joe

    2008-01-01

    Integrated rate plots are frequently used in reaction kinetics to determine orders of reactions. It is often emphasised, when using this methodology in practice, that it is necessary to monitor the reaction to a substantial fraction of completion for these plots to yield unambiguous orders. The present article gives a theoretical and statistical…

  2. FERMI/GLAST Integrated Trending and Plotting System Release 5.0

    Science.gov (United States)

    Ritter, Sheila; Brumer, Haim; Reitan, Denise

    2012-01-01

    An Integrated Trending and Plotting System (ITPS) is a trending, analysis, and plotting system used by space missions to determine performance and status of spacecraft and its instruments. ITPS supports several NASA mission operational control centers providing engineers, ground controllers, and scientists with access to the entire spacecraft telemetry data archive for the life of the mission, and includes a secure Web component for remote access. FERMI/GLAST ITPS Release 5.0 features include the option to display dates (yyyy/ddd) instead of orbit numbers along orbital Long-Term Trend (LTT) plot axis, the ability to save statistics from daily production plots as image files, and removal of redundant edit/create Input Definition File (IDF) screens. Other features are a fix to address invalid packet lengths, a change in naming convention of image files in order to use in script, the ability to save all ITPS plot images (from Windows or the Web) as GIF or PNG format, the ability to specify ymin and ymax on plots where previously only the desired range could be specified, Web interface capability to plot IDFs that contain out-oforder page and plot numbers, and a fix to change all default file names to show yyyydddhhmmss time stamps instead of hhmmssdddyyyy. A Web interface capability sorts files based on modification date (with newest one at top), and the statistics block can be displayed via a Web interface. Via the Web, users can graphically view the volume of telemetry data from each day contained in the ITPS archive in the Web digest. The ITPS could be also used in nonspace fields that need to plot data or trend data, including financial and banking systems, aviation and transportation systems, healthcare and educational systems, sales and marketing, and housing and construction.

  3. SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases

    Science.gov (United States)

    Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.

    2017-10-01

    SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.

  4. Image files of PCR data plotted on the FACS profiles - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plab...earch . Data file File name: planaria_facs_profile.zip File URL: http://togodb.biosciencedbc.jp/togodb/view/plab...d License Update History of This Database Site Policy | Contact Us Image files of PCR data plotted on the FACS profiles - Plabrain DB | LSDB Archive ...

  5. [Cost-effectiveness analysis of integrated control strategy of parasitic diseases in demonstration plots].

    Science.gov (United States)

    Ying-Dan, Chen; Ju-Jun, Wang; Wei, Zang; Men-Bao, Qian; Long-Qi, Xu

    2011-10-01

    To study the cost-effectiveness of different deworming schemes in demonstration plots of integrated control of parasitic diseases. The cost-effectiveness was analyzed between mass drug administration and drug administration to focal population according to the different infection rates of parasites. In the demonstration plots of soil-born nematodes control, the costs for reducing one infected case and the cost for reducing 1% infection rate per ten thousand people in mass drug administration groups (Group 1 and Group 2) and drug administration to focal population were 20.73, 14.42 Yuan and 14.33 Yuan, and 1 700.49, 1 503.19 Yuan and 145.41 Yuan, respectively. In the demonstration plots of control of clonorchiasis sinensis, the costs for reducing one infected case and the cost for reducing 1% infection rate per ten thousand people in mass drug administration group and drug administration to focal population were 31.03 Yuan and 37.01 Yuan, and 3 115.10 Yuan and 3841.38 Yuan, respectively. The multiple effectiveness indexes for control of soil-transmitted nematodes in the mass drug administration groups (Group 1 and Group 2) and drug administration to focal population were 76.72, 80.27 and 97.64, respectively. The multiple effectiveness indexes for control of clonorchiasis sinensis in the mass drug administration group and the drug administration to focal population group were 112.93 and 65.49, respectively. We should choose the deworming schemes not only to get a great reduction of human parasite infection rate and a rapid effective reduction of the source of infection, but also to make a full use of the limited funds on target population.

  6. European Vegetation Archive (EVA): an integrated database of European vegetation plots

    DEFF Research Database (Denmark)

    Chytrý, M; Hennekens, S M; Jiménez-Alfaro, B

    2015-01-01

    The European Vegetation Archive (EVA) is a centralized database of European vegetation plots developed by the IAVS Working Group European Vegetation Survey. It has been in development since 2012 and first made available for use in research projects in 2014. It stores copies of national and regional...... data source for large-scale analyses of European vegetation diversity both for fundamental research and nature conservation applications. Updated information on EVA is available online at http://euroveg.org/eva-database....

  7. Plot 3

    DEFF Research Database (Denmark)

    Lund, Inger-Lise; Gjessing, Susanne; Hermansen, Anne-Mette

    Plot 3 er første udgivelse af et alsidigt dansksystem til mellemtrinnet, hvor digitale medier er integreret i den daglige undervisning.......Plot 3 er første udgivelse af et alsidigt dansksystem til mellemtrinnet, hvor digitale medier er integreret i den daglige undervisning....

  8. DEVELOPMENT OF AN INTEGRATED AIR POLLUTION MAPS ON KEY PLOT OF KRASNOYARSK REGION

    Directory of Open Access Journals (Sweden)

    E. A. Bozhilina

    2016-01-01

    Full Text Available The paper suggested the construction of a comprehensive air pollution map as an example of the key area of the Krasnoyarsk Territory. To create a map developed an original technique for limiting emissions spread zones in the atmosphere from industrial plants near the cities on the basis of climatic data. The proposed method is based on taking into account the repeatability wind speed and direction and length of time of pollutants in the atmosphere. The used methods of cartographic representation – quantitative background (emissions per unit area within the zones of the potential spread of contaminants, localized diagrams (emissions and air pollution index for the city, contour lines (the value of air pollution potential. Using an integrated map allows you to specify the impact of the transfer of pollutants in the formation of the level of pollution in the city, together with the volumes and values of emissions of air pollution potential.

  9. Computer program TRACK_TEST for calculating parameters and plotting profiles for etch pits in nuclear track materials

    Science.gov (United States)

    Nikezic, D.; Yu, K. N.

    2006-01-01

    A computer program called TRACK_TEST for calculating parameters (lengths of the major and minor axes) and plotting profiles in nuclear track materials resulted from light-ion irradiation and subsequent chemical etching is described. The programming steps are outlined, including calculations of alpha-particle ranges, determination of the distance along the particle trajectory penetrated by the chemical etchant, calculations of track coordinates, determination of the lengths of the major and minor axes and determination of the contour of the track opening. Descriptions of the program are given, including the built-in V functions for the two commonly employed nuclear track materials commercially known as LR 115 (cellulose nitrate) and CR-39 (poly allyl diglycol carbonate) irradiated by alpha particles. Program summaryTitle of the program:TRACK_TEST Catalogue identifier:ADWT Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWT Computer:Pentium PC Operating systems:Windows 95+ Programming language:Fortran 90 Memory required to execute with typical data:256 MB No. of lines in distributed program, including test data, etc.: 2739 No. of bytes in distributed program, including test data, etc.:204 526 Distribution format:tar.gz External subprograms used:The entire code must be linked with the MSFLIB library Nature of problem: Fast heavy charged particles (like alpha particles and other light ions etc.) create latent tracks in some dielectric materials. After chemical etching in aqueous NaOH or KOH solutions, these tracks become visible under an optical microscope. The growth of a track is based on the simultaneous actions of the etchant on undamaged regions (with the bulk etch rate V) and along the particle track (with the track etch rate V). Growth of the track is described satisfactorily by these two parameters ( V and V). Several models have been presented in the past describing

  10. Plot 4

    DEFF Research Database (Denmark)

    Lund, Inger-Lise; Hermansen, Anne-Mette; Ferdinand, Trine

    Danskfaglig vejledning informerer om de tanker, der ligger til grund for Plot 4, og beskriver danskfaget ud fra nyere forskning inden for fagets mange delområder. Kapitelvejledning introducerer bogens tekster, forklarer hensigten med kapitlernes opgaver, giver forslag til undervisningen og brugen...

  11. Plot 5

    DEFF Research Database (Denmark)

    Lund, Inger-Lise; Hermansen, Anne-Mette; Ferdinand, Trine

    Danskfaglig vejledning informerer om de tanker, der ligger til grund for Plot 5, og beskriver danskfaget ud fra nyere forskning inden for fagets mange delområder. Kapitelvejledning introducerer bogens tekster, forklarer hensigten med kapitlernes opgaver, giver forslag til undervisningen og brugen...

  12. Complexity Plots

    KAUST Repository

    Thiyagalingam, Jeyarajan

    2013-06-01

    In this paper, we present a novel visualization technique for assisting the observation and analysis of algorithmic complexity. In comparison with conventional line graphs, this new technique is not sensitive to the units of measurement, allowing multivariate data series of different physical qualities (e.g., time, space and energy) to be juxtaposed together conveniently and consistently. It supports multivariate visualization as well as uncertainty visualization. It enables users to focus on algorithm categorization by complexity classes, while reducing visual impact caused by constants and algorithmic components that are insignificant to complexity analysis. It provides an effective means for observing the algorithmic complexity of programs with a mixture of algorithms and black-box software through visualization. Through two case studies, we demonstrate the effectiveness of complexity plots in complexity analysis in research, education and application. © 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and Blackwell Publishing Ltd.

  13. Integrating field plots, lidar, and landsat time series to provide temporally consistent annual estimates of biomass from 1990 to present

    Science.gov (United States)

    Warren B. Cohen; Hans-Erik Andersen; Sean P. Healey; Gretchen G. Moisen; Todd A. Schroeder; Christopher W. Woodall; Grant M. Domke; Zhiqiang Yang; Robert E. Kennedy; Stephen V. Stehman; Curtis Woodcock; Jim Vogelmann; Zhe Zhu; Chengquan. Huang

    2015-01-01

    We are developing a system that provides temporally consistent biomass estimates for national greenhouse gas inventory reporting to the United Nations Framework Convention on Climate Change. Our model-assisted estimation framework relies on remote sensing to scale from plot measurements to lidar strip samples, to Landsat time series-based maps. As a demonstration, new...

  14. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. Contact : gorodkin@cbs.dtu.dk...

  15. Integration of seismic reflection and geologically balanced profiles; Integration reflexionsseismischer und geologisch bilanzierter Profile

    Energy Technology Data Exchange (ETDEWEB)

    Lambrecht, A. [Trappe Erdoel Erdgas Consultant, Isernhagen (Germany)

    1998-12-31

    Geophysics and geology employ different kinds of techniques in order to preserve the underground structure. These techniques are based on different sets of data, i.e. seismic or geological data. A sensible combination of the two techniques should produce a better model of the ground structure. This study attempts to integrate geologically balanced profiles and seismic reflection data. A balanced geological profile can than be compared with seismic reflection data measured in the field. The geological model is then changed into a seismic model of the underground by means of seismic modeling. Synthetic modeling is based on the acquisition of available field data. The synthetic stack section or the synthetic migration image are then compared to the field data. Deviations between the two can be attributed to speed errors and the fact that balances will never give an unequivocal solution but always present a group of solutions. (orig. MSK). [Deutsch] In der Geophysik und der Geologie werden verschiedene Techniken verwendet, um die Untergrundstruktur zu erhalten. Diese Techniken basieren auf verschiedenen Datensaetzen, z.B. seismische und geologische Daten. Eine sinnvolle Kombination der Techniken sollte ein besseres Abbild des Untergrundes liefern. In dieser Studie wird ein Versuch unternommen geologisch bilanzierte Profile und reflexionsseismische Daten zu integrieren. Soll ein bilanziertes geologisches Profil mit im Feld gemessenen reflexionsseismischen Daten verglichen werden, dann wird das geologische Modell mit Hilfe der seismischen Modellierung in ein seismisches Abbild des Untergrundes verwandelt. Dabei wird die synthetische Modellierung entsprechend der Aquisition der vorliegenden Felddaten durchgefuehrt. Die synthetische Stapelsektion oder das synthetische Migrationsimage werden anschliessend mit den Felddaten verglichen. Abweichungen zwischen beobachteten und Felddaten haben ihre Ursachen sowohl in Geschwindigkeitsfehlern, als auch in der Tatsache, dass eine

  16. Moving Toward Integrating Gene Expression Profiling into ...

    Science.gov (United States)

    Microarray profiling of chemical-induced effects is being increasingly used in medium and high-throughput formats. In this study, we describe computational methods to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally-diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through ChIP-Seq analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression data sets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including “very weak” agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals,

  17. Profil Antisipasi Siswa SMA Dalam Memecahkan Masalah Integral

    Directory of Open Access Journals (Sweden)

    Erfan Yudianto

    2015-06-01

    Full Text Available Penelitian ini dilatarbelakangi oleh sulitnya siswa dalam menyelesaikan masalah integral khusunya luas daerah. Banyak siswa hanya menyelesaikan masalah integral hanya berdasarkan rumus yang sudah disediakan. Siswa jarang mengaitkan konsep-konsep yang saling terkait, dalam hal ini konsep integral subpokokbahasan luas daerah.Tujuan penelitian ini untuk mendeskripsikan Profil antisipasi siswa SMA dalam memecahkan masalah integral. Hasil penelitian ini dapat dimanfaatkan oleh guru untuk membantu siswa mengaitkan konsep-konsep yang belum terkait.  Penelitian ini menggunakan metode tes dan wawancara. Tes berupa  tes kemampuan matematika yang diberikan kepada siswa, sehingga diperoleh siswa berkemampuan tinggi dan wawancara diberikan kepada siswa yang bersangkutan untuk menggali dan melihat jaringan konsep yang dimiliki siswa dalam menyelesaikan masalah integral. Subjek dalam penelitian ini termasuk dalam antisipasi terinternasilsasi dikarenakan siswa secara spontan menerapkan rumus integral tanpa menganalisis soal yang diberikan.This research is motivated by the difficulty of students in solving integral problems especially the area. Many students just completed the integral problems just based on a formula that has been provided. Students rarely associate the concepts are interrelated, in this case the integral concept of the area. The purpose of this study was to describe the profile anticipation of high school students in problem solving integrals. The results could be used by teachers to help students link the concepts are not related. This study uses tests and interviews. The tests such as math skills test given to students, in order to obtain a high ability students and interviews given to the student to explore and see the network concept of the students in problem solving integrals. Subjects in this study are included in anticipation terinternasilsasi because students spontaneously apply the integral formula without analyzing the questions

  18. The Practice Integration Profile: Rationale, development, method, and research.

    Science.gov (United States)

    Macchi, C R; Kessler, Rodger; Auxier, Andrea; Hitt, Juvena R; Mullin, Daniel; van Eeghen, Constance; Littenberg, Benjamin

    2016-12-01

    Insufficient knowledge exists regarding how to measure the presence and degree of integrated care. Prior estimates of integration levels are neither grounded in theory nor psychometrically validated. They provide scant guidance to inform improvement activities, compare integration efforts, discriminate among practices by degree of integration, measure the effect of integration on quadruple aim outcomes, or address the needs of clinicians, regulators, and policymakers seeking new models of health care delivery and funding. We describe the development of the Practice Integration Profile (PIP), a novel instrument designed to measure levels of integrated behavioral health care within a primary care clinic. The PIP draws upon the Agency for Health care Research & Quality's (AHRQ) Lexicon of Collaborative Care which provides theoretic justification for a paradigm case of collaborative care. We used the key clauses of the Lexicon to derive domains of integration and generate measures corresponding to those key clauses. After reviewing currently used methods for identifying collaborative care, or integration, and identifying the need to improve on them, we describe a national collaboration to describe and evaluate the PIP. We also describe its potential use in practice improvement, research, responsiveness to multiple stakeholder needs, and other future directions. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  19. A parameter optimization tool for evaluating the physical consistency of the plot-scale water budget of the integrated eco-hydrological model GEOtop in complex terrain

    Science.gov (United States)

    Bertoldi, Giacomo; Cordano, Emanuele; Brenner, Johannes; Senoner, Samuel; Della Chiesa, Stefano; Niedrist, Georg

    2017-04-01

    In mountain regions, the plot- and catchment-scale water and energy budgets are controlled by a complex interplay of different abiotic (i.e. topography, geology, climate) and biotic (i.e. vegetation, land management) controlling factors. When integrated, physically-based eco-hydrological models are used in mountain areas, there are a large number of parameters, topographic and boundary conditions that need to be chosen. However, data on soil and land-cover properties are relatively scarce and do not reflect the strong variability at the local scale. For this reason, tools for uncertainty quantification and optimal parameters identification are essential not only to improve model performances, but also to identify most relevant parameters to be measured in the field and to evaluate the impact of different assumptions for topographic and boundary conditions (surface, lateral and subsurface water and energy fluxes), which are usually unknown. In this contribution, we present the results of a sensitivity analysis exercise for a set of 20 experimental stations located in the Italian Alps, representative of different conditions in terms of topography (elevation, slope, aspect), land use (pastures, meadows, and apple orchards), soil type and groundwater influence. Besides micrometeorological parameters, each station provides soil water content at different depths, and in three stations (one for each land cover) eddy covariance fluxes. The aims of this work are: (I) To present an approach for improving calibration of plot-scale soil moisture and evapotranspiration (ET). (II) To identify the most sensitive parameters and relevant factors controlling temporal and spatial differences among sites. (III) Identify possible model structural deficiencies or uncertainties in boundary conditions. Simulations have been performed with the GEOtop 2.0 model, which is a physically-based, fully distributed integrated eco-hydrological model that has been specifically designed for mountain

  20. Low profile, low cost, new geometry integrated inductors

    DEFF Research Database (Denmark)

    Ouyang, Ziwei; Thomsen, Ole Cornelius; Andersen, Michael A. E.

    2011-01-01

    A new geometry of integrated inductors with low profile and low cost is presented in this paper. The new geometry integrates two inductors by stacking three I-cores. The middle I-core provides a shared low reluctance flux path. The air gaps are formed by separating the I-cores using copper foil w...... digital applications. Experiment results obtained from a 48V-12V 30A two-phase interleaved bidirectional DC/DC converter, demonstrates the characteristic of new geometry and difference between inverse coupling and direct coupling....... windings with well-defined thickness. Many advantages and disadvantages are described in depth. In this work, inverse coupling and direct coupling in the new geometry integrated inductors have been analyzed. Coupling characteristic caused by a special saturation behavior has been emphasis. And also...

  1. GlobPlot

    DEFF Research Database (Denmark)

    Linding, Rune; Russell, Robert B; Neduva, Victor

    2003-01-01

    are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http://globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples...... with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional...... N- or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome...

  2. Difference and ratio plots

    DEFF Research Database (Denmark)

    Svendsen, Anders Jørgen; Holmskov, U; Bro, Peter

    1995-01-01

    hitherto unnoted differences between controls and patients with either rheumatoid arthritis or systemic lupus erythematosus. For this we use simple, but unconventional, graphic representations of the data, based on difference plots and ratio plots. Differences between patients with Burkitt's lymphoma...... and systemic lupus erythematosus from another previously published study (Macanovic, M. and Lachmann, P.J. (1979) Clin. Exp. Immunol. 38, 274) are also represented using ratio plots. Our observations indicate that analysis by regression analysis may often be misleading....

  3. Two-region mass transfer to account for 2D profile scale heterogeneity in a 1D effective plot scale flow model

    Science.gov (United States)

    Filipovic, Vilim; Coquet, Yves; Gerke, Horst H.

    2017-04-01

    In arable soil landscapes, specific spatial heterogeneities related to tillage and trafficking can influence the movement of water and chemicals. The structure in the topsoil is characterized by spatial patterns with locally compacted zones. The contrasting hydraulic properties of more-and-less compacted soil zones can result in heterogeneous flow fields and preferential flow. Two- or three-dimensional models used to account for soil spatial variability are relatively too complex when trying to include local heterogeneities in the description of field scale flow and transport problems. The idea was to reduce the model complexity linked to the explicit description of heterogeneities in 2D or 3D without deteriorating the validity of simulation results. When reducing the spatial dimensionality, the geometry in a 2D, cross-sectional explicit plot description is removed on the expense of an increased complexity of the 1D model with two flow domains and mass exchange between them. Our objective was to design a simplified 1D model approach that effectively accounts for plot-scale soil structural variability. In this simplified 1D model, effective soil hydraulic parameters can be assigned to each of the two domains separately. Different theoretical scenarios simulating different shape, size and arrangement of compacted clods in the tilled layer were set to estimate their effect on solute behaviour. The mass exchange parameters could be determined from structure quantification and by comparing simplified 1D with reference 2D results accounting for defined soil structural (i.e., here the compacted regions) geometries. The mass exchange is strongly related to the geometry of the compacted zones including their distribution and size within the non-compacted soil. Additionally, the simplified model approach was tested by comparing it with measured results from a field tracer experiment.

  4. Distributed plot-making

    DEFF Research Database (Denmark)

    Jensen, Lotte Groth; Bossen, Claus

    2016-01-01

    different socio-technical systems (paper-based and electronic patient records). Drawing on the theory of distributed cognition and narrative theory, primarily inspired by the work done within health care by Cheryl Mattingly, we propose that the creation of overview may be conceptualised as ‘distributed plot......-making’. Distributed cognition focuses on the role of artefacts, humans and their interaction in information processing, while narrative theory focuses on how humans create narratives through the plot construction. Hence, the concept of distributed plot-making highlights the distribution of information processing...... between different social actors and artefacts, as well as the filtering, sorting and ordering of such information into a narrative that is made coherent by a plot. The analysis shows that the characteristics of paper-based and electronic patient records support or obstruct the creation of overview in both...

  5. BoxPlot++

    OpenAIRE

    Azmeh, Zeina; Hamoui, Fady; Huchard, Marianne

    2011-01-01

    We propose the BoxPlot++ as an extension of Tukey's boxplot. We improve the resulting data values distribution by removing the repeated values and by calculating distances between the points and the nearest median.

  6. Multiple plots in R

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon

    2012-01-01

    In this chapter I will investigate how to combine multiple plots into a single. The scenario is a dataset of a series of measurements, on three samples in three situations. There are many ways we can display this, e.g. 3d graphs or faceting. 3d graphs are not good for displaying static data so we...... will not go there. Faceting is strictly speaking for plotting all variable / classes against each other....

  7. Density Distribution Sunflower Plots

    Directory of Open Access Journals (Sweden)

    William D. Dupont

    2003-01-01

    Full Text Available Density distribution sunflower plots are used to display high-density bivariate data. They are useful for data where a conventional scatter plot is difficult to read due to overstriking of the plot symbol. The x-y plane is subdivided into a lattice of regular hexagonal bins of width w specified by the user. The user also specifies the values of l, d, and k that affect the plot as follows. Individual observations are plotted when there are less than l observations per bin as in a conventional scatter plot. Each bin with from l to d observations contains a light sunflower. Other bins contain a dark sunflower. In a light sunflower each petal represents one observation. In a dark sunflower, each petal represents k observations. (A dark sunflower with p petals represents between /2-pk k and /2+pk k observations. The user can control the sizes and colors of the sunflowers. By selecting appropriate colors and sizes for the light and dark sunflowers, plots can be obtained that give both the overall sense of the data density distribution as well as the number of data points in any given region. The use of this graphic is illustrated with data from the Framingham Heart Study. A documented Stata program, called sunflower, is available to draw these graphs. It can be downloaded from the Statistical Software Components archive at http://ideas.repec.org/c/boc/bocode/s430201.html . (Journal of Statistical Software 2003; 8 (3: 1-5. Posted at http://www.jstatsoft.org/index.php?vol=8 .

  8. Plot Description (PD)

    Science.gov (United States)

    Robert E. Keane

    2006-01-01

    The Plot Description (PD) form is used to describe general characteristics of the FIREMON macroplot to provide ecological context for data analyses. The PD data characterize the topographical setting, geographic reference point, general plant composition and cover, ground cover, fuels, and soils information. This method provides the general ecological data that can be...

  9. Integrated work-flow for quantitative metabolome profiling of plants, Peucedani Radix as a case.

    Science.gov (United States)

    Song, Yuelin; Song, Qingqing; Liu, Yao; Li, Jun; Wan, Jian-Bo; Wang, Yitao; Jiang, Yong; Tu, Pengfei

    2017-02-08

    Universal acquisition of reliable information regarding the qualitative and quantitative properties of complicated matrices is the premise for the success of metabolomics study. Liquid chromatography-mass spectrometry (LC-MS) is now serving as a workhorse for metabolomics; however, LC-MS-based non-targeted metabolomics is suffering from some shortcomings, even some cutting-edge techniques have been introduced. Aiming to tackle, to some extent, the drawbacks of the conventional approaches, such as redundant information, detector saturation, low sensitivity, and inconstant signal number among different runs, herein, a novel and flexible work-flow consisting of three progressive steps was proposed to profile in depth the quantitative metabolome of plants. The roots of Peucedanum praeruptorum Dunn (Peucedani Radix, PR) that are rich in various coumarin isomers, were employed as a case study to verify the applicability. First, offline two dimensional LC-MS was utilized for in-depth detection of metabolites in a pooled PR extract namely universal metabolome standard (UMS). Second, mass fragmentation rules, notably concerning angular-type pyranocoumarins that are the primary chemical homologues in PR, and available databases were integrated for signal assignment and structural annotation. Third, optimum collision energy (OCE) as well as ion transition for multiple monitoring reaction measurement was online optimized with a reference compound-free strategy for each annotated component and large-scale relative quantification of all annotated components was accomplished by plotting calibration curves via serially diluting UMS. It is worthwhile to highlight that the potential of OCE for isomer discrimination was described and the linearity ranges of those primary ingredients were extended by suppressing their responses. The integrated workflow is expected to be qualified as a promising pipeline to clarify the quantitative metabolome of plants because it could not only

  10. Distributed plot-making

    DEFF Research Database (Denmark)

    Jensen, Lotte Groth; Bossen, Claus

    2016-01-01

    similar and distinct ways. In the light of the current move towards electronic patient records, we explore the ways in which the benefits of paper records may be carried over into the electronic patient record as well as the ways in which the possibilities afforded by digital artefacts may be exploited...... different socio-technical systems (paper-based and electronic patient records). Drawing on the theory of distributed cognition and narrative theory, primarily inspired by the work done within health care by Cheryl Mattingly, we propose that the creation of overview may be conceptualised as ‘distributed plot...... between different social actors and artefacts, as well as the filtering, sorting and ordering of such information into a narrative that is made coherent by a plot. The analysis shows that the characteristics of paper-based and electronic patient records support or obstruct the creation of overview in both...

  11. Plot til lyst

    DEFF Research Database (Denmark)

    Sandvik, Kjetil

    Den velfungerende krimi faciliterer denne dobbelte plotlæsning ved at muliggøre en særlig form for legende og udforskende interaktion mellem læser og plot: Ved at lægge spor ud og holde tolkningsmuligheder og løsningsmuligheder åbne får vi mulighed for at påtage os og udføre opklaringsarbejdet side......, der inviterer os med ind i selve handlingens rum og forløb og giver os forskellige handlingsmuligheder i forhold til disse. I bogen omtales denne særlige form for plot for forlystelsesplot med henvisning til forlystelsesparken og den særlige form for interaktiv fortælleform, som vi finder der: en...

  12. The Half-Half Plot

    NARCIS (Netherlands)

    Einmahl, J.H.J.; Gantner, M.

    2009-01-01

    The Half-Half (HH) plot is a new graphical method to investigate qualitatively the shape of a regression curve. The empirical HH-plot counts observations in the lower and upper quarter of a strip that moves horizontally over the scatter plot. The plot displays jumps clearly and reveals further

  13. matplotlib plotting cookbook

    CERN Document Server

    Devert, Alexandre

    2014-01-01

    This book follows a cookbook style approach that puts orthogonal and non-redundant recipes in your hands. Rather than rehashing the user manual, the explanations expose the underlying logic behind Matplotlib. If you are an engineer or scientist who wants to create great visualizations with Python, rather than yet another specialized language, this is the book for you. While there are several very competent plotting packages, Matplotlib is ""just"" a Python module. Thus, if you know some Python already, you will feel at home from the first steps on. In case you are an application writer, you wo

  14. Plotting Gothic: A Paradox

    Directory of Open Access Journals (Sweden)

    Stephen Murray

    2014-06-01

    Full Text Available The paradox of the title is that while most historians of medieval architecture agree that a combination of geometric and arithmetic methods was generally used to lay out a medieval church, there has been little consensus on the specifics of the process in relation to the design of any particular edifice. I begin by identifying four premises which underlie the debate. I then ask whether the new technologies — laser scanning and computer assisted design/drafting applications — can help. A case study uses newly generated point cloud data from a laser scan of the choir of Beauvais Cathedral. Finally, the notion of ‘plotting’ introduces essential sociological, anthropological and rhetorical dimensions. In the spirit of Roland Barthes ('Le plaisir du texte' and Peter Brooks ('Reading for the Plot', we can understand the urgency with which the architectural historian may seek to unscramble the hidden codes of the building as compulsive ‘reading for the plot’.

  15. The half-half plot

    NARCIS (Netherlands)

    Einmahl, J.H.J.; Gantner, M.

    2012-01-01

    The Half-Half (HH) plot is a new graphical method to investigate qualitatively the shape of a regression curve. The empirical HH-plot counts observations in the lower and upper quarter of a strip that moves horizontally over the scatterplot. The plot displays jumps clearly and reveals further

  16. Retroviral integration profiles: their determinants and implications for gene therapy

    Directory of Open Access Journals (Sweden)

    Kwang-il Lim

    2012-04-01

    Full Text Available Retroviruses have often been used for gene therapy because oftheir capacity for the long-term expression of transgenes via stableintegration into the host genome. However, retroviral integrationcan also result in the transformation of normal cells into cancercells, as demonstrated by the incidence of leukemia in a recentretroviral gene therapy trial in Europe. This unfortunate outcomehas led to the rapid initiation of studies examining variousbiological and pathological aspects of retroviral integration. Thisreview summarizes recent findings from these studies, includingthe global integration patterns of various types of retroviruses,viral and cellular determinants of integration, implications ofintegration for gene therapy and retrovirus-mediated infectiousdiseases, and strategies to shift integration to safe host genomicloci. A more comprehensive and mechanistic understanding ofretroviral integration processes will eventually make it possible togenerate safer retroviral vector platforms in the near future. [BMBreports 2012; 45(4: 207-212

  17. Two-dimensional box plot

    OpenAIRE

    Phattrawan Tongkumchum

    2005-01-01

    In this paper we propose a two-dimensional box plot, a simple bivariate extension of the box plot and the scatter plot. This plot comprises a pair of trapeziums oriented in the direction of a fitted straight line, with symbols denoting extreme values. The choice for the fitted straight resistant line showing the relationship between the two variables is Tukey’s resistance line. The main components of the plot are an inner box containing 50% of the projection points of the observations on the ...

  18. BPMO HISTOS plots

    Energy Technology Data Exchange (ETDEWEB)

    Clendenin, J.; Williams, S.

    1983-08-23

    Early experience (1981-1982) with jittery position measurements in the CID (Collider Injector Development) and Sector 1 BPM (beam position monitor) system led us to ask whether the source of the observed noise was in the beam or in the BPM electronics. Prior to July, 1983, the signal from each BPM strip was individually processed. It occurred to us that the signal from each strip, when normalized by the sum of the signals from the two adjacent strips, made possible two independent measurements of the beam position in the plane containing the strip. When a single parameter is measured twice, one can look at the correlation of the measurements over a statistical sample of events. This will allow one to distinguish real parameter variations from measurement errors. In this case, a strong correlation in the two measurements from a given strip indicates beam jitter, whereas a lack of correlation indicates either that there is beam jitter in the normalizing plane or that the processing electronics is noisy in at least one channel. The five possible cases are illustrated. These plots are interpreted.

  19. Profiling Patients’ Healthcare Needs to Support Integrated, Person-Centered Models for Long-Term Disease Management (Profile: Research Design

    Directory of Open Access Journals (Sweden)

    Arianne MJ Elissen

    2016-04-01

    Full Text Available Background: This article presents the design of PROFILe, a study investigating which (biomedical and non-(biomedical patient characteristics should guide more tailored chronic care. Based on this insight, the project aims to develop and validate ‘patient profiles’ that can be used in practice to determine optimal treatment strategies for subgroups of chronically ill with similar healthcare needs and preferences. Methods/Design: PROFILe is a practice-based research comprising four phases. The project focuses on patients with type 2 diabetes. During the first study phase, patient profiles are drafted based on a systematic literature research, latent class growth modeling, and expert collaboration. In phase 2, the profiles are validated from a clinical, patient-related and statistical perspective. Phase 3 involves a discrete choice experiment to gain insight into the patient preferences that exist per profile. In phase 4, the results from all analyses are integrated and recommendations formulated on which patient characteristics should guide tailored chronic care. Discussion: PROFILe is an innovative study which uses a uniquely holistic approach to assess the healthcare needs and preferences of chronically ill. The patient profiles resulting from this project must be tested in practice to investigate the effects of tailored management on patient experience, population health and costs.

  20. Computer-Integrated Manufacturing Technology. Tech Prep Competency Profile.

    Science.gov (United States)

    Lakeland Tech Prep Consortium, Kirtland, OH.

    This tech prep competency profile covers these occupations: manufacturing technician, computer-assisted design and drafting (CADD) technician, quality technician, and mechanical technician. Section 1 provides occupation definitions. Section 2 lists development committee members. Section 3 provides the leveling codes---abbreviations for grade level…

  1. Temporal profiles of response enhancement in multisensory integration

    Directory of Open Access Journals (Sweden)

    Benjamin A Rowland

    2008-12-01

    Full Text Available Animals have evolved multiple senses that transduce different forms of energy as a way of increasing their sensitivity to environmental events. Each sense provides a unique and independent perspective on the world, and very often a single event stimulates several of them. In order to make best use of the available information, the brain has also evolved the capacity to integrate information across the senses (“multisensory integration”. This facilitates the detection, localization, and identification of a given event, and has obvious survival value for the individual and the species. Multisensory responses in the superior colliculus (SC evidence shorter latencies and are more robust at their onset. This is the phenomenon of initial response enhancement in multisensory integration, which is believed to a real time fusion of information across the senses. The present paper reviews two recent reports describing how the timing and robustness of sensory responses changes as a consequence of multisensory integration in the model system of the SC.

  2. Box-and-Whisker Plots.

    Science.gov (United States)

    Larsen, Russell D.

    1985-01-01

    Box-and-whisker plots (which give rapid visualization of batches of data) can be effectively used to present diverse collections of data used in traditional first-year chemistry courses. Construction of box-and-whisker plots and their use with bond energy data and data on heats of formation and solution are discussed. (JN)

  3. S2PLOT: Three-dimensional (3D) Plotting Library

    Science.gov (United States)

    Barnes, D. G.; Fluke, C. J.; Bourke, P. D.; Parry, O. T.

    2011-03-01

    We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - S2PLOT - is written in C and can be used by C, C++ and FORTRAN programs on GNU/Linux and Apple/OSX systems. S2PLOT draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a PGPLOT inspired interface, S2PLOT provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The S2PLOT architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce S2PLOT to the astronomical community, describe its potential applications, and present some example uses of the library.

  4. Trellis plots as visual aids for analyzing split plot experiments

    DEFF Research Database (Denmark)

    Kulahci, Murat; Menon, Anil

    2017-01-01

    The analysis of split plot experiments can be challenging due to a complicated error structure resulting from restrictions on complete randomization. Similarly, standard visualization methods do not provide the insight practitioners desire to understand the data, think of explanations, generate...... hypotheses, build models, or decide on next steps. This article demonstrates the effective use of trellis plots in the preliminary data analysis for split plot experiments to address this problem. Trellis displays help to visualize multivariate data by allowing for conditioning in a general way. They can...

  5. A new method to identify the foot of continental slope based on an integrated profile analysis

    Science.gov (United States)

    Wu, Ziyin; Li, Jiabiao; Li, Shoujun; Shang, Jihong; Jin, Xiaobin

    2017-06-01

    A new method is proposed to identify automatically the foot of the continental slope (FOS) based on the integrated analysis of topographic profiles. Based on the extremum points of the second derivative and the Douglas-Peucker algorithm, it simplifies the topographic profiles, then calculates the second derivative of the original profiles and the D-P profiles. Seven steps are proposed to simplify the original profiles. Meanwhile, multiple identification methods are proposed to determine the FOS points, including gradient, water depth and second derivative values of data points, as well as the concave and convex, continuity and segmentation of the topographic profiles. This method can comprehensively and intelligently analyze the topographic profiles and their derived slopes, second derivatives and D-P profiles, based on which, it is capable to analyze the essential properties of every single data point in the profile. Furthermore, it is proposed to remove the concave points of the curve and in addition, to implement six FOS judgment criteria.

  6. Integration profile and safety of an adenovirus hybrid-vector utilizing hyperactive sleeping beauty transposase for somatic integration.

    Directory of Open Access Journals (Sweden)

    Wenli Zhang

    Full Text Available We recently developed adenovirus/transposase hybrid-vectors utilizing the previously described hyperactive Sleeping Beauty (SB transposase HSB5 for somatic integration and we could show stabilized transgene expression in mice and a canine model for hemophilia B. However, the safety profile of these hybrid-vectors with respect to vector dose and genotoxicity remains to be investigated. Herein, we evaluated this hybrid-vector system in C57Bl/6 mice with escalating vector dose settings. We found that in all mice which received the hyperactive SB transposase, transgene expression levels were stabilized in a dose-dependent manner and that the highest vector dose was accompanied by fatalities in mice. To analyze potential genotoxic side-effects due to somatic integration into host chromosomes, we performed a genome-wide integration site analysis using linker-mediated PCR (LM-PCR and linear amplification-mediated PCR (LAM-PCR. Analysis of genomic DNA samples obtained from HSB5 treated female and male mice revealed a total of 1327 unique transposition events. Overall the chromosomal distribution pattern was close-to-random and we observed a random integration profile with respect to integration into gene and non-gene areas. Notably, when using the LM-PCR protocol, 27 extra-chromosomal integration events were identified, most likely caused by transposon excision and subsequent transposition into the delivered adenoviral vector genome. In total, this study provides a careful evaluation of the safety profile of adenovirus/Sleeping Beauty transposase hybrid-vectors. The obtained information will be useful when designing future preclinical studies utilizing hybrid-vectors in small and large animal models.

  7. The spatio-temporal profile of multisensory integration.

    Science.gov (United States)

    Starke, Johanna; Ball, Felix; Heinze, Hans-Jochen; Noesselt, Toemme

    2017-10-23

    Task-irrelevant visual stimuli can enhance auditory perception. However, while there is some neurophysiological evidence for mechanisms that underlie the phenomenon, the neural basis of visually induced effects on auditory perception remains unknown. Combining fMRI and EEG with psychophysical measurements in two independent studies, we identified the neural underpinnings and temporal dynamics of visually induced auditory enhancement. Lower- and higher-intensity sounds were paired with a non-informative visual stimulus, while participants performed an auditory detection task. Behaviourally, visual co-stimulation enhanced auditory sensitivity. Using fMRI, enhanced BOLD signals were observed in primary auditory cortex for low-intensity audiovisual stimuli which scaled with subject-specific enhancement in perceptual sensitivity. Concordantly, a modulation of event-related potentials could already be observed over frontal electrodes at an early latency (30-80 ms), which again scaled with subject-specific behavioural benefits. Later modulations starting around 280 ms, that is in the time range of the P3, did not fit this pattern of brain-behaviour correspondence. Hence, the latency of the corresponding fMRI-EEG brain-behaviour modulation points at an early interplay of visual and auditory signals in low-level auditory cortex, potentially mediated by crosstalk at the level of the thalamus. However, fMRI signals in primary auditory cortex, auditory thalamus and the P50 for higher-intensity auditory stimuli were also elevated by visual co-stimulation (in the absence of any behavioural effect) suggesting a general, intensity-independent integration mechanism. We propose that this automatic interaction occurs at the level of the thalamus and might signify a first step of audiovisual interplay necessary for visually induced perceptual enhancement of auditory perception. © 2017 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  8. Numerical computation of Pop plot

    Energy Technology Data Exchange (ETDEWEB)

    Menikoff, Ralph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-03-23

    The Pop plot — distance-of-run to detonation versus initial shock pressure — is a key characterization of shock initiation in a heterogeneous explosive. Reactive burn models for high explosives (HE) must reproduce the experimental Pop plot to have any chance of accurately predicting shock initiation phenomena. This report describes a methodology for automating the computation of a Pop plot for a specific explosive with a given HE model. Illustrative examples of the computation are shown for PBX 9502 with three burn models (SURF, WSD and Forest Fire) utilizing the xRage code, which is the Eulerian ASC hydrocode at LANL. Comparison of the numerical and experimental Pop plot can be the basis for a validation test or as an aid in calibrating the burn rate of an HE model. Issues with calibration are discussed.

  9. Box Plots: Basic and Advanced.

    Science.gov (United States)

    Mullenex, James L.

    1990-01-01

    Describes a five-number summary which is a display of the minimum value, lower quartile, median, upper quartile, and maximum value. Indicates how to draw box plots as graphical representations of a five-number summary. (YP)

  10. Plotting Orbital Trajectories For Maneuvers

    Science.gov (United States)

    Brody, Adam R.

    1991-01-01

    Interactive Orbital Trajectory Planning Tool (EIVAN) computer program is forward-looking interactive orbit-trajectory-plotting software tool for use with proximity operations (operations occurring within 1-km sphere of space station) and other maneuvers. Developed to plot resulting trajectories, to provide better comprehension of effects of orbital mechanics, and to help user develop heuristics for planning missions on orbit. Program runs with Microsoft's Excel for execution on MacIntosh computer running MacIntosh OS.

  11. Normal probability plots with confidence.

    Science.gov (United States)

    Chantarangsi, Wanpen; Liu, Wei; Bretz, Frank; Kiatsupaibul, Seksan; Hayter, Anthony J; Wan, Fang

    2015-01-01

    Normal probability plots are widely used as a statistical tool for assessing whether an observed simple random sample is drawn from a normally distributed population. The users, however, have to judge subjectively, if no objective rule is provided, whether the plotted points fall close to a straight line. In this paper, we focus on how a normal probability plot can be augmented by intervals for all the points so that, if the population distribution is normal, then all the points should fall into the corresponding intervals simultaneously with probability 1-α. These simultaneous 1-α probability intervals provide therefore an objective mean to judge whether the plotted points fall close to the straight line: the plotted points fall close to the straight line if and only if all the points fall into the corresponding intervals. The powers of several normal probability plot based (graphical) tests and the most popular nongraphical Anderson-Darling and Shapiro-Wilk tests are compared by simulation. Based on this comparison, recommendations are given in Section 3 on which graphical tests should be used in what circumstances. An example is provided to illustrate the methods. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Integration based profile likelihood calculation for PDE constrained parameter estimation problems

    Science.gov (United States)

    Boiger, R.; Hasenauer, J.; Hroß, S.; Kaltenbacher, B.

    2016-12-01

    Partial differential equation (PDE) models are widely used in engineering and natural sciences to describe spatio-temporal processes. The parameters of the considered processes are often unknown and have to be estimated from experimental data. Due to partial observations and measurement noise, these parameter estimates are subject to uncertainty. This uncertainty can be assessed using profile likelihoods, a reliable but computationally intensive approach. In this paper, we present the integration based approach for the profile likelihood calculation developed by (Chen and Jennrich 2002 J. Comput. Graph. Stat. 11 714-32) and adapt it to inverse problems with PDE constraints. While existing methods for profile likelihood calculation in parameter estimation problems with PDE constraints rely on repeated optimization, the proposed approach exploits a dynamical system evolving along the likelihood profile. We derive the dynamical system for the unreduced estimation problem, prove convergence and study the properties of the integration based approach for the PDE case. To evaluate the proposed method, we compare it with state-of-the-art algorithms for a simple reaction-diffusion model for a cellular patterning process. We observe a good accuracy of the method as well as a significant speed up as compared to established methods. Integration based profile calculation facilitates rigorous uncertainty analysis for computationally demanding parameter estimation problems with PDE constraints.

  13. Thermal integrity profiling for augered cast-in-place piles - implementation plan.

    Science.gov (United States)

    2017-08-01

    This study was the second in a two-part research program focused on assessing the feasibility of using thermal integrity profiling (TIP) as a quality assurance tool for Augered Cast-In-Place (ACIP) piles. This was made possible by coordinating with t...

  14. Device- and service profiles for integrated or systems based on open standards

    Directory of Open Access Journals (Sweden)

    Mildner Alexander

    2015-09-01

    Full Text Available Integrated OR systems nowadays are closed and proprietary, so that the interconnection of components from third-party vendors is only possible with high time and cost effort. An integrated operating theatre with open interfaces, giving clinical operators the opportunity to choose individual medical devices from different manufacturers, is currently being developed in the framework of the BMBF (Federal Ministry of Education and Research funded project OR.NET [1]. Actual standards and concepts regarding technical feasibility and accreditation process do not cope with the requirements for modular integration based on an open standard. Therefore, strategies as well as service and device profiles to enable a procedure for risk management and certifiability are in the focus of the project work. Amongst others, a concept for User Interface Profiles (UI-Profiles has been conceived in order to describe medical device functions and the entire user interface regarding Human-Machine-Interaction (HMI characteristics with the aim to identify human-induced risks of central user interfaces. The use of standardized device and service profiles shall allow the manufacturers to integrate their medical devices in the OR.NET network, without disclosing the medical devices’ risk analysis and related confidential knowledge or proprietary information.

  15. Uncertainty of Integrated Intensity Following Line Profile Fitting of Multiline Spectra.

    Science.gov (United States)

    Surmick, David M; Boukari, Hacene; Woodward, Jonathan; Stowe, Ashley C; Melikechi, Noureddine

    2018-01-01

    A novel method of determining the total uncertainty in the integrated intensity of fitted emission lines in multipeaked emission spectra is presented. The proposed method does not require an assumption of the type of line profile to be specified. The absolute difference between a fit and measured spectrum defines the uncertainty of the integrated signal intensity and is subsequently decomposed to determine the uncertainty of each peak in multiline fits. Decomposition relies on tabulating a weighting factor, which describes how each peak contributes to the total integral uncertainty. Applications of this method to quantitative approaches in laser-induced breakdown spectroscopy analysis are described.

  16. High throughput gene expression profiling: a molecular approach to integrative physiology

    Science.gov (United States)

    Liang, Mingyu; Cowley, Allen W; Greene, Andrew S

    2004-01-01

    Integrative physiology emphasizes the importance of understanding multiple pathways with overlapping, complementary, or opposing effects and their interactions in the context of intact organisms. The DNA microarray technology, the most commonly used method for high-throughput gene expression profiling, has been touted as an integrative tool that provides insights into regulatory pathways. However, the physiology community has been slow in acceptance of these techniques because of early failure in generating useful data and the lack of a cohesive theoretical framework in which experiments can be analysed. With recent advances in both technology and analysis, we propose a concept of multidimensional integration of physiology that incorporates data generated by DNA microarray and other functional, genomic, and proteomic approaches to achieve a truly integrative understanding of physiology. Analysis of several studies performed in simpler organisms or in mammalian model animals supports the feasibility of such multidimensional integration and demonstrates the power of DNA microarray as an indispensable molecular tool for such integration. Evaluation of DNA microarray techniques indicates that these techniques, despite limitations, have advanced to a point where the question-driven profiling research has become a feasible complement to the conventional, hypothesis-driven research. With a keen sense of homeostasis, global regulation, and quantitative analysis, integrative physiologists are uniquely positioned to apply these techniques to enhance the understanding of complex physiological functions. PMID:14678487

  17. Hypothetical Outcome Plots Outperform Error Bars and Violin Plots for Inferences about Reliability of Variable Ordering.

    Directory of Open Access Journals (Sweden)

    Jessica Hullman

    Full Text Available Many visual depictions of probability distributions, such as error bars, are difficult for users to accurately interpret. We present and study an alternative representation, Hypothetical Outcome Plots (HOPs, that animates a finite set of individual draws. In contrast to the statistical background required to interpret many static representations of distributions, HOPs require relatively little background knowledge to interpret. Instead, HOPs enables viewers to infer properties of the distribution using mental processes like counting and integration. We conducted an experiment comparing HOPs to error bars and violin plots. With HOPs, people made much more accurate judgments about plots of two and three quantities. Accuracy was similar with all three representations for most questions about distributions of a single quantity.

  18. Hypothetical Outcome Plots Outperform Error Bars and Violin Plots for Inferences about Reliability of Variable Ordering.

    Science.gov (United States)

    Hullman, Jessica; Resnick, Paul; Adar, Eytan

    2015-01-01

    Many visual depictions of probability distributions, such as error bars, are difficult for users to accurately interpret. We present and study an alternative representation, Hypothetical Outcome Plots (HOPs), that animates a finite set of individual draws. In contrast to the statistical background required to interpret many static representations of distributions, HOPs require relatively little background knowledge to interpret. Instead, HOPs enables viewers to infer properties of the distribution using mental processes like counting and integration. We conducted an experiment comparing HOPs to error bars and violin plots. With HOPs, people made much more accurate judgments about plots of two and three quantities. Accuracy was similar with all three representations for most questions about distributions of a single quantity.

  19. Action Between Plot and Discourse

    DEFF Research Database (Denmark)

    Grünbaum, Thor

    2007-01-01

    , these narrated actions disrupt the theoretical divisions, on the one hand, between the narrated story and the narrating discourse, and on the other hand, between plot-narratology and discourse-narratology. As narrated actions, they seem to belong to the domain of plot-narratology, but insofar as they serve...... an important visualizing function, these narrated actions have a communicative function and, as such, they can be said to belong to the domain of discourse-narratology. In the first part of the article, I argue that a certain type of plot-narratology, due to its retrospective epistemology and abstract...... definition of action, is unable to conceive of this visualizing function. In the second part, I argue that discourse-narratology fares no better since the visualizing function is independent of voice and focalization. In the final part, I sketch a possible account of the visualizing function of simple...

  20. Integration of ALS and TLS for calibration and validation of LAI profiles from large footprint lidar

    Science.gov (United States)

    Armston, J.; Tang, H.; Hancock, S.; Hofton, M. A.; Dubayah, R.; Duncanson, L.; Fatoyinbo, T. E.; Blair, J. B.; Disney, M.

    2016-12-01

    The Global Ecosystem Dynamics Investigation (GEDI) is designed to provide measurements of forest vertical structure and above-ground biomass density (AGBD) over tropical and temperate regions. The GEDI is a multi-beam waveform lidar that will acquire transects of forest canopy vertical profiles in conditions of up to 99% canopy cover. These are used to produce a number of canopy height and profile metrics to model habitat suitability and AGBD. These metrics include vertical leaf area index (LAI) profiles, which require some pre-launch refinement of large-footprint waveform processing methods for separating canopy and ground returns and estimation of their reflectance. Previous research developments in modelling canopy gap probability to derive canopy and ground reflectance from waveforms have primarily used data from small-footprint instruments, however development of a generalized spatial model with uncertainty will be useful for interpreting and modelling waveforms from large-footprint instruments such as the NASA Land Vegetation and Ice Sensor (LVIS) with a view to implementation for GEDI. Here we present an analysis of waveform lidar data from the NASA Land Vegetation and Ice Sensor (LVIS), which were acquired in Gabon in February 2016 to support the NASA/ESA AfriSAR campaign. AfriSAR presents a unique opportunity to test refined methods for retrieval of LAI profiles in high above-ground biomass rainforests (up to 600 Mg/ha) with dense canopies (>90% cover), where the greatest uncertainty exists. Airborne and Terrestrial Laser Scanning data (TLS) were also collected, enabling quantification of algorithm performance in plots of dense canopy cover. Refinement of canopy gap probability and LAI profile modelling from large-footprint lidar was based on solving for canopy and ground reflectance parameters spatially by penalized least-squares. The sensitivities of retrieved cover and LAI profiles to variation in canopy and ground reflectance showed improvement

  1. HRR Profiling on Integrated Radar-Communication Systems Using OFDM-PCSF Signals

    Directory of Open Access Journals (Sweden)

    Xuanxuan Tian

    2017-01-01

    Full Text Available In order to improve both the transmission data rate and the range resolution simultaneously in integrated radar-communication (RadCom systems, orthogonal frequency-division multiplexing with phase-coded and stepped-frequency (OFDM-PCSF waveform is proposed. A corresponding high resolution range (HRR profile generation method is also presented. We first perform OFDM-PCSF waveform design by combining the intrapulse phase coding with the interpulse stepped-frequency modulation. We then give the ambiguity function (AF based on the presented waveforms. Then, the synthetic range profile (SRP processing to achieve HRR performance is analyzed. Theoretical analysis and simulation results show that the proposed methods can achieve HRR profiles of the targets and high data rate transmissions, while a relative low computational complexity can be achieved.

  2. Ontology-based Integration of Web Navigation for Dynamic User Profiling

    Directory of Open Access Journals (Sweden)

    Anett HOPPE

    2015-01-01

    Full Text Available The development of technology for handling information on a Big Data-scale is a buzzing topic of current research. Indeed, improved techniques for knowledge discovery are crucial for scientific and economic exploitation of large-scale raw data. In research collaboration with an industrial actor, we explore the applicability of ontology-based knowledge extraction and representation for today's biggest source of large-scale data, the Web. The goal is to develop a profil-ing application, based on the implicit information that every user leaves while navigating the online, with the goal to identify and model preferences and interests in a detailed user profile. This includes the identification of current tendencies as well as the prediction of possible future interests, as far as they are deducible from the collected browsing information, and integrated expert domain knowledge. The article at hand gives an overview on the current state of the research, the developments made and insights gained.

  3. Aluminum integral foams with tailored density profile by adapted blowing agents

    Science.gov (United States)

    Hartmann, Johannes; Fiegl, Tobias; Körner, Carolin

    2014-05-01

    The goal of the present work is the variation of the structure of aluminum integral foams regarding the thickness of the integral solid skin as well as the density profile. A modified die casting process, namely integral foam molding, is used in which an aluminum melt and blowing agent particles (magnesium hydride MgH2) are injected in a permanent steel mold. The high solidification rates at the cooled walls of the mold lead to the formation of a solid skin. In the inner region, hydrogen is released by thermal decomposition of MgH2 particles. Thus, the pore formation takes place parallel to the continuing solidification of the melt. The thickness of the solid skin and the density profile of the core strongly depend on the interplay between solidification velocity and kinetics of hydrogen release. By varying the melt and blowing agent properties, the structure of integral foams can be systematically changed to meet the requirements of the desired field of application of the produced component.

  4. The Box-Percentile Plot

    OpenAIRE

    Esty, Warren W.; Jeff Banfield

    2003-01-01

    A variant of the boxplot is proposed in which the sides contain the information of a percentile plot (which is equivalent to the empirical cumulative distribution function). Unlike boxplots, there is no question about how long to draw the whiskers, nor is there loss of information due to grouping. Side-by-side comparisons of distributions are especially effective. In spite of including more detail, the impact on statistically-untrained readers remains similar to that of traditional boxplots.

  5. Convergence of Place and Plot

    DEFF Research Database (Denmark)

    Sandvik, Kjetil

    2010-01-01

    efterladt sig en række mærker og spor som kan læses og fortolkes. Blodspor, rester af negle, hår udgør forskellige (DNA)koder som kan dekrypteres og dechifreres på samme måde som krudtslam, skudhuller, fysiske skader er tegn som skal læses og fortolkes. Som sådan rummer stedet et plot (en fortælling) som...

  6. The forest inventory and analysis plot design

    Science.gov (United States)

    William Bechtold; Charles T. Scott

    2005-01-01

    This chapter describes the prescribed core plot2 design currently used by Forest Inventory and Analysis (FIA) for Phase 2 and Phase 3 ground sampling. FIA ground plots relate to the sampling frame discussed in the previous chapter as follows: One plot has been randomly located within each 6,000-acre hexagon. Each plot has been assigned to one of five panels as...

  7. Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry.

    Science.gov (United States)

    Souda, Puneet; Ryan, Christopher M; Cramer, William A; Whitelegge, Julian

    2011-12-01

    Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein's native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electron-capture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Model Predictive Control with Integral Action for Current Density Profile Tracking in NSTX-U

    Science.gov (United States)

    Ilhan, Z. O.; Wehner, W. P.; Schuster, E.; Boyer, M. D.

    2016-10-01

    Active control of the toroidal current density profile may play a critical role in non-inductively sustained long-pulse, high-beta scenarios in a spherical torus (ST) configuration, which is among the missions of the NSTX-U facility. In this work, a previously developed physics-based control-oriented model is embedded in a feedback control scheme based on a model predictive control (MPC) strategy to track a desired current density profile evolution specified indirectly by a desired rotational transform profile. An integrator is embedded into the standard MPC formulation to reject various modeling uncertainties and external disturbances. Neutral beam powers, electron density, and total plasma current are used as actuators. The proposed MPC strategy incorporates various state and actuator constraints directly into the control design process by solving a constrained optimization problem in real-time to determine the optimal actuator requests. The effectiveness of the proposed controller in regulating the current density profile in NSTX-U is demonstrated in closed-loop nonlinear simulations. Supported by the US DOE under DE-AC02-09CH11466.

  9. Chiral Ramachandran Plots I: Glycine.

    Science.gov (United States)

    Baruch-Shpigler, Yael; Wang, Huan; Tuvi-Arad, Inbal; Avnir, David

    2017-10-24

    Ramachandran plots (RPs) map the wealth of conformations of the polypeptide backbone and are widely used to characterize protein structures. A limitation of the RPs is that they are based solely on two dihedral angles for each amino acid residue and provide therefore only a partial picture of the conformational richness of the protein. Here we extend the structural RP analysis of proteins from a two-dimensional (2D) map to a three-dimensional map by adding the quantitative degree of chirality-the continuous chirality measure (CCM)-of the amino acid residue at each point in the RP. This measure encompasses all bond angles and bond lengths of an amino acid residue. We focus in this report on glycine (Gly) because, due to its flexibility, it occupies a large portion of the 2D map, thus allowing a detailed study of the chirality measure, and in order to evaluate the justification of classically labeling Gly as the only achiral amino acid. We have analyzed in detail 4366 Gly residues extracted from high resolution crystallographic data of 160 proteins. This analysis reveals not only that Gly is practically always conformationally chiral, but that upon comparing with the backbone of all amino acids, the quantitative chirality values of Gly are of similar magnitudes to those of the (chiral) amino acids. Structural trends and energetic considerations are discussed in detail. Generally we show that adding chirality to Ramachandran plots creates far more informative plots that highlight the sensitivity of the protein structure to minor conformational changes.

  10. AUTOMATED TECHNIQUE FOR CREATING LITHOLOGIC LOG PLOTS

    Directory of Open Access Journals (Sweden)

    Kristijan Posavec

    2006-12-01

    Full Text Available Paper presents automated technique for creating lithologic log plots. Technique is based on three computer tools: Microsoft (MS Access program, LogPlot program, and Visual Basic (VB macros for MS Excel. MS Access ensures professional storage of lithologic data which can be in that way easier and faster entered, searched, updated, and also used for different purposes, while LogPlot provides tools for creating lithologic log plots. VB macros enable transfer of lithologic data from MS Access to LogPlot. Data stored in MS Access are exported in ASCII files which are later used by LogPlot for creation of lithologic log plots. Presented concept facilitates creation of lithologic log plots, and automated technique enables processing of a large number of data i.e. creation of lareg number lithologic log plots in a short period of time (the paper is published in Croatian.

  11. Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification

    DEFF Research Database (Denmark)

    Hauschild, A.C.; Baumbach, Jan; Baumbach, J.

    2012-01-01

    as from 35 healthy volunteers, comprising a control group (CG). We standardized and integrated several statistical learning methods to provide a broad overview of their potential for distinguishing the patient groups. We found that there is strong potential for separating MCC/IMS chromatograms of healthy...... patients from healthy controls. We conclude that these statistical learning methods have a generally high accuracy when applied to well-structured, medical MCC/IMS data....... in every day practice. However, the potential of this methodology depends on successful application of computational approaches for finding relevant VOCs and classification of patients into disease-specific profile groups based on the detected VOCs. We developed an integrated state-of-the-art system using...

  12. ANALYZING THE CONSUMER PROFILING FOR IMPROVING EFFORTS OF INTEGRATED MARKETING COMMUNICATION

    Directory of Open Access Journals (Sweden)

    Olimpia OANCEA

    2014-06-01

    Full Text Available In an economy with a strong concurential character, organizations must capitalize the integrated marketing communication in the most effective way, to ensure the creation and maintenance of long-term relationships with current and potential customers. Building and managing the relationships with customers can have a direct and favourable effect on the efficiency of an organization's communication efforts. The integrated marketing communication identifies with the nowadays market dynamics and learns the organizations how easy can be to prosper in an environment where changes occur in an alarming way. Therefore, the purpose of this paper is to analyze the socio-demographic profile of the consumers of bread in Arges County, as well as the preferences and purchasing behaviour at the level of the market segments identified using the K-Means Cluster Analysis method.

  13. ACTRIS aerosol vertical profile data and observations: potentiality and first examples of integrated studies with models

    Science.gov (United States)

    Mona, Lucia; Benedetti, Angela; D'Amico, Giuseppe; Myhre, Cathrine Lund; Schulz, Michael; Wandinger, Ulla; Laj, Paolo; Pappalardo, Gelsomina

    2016-04-01

    The ACTRIS-2 project, funded by Horizon 2020, addresses the scope of integrating state-of-the-art European ground-based stations for long term observations of aerosols, clouds and short lived gases, capitalizing on the work of FP7-ACTRIS. It aims at achieving the construction of a user-oriented RI, unique in the EU-RI landscape for providing 4-D integrated high-quality data from near-surface to high altitude (vertical profiles and total-column) which are relevant to climate and air-quality research. ACTRIS-2 develops and implements, in a large network of stations in Europe and beyond, observational protocols that permit the harmonization of collected data and their dissemination. ACTRIS secures provision and dissemination of a unique set of data and data-products that would not otherwise be available with the same level of quality and standardization. This results from a 10-year plus effort in constructing a research infrastructure capable of responding to community needs and requirements, and has been engaged since the start of the FP5 EU commission program. ACTRIS ensures compliance with reporting requirements (timing, format, traceability) defined by the major global observing networks. EARLINET (European Aerosol research Lidar NETwork), the aerosol vertical profiling component of ACTRIS, is providing since May 2000 vertical profiles of aerosol extinction and backscatter over Europe. A new structure of the EARLINET database has been designed in a more user oriented approach reporting new data products which are more effective for specific uses of different communities. In particular, a new era is starting with the Copernicus program during which the aerosol vertical profiling capability will be fundamental for assimilation and validation purposes. The new data products have been designed thanks to a strong link with EARLINET data users, first of all modeling and satellite communities, established since the beginning of EARLINET and re-enforced within ACTRIS2

  14. Integrated modeling of temperature profiles in L-mode tokamak discharges

    Energy Technology Data Exchange (ETDEWEB)

    Rafiq, T.; Kritz, A. H.; Tangri, V. [Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015 (United States); Pankin, A. Y. [Tech-X Corporation, Boulder, Colorado 80303 (United States); Voitsekhovitch, I. [CCFE, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Budny, R. V. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)

    2014-12-15

    Simulations of doublet III-D, the joint European tokamak, and the tokamak fusion test reactor L-mode tokamak plasmas are carried out using the PTRANSP predictive integrated modeling code. The simulation and experimental temperature profiles are compared. The time evolved temperature profiles are computed utilizing the Multi-Mode anomalous transport model version 7.1 (MMM7.1) which includes transport associated with drift-resistive-inertial ballooning modes (the DRIBM model [T. Rafiq et al., Phys. Plasmas 17, 082511 (2010)]). The tokamak discharges considered involved a broad range of conditions including scans over gyroradius, ITER like current ramp-up, with and without neon impurity injection, collisionality, and low and high plasma current. The comparison of simulation and experimental temperature profiles for the discharges considered is shown for the radial range from the magnetic axis to the last closed flux surface. The regions where various modes in the Multi-Mode model contribute to transport are illustrated. In the simulations carried out using the MMM7.1 model it is found that: The drift-resistive-inertial ballooning modes contribute to the anomalous transport primarily near the edge of the plasma; transport associated with the ion temperature gradient and trapped electron modes contribute in the core region but decrease in the region of the plasma boundary; and neoclassical ion thermal transport contributes mainly near the center of the discharge.

  15. Modular injector integrated linear apparatus with motion profile optimization for spatial atomic layer deposition

    Science.gov (United States)

    Wang, Xiaolei; Li, Yun; Lin, Jilong; Shan, Bin; Chen, Rong

    2017-11-01

    A spatial atomic layer deposition apparatus integrated with a modular injector and a linear motor has been designed. It consists of four parts: a precursor delivery manifold, a modular injector, a reaction zone, and a driving unit. An injector with multi-layer structured channels is designed to help improve precursor distribution homogeneity. During the back and forth movement of the substrate at high speed, the inertial impact caused by jerk and sudden changes of acceleration will degrade the film deposition quality. Such residual vibration caused by inertial impact will aggravate the fluctuation of the gap distance between the injector and the substrate in the deposition process. Thus, an S-curve motion profile is implemented to reduce the large inertial impact, and the maximum position error could be reduced by 84%. The microstructure of the film under the S-curve motion profile shows smaller root-mean-square and scanning voltage amplitude under an atomic force microscope, which verifies the effectiveness of the S-curve motion profile in reducing the residual vibration and stabilizing the gap distance between the injector and the substrate. The film deposition rate could reach 100 nm/min while maintaining good uniformity without obvious periodic patterns on the surface.

  16. Evaluating Plot Designs for the Tropics

    Science.gov (United States)

    Paul C. van Deusen; Bruce Bayle

    1991-01-01

    Theory and procedures are reviewed for determining the best type of plot for a given forest inventory. A general methodology is given that clarifies the relationship between different plot designs and the associated methods to produce the inventory estimates.

  17. Multiple hypothesis clustering in radar plot extraction

    NARCIS (Netherlands)

    Huizing, A.G.; Theil, A.; Dorp, Ph. van; Ligthart, L.P.

    1995-01-01

    False plots and plots with inaccurate range and Doppler estimates may severely degrade the performance of tracking algorithms in radar systems. This paper describes how a multiple hypothesis clustering technique can be applied to mitigate the problems involved in plot extraction. The measures of

  18. Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models

    Directory of Open Access Journals (Sweden)

    Greenwood Celia MT

    2005-05-01

    Full Text Available Abstract Background With the explosion of microarray studies, an enormous amount of data is being produced. Systematic integration of gene expression data from different sources increases statistical power of detecting differentially expressed genes and allows assessment of heterogeneity. The challenge, however, is in designing and implementing efficient analytic methodologies for combination of data generated by different research groups. Results We extended traditional effect size models to combine information from different microarray datasets by incorporating a quality measure for each gene in each study into the effect size estimation. We illustrated our method by integrating two datasets generated using different Affymetrix oligonucleotide types. Our results indicate that the proposed quality-adjusted weighting strategy for modelling inter-study variation of gene expression profiles not only increases consistency and decreases heterogeneous results between these two datasets, but also identifies many more differentially expressed genes than methods proposed previously. Conclusion Data integration and synthesis is becoming increasingly important. We live in a high-throughput era where technologies constantly change leaving behind a trail of data with different forms, shapes and sizes. Statistical and computational methodologies are therefore critical for extracting the most out of these related but not identical sources of data.

  19. Integrating Wind Profiling Radars and Radiosonde Observations with Model Point Data to Develop a Decision Support Tool to Assess Upper-Level Winds for Space Launch

    Science.gov (United States)

    Bauman, William H., III; Flinn, Clay

    2013-01-01

    On the day-of-launch, the 45th Weather Squadron (45 WS) Launch Weather Officers (LWOs) monitor the upper-level winds for their launch customers to include NASA's Launch Services Program and NASA's Ground Systems Development and Operations Program. They currently do not have the capability to display and overlay profiles of upper-level observations and numerical weather prediction model forecasts. The LWOs requested the Applied Meteorology Unit (AMU) develop a tool in the form of a graphical user interface (GUI) that will allow them to plot upper-level wind speed and direction observations from the Kennedy Space Center (KSC) 50 MHz tropospheric wind profiling radar, KSC Shuttle Landing Facility 915 MHz boundary layer wind profiling radar and Cape Canaveral Air Force Station (CCAFS) Automated Meteorological Processing System (AMPS) radiosondes, and then overlay forecast wind profiles from the model point data including the North American Mesoscale (NAM) model, Rapid Refresh (RAP) model and Global Forecast System (GFS) model to assess the performance of these models. The AMU developed an Excel-based tool that provides an objective method for the LWOs to compare the model-forecast upper-level winds to the KSC wind profiling radars and CCAFS AMPS observations to assess the model potential to accurately forecast changes in the upperlevel profile through the launch count. The AMU wrote Excel Visual Basic for Applications (VBA) scripts to automatically retrieve model point data for CCAFS (XMR) from the Iowa State University Archive Data Server (http://mtarchive.qeol.iastate.edu) and the 50 MHz, 915 MHz and AMPS observations from the NASA/KSC Spaceport Weather Data Archive web site (http://trmm.ksc.nasa.gov). The AMU then developed code in Excel VBA to automatically ingest and format the observations and model point data in Excel to ready the data for generating Excel charts for the LWO's. The resulting charts allow the LWOs to independently initialize the three models 0

  20. Hybrid Lentivirus-transposon Vectors With a Random Integration Profile in Human Cells

    DEFF Research Database (Denmark)

    Staunstrup, Nicklas H; Moldt, Brian; Mátés, Lajos

    2009-01-01

    Gene delivery by human immunodeficiency virus type 1 (HIV-1)-based lentiviral vectors (LVs) is efficient, but genomic integration of the viral DNA is strongly biased toward transcriptionally active loci resulting in an increased risk of insertional mutagenesis in gene therapy protocols. Nonviral...... Sleeping Beauty (SB) transposon vectors have a significantly safer insertion profile, but efficient delivery into relevant cell/tissue types is a limitation. In an attempt to combine the favorable features of the two vector systems we established a novel hybrid vector technology based on SB transposase......-mediated insertion of lentiviral DNA circles generated during transduction of target cells with integrase (IN)-defective LVs (IDLVs). By construction of a lentivirus-transposon hybrid vector allowing transposition exclusively from circular viral DNA substrates, we demonstrate that SB transposase added in trans...

  1. Profiling Patients’ Healthcare Needs to Support Integrated, Person-Centered Models for Long-Term Disease Management (Profile): Research Design

    OpenAIRE

    Arianne MJ Elissen; Dorijn FL Hertroijs; Shaper, Nicolaas C; Hubertus JM Vrijhoef; Dirk Ruwaard

    2016-01-01

    Background: This article presents the design of PROFILe, a study investigating which (bio)medical and non-(bio)medical patient characteristics should guide more tailored chronic care. Based on this insight, the project aims to develop and validate ‘patient profiles’ that can be used in practice to determine optimal treatment strategies for subgroups of chronically ill with similar healthcare needs and preferences. Methods/Design: PROFILe is a practice-based research comprising four phases. Th...

  2. Reciprocal data acquisition and subsequent waveform matching for integrated onshore-offshore seismic profiling

    Science.gov (United States)

    Katou, Masafumi; Abe, Susumu; Saito, Hideo; Sato, Hiroshi

    2018-01-01

    In this study, experiments on seismic reciprocity utilizing various acquisition tools, including airguns, vibrators, dynamite, hydrophones and geophones, in combination are conducted on onshore-offshore transects that crossed the coastline. Because airguns, vibrators and dynamite generate different wavelets (i.e. have different source functions) and because hydrophones and geophones observe different physical field quantities, waveform matching processes must be applied to the recorded time-series to perform integrated seismic profiling. For the best integration of data acquired with onshore and offshore instruments, processes which compensate the instrumental differences with no loss of bandwidth should be employed. We present a combined onshore-offshore acquisition system and associated signal processing procedures for obtaining broad-band seismograms that support the comparison of reciprocal data. In the first of two experiments, we considered the data acquired by using two receiver-source pairs, one consisting of an onshore geophone and offshore airgun and the other consisting of an offshore hydrophone and onshore vibrator. The two waveforms were found to be in very good agreement after applying data processing including signature deconvolution. In the second experiment, we succeeded in matching time-series data from a pair consisting of an onshore geophone and offshore airgun and a pair consisting of an offshore hydrophone and an onshore dynamite source, by tracing subsurface dilatation through the use of a buried array of multicomponent geophones and the moving least squares method. Both signature deconvolution and the moving least squares method preserved the bandwidth of each recorded seismogram and were noise-independent. This study confirms that seismic reciprocity for onshore-offshore seismic profiling can be achieved with a combined survey system using all required instrument types and modern data processing preserving recorded bandwidth.

  3. Integration of polystyrene microlenses with both convex and concave profiles in a polymer-based microfluidic system

    KAUST Repository

    Fan, Yiqiang

    2013-12-20

    This paper reports a new technique of fabricating polystyrene microlenses with both convex and concave profiles that are integrated in polymer-based microfluidic system. The polystyrene microlenses, or microlens array, are fabricated using the free-surface thermal compression molding method. The laser fabricated poly(methyl methacrylate) (PMMA) sheet is used as the mold for the thermal compression molding process. With different surface treatment methods of the PMMA mold, microlenses with either convex or concave profiles could be achieved during the thermal molding process. By integrating the microlenses in the microfluidic systems, observing the flow inside the microchannels is easier. This new technique is rapid, low cost, and it does not require cleanroom facilities. Microlenses with both convex and concave profiles can be easily fabricated and integrated in microfluidic system with this technique. © 2013 Springer-Verlag Berlin Heidelberg.

  4. Latent profile analysis of students’ motivation and outcomes in mathematics: an organismic integration theory perspective

    Directory of Open Access Journals (Sweden)

    Chee Keng John Wang

    2017-05-01

    Full Text Available The purpose of the current study was to identify the motivation profiles at the intraindividual level using a latent profile analyses (LPA approach. A total of 1151 secondary school students aged 13 to 17 years old from Singapore took part in the study. Using LPA, four distinct motivational profiles were identified based on four motivation regulations. Profile 1 has very low introjected and low autonomous motivation (6% of sample. Profile 2 had high external and identified regulations and very low intrinsic regulation (10%. Profile 3 consisted of students with high identified and intrinsic regulations (51%. Profile 4 had moderately low identified and intrinsic regulations (33%. The results showed that the four profiles differed significantly in terms of effort, competence, value, and time spent on math beyond homework. The best profile (Profile 3 reported highest scores in effort, value, competence and time spent on Math beyond homework. The worst profile (Profile 1 reported lowest scores in all the four outcome variables.

  5. Profile of Metacognition of Mathematics Pre-Service Teachers in Understanding the Concept of Integral Calculus with Regard Gender Differences

    Science.gov (United States)

    Misu, L.; Budayasa, I. K.; Lukito, A.

    2018-01-01

    This research is to describe metacognition profile of female and male mathematics’ pre-service teachers in understanding the concept of integral calculus. The subjects of this study are one female and 1 male mathematics’ pre-service teachers who have studied integral calculus. This research type is an explorative study with the qualitative approach. The main data collection of this research was obtained by using Interview technique. In addition, there are supporting data which is the result of the written work of research subjects (SP) in understanding the question of integral calculus. The results of this study are as follows: There is a difference in metacognition profiles between male and female mathematics’ pre-service teachers in the understanding concept of integral calculus in the interpreting category, especially the definite integral concept. While in the category of exemplifying, there is no difference in metacognition profile between male and female mathematics’ pre-service teachers either the definite integral concept and the indefinite integral concept.

  6. Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia.

    Science.gov (United States)

    Taskesen, Erdogan; Babaei, Sepideh; Reinders, Marcel M J; de Ridder, Jeroen

    2015-01-01

    Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and the gene signatures derived from GEP, can be used for the prediction of subtypes in AML. Similarly, successful prediction was also achieved by exploiting DNA-methylation profiles (DMP). There are, however, no studies that compared classification accuracy and performance between GEP and DMP, neither are there studies that integrated both types of data to determine whether predictive power can be improved. Here, we used 344 well-characterized AML samples for which both gene expression and DNA-methylation profiles are available. We created three different classification strategies including early, late and no integration of these datasets and used them to predict AML subtypes using a logistic regression model with Lasso regularization. We illustrate that both gene expression and DNA-methylation profiles contain distinct patterns that contribute to discriminating AML subtypes and that an integration strategy can exploit these patterns to achieve synergy between both data types. We show that concatenation of features from both data sets, i.e. early integration, improves the predictive power compared to classifiers trained on GEP or DMP alone. A more sophisticated strategy, i.e. the late integration strategy, employs a two-layer classifier which outperforms the early integration strategy. We demonstrate that prediction of known cytogenetic and molecular abnormalities in AML can be further improved by integrating GEP and DMP profiles.

  7. Fifth International Symposium on Recurrence Plot

    CERN Document Server

    Riley, Michael; Giuliani, Alessandro; Webber, Charles; Jr, Jr; Translational Recurrences : From Mathematical Theory to Real-World Applications

    2014-01-01

    This book features 13 papers presented at the Fifth International Symposium on Recurrence Plots, held August 2013 in Chicago, IL. It examines recent applications and developments in recurrence plots and recurrence quantifi cation analysis (RQA) with special emphasis on biological and cognitive systems and the analysis of coupled systems using cross-recurrence methods. Readers will discover new applications and insights into a range of systems provided by recurrence plot analysis and new theoretical and mathematical developments in recurrence plots. Recurrence plot based analysis is a powerful tool that operates on real-world complex systems that are nonlinear, non-stationary, noisy, of any statistical distribution, free of any particular model type, and not particularly long. Quantitative analyses promote the detection of system state changes, synchronized dynamical regimes, or classifi cation of system states. Th e book will be of interest to an interdisciplinary audience of recurrence plot users and researc...

  8. An Excel macro for generating trilinear plots.

    Science.gov (United States)

    Shikaze, Steven G; Crowe, Allan S

    2007-01-01

    This computer note describes a method for creating trilinear plots in Microsoft Excel. Macros have been created in MS Excel's internal language: Visual Basic for Applications (VBA). A simple form has been set up to allow the user to input data from an Excel worksheet. The VBA macro is used to convert the triangular data (which consist of three columns of percentage data) into X-Y data. The macro then generates the axes, labels, and grid for the trilinear plot. The X-Y data are plotted as scatter data in Excel. By providing this macro in Excel, users can create trilinear plots in a quick, inexpensive manner.

  9. The relationship between technology leadership roles and profiles of school principals and technology integration in primary school classrooms

    Directory of Open Access Journals (Sweden)

    Mustafa SAMANCIOĞLU

    2015-12-01

    Full Text Available The purpose of this study was to investigate the relationship between technology leadership behaviors of school principals and teachers’ level of technology integration, and to determine technology leadership profiles based on teacher views and examine their association with technology integration. The researchers administered two questionnaires to 352 teachers working at sixteen primary schools in a large city in southeastern Turkey. The results revealed a positive, but weak relationship between technology leadership and technology integration. Furthermore, it was concluded that there were positive but weak relationships among technology integration and human centeredness, communication and collaboration, vision and support sub-dimensions of technology leadership. Two technology leadership profiles (high-TLP=65.6% and low-TLP=34.4% were constructed as a result of cluster analysis. A statistically significant difference was detected between teachers’ technology integration perceptions which were categorized into two profiles. The paper concludes by suggestions for implications to strengthen the link between technology leadership and technology integration.

  10. Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

    Directory of Open Access Journals (Sweden)

    Beisser Daniela

    2012-06-01

    Full Text Available Abstract Background Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. Results In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites and 4,378 edges (reactions. Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from

  11. Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma.

    Directory of Open Access Journals (Sweden)

    David Lindgren

    Full Text Available Similar to other malignancies, urothelial carcinoma (UC is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21, and BCL2L1 (20q11. We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.

  12. Profile of the Treated Patients at the Implantology Clinic of Integrated Schools of Adamantina (FAI

    Directory of Open Access Journals (Sweden)

    Jean Paulo Rodolfo Ferreira

    2015-05-01

    Full Text Available Objective: The aim of this study was to identify the profile of patients treated at the Implantology clinic of the Integrated Schools of Adamantina-FAI, Adamantina-SP, Brazil, through analysis of medical records, appliance of questionnaire and execution of clinical examination. Material and methods: The sample universe of this study consisted of 96 medical records and 96 patients seen over the 9 years of FAI’s experience in the discipline of Implantology. The results were analyzed in the IBM SPSS StatisticsVersion 19 program and the Fisher’s exact and chi-square tests were also applied. Discussion / Results: It was observed that 53.97 % of the participants have lost their natural teeth due to caries. The type of implant prosthesis most used was the fixed denture (88 %. It is also important to note that almost all of the patients had no loss of implant, and these individuals were mostly aged less than or equal to 49 years for women (73.8 % and greater than or equal to 50 years for men (61.8 %. In relation to the quantity of implant elements, the use of 2 implants or less was the most common rehabilitation for both sexes. Another important observation is that only 15.8 % of the participants have the habit of smoking. Conclusion: Thus, the profile of the treated patient at the Implantology clinic of FAI, is mostly women, healthy, aged less than 49 years old, non-smoking, which rehabilitated 1 or 2 teeth, with almost no incidence of implant lost and who opted for fixed denture supported by the implants.

  13. Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling.

    Science.gov (United States)

    Roson-Burgo, Beatriz; Sanchez-Guijo, Fermin; Del Cañizo, Consuelo; De Las Rivas, Javier

    2016-11-21

    Mesenchymal Stromal/Stem Cells (MSCs), isolated under the criteria established by the ISCT, still have a poorly characterized phenotype that is difficult to distinguish from similar cell populations. Although the field of transcriptomics and functional genomics has quickly grown in the last decade, a deep comparative analysis of human MSCs expression profiles in a meaningful cellular context has not been yet performed. There is also a need to find a well-defined MSCs gene-signature because many recent biomedical studies show that key cellular interaction processes (i.e. inmuno-modulation, cellular cross-talk, cellular maintenance, differentiation, epithelial-mesenchymal transition) are dependent on the mesenchymal stem cells within the stromal niche. In this work we define a core mesenchymal lineage signature of 489 genes based on a deep comparative analysis of multiple transcriptomic expression data series that comprise: (i) MSCs of different tissue origins; (ii) MSCs in different states of commitment; (iii) other related non-mesenchymal human cell types. The work integrates several public datasets, as well as de-novo produced microarray and RNA-Seq datasets. The results present tissue-specific signatures for adipose tissue, chorionic placenta, and bone marrow MSCs, as well as for dermal fibroblasts; providing a better definition of the relationship between fibroblasts and MSCs. Finally, novel CD marker patterns and cytokine-receptor profiles are unravelled, especially for BM-MSCs; with MCAM (CD146) revealed as a prevalent marker in this subtype of MSCs. The improved biomolecular characterization and the released genome-wide expression signatures of human MSCs provide a comprehensive new resource that can drive further functional studies and redesigned cell therapy applications.

  14. Predicting miRNA Targets by Integrating Gene Regulatory Knowledge with Expression Profiles.

    Directory of Open Access Journals (Sweden)

    Weijia Zhang

    Full Text Available microRNAs (miRNAs play crucial roles in post-transcriptional gene regulation of both plants and mammals, and dysfunctions of miRNAs are often associated with tumorigenesis and development through the effects on their target messenger RNAs (mRNAs. Identifying miRNA functions is critical for understanding cancer mechanisms and determining the efficacy of drugs. Computational methods analyzing high-throughput data offer great assistance in understanding the diverse and complex relationships between miRNAs and mRNAs. However, most of the existing methods do not fully utilise the available knowledge in biology to reduce the uncertainty in the modeling process. Therefore it is desirable to develop a method that can seamlessly integrate existing biological knowledge and high-throughput data into the process of discovering miRNA regulation mechanisms.In this article we present an integrative framework, CIDER (Causal miRNA target Discovery with Expression profile and Regulatory knowledge, to predict miRNA targets. CIDER is able to utilise a variety of gene regulation knowledge, including transcriptional and post-transcriptional knowledge, and to exploit gene expression data for the discovery of miRNA-mRNA regulatory relationships. The benefits of our framework is demonstrated by both simulation study and the analysis of the epithelial-to-mesenchymal transition (EMT and the breast cancer (BRCA datasets. Our results reveal that even a limited amount of either Transcription Factor (TF-miRNA or miRNA-mRNA regulatory knowledge improves the performance of miRNA target prediction, and the combination of the two types of knowledge enhances the improvement further. Another useful property of the framework is that its performance increases monotonically with the increase of regulatory knowledge.

  15. Emotional characters for automatic plot creation

    NARCIS (Netherlands)

    Theune, Mariet; Rensen, S.; op den Akker, Hendrikus J.A.; Heylen, Dirk K.J.; Nijholt, Antinus; Göbel, S.; Spierling, U.; Hoffmann, A.; Iurgel, I.; Schneider, O.; Dechau, J.; Feix, A.

    The Virtual Storyteller is a multi-agent framework for automatic story generation. In this paper we describe how plots emerge from the actions of semi-autonomous character agents, focusing on the influence of the characters’ emotions on plot development.

  16. Box Plots in the Australian Curriculum

    Science.gov (United States)

    Watson, Jane M.

    2012-01-01

    This article compares the definition of "box plot" as used in the "Australian Curriculum: Mathematics" with other definitions used in the education community; describes the difficulties students experience when dealing with box plots; and discusses the elaboration that is necessary to enable teachers to develop the knowledge…

  17. Digital data collection in forest dynamics plots

    Science.gov (United States)

    Faith Inman-Narahari; Christian Giardina; Rebecca Ostertag; Susan Cordell; Lawren Sack

    2010-01-01

    Summary 1. Computers are widely used in all aspects of research but their application to in-field data collection for forest plots has rarely been evaluated. 2. We developed digital data collection methods using ESRI mapping software and ruggedized field computers to map and measure ~30 000 trees in two 4-ha forest dynamics plots in wet and dry...

  18. The Heuristic Interpretation of Box Plots

    Science.gov (United States)

    Lem, Stephanie; Onghena, Patrick; Verschaffel, Lieven; Van Dooren, Wim

    2013-01-01

    Box plots are frequently used, but are often misinterpreted by students. Especially the area of the box in box plots is often misinterpreted as representing number or proportion of observations, while it actually represents their density. In a first study, reaction time evidence was used to test whether heuristic reasoning underlies this…

  19. Corrections for Cluster-Plot Slop

    Science.gov (United States)

    Harry T. Valentine; Mark J. Ducey; Jeffery H. Gove; Adrian Lanz; David L.R. Affleck

    2006-01-01

    Cluster-plot designs, including the design used by the Forest Inventory and Analysis program of the USDA Forest Service (FIA), are attended by a complicated boundary slopover problem. Slopover occurs where inclusion zones of objects of interest cross the boundary of the area of interest. The dispersed nature of inclusion zones that arise from the use of cluster plots...

  20. SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics.

    Science.gov (United States)

    Stempor, Przemyslaw; Ahringer, Julie

    2016-01-01

    Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps. We found that available plotting software was either slow and laborious or difficult to use by investigators with little computational training, which inhibited wide data exploration. To address this need, we developed SeqPlots, a user-friendly exploratory data analysis (EDA) and visualization software for genomics. After choosing groups of signal and feature files and defining plotting parameters, users can generate profile plots of average signal or heatmaps clustered using different algorithms in a matter of seconds through the graphical user interface (GUI) controls. SeqPlots accepts all major genomic file formats as input and can also generate and plot user defined motif densities. Profile plots and heatmaps are highly configurable and batch operations can be used to generate a large number of plots at once. SeqPlots is available as a GUI application for Mac or Windows and Linux, or as an R/Bioconductor package. It can also be deployed on a server for remote and collaborative usage. The analysis features and ease of use of SeqPlots encourages wide data exploration, which should aid the discovery of novel genomic associations.

  1. Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile.

    Science.gov (United States)

    Zhang, Deng-Feng; Wang, Dong; Li, Yu-Ye; Yao, Yong-Gang

    2016-04-01

    Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors. To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy. We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses. A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes. Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. plotKML: Scientific Visualization of Spatio-Temporal Data

    Directory of Open Access Journals (Sweden)

    Tomislav Hengl

    2015-02-01

    Full Text Available plotKML is an R package that provides methods for writing the most common R spatial classes into KML files. It builds up on the existing XML parsing functionality (XML package, and provides similar plotting functionality as the lattice package. Its main objective is to provide a simple interface to generate KML files with a small number of arguments, and allows users to visually explore spatio-temporal data available in R: points, polygons, gridded maps, trajectory-type data, vertical profiles, ground photographs, time series vector objects or raster images, along with the results of spatial analysis such as geostatistical mapping, spatial simulations of vector and gridded objects, optimized sampling designs, species distribution models and similar. A generic plotKML( function automatically determines the parsing order and visualizes data directly from R; lower level functions can be combined to allow for new user-created visualization templates. In comparison to other packages writing KML, plotKML seems to be more object oriented, it links more closely to the existing R classes for spatio-temporal data (sp, spacetime and raster packages than the alternatives, and provides users with the possibility to create their own templates.

  3. Adding uncertainty to forest inventory plot locations: effects on analyses using geospatial data

    Science.gov (United States)

    Alexia A. Sabor; Volker C. Radeloff; Ronald E. McRoberts; Murray Clayton; Susan I. Stewart

    2007-01-01

    The Forest Inventory and Analysis (FIA) program of the USDA Forest Service alters plot locations before releasing data to the public to ensure landowner confidentiality and sample integrity, but using data with altered plot locations in conjunction with other spatially explicit data layers produces analytical results with unknown amounts of error. We calculated the...

  4. The hexagon/panel system for selecting FIA plots under an annual inventory

    Science.gov (United States)

    Gary J. Brand; Mark D. Nelson; Daniel G. Wendt; Kevin K. Nimerfro

    2000-01-01

    Forest Inventory and Analysis (FIA) is changing to an annual nationwide forest inventory. This paper describes the sampling grid used to distribute FIA plots across the landscape and to allocate them to a particular measurement year. We also describe the integration of the F1A and Forest Health Monitoring (FHM) plot networks.

  5. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice

    Directory of Open Access Journals (Sweden)

    Tu Yuanyuan

    2010-12-01

    Full Text Available Abstract Background The cellulose synthase and cellulose synthase-like gene superfamily (CESA/CSL is proposed to encode enzymes for cellulose and non-cellulosic matrix polysaccharide synthesis in plants. Although the rice (Oryza sativa L. genome has been sequenced for a few years, the global expression profiling patterns and functions of the OsCESA/CSL superfamily remain largely unknown. Results A total of 45 identified members of OsCESA/CSL were classified into two clusters based on phylogeny and motif constitution. Duplication events contributed largely to the expansion of this superfamily, with Cluster I and II mainly attributed to tandem and segmental duplication, respectively. With microarray data of 33 tissue samples covering the entire life cycle of rice, fairly high OsCESA gene expression and rather variable OsCSL expression were observed. While some members from each CSL family (A1, C9, D2, E1, F6 and H1 were expressed in all tissues examined, many of OsCSL genes were expressed in specific tissues (stamen and radicles. The expression pattern of OsCESA/CSL and OsBC1L which extensively co-expressed with OsCESA/CSL can be divided into three major groups with ten subgroups, each showing a distinct co-expression in tissues representing typically distinct cell wall constitutions. In particular, OsCESA1, -3 & -8 and OsCESA4, -7 & -9 were strongly co-expressed in tissues typical of primary and secondary cell walls, suggesting that they form as a cellulose synthase complex; these results are similar to the findings in Arabidopsis. OsCESA5/OsCESA6 is likely partially redundant with OsCESA3 for OsCESA complex organization in the specific tissues (plumule and radicle. Moreover, the phylogenetic comparison in rice, Arabidopsis and other species can provide clues for the prediction of orthologous gene expression patterns. Conclusions The study characterized the CESA/CSL of rice using an integrated approach comprised of phylogeny, transcriptional

  6. Experimental Garden Plots for Botany Lessons

    Science.gov (United States)

    Gorodnicheva, V. V.; Vasil'eva, E. I.

    1976-01-01

    Discussion of the botany lessons used at two schools points out the need for fifth and sixth grade students to be taught the principles of plant life through observations made at an experimental garden plot at the school. (ND)

  7. Split-plot designs for multistage experimentation

    DEFF Research Database (Denmark)

    Kulahci, Murat; Tyssedal, John

    2016-01-01

    at the same time will be more efficient. However, there have been only a few attempts in the literature to provide an adequate and easy-to-use approach for this problem. In this paper, we present a novel methodology for constructing two-level split-plot and multistage experiments. The methodology is based...... be accommodated in each stage. Furthermore, split-plot designs for multistage experiments with good projective properties are also provided....

  8. SUPPLY CHAIN MANAGERS: PROFESSIONAL PROFILE AND THE ROLE IN THE CROSS-FUNCTIONAL INTEGRATION OF SUPPLY CHAIN MANAGEMENT

    OpenAIRE

    Andréia de Abreu; Rosane Lúcia Chicarelli Alcântara

    2015-01-01

    Supply Chain Management can be seen as a way to achieve integration of all corporate functions. In practice, Supply Chain Management is complex and characterized by numerous activities spread over multiple functions and organizations, which pose challenges to reach effective implementation. Based on literature review, the objective of this paper is to present the theoretical indications regarding professional profile recommended for the Supply Chain Management and discuss the role of these pr...

  9. Extended device profiles and testing procedures for the approval process of integrated medical devices using the IEEE 11073 communication standard.

    Science.gov (United States)

    Janß, Armin; Thorn, Johannes; Schmitz, Malte; Mildner, Alexander; Dell'Anna-Pudlik, Jasmin; Leucker, Martin; Radermacher, Klaus

    2018-02-23

    Nowadays, only closed and proprietary integrated operating room systems (IORS) from big manufacturers are available on the market. Hence, the interconnection of components from third-party vendors is only possible with increased time and costs. In the context of the German Federal Ministry of Education and Research (BMBF)-funded project OR.NET (2012-2016), the open integration of medical devices from different manufacturers was addressed. An integrated operating theater based on the open communication standard IEEE 11073 shall give clinical operators the opportunity to choose medical devices independently of the manufacturer. This approach would be advantageous especially for hospital operators and small- and medium-sized enterprises (SME) of medical devices. Actual standards and concepts regarding technical feasibility and the approval process do not cope with the requirements for a modular integration of medical devices in the operating room (OR), based on an open communication standard. Therefore, innovative approval strategies and corresponding certification and test procedures, which cover actual legal and normative standards, have to be developed in order to support the future risk management and the usability engineering process of open integrated medical devices in the OR. The use of standardized device and service profiles and a three-step testing procedure, including conformity, interoperability and integration tests are described in this paper and shall support the manufacturers to integrate their medical devices without disclosing the medical devices' risk analysis and related confidential expertise or proprietary information.

  10. Functional and integrative analysis of the proteomic profile of radish root under Pb exposure

    Directory of Open Access Journals (Sweden)

    Yan Wang

    2016-12-01

    Full Text Available Lead (Pb is one of the most abundant heavy metal pollutants, which can penetrate the plant through the root and then enter the food chain causing in potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification respectively upon Pb(NO32 at 500 mg L-1(Pb500 and Pb(NO32 at 1000 mg L-1(Pb1000 exposure. A total of 3, 898 protein species were successfully detected and 2,141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes during both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS scavenging, photosynthesis and respiration and carbon metabolism were successfully identified. Gene Ontology (GO and pathway enrichment analysis of the 135 differential abundance protein species revealed that the overrepresented GO terms were include in ‘cell wall’, ‘apoplast’, ‘response to metal ion’, ‘vacuole’ and ‘peroxidase activity’, and the critical enriched pathways were involved in ‘citric acid (TCA cycle and respiratory electron transport’, ‘pyruvate metabolism’, ‘phenylalanine metabolism’, ‘phenylpropanoid biosynthesis’ and ‘carbon metabolism’. Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomic and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e. ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase involved in the glycolysis and TCA cycle were severely affected, which ultimately cause

  11. Plotting equation for gaussian percentiles and a spreadsheet program for generating probability plots

    Science.gov (United States)

    Balsillie, J.H.; Donoghue, J.F.; Butler, K.M.; Koch, J.L.

    2002-01-01

    Two-dimensional plotting tools can be of invaluable assistance in analytical scientific pursuits, and have been widely used in the analysis and interpretation of sedimentologic data. We consider, in this work, the use of arithmetic probability paper (APP). Most statistical computer applications do not allow for the generation of APP plots, because of apparent intractable nonlinearity of the percentile (or probability) axis of the plot. We have solved this problem by identifying an equation(s) for determining plotting positions of Gaussian percentiles (or probabilities), so that APP plots can easily be computer generated. An EXCEL example is presented, and a programmed, simple-to-use EXCEL application template is hereby made publicly available, whereby a complete granulometric analysis including data listing, moment measure calculations, and frequency and cumulative APP plots, is automatically produced.

  12. An Integrated Approach to Study Mud Banks of Alleppey Kerala using the Autonomous Vertical Profiler (AVP)

    Digital Repository Service at National Institute of Oceanography (India)

    Mascarenhas, A.A.M.Q.; Afzulpurkar, S.; Navelkar, G.S.; Madhan, R.; Maurya, P.; Desa, E.S.; Prabhudesai, S.P.; Dabholkar, N.A.; Lamani, V.; Manoharan, V.; Naik, N.; Thottam, T.J.; DineshKumar, P.K.; deAraujo, B.A.

    and estuaries. It consists of a hands-free, motor driven in-situ robot profiler that requires no operator skill or deployment gear, while fulfilling the requirements of repetitive sampling in coastal waters. It uses standard oceanographic sensors, ie...

  13. Quality Control Algorithms and Proposed Integration Process for Wind Profilers Used by Launch Vehicle Systems

    Science.gov (United States)

    Decker, Ryan; Barbre, Robert E., Jr.

    2011-01-01

    Impact of winds to space launch vehicle include Design, Certification Day-of-launch (DOL) steering commands (1)Develop "knockdowns" of load indicators (2) Temporal uncertainty of flight winds. Currently use databases from weather balloons. Includes discrete profiles and profile pair datasets. Issues are : (1)Larger vehicles operate near design limits during ascent 150 discrete profiles per month 110-217 seasonal 2.0 and 3.5-hour pairs Balloon rise time (one hour) and drift (up to 100 n mi) Advantages of the Alternative approach using Doppler Radar Wind Profiler (DRWP) are: (1) Obtain larger sample size (2) Provide flexibility for assessing trajectory changes due to winds (3) Better representation of flight winds.

  14. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.

    Science.gov (United States)

    Lu, Kun; Abo, Ryan Phillip; Schlieper, Katherine Ann; Graffam, Michelle E; Levine, Stuart; Wishnok, John S; Swenberg, James A; Tannenbaum, Steven R; Fox, James G

    2014-03-01

    The human intestine is host to an enormously complex, diverse, and vast microbial community-the gut microbiota. The gut microbiome plays a profound role in metabolic processing, energy production, immune and cognitive development, epithelial homeostasis, and so forth. However, the composition and diversity of the gut microbiome can be readily affected by external factors, which raises the possibility that exposure to toxic environmental chemicals leads to gut microbiome alteration, or dysbiosis. Arsenic exposure affects large human populations worldwide and has been linked to a number of diseases, including cancer, diabetes, and cardiovascular disorders. We investigated the impact of arsenic exposure on the gut microbiome composition and its metabolic profiles. We used an integrated approach combining 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling to examine the functional impact of arsenic exposure on the gut microbiome. 16S rRNA gene sequencing revealed that arsenic significantly perturbed the gut microbiome composition in C57BL/6 mice after exposure to 10 ppm arsenic for 4 weeks in drinking water. Moreover, metabolomics profiling revealed a concurrent effect, with a number of gut microflora-related metabolites being perturbed in multiple biological matrices. Arsenic exposure not only alters the gut microbiome community at the abundance level but also substantially disturbs its metabolic profiles at the function level. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism by which arsenic exposure leads to or exacerbates human diseases. Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.

  15. Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics.

    Science.gov (United States)

    Gilroy, Kathryn L; Terry, Anne; Naseer, Asif; de Ridder, Jeroen; Allahyar, Amin; Wang, Weiwei; Carpenter, Eric; Mason, Andrew; Wong, Gane K-S; Cameron, Ewan R; Kilbey, Anna; Neil, James C

    2016-01-01

    Retroviruses have been foundational in cancer research since early studies identified proto-oncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types. Analysis of FeLV insertion sites in the MCF-7 mammary carcinoma cell line revealed strong bias towards active chromatin marks with no evidence of significant post-integration growth selection. The most prominent FeLV integration targets had little overlap with the most abundantly expressed transcripts, but were strongly enriched for annotated cancer genes. A meta-analysis based on several gamma-retrovirus integration profiling (GRIP) studies in human cells (CD34+, K562, HepG2) revealed a similar cancer gene bias but also remarkable cell-type specificity, with prominent exceptions including a universal integration hotspot at the long non-coding RNA MALAT1. Comparison of GRIP targets with databases of super-enhancers from the same cell lines showed that these have only limited overlap and that GRIP provides unique insights into the upstream drivers of cell growth. These observations elucidate the oncogenic potency of the gamma-retroviruses and support the wider application of GRIP to identify the genes and growth regulatory circuits that drive distinct cancer types.

  16. 6th International Symposium on Recurrence Plots

    CERN Document Server

    Jr, Jr; Ioana, Cornel; Marwan, Norbert

    2016-01-01

    The chapters in this book originate from the research work and contributions presented at the Sixth International Symposium on Recurrence Plots held in Grenoble, France in June 2015. Scientists from numerous disciplines gathered to exchange knowledge on recent applications and developments in recurrence plots and recurrence quantification analysis. This meeting was remarkable because of the obvious expansion of recurrence strategies (theory) and applications (practice) into ever-broadening fields of science. It discusses real-world systems from various fields, including mathematics, strange attractors, applied physics, physiology, medicine, environmental and earth sciences, as well as psychology and linguistics. Even readers not actively researching any of these particular systems will benefit from discovering how other scientists are finding practical non-linear solutions to specific problems. The book is of interest to an interdisciplinary audience of recurrence plot users and researchers interested in time...

  17. Analysis of photonic spot profile converter and bridge structure on SOI platform for horizontal and vertical integration

    Science.gov (United States)

    Majumder, Saikat; Jha, Amit Kr.; Biswas, Aishik; Banerjee, Debasmita; Ganguly, Dipankar; Chakraborty, Rajib

    2017-08-01

    Horizontal spot size converter required for horizontal light coupling and vertical bridge structure required for vertical integration are designed on high index contrast SOI platform in order to form more compact integrated photonic circuits. Both the structures are based on the concept of multimode interference. The spot size converter can be realized by successive integration of multimode interference structures with reducing dimension on horizontal plane, whereas the optical bridge structure consists of a number of vertical multimode interference structure connected by single mode sections. The spot size converter can be modified to a spot profile converter when the final single mode waveguide is replaced by a slot waveguide. Analysis have shown that by using three multimode sections in a spot size converter, an Gaussian input having spot diameter of 2.51 μm can be converted to a spot diameter of 0.25 μm. If the output single mode section is replaced by a slot waveguide, this input profile can be converted to a flat top profile of width 50 nm. Similarly, vertical displacement of 8μm is possible by using a combination of two multimode sections and three single mode sections in the vertical bridge structure. The analyses of these two structures are carried out for both TE and TM modes at 1550 nm wavelength using the semi analytical matrix method which is simple and fast in computation time and memory. This work shows that the matrix method is equally applicable for analysis of horizontally as well as vertically integrated photonic circuit.

  18. Increasing biomass in Amazonian forest plots.

    OpenAIRE

    Baker, Timothy R; Phillips, Oliver L; Malhi, Yadvinder; Almeida, Samuel; Arroyo, Luzmila; Di Fiore, Anthony; Erwin, Terry; Higuchi, Niro; Killeen, Timothy J; Laurance, Susan G; Laurance, William F; Lewis, Simon L; Monteagudo, Abel; Neill, David A; Vargas, Percy Núñez

    2004-01-01

    A previous study by Phillips et al. of changes in the biomass of permanent sample plots in Amazonian forests was used to infer the presence of a regional carbon sink. However, these results generated a vigorous debate about sampling and methodological issues. Therefore we present a new analysis of biomass change in old-growth Amazonian forest plots using updated inventory data. We find that across 59 sites, the above-ground dry biomass in trees that are more than 10 cm in diameter (AGB) has i...

  19. Displaying New Measurements on WDS Orbit Plots

    Science.gov (United States)

    Buchheim, Robert

    2017-04-01

    Students who observe and measure a visual double star often want to see how their measurement compares with the historical record and with the orbit (if one has been determined). This paper describes how PowerPoint’s graphical tools can display a newly-measured data point on the orbit plot from USNO’s 6th Orbit Catalog, and how a simple spreadsheet can transform measurements expressed as (rho,theta) into a Cartesian plot of the sky positions (E, N). This information is presented as a resource for future students.

  20. A Study of Plot in Siavash Story

    OpenAIRE

    Jafari, A.(Université Catholique de Louvain, Louvain-la-Neuve, Belgium)

    2012-01-01

    Plot is the main element of a story based on a temporal chain and causality. Although Siavash story is an epic story, there are some structural elements on the basis of which we should call the first episode of this story âfrom Siavash birth till his emigrationâ a âDramatic storyâ and its second episode âfrom his emigration till being killedâ a âTragic storyâ. Analysing the plot of this story, we can summarize it in three sequences. Every sequence consists of three to five functions and ev...

  1. Half a century of Ramachandran plots.

    Science.gov (United States)

    Carugo, Oliviero; Djinovic-Carugo, Kristina

    2013-08-01

    On the occasion of their fiftieth birthday, it is opportune to review the first half century of Ramachandran plots. In the present review, some of the most relevant aspects of this fifty-year history are summarized, from the original ideas of Gopalasamudram Narayana Ramachandran to subsequent revisions and to applications in structural biology. This will not be a guided walk through five decades of Ramachandran plots, but a commented summary of the lines along which the original ideas evolved and continue to develop, and of their applications.

  2. Person and consumption profiles. Building integrated energy supply; Person- og forbrugsprofiler. Bygningsintegreret energiforsyning

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Rasmus L.; Noergaard, J.; Daniels, O.; Justesen, R.O.

    2011-08-15

    In the future, buildings will not only act as consumers of energy but as producers as well. For these ''prosumers'', energy production by use of solar panels, photovoltaics and heat pumps etc will be essential. The objective of this project was to find the most optimal combinations of building insulation and use of renewable energy sources in existing buildings in terms of economics and climate impacts. Five houses were analyzed based on different personal load, consumption profiles, solar orientation and proposed building envelope improvements and use of combinations of renewable energy systems. The present report describes how person and consumption profiles used in this project are developed, and which data that form the basis for these profiles. The increasing requirements for energy in the building sector mean that the primary energy consumption ends close to or below zero within the next years. Therefore, the consumption in buildings becomes a relatively larger and larger part of the total energy demand in dwellings. It is important to investigate whether there are seasonal distributions of power and water consumption, because it might give a more exact result and describe the reality better than by using yearly values. First, the personal load determined, and then humidity and consumption of both power and hot water is defined. Second, the hourly profiles are developed based on analyses of seasonal distributions. These profiles also include cold domestic water to see whether there is a correlation between this and hot domestic water. (ln)

  3. SUPPLY CHAIN MANAGERS: PROFESSIONAL PROFILE AND THE ROLE IN THE CROSS-FUNCTIONAL INTEGRATION OF SUPPLY CHAIN MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Andréia de Abreu

    2015-03-01

    Full Text Available Supply Chain Management can be seen as a way to achieve integration of all corporate functions. In practice, Supply Chain Management is complex and characterized by numerous activities spread over multiple functions and organizations, which pose challenges to reach effective implementation. Based on literature review, the objective of this paper is to present the theoretical indications regarding professional profile recommended for the Supply Chain Management and discuss the role of these professionals in cross-functional business processes. The literature review demonstrated a growing interest in the thematic, especially because the “soft” aspects (human and behavioral to achieve supply chain internal and external integration. All functions must be involved in Supply Chain Management and supply chain managers have a critical role to play: challenge the supremacy of functions in the organizational structure, implementing the practice of "horizontal work" through cross-functional teams. Overall, this research contributes to academic and practical professionals by the description of the job profile of the supply chain managers and presentation of forms to achieve internal integration.

  4. Phasor plots of luminescence decay functions

    Energy Technology Data Exchange (ETDEWEB)

    Berberan-Santos, Mário N., E-mail: berberan@tecnico.ulisboa.pt

    2015-03-01

    Highlights: • First complete study of the phasor plots of a sum of two exponentials (2E). • The existence of a 2E limiting curve (outer boundary) is demonstrated. • A generalization of the lever rule is presented. • Virtual phasor concept. • Study of several decay laws displaying a diversity of patterns. - Abstract: Luminescence decay functions describe the time dependence of the intensity of radiation emitted by electronically excited species. Decay phasor plots (plots of the Fourier sine transform vs. the Fourier cosine transform, for one or several angular frequencies) are being increasingly used in fluorescence, namely in lifetime imaging microscopy (FLIM). In this work, a detailed study of the sum of two exponentials decay function is carried out revealing that sub-exponential, super-exponential and unimodal decays have different phasor signatures. A generalization of the lever rule is obtained, and the existence of an outermost phasor curve corresponding to intermediate-like decays is demonstrated. A study of the behavior of more complex decay functions (sum of three exponentials, stretched and compressed exponentials, phosphorescence with reabsorption and triplet–triplet annihilation, fluorescence with quantum beats) allows concluding that a rich diversity of phasor plot patterns exists. In particular, super-exponential decays can present complex shapes, spiraling at high frequencies. The concept of virtual phasor is also introduced.

  5. Purging Plot from Film and Literature Courses.

    Science.gov (United States)

    Peavler, Terry J.

    1983-01-01

    Argues that film and literature courses must get beyond discussions of plot to explorations of narrative perspective and structure, communication techniques, and critical methodologies in order to give students an awareness of the inherent natures, limitations, and possibilities of film and literature. (DMM)

  6. Comparing Box Plot Distributions: A Teacher's Reasoning

    Science.gov (United States)

    Pfannkuch, Maxine

    2006-01-01

    Drawing conclusions from the comparison of datasets using informal statistical inference is a challenging task since the nature and type of reasoning expected is not fully understood. In this paper a secondary teacher's reasoning from the comparison of box plot distributions during the teaching of a Year 11 (15-year-old) class is analyzed. From…

  7. Activities: Exploring Data with Box Plots.

    Science.gov (United States)

    Bryan, Elizabeth H.

    1988-01-01

    This set of activity sheets requires students to organize and display data with a box-and-whiskers graph. Students use the plot as a summary display to detect patterns and to highlight the important features of the data for purposes of comparison. (PK)

  8. Historical growth plots in the Pacific Southwest

    Science.gov (United States)

    Lawrence A. Rabin; William W. Oliver; Robert F. Powers; Martin W. Ritchie; Matt D. Busse; Eric E. Knapp

    2009-01-01

    In the past, researchers from the Pacific Southwest Research Station (PSW) undertook forest growth studies to evaluate how best to manage timber resources. However, historical and future data collected at PSW growth plots also have the potential to increase our understanding of the ecological processes occurring in our forests and shed light on national issues of...

  9. Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

    Energy Technology Data Exchange (ETDEWEB)

    Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M.; Young, Vincent B.; Jansson, Janet K.; Fredricks, David N.; Borenstein, Elhanan; Sanchez, Laura M.

    2015-12-22

    ABSTRACT

    Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in

  10. DEEP: Dallas EEProm Equipment Profile for Rapid Integration and Automatic System Modeling

    OpenAIRE

    Rogers-Marcovitz, Forrest; Williams, Phelps

    2007-01-01

    The Responsive Space Initiative, the ability for mission-specific payloads and support systems to be rapidly integrated within a short period, is a goal within the spacecraft community. However, as components are added to the spacecraft, the complex interactions between subsystems must be noted and, if possible, modeled. This process is extremely time consuming and if not done properly, can be a major contributor to spacecraft failure. A new paradigm is needed for Rapid Integration and System...

  11. An exploratory drilling exhaustion sequence plot program

    Science.gov (United States)

    Schuenemeyer, J.H.; Drew, L.J.

    1977-01-01

    The exhaustion sequence plot program computes the conditional area of influence for wells in a specified rectangular region with respect to a fixed-size deposit. The deposit is represented by an ellipse whose size is chosen by the user. The area of influence may be displayed on computer printer plots consisting of a maximum of 10,000 grid points. At each point, a symbol is presented that indicates the probability of that point being exhausted by nearby wells with respect to a fixed-size ellipse. This output gives a pictorial view of the manner in which oil fields are exhausted. In addition, the exhaustion data may be used to estimate the number of deposits remaining in a basin. ?? 1977.

  12. Can the box plot be improved?

    OpenAIRE

    Chamnein Choonpradub; Don McNeil

    2005-01-01

    Invented by Spear in 1952 and popularized by Tukey in 1977, the box plot is widely used for displaying and comparing samples of continuous observations. Despite its popularity, it is less effective for showing shape behaviour of distributions, particularly bimodality. Using robust estimators of data skewness and kurtosis to classify the distribution into categories, we suggest a simple enhancement for indicating bimodality, central peakedness, and skewness. We also suggest a new graphical met...

  13. Research note on a parabolic heat-balance integral method with unspecified exponent: An entropy generation approach in optimal profile determination

    Directory of Open Access Journals (Sweden)

    Hristov Jordan

    2009-01-01

    Full Text Available The heat-balance integral method of Goodman is studied with two simple 1-D heat conduction problems with prescribed temperature and flux boundary conditions. These classical problems with well known exact solutions enable to demonstrate the heat-balance integral method performance by a parabolic profile and the entropy generation minimization concept in definition of the appropriate profile exponent. The basic assumption generating the additional constraints needed to perform the solution is based on the requirement to minimize the difference in the local thermal entropy generation rates calculated by the approximate and the exact profile, respectively. This concept is easily applicable since the general concept has simple implementation of the condition requiring the thermal entropy generations calculated through both profiles to be the same at the boundary. The entropy minimization generation approach automatically generates the additional requirement which is deficient in the set of conditions defined by the heat-balance integral method concept.

  14. Microwave measurements of temperature profiles, integrated water vapour, and liquid water path at Thule Air Base, Greenland.

    Science.gov (United States)

    Pace, Giandomenico; Di Iorio, Tatiana; di Sarra, Alcide; Iaccarino, Antonio; Meloni, Daniela; Mevi, Gabriele; Muscari, Giovanni; Cacciani, Marco

    2017-04-01

    A RPG Humidity And Temperature PROfiler (HATPRO-G2 ) radiometer was installed at Thule Air Base (76.5° N, 68.8° W), Greenland, in June 2016 in the framework of the Study of the water VApour in the polar AtmosPhere (SVAAP) project. The Danish Meteorological Institute started measurements of atmospheric properties at Thule Air Base in early '90s. The Thule High Arctic Atmospheric Observatory (THAAO) has grown in size and observing capabilities during the last three decades through the international effort of United States (NCAR and University of Alaska Fairbanks) and Italian (ENEA, INGV, University of Roma and Firenze) institutions (http://www.thuleatmos-it.it). Within this context, the intensive field campaign of the SVAAP project was aimed at the investigation of the surface radiation budget and took place from 5 to 28 July, 2016. After the summer campaign the HATPRO has continued to operate in order to monitor the annual variability of the temperature profile and integrated water vapour as well as the presence and characteristics of liquid clouds in the Artic environment. The combined use of the HATPRO together with other automatic instruments, such as a new microwave spectrometer (the water Vapour Emission Spectrometer for Polar Atmosphere VESPA-22), upward- and downward-looking pyranometers and pyrgeometers, a zenith-looking pyrometer operating in the 9.6-11.5 µm spectral range, an all sky camera, and a meteorological station, allows to investigate the clouds' physical and optical properties, as well as their impact on the surface radiation budget. This study will present and discuss the first few months of HATPRO observations; the effectiveness of the statistical retrieval used to derive the physical parameters from the HATPRO brightness temperatures will also be investigated through the comparison of the temperature and humidity profiles, and integrated water vapour, with data from radiosondes launched during the summer campaign and in winter time.

  15. Managing multimorbidity: profiles of integrated care approaches targeting people with multiple chronic conditions in Europe.

    NARCIS (Netherlands)

    Rijken, M.; Hujala, A.; Ginneken, E. van; Melchiorre, M.G.; Groenewegen, P.; Schellevis, F.

    2017-01-01

    In response to the growing populations of people with multiple chronic diseases, new models of care are currently being developed in European countries to better meet the needs of these people. This paper aims to describe the occurrence and characteristics of various types of integrated care

  16. Citation Mining: Integrating Text Mining and Bibliometrics for Research User Profiling.

    Science.gov (United States)

    Kostoff, Ronald N.; del Rio, J. Antonio; Humenik, James A.; Garcia, Esther Ofilia; Ramirez, Ana Maria

    2001-01-01

    Discusses the importance of identifying the users and impact of research, and describes an approach for identifying the pathways through which research can impact other research, technology development, and applications. Describes a study that used citation mining, an integration of citation bibliometrics and text mining, on articles from the…

  17. Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling.

    Science.gov (United States)

    Castillo, Daniel; Gálvez, Juan Manuel; Herrera, Luis Javier; Román, Belén San; Rojas, Fernando; Rojas, Ignacio

    2017-11-21

    Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more recent Next Generation Sequencing technologies, such as RNA-Seq. In any case, information from microarrays is truthful and robust, thus it can be exploited through the integration of microarray data with RNA-Seq data. Additionally, information extraction and acquisition of large number of samples in RNA-Seq still entails very high costs in terms of time and computational resources.This paper proposes a new model to find the gene signature of breast cancer cell lines through the integration of heterogeneous data from different breast cancer datasets, obtained from microarray and RNA-Seq technologies. Consequently, data integration is expected to provide a more robust statistical significance to the results obtained. Finally, a classification method is proposed in order to test the robustness of the Differentially Expressed Genes when unseen data is presented for diagnosis. The proposed data integration allows analyzing gene expression samples coming from different technologies. The most significant genes of the whole integrated data were obtained through the intersection of the three gene sets, corresponding to the identified expressed genes within the microarray data itself, within the RNA-Seq data itself, and within the integrated data from both technologies. This intersection reveals 98 possible technology-independent biomarkers. Two different heterogeneous datasets were distinguished for the classification tasks: a training dataset for gene expression identification and classifier validation, and a test dataset with unseen data for testing the classifier. Both of them achieved great classification accuracies, therefore confirming the validity of the obtained set of genes as possible biomarkers for breast cancer. Through a feature selection process, a final

  18. 9 CFR 108.3 - Preparation of plot plans.

    Science.gov (United States)

    2010-01-01

    ... on the plot plan the use of immediate adjacent properties such as, residential area, pasture, box... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Preparation of plot plans. 108.3... LICENSED ESTABLISHMENTS § 108.3 Preparation of plot plans. Plot plans shall show all of the buildings on a...

  19. Subsurface profiling using integrated geophysical methods for 2D site response analysis in Bangalore city, India: a new approach

    Science.gov (United States)

    Chandran, Deepu; Anbazhagan, P.

    2017-10-01

    Recently, site response analysis has become a mandatory step for the design of important structures. Subsurface investigation is an essential step, from where the input parameters for the site response study like density, shear wave velocity (Vs), thickness and damping characteristics, etc, are obtained. Most site response studies at shallow bedrock sites are one-dimensional (1D) and are usually carried out by using Vs from multi-channel analysis of surface waves (MASW) or a standard penetration test (SPT) for N values with assumptions that soil layers are horizontal, uniform and homogeneous. These assumptions are not completely true in shallow bedrock regions as soil deposits are heterogeneous. The objective of this study is to generate the actual subsurface profiles in two-dimensions at shallow bedrock regions using integrated subsurface investigation testing. The study area selected for this work is Bangalore, India. Three survey lines were selected in Bangalore at two different locations; one at the Indian Institute of Science (IISc) Campus and the other at Whitefield. Geophysical surveys like ground penetrating radar (GPR) and 2D MASW were carried out at these survey lines. Geophysical test results are compared and validated with a conventional geotechnical SPT. At the IISc site, the soil profile is obtained from a trench excavated for a proposed pipeline used to compare the geophysical test results. Test results show that GPR is very useful to delineate subsurface layers, especially for shallow depths at both sites (IISc Campus and Whitefield). MASW survey results show variation of Vs values and layer thickness comparatively at deeper depths for both sites. They also show higher density soil strata with high Vs value obtained at the IISc Campus site, whereas at the Whitefield site weaker soil with low shear velocity is observed. Combining these two geophysical methods helped to generate representative 2D subsurface profiles. These subsurface profiles can be

  20. Split-Plot Designs with Mirror Image Pairs as Subplots

    DEFF Research Database (Denmark)

    Tyssedal, John; Kulahci, Murat; Bisgaard, Soren

    2011-01-01

    In this article we investigate two-level split-plot designs where the sub-plots consist of only two mirror image trials. Assuming third and higher order interactions negligible, we show that these designs divide the estimated effects into two orthogonal sub-spaces, separating sub-plot main effects...... and sub-plot by whole-plot interactions from the rest. Further we show how to construct split-plot designs of projectivity P≥3. We also introduce a new class of split-plot designs with mirror image pairs constructed from non-geometric Plackett–Burman designs. The design properties of such designs are very...

  1. Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors.

    Directory of Open Access Journals (Sweden)

    Joseph J Babcock

    Full Text Available Growing evidence suggests that drugs interact with diverse molecular targets mediating both therapeutic and toxic effects. Prediction of these complex interactions from chemical structures alone remains challenging, as compounds with different structures may possess similar toxicity profiles. In contrast, predictions based on systems-level measurements of drug effect may reveal pharmacologic similarities not evident from structure or known therapeutic indications. Here we utilized drug-induced transcriptional responses in the Connectivity Map (CMap to discover such similarities among diverse antagonists of the human ether-à-go-go related (hERG potassium channel, a common target of promiscuous inhibition by small molecules. Analysis of transcriptional profiles generated in three independent cell lines revealed clusters enriched for hERG inhibitors annotated using a database of experimental measurements (hERGcentral and clinical indications. As a validation, we experimentally identified novel hERG inhibitors among the unannotated drugs in these enriched clusters, suggesting transcriptional responses may serve as predictive surrogates of cardiotoxicity complementing existing functional assays.

  2. Tissue specific profiling of females of Schistosoma japonicum by integrated laser microdissection microscopy and microarray analysis.

    Directory of Open Access Journals (Sweden)

    Geoffrey N Gobert

    2009-06-01

    Full Text Available The functions of many schistosome gene products remain to be characterized. A major step towards elucidating function of these genes would be in defining their sites of expression. This goal is rendered difficult to achieve by the generally small size of the parasites and the lack of a body cavity, which precludes analysis of transcriptional profiles of the tissues in isolation.Here, we describe a combined laser microdissection microscopy (LMM and microarray analysis approach to expedite tissue specific profiling and gene atlasing for tissues of adult female Schistosoma japonicum. This approach helps to solve the gene characterization "bottle-neck" brought about by acoelomy and the size of these parasites. Complementary RNA obtained after isolation from gastrodermis (parasite gut mucosa, vitelline glands and ovary by LMM were subjected to microarray analyses, resulting in identification of 147 genes upregulated in the gastrodermis, 4,149 genes in the ovary and 2,553 in the vitellaria.This work will help to shed light on the molecular pathobiology of this debilitating human parasite and aid in the discovery of new targets for the development of anti-schistosome vaccines and drugs.

  3. Encounters with neighbours : current developments of concepts based on recurrence plots and their applications

    Science.gov (United States)

    Marwan, Norbert

    2003-09-01

    In this work, different aspects and applications of the recurrence plot analysis are presented. First, a comprehensive overview of recurrence plots and their quantification possibilities is given. New measures of complexity are defined by using geometrical structures of recurrence plots. These measures are capable to find chaos-chaos transitions in processes. Furthermore, a bivariate extension to cross recurrence plots is studied. Cross recurrence plots exhibit characteristic structures which can be used for the study of differences between two processes or for the alignment and search for matching sequences of two data series. The selected applications of the introduced techniques to various kind of data demonstrate their ability. Analysis of recurrence plots can be adopted to the specific problem and thus opens a wide field of potential applications. Regarding the quantification of recurrence plots, chaos-chaos transitions can be found in heart rate variability data before the onset of life threatening cardiac arrhythmias. This may be of importance for the therapy of such cardiac arrhythmias. The quantification of recurrence plots allows to study transitions in brain during cognitive experiments on the base of single trials. Traditionally, for the finding of these transitions the averaging of a collection of single trials is needed. Using cross recurrence plots, the existence of an El Niño/Southern Oscillation-like oscillation is traced in northwestern Argentina 34,000 yrs. ago. In further applications to geological data, cross recurrence plots are used for time scale alignment of different borehole data and for dating a geological profile with a reference data set. Additional examples from molecular biology and speech recognition emphasize the suitability of cross recurrence plots. Diese Arbeit beschäftigt sich mit verschiedenen Aspekten und Anwendungen von Recurrence Plots. Nach einer Übersicht über Methoden, die auf Recurrence Plots basieren, werden neue

  4. Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.

    Science.gov (United States)

    Zhang, Lei; Ma, Shiyun; Wang, Huailiang; Su, Hang; Su, Ke; Li, Longjie

    2017-11-15

    The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA. Copyright © 2017. Published by Elsevier B.V.

  5. Development of carbon response trajectories using FIA plot data and FVS growth simulator: challenges of a large scale simulation project

    Science.gov (United States)

    James B. McCarter; Sean. Healey

    2015-01-01

    The Forest Carbon Management Framework (ForCaMF) integrates Forest Inventory and Analysis (FIA) plot inventory data, disturbance histories, and carbon response trajectories to develop estimates of disturbance and management effects on carbon pools for the National Forest System. All appropriate FIA inventory plots are simulated using the Forest Vegetation Simulator (...

  6. Authentication of Zanthoxylum Species Based on Integrated Analysis of Complete Chloroplast Genome Sequences and Metabolite Profiles.

    Science.gov (United States)

    Lee, Hyeon Ju; Koo, Hyun Jo; Lee, Jonghoon; Lee, Sang-Choon; Lee, Dong Young; Giang, Vo Ngoc Linh; Kim, Minjung; Shim, Hyeonah; Park, Jee Young; Yoo, Ki-Oug; Sung, Sang Hyun; Yang, Tae-Jin

    2017-11-29

    We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species. Metabolite profile analysis pointed to three metabolic groups, one with Korean Z. piperitum samples, one with Korean Z. schinifolium samples, and the last containing all the tested Chinese Zanthoxylum species samples, which are considered to be Z. bungeanum based on our results. Two markers were capable of distinguishing among these three groups. The chloroplast genome sequences identified in this study represent a valuable genomics resource for exploring diversity in Rutaceae, and the molecular markers will be useful for authenticating dried Zanthoxylum berries in the marketplace.

  7. Can the box plot be improved?

    Directory of Open Access Journals (Sweden)

    Chamnein Choonpradub

    2005-05-01

    Full Text Available Invented by Spear in 1952 and popularized by Tukey in 1977, the box plot is widely used for displaying and comparing samples of continuous observations. Despite its popularity, it is less effective for showing shape behaviour of distributions, particularly bimodality. Using robust estimators of data skewness and kurtosis to classify the distribution into categories, we suggest a simple enhancement for indicating bimodality, central peakedness, and skewness. We also suggest a new graphical method for displaying confidence intervals when comparing several samples of continuous data.

  8. Integrating chromosomal aberrations and gene expression profiles to dissect rectal tumorigenesis

    Directory of Open Access Journals (Sweden)

    Eilers Paul HC

    2008-10-01

    Full Text Available Abstract Background Accurate staging of rectal tumors is essential for making the correct treatment choice. In a previous study, we found that loss of 17p, 18q and gain of 8q, 13q and 20q could distinguish adenoma from carcinoma tissue and that gain of 1q was related to lymph node metastasis. In order to find markers for tumor staging, we searched for candidate genes on these specific chromosomes. Methods We performed gene expression microarray analysis on 79 rectal tumors and integrated these data with genomic data from the same sample series. We performed supervised analysis to find candidate genes on affected chromosomes and validated the results with qRT-PCR and immunohistochemistry. Results Integration of gene expression and chromosomal instability data revealed similarity between these two data types. Supervised analysis identified up-regulation of EFNA1 in cases with 1q gain, and EFNA1 expression was correlated with the expression of a target gene (VEGF. The BOP1 gene, involved in ribosome biogenesis and related to chromosomal instability, was over-expressed in cases with 8q gain. SMAD2 was the most down-regulated gene on 18q, and on 20q, STMN3 and TGIF2 were highly up-regulated. Immunohistochemistry for SMAD4 correlated with SMAD2 gene expression and 18q loss. Conclusion On basis of integrative analysis this study identified one well known CRC gene (SMAD2 and several other genes (EFNA1, BOP1, TGIF2 and STMN3 that possibly could be used for rectal cancer characterization.

  9. Integrated Analysis of Dysregulated ncRNA and mRNA Expression Profiles in Humans Exposed to Carbon Nanotubes.

    Directory of Open Access Journals (Sweden)

    Anna A Shvedova

    Full Text Available As the application of carbon nanotubes (CNT in consumer products continues to rise, studies have expanded to determine the associated risks of exposure on human and environmental health. In particular, several lines of evidence indicate that exposure to multi-walled carbon nanotubes (MWCNT could pose a carcinogenic risk similar to asbestos fibers. However, to date the potential markers of MWCNT exposure are not yet explored in humans.In the present study, global mRNA and ncRNA expression profiles in the blood of exposed workers, having direct contact with MWCNT aerosol for at least 6 months (n = 8, were compared with expression profiles of non-exposed (n = 7 workers (e.g., professional and/or technical staff from the same manufacturing facility.Significant changes in the ncRNA and mRNA expression profiles were observed between exposed and non-exposed worker groups. An integrative analysis of ncRNA-mRNA correlations was performed to identify target genes, functional relationships, and regulatory networks in MWCNT-exposed workers. The coordinated changes in ncRNA and mRNA expression profiles revealed a set of miRNAs and their target genes with roles in cell cycle regulation/progression/control, apoptosis and proliferation. Further, the identified pathways and signaling networks also revealed MWCNT potential to trigger pulmonary and cardiovascular effects as well as carcinogenic outcomes in humans, similar to those previously described in rodents exposed to MWCNTs.This study is the first to investigate aberrant changes in mRNA and ncRNA expression profiles in the blood of humans exposed to MWCNT. The significant changes in several miRNAs and mRNAs expression as well as their regulatory networks are important for getting molecular insights into the MWCNT-induced toxicity and pathogenesis in humans. Further large-scale prospective studies are necessary to validate the potential applicability of such changes in mRNAs and miRNAs as prognostic markers

  10. Holey buckets! Monitoring plot-scale runoff

    Science.gov (United States)

    Rupp, D. E.; Stewart, R. D.; Abou Najm, M. R.; Selker, J. S.; Selker, F.; Van De Giesen, N.

    2011-12-01

    Measurement of plot-scale surface runoff is commonly achieved by diverting flow through a flume or tipping bucket system, or into a storage tank, such as bucket. The principle advantages of the "bucket method" are relative simplicity and low cost. The principle drawback is that the bucket requires frequent emptying during heavy runoff, unless the bucket volume is very large. As a solution to the problem of emptying the bucket while still retaining the properties of simplicity and economy, we used a holey bucket. Our "bucket" is vertical 4"-diameter ABS pipe, sealed at the bottom, and with holes along the side of the pipe. A screen in the pipe catches debris that could block the holes. The holes' diameters and locations were chosen to capture both low (100 L min-1) flows. Runoff is diverted into the top of the pipe. The runoff rate is determined from the water level and the rate of change in water level: the water level gives the flow rate out of the submerged holes (using Torricelli's Law) and the change in water level gives the rate of change in storage in the pipe. The runoff is calculated as the sum of the hole discharge and the rate of change in storage. A calibration parameter is applied to account for departures from assumptions of the theory. The design is currently being utilized to monitor runoff from experimental plots on a rural hillslope in Chile.

  11. Flyby Error Analysis Based on Contour Plots for the Cassini Tour

    Science.gov (United States)

    Stumpf, P. W.; Gist, E. M.; Goodson, T. D.; Hahn, Y.; Wagner, S. V.; Williams, P. N.

    2008-01-01

    The maneuver cancellation analysis consists of cost contour plots employed by the Cassini maneuver team. The plots are two-dimensional linear representations of a larger six-dimensional solution to a multi-maneuver, multi-encounter mission at Saturn. By using contours plotted with the dot product of vectors B and R and the dot product of vectors B and T components, it is possible to view the effects delta V on for various encounter positions in the B-plane. The plot is used in operations to help determine if the Approach Maneuver (ensuing encounter minus three days) and/or the Cleanup Maneuver (ensuing encounter plus three days) can be cancelled and also is a linear check of an integrated solution.

  12. A DICOM-based 2nd generation Molecular Imaging Data Grid implementing the IHE XDS-i integration profile.

    Science.gov (United States)

    Lee, Jasper; Zhang, Jianguo; Park, Ryan; Dagliyan, Grant; Liu, Brent; Huang, H K

    2012-07-01

    A Molecular Imaging Data Grid (MIDG) was developed to address current informatics challenges in archival, sharing, search, and distribution of preclinical imaging studies between animal imaging facilities and investigator sites. This manuscript presents a 2nd generation MIDG replacing the Globus Toolkit with a new system architecture that implements the IHE XDS-i integration profile. Implementation and evaluation were conducted using a 3-site interdisciplinary test-bed at the University of Southern California. The 2nd generation MIDG design architecture replaces the initial design's Globus Toolkit with dedicated web services and XML-based messaging for dedicated management and delivery of multi-modality DICOM imaging datasets. The Cross-enterprise Document Sharing for Imaging (XDS-i) integration profile from the field of enterprise radiology informatics was adopted into the MIDG design because streamlined image registration, management, and distribution dataflow are likewise needed in preclinical imaging informatics systems as in enterprise PACS application. Implementation of the MIDG is demonstrated at the University of Southern California Molecular Imaging Center (MIC) and two other sites with specified hardware, software, and network bandwidth. Evaluation of the MIDG involves data upload, download, and fault-tolerance testing scenarios using multi-modality animal imaging datasets collected at the USC Molecular Imaging Center. The upload, download, and fault-tolerance tests of the MIDG were performed multiple times using 12 collected animal study datasets. Upload and download times demonstrated reproducibility and improved real-world performance. Fault-tolerance tests showed that automated failover between Grid Node Servers has minimal impact on normal download times. Building upon the 1st generation concepts and experiences, the 2nd generation MIDG system improves accessibility of disparate animal-model molecular imaging datasets to users outside a molecular

  13. Effects of the sesquiterpene lactone parthenolide on prostate tumor-initiating cells: an integrated molecular profiling approach

    Science.gov (United States)

    Kawasaki, Brian T.; Hurt, Elaine M.; Kalathur, Madhuri; Duhagon, Maria Ana; Milner, John A.; Kim, Young S.; Farrar, William L.

    2009-01-01

    Recent evidence suggests tumor-initating cells (TICs), also called cancer stem cells, are responsible for tumor initiation and progression; therefore, they represent an important cell population for development of future anti-cancer therapies. In this study, we show that the sesquiterpene lactone parthenolide (PTL) is cytotoxic to prostate TICs isolated from prostate cancer cell lines: DU145, PC3, VCAP and LAPC4, as well as primary prostate TICs. Furthermore, PTL inhibited TIC-driven tumor formation in mouse xenografts. Using an integrated molecular profiling approach encompassing proteomics, profiles of activated transcription factors and genomics we ascertained the effects of PTL on prostate cancer cells. In addition to the previously described effects of PTL, we determined that the non-receptor tyrosine kinase src, and many src signaling components, including: Csk, FAK, β1-arrestin, FGFR2, PKC, MEK/MAPK, CaMK, ELK-1 and ELK-1-dependent genes are novel targets of PTL action. Furthermore, PTL altered the binding of transcription factors important in prostate cancer including: C/EBP-α, fos related antigen-1 (FRA-1), HOXA-4, c-MYB, SNAIL, SP1, serum response factor (SRF), STAT3, X-box binding protein-1 (XBP1) and p53. In summary, we show PTL is cytotoxic to prostate TICs and describe the molecular events of PTL-mediated cytotoxicity. Therefore, PTL represents a promising therapeutic for prostate cancer treatment. PMID:19204913

  14. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

    Science.gov (United States)

    Farshidfar, Farshad; Zheng, Siyuan; Gingras, Marie-Claude; Newton, Yulia; Shih, Juliann; Robertson, A Gordon; Hinoue, Toshinori; Hoadley, Katherine A; Gibb, Ewan A; Roszik, Jason; Covington, Kyle R; Wu, Chia-Chin; Shinbrot, Eve; Stransky, Nicolas; Hegde, Apurva; Yang, Ju Dong; Reznik, Ed; Sadeghi, Sara; Pedamallu, Chandra Sekhar; Ojesina, Akinyemi I; Hess, Julian M; Auman, J Todd; Rhie, Suhn K; Bowlby, Reanne; Borad, Mitesh J; Zhu, Andrew X; Stuart, Josh M; Sander, Chris; Akbani, Rehan; Cherniack, Andrew D; Deshpande, Vikram; Mounajjed, Taofic; Foo, Wai Chin; Torbenson, Michael S; Kleiner, David E; Laird, Peter W; Wheeler, David A; McRee, Autumn J; Bathe, Oliver F; Andersen, Jesper B; Bardeesy, Nabeel; Roberts, Lewis R; Kwong, Lawrence N

    2017-03-14

    Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

    Directory of Open Access Journals (Sweden)

    Farshad Farshidfar

    2017-03-01

    Full Text Available Cholangiocarcinoma (CCA is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

  16. iTagPlot: an accurate computation and interactive drawing tool for tag density plot.

    Science.gov (United States)

    Kim, Sung-Hwan; Ezenwoye, Onyeka; Cho, Hwan-Gue; Robertson, Keith D; Choi, Jeong-Hyeon

    2015-07-15

    Tag density plots are very important to intuitively reveal biological phenomena from capture-based sequencing data by visualizing the normalized read depth in a region. We have developed iTagPlot to compute tag density across functional features in parallel using multicores and a grid engine and to interactively explore it in a graphical user interface. It allows us to stratify features by defining groups based on biological function and measurement, summary statistics and unsupervised clustering. http://sourceforge.net/projects/itagplot/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. An Integrated Strategy for Global Qualitative and Quantitative Profiling of Traditional Chinese Medicine Formulas: Baoyuan Decoction as a Case

    Science.gov (United States)

    Ma, Xiaoli; Guo, Xiaoyu; Song, Yuelin; Qiao, Lirui; Wang, Wenguang; Zhao, Mingbo; Tu, Pengfei; Jiang, Yong

    2016-12-01

    Clarification of the chemical composition of traditional Chinese medicine formulas (TCMFs) is a challenge due to the variety of structures and the complexity of plant matrices. Herein, an integrated strategy was developed by hyphenating ultra-performance liquid chromatography (UPLC), quadrupole time-of-flight (Q-TOF), hybrid triple quadrupole-linear ion trap mass spectrometry (Qtrap-MS), and the novel post-acquisition data processing software UNIFI to achieve automatic, rapid, accurate, and comprehensive qualitative and quantitative analysis of the chemical components in TCMFs. As a proof-of-concept, the chemical profiling of Baoyuan decoction (BYD), which is an ancient TCMF that is clinically used for the treatment of coronary heart disease that consists of Ginseng Radix et Rhizoma, Astragali Radix, Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle, and Cinnamomi Cortex, was performed. As many as 236 compounds were plausibly or unambiguously identified, and 175 compounds were quantified or relatively quantified by the scheduled multiple reaction monitoring (sMRM) method. The findings demonstrate that the strategy integrating the rapidity of UNIFI software, the efficiency of UPLC, the accuracy of Q-TOF-MS, and the sensitivity and quantitation ability of Qtrap-MS provides a method for the efficient and comprehensive chemome characterization and quality control of complex TCMFs.

  18. Tracker Alignment Performance Plots after Commissioning

    CERN Document Server

    CMS Collaboration

    2017-01-01

    During the LHC shutdown in Winter 2016/17, the CMS pixel detector, the inner component of the CMS Tracker, was replaced by the Phase-1 upgrade detector. Among others improvements, the new pixel detector consists of four instead of three layers in the central barrel region (BPIX) and three instead of two disks in the endcap regions (FPIX). In this report, performance plots of pixel detector alignment results are presented, which were obtained with both cosmic-ray and pp collision data acquired at the beginning of the 2017 LHC operation. Alignment constants have been derived for each data-taking period to the level of single module positions in both the pixel and the strip detectors. The complete understanding of the alignment and biases was derived by using two algorithms, Millepede-II and HipPy. The results confirm each other.

  19. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

    Science.gov (United States)

    Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita

    2016-01-01

    We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution. PMID:27803195

  20. MetaTopics: an integration tool to analyze microbial community profile by topic model.

    Science.gov (United States)

    Yan, Jifang; Chuai, Guohui; Qi, Tao; Shao, Fangyang; Zhou, Chi; Zhu, Chenyu; Yang, Jing; Yu, Yifei; Shi, Cong; Kang, Ning; He, Yuan; Liu, Qi

    2017-01-25

    Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown. MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes. Furthermore, a quantitative measurement, Quetelet Index, is defined to estimate the influence of a latent sub-community on a certain disease status for given samples. An analysis of our in-house oral metagenomics data and public gut microbe data was presented to demonstrate the application and usefulness of MetaTopics. To preset a user-friendly R package, we have built a dedicated website, https://github.com/bm2-lab/MetaTopics , which includes free downloads, detailed tutorials and illustration examples. MetaTopics is the first interactive R package to integrate the state-of-arts topic model derived from statistical learning community to analyze and visualize the metagenomics taxonomy data.

  1. Profiles of rural longitudinal integrated clerkship students: a descriptive study of six consecutive student cohorts *.

    Science.gov (United States)

    Brooks, Kathleen D; Eley, Diann S; Zink, Therese

    2014-02-01

    Medical schools worldwide are challenged to address the rural primary care workforce shortage by creating community-engaged curricula to nurture student interest in rural practice. To examine the personal characteristics of six consecutive rural longitudinal integrated clerkship student cohorts to understand whom the programs attract and select and thus inform the development of such programs. A cross-sectional cohort design was used. Six cohorts (2007-2012) completed a survey on demographics and factors that influenced their choice of rural primary care. The Temperament and Character Inventory was used to measure personality. Analysis was mainly descriptive. Where appropriate univariate analysis compared variables between groups. Sample size was 205 with the majority female (61%), between 25 and 29 years (64%), single (60%) and lived longest in rural communities with populations less than 20,000 (60%). Rural lifestyle, background and desire to work in underserved areas were noted to impact rural medicine interest. Professional satisfaction, personal and professional goals and family needs had the highest impact on career decisions, and financial concerns lowest. The stability of students' personal characteristics across cohorts and the workforce outcomes of this program suggest the recruitment process successfully nurtures students who will fit well into future rural practice.

  2. Integration of miRNA and protein profiling reveals coordinated neuroadaptations in the alcohol-dependent mouse brain.

    Directory of Open Access Journals (Sweden)

    Giorgio Gorini

    Full Text Available The molecular mechanisms underlying alcohol dependence involve different neurochemical systems and are brain region-dependent. Chronic Intermittent Ethanol (CIE procedure, combined with a Two-Bottle Choice voluntary drinking paradigm, represents one of the best available animal models for alcohol dependence and relapse drinking. MicroRNAs, master regulators of the cellular transcriptome and proteome, can regulate their targets in a cooperative, combinatorial fashion, ensuring fine tuning and control over a large number of cellular functions. We analyzed cortex and midbrain microRNA expression levels using an integrative approach to combine and relate data to previous protein profiling from the same CIE-subjected samples, and examined the significance of the data in terms of relative contribution to alcohol consumption and dependence. MicroRNA levels were significantly altered in CIE-exposed dependent mice compared with their non-dependent controls. More importantly, our integrative analysis identified modules of coexpressed microRNAs that were highly correlated with CIE effects and predicted target genes encoding differentially expressed proteins. Coexpressed CIE-relevant proteins, in turn, were often negatively correlated with specific microRNA modules. Our results provide evidence that microRNA-orchestrated translational imbalances are driving the behavioral transition from alcohol consumption to dependence. This study represents the first attempt to combine ex vivo microRNA and protein expression on a global scale from the same mammalian brain samples. The integrative systems approach used here will improve our understanding of brain adaptive changes in response to drug abuse and suggests the potential therapeutic use of microRNAs as tools to prevent or compensate multiple neuroadaptations underlying addictive behavior.

  3. Heterogeneous Molecular Catalysis of Electrochemical Reactions: Volcano Plots and Catalytic Tafel Plots.

    Science.gov (United States)

    Costentin, Cyrille; Savéant, Jean-Michel

    2017-06-14

    We analyze here, in the framework of heterogeneous molecular catalysis, the reasons for the occurrence or nonoccurrence of volcanoes upon plotting the kinetics of the catalytic reaction versus the stabilization free energy of the primary intermediate of the catalytic process. As in the case of homogeneous molecular catalysis or catalysis by surface-active metallic sites, a strong motivation of such studies relates to modern energy challenges, particularly those involving small molecules, such as water, hydrogen, oxygen, proton, and carbon dioxide. This motivation is particularly pertinent for what concerns heterogeneous molecular catalysis, since it is commonly preferred to homogeneous molecular catalysis by the same molecules if only for chemical separation purposes and electrolytic cell architecture. As with the two other catalysis modes, the main drawback of the volcano plot approach is the basic assumption that the kinetic responses depend on a single descriptor, viz., the stabilization free energy of the primary intermediate. More comprehensive approaches, investigating the responses to the maximal number of experimental factors, and conveniently expressed as catalytic Tafel plots, should clearly be preferred. This is more so in the case of heterogeneous molecular catalysis in that additional transport factors in the supporting film may additionally affect the current-potential responses. This is attested by the noteworthy presence of maxima in catalytic Tafel plots as well as their dependence upon the cyclic voltammetric scan rate.

  4. Visualising disease progression on multiple variables with vector plots and path plots

    Directory of Open Access Journals (Sweden)

    Michell Andrew W

    2009-05-01

    Full Text Available Abstract Background It is often desirable to observe how a disease progresses over time in individual patients, rather than graphing group averages; and since multiple outcomes are typically recorded on each patient, it would be advantageous to visualise disease progression on multiple variables simultaneously. Methods A variety of vector plots and a path plot have been developed for this purpose, and data from a longitudinal Huntington's disease study are used to illustrate the utility of these graphical methods for exploratory data analysis. Results Initial and final values for three outcome variables can be easily visualised per patient, along with the change in these variables over time. In addition to the disease trajectory, the path individual patients take from initial to final observation can be traced. Categorical variables can be coded with different types of vectors or paths (e.g. different colours, line types, line thickness and separate panels can be used to include further categorical or continuous variables, allowing clear visualisation of further information for each individual. In addition, summary statistics such as mean vectors, bivariate interquartile ranges and convex polygons can be included to assist in interpreting trajectories, comparing groups, and detecting multivariate outliers. Conclusion Vector and path plots are useful graphical methods for exploratory data analysis when individual-level information on multiple variables over time is desired, and they have several advantages over plotting each variable separately.

  5. Institutional profile: integrated center for research and treatment of vertigo, balance and ocular motor disorders.

    Science.gov (United States)

    Brandt, Thomas; Zwergal, Andreas; Jahn, Klaus; Strupp, Michael

    2010-01-01

    In 2009 the German BMBF (German Ministry of Education and Research) established an Integrated Center for Research and Treatment (IFB(LMU)) of Vertigo, Balance and Ocular Motor Disorders in Munich. After the 10-year period of funding by the BMBF, it is envisioned that the (IFB(LMU)) will continue over the long term with the joint support of the University Hospital, the Medical Faculty, and the Bavarian State. Vertigo is one of the most common complaints in medicine. Despite its high prevalence, patients with vertigo generally receive either inappropriate or inadequate treatment. This deplorable situation is internationally well known and its causes are multiple: insufficient interdisciplinary cooperation, no standardized diagnostics and therapy, the failure to translate findings of basic science into clinical applications, and the scarcity of clinical multicenter studies. The (IFB(LMU)) will constitute a suitable tool with which these structural, clinical, and scientific deficits can be overcome. It will also make possible the establishment of an international interdisciplinary referral center. Munich has become the site of a unique concentration of leading experts on vertigo, balance and ocular motor disorders, both in the clinical and basic sciences. Academic structures have paved the way for the creation of an interdisciplinary horizontal network that also allows structured, vertical academic career paths via the Bachelor's and Master's degree programs in Neuroscience, a Graduate School of Systemic Neurosciences, and the Munich Center for Neurosciences - Brain and Mind. The (IFB(LMU)) has the following objectives as regards structure and content: to create an independent patient-oriented clinical research center under the auspices of the Medical Faculty but with autonomous administration and budget; to overcome existing clinical and academic barriers separating the traditional specializations; to establish a standardized interdisciplinary longitudinal and

  6. Toward an integrated profile of emotional intelligence: introducing a brief measure.

    Science.gov (United States)

    Kemp, Andrew H; Cooper, Nicholas J; Hermens, Gerard; Gordon, Evian; Bryant, Richard; Williams, Leanne M

    2005-03-01

    Over the last decade, an increasing number of research studies have focused on the construct of Emotional Intelligence (EI), which may be broadly defined as the capacity to perceive and regulate emotions in oneself as well as those of others. Researchers have generally adopted an organizational or management focus to the study of EI, however studies which adopt a more integrated perspective by combining psychological with biological measures, may help in further elucidating this relatively abstract construct. The first objective of this paper was to report on the psychometric properties of a brief, self-report measure of EI (Brain Resource Inventory for Emotional intelligence Factors or BRIEF), comprising internal emotional capacity (IEC), external emotional capacity (EEC) and self concept (SELF). Second, we further explored the validity of the measure by assessing the relationships between the BRIEF and variables considered relevant to the understanding of EI (including gender, age, personality, cognitive intelligence and resting state electroencephalography, EEG). The BRIEF possessed sound psychometric properties (internal consistency, r=0.68-0.81; test-retest reliability, r=0.92; construct validity with the Self Report Emotional Intelligence Test, r=0.70). As hypothesized, females were found to score higher than males on EI. EI was associated more with personality than with cognitive ability, and EEG was found to explain a significant portion of the variance in EI scores. The finding that low EI is related to underarousal of the left-frontal cortex (increased theta EEG) is consistent with research on patients with depression, as well as attention deficit hyperactivity disorder. Although EI did not display age-related increases, this might relate to the exclusion of adolescents from our sample. In conclusion, examination of the way in which EI measures relate to a complementary range of psychological and biological measures may help to further elucidate this

  7. Integrated near-surface refraction and reflection profiling across the Carlsberg Fault, Denmark

    Science.gov (United States)

    Jorgensen, M. I.; Nielsen, L.; Thybo, H.; Fallesen, J.

    2003-04-01

    An integrated refraction and normal-incidence reflection seismic experiment has been conducted in order to resolve the near-surface part of the Carlsberg Fault in the easternmost part of the Danish basin. The primary objectives of the seismic experiment are to: 1) determine the fault structure; 2) image possible velocity contrasts across the fault; and 3) estimate how much the fault offsets the individual sedimentary layers at the different depth levels. The upper sedimentary strata in the study area consist of Cretaceous and Danian chalk and younger sediments dominated by sand and clay. The Carlsberg Fault is a NNW-SSE striking fault, which offsets the different sedimentary lithologies. It was probably created due to extensional stresses in a strike-slip system of the Sorgenfrei-Tornquist Zone, which is situated approximately 50 km east of the study area. Geodetic measurements indicate that the Carlsberg Fault may have been active during the last 100 years. The 1100 m long seismic reflection section, which was collected in 1995, shows a pronounced flower structure across the Carlsberg Fault, indicative of lateral movements along the fault plane. The seismic experiments were conducted in the SE part of Copenhagen, and urban noise was a major obstacle during collection of the refraction data in 2002. Nevertheless, both first arrivals and wide-angle reflections are prominent along the 3000 m long refraction line. From seismic travel time modelling we find that the P-wave velocity structure changes across the fault zone. The P-wave velocities in the chalk layers are relatively high (typically more than 3.0 km/s) compared to velocities from well log data of similar rock types elsewhere in the Danish area. The estimated velocity structure allows us to depth convert the reflection seismic sections. Vertical offsets of up to 90 m are observed for layers across the fault zone.

  8. Functional profile of the binary brain corticosteroid receptor system: mediating, multitasking, coordinating, integrating.

    Science.gov (United States)

    de Kloet, E R

    2013-11-05

    This contribution is focused on the action of the naturally occurring corticosteroids, cortisol and corticosterone, which are secreted from the adrenals in hourly pulses and after stress with the goal to maintain resilience and health. To achieve this goal the action of the corticosteroids displays an impressive diversity, because it is cell-specific and context-dependent in coordinating the individual's response to changing environments. These diverse actions of corticosterone are mediated by mineralocorticoid- and glucocorticoid-receptors that operate as a binary system in concert with neurotransmitter and neuropeptide signals to activate and inhibit stress reactions, respectively. Classically MR and GR are gene transcription factors, but recently these receptors appear to mediate also rapid non-genomic actions on excitatory neurotransmission suggesting that they integrate functions over time. Hence the balance of receptor-mediated actions is crucial for homeostasis. This balanced function of mineralo- and glucocorticoid-receptors can be altered epigenetically by a history of traumatic (early) life events and the experience of repeated stressors as well as by predisposing genetic variants in signaling pathways of these receptors. One of these variants, mineralocorticoid receptor haplotype 2, is associated with dispositional optimism in appraisal of environmental challenges. Imbalance in receptor-mediated corticosterone actions was found to leave a genomic signature highlighting the role of master switches such as cAMP response element-binding protein and mammalian target of rapamycin to compromise health, and to promote vulnerability to disease. Diabetic encephalopathy is a pathology of imbalanced corticosterone action, which can be corrected in its pre-stage by a brief treatment with the antiglucocorticoid mifepristone. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Integrating circadian activity and gene expression profiles to predict chronotoxicity of Drosophila suzukii response to insecticides.

    Directory of Open Access Journals (Sweden)

    Kelly A Hamby

    Full Text Available Native to Southeast Asia, Drosophila suzukii (Matsumura is a recent invader that infests intact ripe and ripening fruit, leading to significant crop losses in the U.S., Canada, and Europe. Since current D. suzukii management strategies rely heavily on insecticide usage and insecticide detoxification gene expression is under circadian regulation in the closely related Drosophila melanogaster, we set out to determine if integrative analysis of daily activity patterns and detoxification gene expression can predict chronotoxicity of D. suzukii to insecticides. Locomotor assays were performed under conditions that approximate a typical summer or winter day in Watsonville, California, where D. suzukii was first detected in North America. As expected, daily activity patterns of D. suzukii appeared quite different between 'summer' and 'winter' conditions due to differences in photoperiod and temperature. In the 'summer', D. suzukii assumed a more bimodal activity pattern, with maximum activity occurring at dawn and dusk. In the 'winter', activity was unimodal and restricted to the warmest part of the circadian cycle. Expression analysis of six detoxification genes and acute contact bioassays were performed at multiple circadian times, but only in conditions approximating Watsonville summer, the cropping season, when most insecticide applications occur. Five of the genes tested exhibited rhythmic expression, with the majority showing peak expression at dawn (ZT0, 6am. We observed significant differences in the chronotoxicity of D. suzukii towards malathion, with highest susceptibility at ZT0 (6am, corresponding to peak expression of cytochrome P450s that may be involved in bioactivation of malathion. High activity levels were not found to correlate with high insecticide susceptibility as initially hypothesized. Chronobiology and chronotoxicity of D. suzukii provide valuable insights for monitoring and control efforts, because insect activity as well as

  10. Variability of Measured Runoff and Soil Loss from Field Plots

    Directory of Open Access Journals (Sweden)

    F. Asadzadeh

    2016-02-01

    Full Text Available Introduction: Field plots are widely used in studies related to the measurements of soil loss and modeling of erosion processes. Research efforts are needed to investigate factors affecting the data quality of plots. Spatial scale or size of plots is one of these factors which directly affects measuring runoff and soil loss by means of field plots. The effect of plot size on measured runoff or soil loss from natural plots is known as plot scale effect. On the other hand, variability of runoff and sediment yield from replicated filed plots is a main source of uncertainty in measurement of erosion from plots which should be considered in plot data interpretation processes. Therefore, there is a demand for knowledge of soil erosion processes occurring in plots of different sizes and of factors that determine natural variability, as a basis for obtaining soil loss data of good quality. This study was carried out to investigate the combined effects of these two factors by measurement of runoff and soil loss from replicated plots with different sizes. Materials and Methods: In order to evaluate the variability of runoff and soil loss data seven plots, differing in width and length, were constructed in a uniform slope of 9% at three replicates at Koohin Research Station in Qazvin province. The plots were ploughed up to down slope in September 2011. Each plot was isolated using soil beds with a height of 30 cm, to direct generated surface runoff to the lower part of the plots. Runoff collecting systems composed of gutters, pipes and tankswere installed at the end of each plot. During the two-year study period of 2011-2012, plots were maintained in bare conditions and runoff and soil loss were measured for each single event. Precipitation amounts and characteristics were directly measured by an automatic recording tipping-bucket rain gauge located about 200 m from the experimental plots. The entire runoff volume including eroded sediment was measured on

  11. Relative Efficiency of Split-plot Design (SPD) to Randomized ...

    African Journals Online (AJOL)

    PROF. O. E. OSUAGWU

    2013-06-01

    Datafield Logistics ..... k level of the poultry manure (split-plot treatments);. ( )jk. AB is the interaction effect of the th j level of the phosphorus (whole-plot treatments) and th k level of the poultry manure (split-plot treatments); ijkl e.

  12. Worm plot to diagnose fit in quantile regression

    NARCIS (Netherlands)

    Buuren, S. van

    2007-01-01

    The worm plot is a series of detrended Q-Q plots, split by covariate levels. The worm plot is a diagnostic tool for visualizing how well a statistical model fits the data, for finding locations at which the fit can be improved, and for comparing the fit of different models. This paper shows how

  13. Worm plot to diagnose fit in quantile regression

    NARCIS (Netherlands)

    Buuren, S. van

    2007-01-01

    The worm plot is a series of detrended Q-Q plots, split by covariate levels. The worm plot is a diagnostic tool for visualizing how well a statistical model fits the data, for finding locations at which the fit can be improved, and for comparing the fit of different models. This paper shows how the

  14. Integrated analysis of gene expression profiles associated with response of platinum/paclitaxel-based treatment in epithelial ovarian cancer.

    Directory of Open Access Journals (Sweden)

    Yong Han

    Full Text Available PURPOSE: This study aims to explore gene expression signatures and serum biomarkers to predict intrinsic chemoresistance in epithelial ovarian cancer (EOC. PATIENTS AND METHODS: Gene expression profiling data of 322 high-grade EOC cases between 2009 and 2010 in The Cancer Genome Atlas project (TCGA were used to develop and validate gene expression signatures that could discriminate different responses to first-line platinum/paclitaxel-based treatments. A gene regulation network was then built to further identify hub genes responsible for differential gene expression between the complete response (CR group and the progressive disease (PD group. Further, to find more robust serum biomarkers for clinical application, we integrated our gene signatures and gene signatures reported previously to identify secretory protein-encoding genes by searching the DAVID database. In the end, gene-drug interaction network was constructed by searching Comparative Toxicogenomics Database (CTD and literature. RESULTS: A 349-gene predictive model and an 18-gene model independent of key clinical features with high accuracy were developed for prediction of chemoresistance in EOC. Among them, ten important hub genes and six critical signaling pathways were identified to have important implications in chemotherapeutic response. Further, ten potential serum biomarkers were identified for predicting chemoresistance in EOC. Finally, we suggested some drugs for individualized treatment. CONCLUSION: We have developed the predictive models and serum biomarkers for platinum/paclitaxel response and established the new approach to discover potential serum biomarkers from gene expression profiles. The potential drugs that target hub genes are also suggested.

  15. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples.

    Science.gov (United States)

    Hintzsche, Jennifer; Kim, Jihye; Yadav, Vinod; Amato, Carol; Robinson, Steven E; Seelenfreund, Eric; Shellman, Yiqun; Wisell, Joshua; Applegate, Allison; McCarter, Martin; Box, Neil; Tentler, John; De, Subhajyoti; Robinson, William A; Tan, Aik Choon

    2016-07-01

    Currently, there is a disconnect between finding a patient's relevant molecular profile and predicting actionable therapeutics. Here we develop and implement the Integrating Molecular Profiles with Actionable Therapeutics (IMPACT) analysis pipeline, linking variants detected from whole-exome sequencing (WES) to actionable therapeutics. The IMPACT pipeline contains 4 analytical modules: detecting somatic variants, calling copy number alterations, predicting drugs against deleterious variants, and analyzing tumor heterogeneity. We tested the IMPACT pipeline on whole-exome sequencing data in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples with known EGFR mutations. We also used IMPACT to analyze melanoma patient tumor samples before treatment, after BRAF-inhibitor treatment, and after BRAF- and MEK-inhibitor treatment. IMPACT Food and Drug Administration (FDA) correctly identified known EGFR mutations in the TCGA lung adenocarcinoma samples. IMPACT linked these EGFR mutations to the appropriate FDA-approved EGFR inhibitors. For the melanoma patient samples, we identified NRAS p.Q61K as an acquired resistance mutation to BRAF-inhibitor treatment. We also identified CDKN2A deletion as a novel acquired resistance mutation to BRAFi/MEKi inhibition. The IMPACT analysis pipeline predicts these somatic variants to actionable therapeutics. We observed the clonal dynamic in the tumor samples after various treatments. We showed that IMPACT not only helped in successful prioritization of clinically relevant variants but also linked these variations to possible targeted therapies. IMPACT provides a new bioinformatics strategy to delineate candidate somatic variants and actionable therapies. This approach can be applied to other patient tumor samples to discover effective drug targets for personalized medicine.IMPACT is publicly available at http://tanlab.ucdenver.edu/IMPACT. © The Author 2016. Published by Oxford University Press on behalf of the American Medical

  16. Investigation Of The Effects Of Reflow Profile Parameters On Lead-free Solder Bump Volumes And Joint Integrity

    Science.gov (United States)

    Amalu, E. H.; Lui, Y. T.; Ekere, N. N.; Bhatti, R. S.; Takyi, G.

    2011-01-01

    The electronics manufacturing industry was quick to adopt and use the Surface Mount Technology (SMT) assembly technique on realization of its huge potentials in achieving smaller, lighter and low cost product implementations. Increasing global customer demand for miniaturized electronic products is a key driver in the design, development and wide application of high-density area array package format. Electronic components and their associated solder joints have reduced in size as the miniaturization trend in packaging continues to be challenged by printing through very small stencil apertures required for fine pitch flip-chip applications. At very narrow aperture sizes, solder paste rheology becomes crucial for consistent paste withdrawal. The deposition of consistent volume of solder from pad-to-pad is fundamental to minimizing surface mount assembly defects. This study investigates the relationship between volume of solder paste deposit (VSPD) and the volume of solder bump formed (VSBF) after reflow, and the effect of reflow profile parameters on lead-free solder bump formation and the associated solder joint integrity. The study uses a fractional factorial design (FFD) of 24-1 Ramp-Soak-Spike reflow profile, with all main effects and two-way interactions estimable to determine the optimal factorial combination. The results from the study show that the percentage change in the VSPD depends on the combination of the process parameters and reliability issues could become critical as the size of solder joints soldered on the same board assembly vary greatly. Mathematical models describe the relationships among VSPD, VSBF and theoretical volume of solder paste. Some factors have main effects across the volumes and a number of interactions exist among them. These results would be useful for R&D personnel in designing and implementing newer applications with finer-pitch interconnect.

  17. Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape

    Directory of Open Access Journals (Sweden)

    Li Dongmei

    2009-05-01

    Full Text Available Abstract Background Universally accepted landmark stages are necessary to highlight key events in plant reproductive development and to facilitate comparisons among species. Domestication and selection of tomato resulted in many varieties that differ in fruit shape and size. This diversity is useful to unravel underlying molecular and developmental mechanisms that control organ morphology and patterning. The tomato fruit shape gene SUN controls fruit elongation. The most dramatic effect of SUN on fruit shape occurs after pollination and fertilization although a detailed investigation into the timing of the fruit shape change as well as gene expression profiles during critical developmental stages has not been conducted. Results We provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new floral and fruit landmarks to present a framework for tomato developmental studies. In addition, gene expression profiles of three key stages in floral and fruit development are presented, namely floral buds 10 days before anthesis (floral landmark 7, anthesis-stage flowers (floral landmark 10 and fruit landmark 1, and 5 days post anthesis fruit (fruit landmark 3. To demonstrate the utility of the landmarks, we characterize the tomato shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post-anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. The expression profiles of the NILs that differ at sun show that only 34 genes were differentially expressed and most of them at a less than 2-fold difference. Conclusion The landmarks for flower and fruit development in tomato were outlined and integrated with the effect of SUN on fruit shape. Although we did not identify many genes differentially expressed in

  18. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  19. Integration of miRNA and mRNA expression profiles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia

    DEFF Research Database (Denmark)

    Moraes, Leonardo N; Fernandez, Geysson J; Vechetti-Júnior, Ivan J

    2017-01-01

    Cardiac cachexia (CC) is a common complication of heart failure (HF) associated with muscle wasting and poor patient prognosis. Although different mechanisms have been proposed to explain muscle wasting during CC, its pathogenesis is still not understood. Here, we described an integrative analysis...... between miRNA and mRNA expression profiles of muscle wasting during CC. Global gene expression profiling identified 1,281 genes and 19 miRNAs differentially expressed in muscle wasting during CC. Several of these deregulated genes are known or putative targets of the altered miRNAs, including miR-29a-3p......, miR-29b-3p, miR-210-5p, miR-214, and miR-489. Gene ontology analysis on integrative mRNA/miRNA expression profiling data revealed miRNA interactions affecting genes that regulate extra-cellular matrix (ECM) organization, proteasome protein degradation, citric acid cycle and respiratory electron...

  20. Intertumor heterogeneity of non-small-cell lung carcinomas revealed by multiplexed mutation profiling and integrative genomics.

    Science.gov (United States)

    Tan, Daniel S W; Camilleri-Broët, Sophie; Tan, Eng Huat; Alifano, Marco; Lim, Wan-Teck; Bobbio, Antonio; Zhang, Shenli; Ng, Quan-Sing; Ang, Mei-Kim; Iyer, N Gopalakrishna; Takano, Angela; Lim, Kiat Hon; Régnard, Jean-François; Tan, Patrick; Broët, Philippe

    2014-09-01

    Non-small-cell lung cancer (NSCLC) is a heterogeneous disease, with a burden of genomic alterations exceeding most other tumors. The goal of our study was to evaluate the frequencies of co-occurring mutations and copy-number aberrations (CNAs) within the same tumor and to evaluate their potential clinical impact. Mass-spectrometry based mutation profiling using a customized lung cancer panel evaluating 214 mutations across 26 key NSCLC genes was performed on 230 nonsquamous NSCLC and integrated with genome-wide CNAs and clinical variables. Among the 138 cases having at least one mutation, one-third (41, 29.7%) showed two or more mutations, either in the same gene (double mutation) or in different genes (co-mutations). In epidermal growth factor receptor (EGFR) mutant cancers, there was a double mutation in 18% and co-mutations in the following genes: TP53 (10%), PIK3CA (8%), STK11 (6%) and MET (4%). Significant relationships were detected between EGFR mutation and 1p, 7p copy gains (harboring the EGFR gene) as well as 13q copy loss. KRAS mutation was significantly related with 1q gain and 3q loss. For Stage I, tumors harboring at least one mutation or PIK3CA mutation were significantly correlated with poor prognosis (p-value = 0.02). When combining CNAs and mutational status, patients having both KRAS mutation and the highest related CNA (3q22.3 copy loss) showed a significant poorer prognosis (p-value = 0.03). Our study highlights the clinical relevance of studying tumor complexity by integrative genomic analysis and the need for developing assays that broadly screen for both "actionable" mutations and copy-number alterations to improve precision of stratified treatment approaches. © 2014 UICC.

  1. iCanPlot: visual exploration of high-throughput omics data using interactive Canvas plotting.

    Directory of Open Access Journals (Sweden)

    Amit U Sinha

    Full Text Available Increasing use of high throughput genomic scale assays requires effective visualization and analysis techniques to facilitate data interpretation. Moreover, existing tools often require programming skills, which discourages bench scientists from examining their own data. We have created iCanPlot, a compelling platform for visual data exploration based on the latest technologies. Using the recently adopted HTML5 Canvas element, we have developed a highly interactive tool to visualize tabular data and identify interesting patterns in an intuitive fashion without the need of any specialized computing skills. A module for geneset overlap analysis has been implemented on the Google App Engine platform: when the user selects a region of interest in the plot, the genes in the region are analyzed on the fly. The visualization and analysis are amalgamated for a seamless experience. Further, users can easily upload their data for analysis--which also makes it simple to share the analysis with collaborators. We illustrate the power of iCanPlot by showing an example of how it can be used to interpret histone modifications in the context of gene expression.

  2. Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models

    Directory of Open Access Journals (Sweden)

    Huaqiang Zhou

    2016-05-01

    Full Text Available Stroke is one of the most common causes of death, only second to heart disease. Molecular investigations about stroke are in acute shortage nowadays. This study is intended to explore a gene expression profile after brain ischemia reperfusion. Meta-analysis, differential expression analysis, and integrated analysis were employed on an eight microarray series. We explored the functions and pathways of target genes in gene ontology (GO enrichment analysis and constructed a protein-protein interaction network. Meta-analysis identified 360 differentially expressed genes (DEGs for Mus musculus and 255 for Rattus norvegicus. Differential expression analysis identified 44 DEGs for Mus musculus and 21 for Rattus norvegicus. Timp1 and Lcn2 were overexpressed in both species. The cytokine-cytokine receptor interaction and chemokine signaling pathway were highly enriched for the Kyoto Encyclopedia of Genes and Genomes (KEGG pathway. We have exhibited a global view of the potential molecular differences between middle cerebral artery occlusion (MCAO animal model and sham for Mus musculus or Rattus norvegicus, including the biological process and enriched pathways in DEGs. This research helps contribute to a clearer understanding of the inflammation process and accurate identification of ischemic infarction stages, which might be transformed into a therapeutic approach.

  3. Integrated analyses for genetic markers of polycystic ovary syndrome with 9 case-control studies of gene expression profiles.

    Science.gov (United States)

    Lu, Chenqi; Liu, Xiaoqin; Wang, Lin; Jiang, Ning; Yu, Jun; Zhao, Xiaobo; Hu, Hairong; Zheng, Saihua; Li, Xuelian; Wang, Guiying

    2017-01-10

    Due to genetic heterogeneity and variable diagnostic criteria, genetic studies of polycystic ovary syndrome are particularly challenging. Furthermore, lack of sufficiently large cohorts limits the identification of susceptibility genes contributing to polycystic ovary syndrome. Here, we carried out a systematic search of studies deposited in the Gene Expression Omnibus database through August 31, 2016. The present analyses included studies with: 1) patients with polycystic ovary syndrome and normal controls, 2) gene expression profiling of messenger RNA, and 3) sufficient data for our analysis. Ultimately, a total of 9 studies with 13 datasets met the inclusion criteria and were performed for the subsequent integrated analyses. Through comprehensive analyses, there were 13 genetic factors overlapped in all datasets and identified as significant specific genes for polycystic ovary syndrome. After quality control assessment, there were six datasets remained. Further gene ontology enrichment and pathway analyses suggested that differentially expressed genes mainly enriched in oocyte pathways. These findings provide potential molecular markers for diagnosis and prognosis of polycystic ovary syndrome, and need in-depth studies on the exact function and mechanism in polycystic ovary syndrome.

  4. [Integrity].

    Science.gov (United States)

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  5. Allan Deviation Plot as a Tool for Quartz-Enhanced Photoacoustic Sensors Noise Analysis.

    Science.gov (United States)

    Giglio, Marilena; Patimisco, Pietro; Sampaolo, Angelo; Scamarcio, Gaetano; Tittel, Frank K; Spagnolo, Vincenzo

    2016-04-01

    We report here on the use of the Allan deviation plot to analyze the long-term stability of a quartz-enhanced photoacoustic (QEPAS) gas sensor. The Allan plot provides information about the optimum averaging time for the QEPAS signal and allows the prediction of its ultimate detection limit. The Allan deviation can also be used to determine the main sources of noise coming from the individual components of the sensor. Quartz tuning fork thermal noise dominates for integration times up to 275 s, whereas at longer averaging times, the main contribution to the sensor noise originates from laser power instabilities.

  6. WCPP-THE WOLF PLOTTING AND CONTOURING PACKAGE

    Science.gov (United States)

    Masaki, G. T.

    1994-01-01

    The WOLF Contouring and Plotting Package provides the user with a complete general purpose plotting and contouring capability. This package is a complete system for producing line printer, SC4020, Gerber, Calcomp, and SD4060 plots. The package has been designed to be highly flexible and easy to use. Any plot from a quick simple plot (which requires only one call to the package) to highly sophisticated plots (including motion picture plots) can be easily generated with only a basic knowledge of FORTRAN and the plot commands. Anyone designing a software system that requires plotted output will find that this package offers many advantages over the standard hardware support packages available. The WCPP package is divided into a plot segment and a contour segment. The plot segment can produce output for any combination of line printer, SC4020, Gerber, Calcomp, and SD4060 plots. The line printer plots allow the user to have plots available immediately after a job is run at a low cost. Although the resolution of line printer plots is low, the quick results allows the user to judge if a high resolution plot of a particular run is desirable. The SC4020 and SD4060 provide high speed high resolution cathode ray plots with film and hard copy output available. The Gerber and Calcomp plotters provide very high quality (of publishable quality) plots of good resolution. Being bed or drum type plotters, the Gerber and Calcomp plotters are usually slow and not suited for large volume plotting. All output for any or all of the plotters can be produced simultaneously. The types of plots supported are: linear, semi-log, log-log, polar, tabular data using the FORTRAN WRITE statement, 3-D perspective linear, and affine transformations. The labeling facility provides for horizontal labels, vertical labels, diagonal labels, vector characters of a requested size (special character fonts are easily implemented), and rotated letters. The gridding routines label the grid lines according to

  7. Storytelling in Earth sciences: The eight basic plots

    Science.gov (United States)

    Phillips, Jonathan

    2012-11-01

    Reporting results and promoting ideas in science in general, and Earth science in particular, is treated here as storytelling. Just as in literature and drama, storytelling in Earth science is characterized by a small number of basic plots. Though the list is not exhaustive, and acknowledging that multiple or hybrid plots and subplots are possible in a single piece, eight standard plots are identified, and examples provided: cause-and-effect, genesis, emergence, destruction, metamorphosis, convergence, divergence, and oscillation. The plots of Earth science stories are not those of literary traditions, nor those of persuasion or moral philosophy, and deserve separate consideration. Earth science plots do not conform those of storytelling more generally, implying that Earth scientists may have fundamentally different motivations than other storytellers, and that the basic plots of Earth Science derive from the characteristics and behaviors of Earth systems. In some cases preference or affinity to different plots results in fundamentally different interpretations and conclusions of the same evidence. In other situations exploration of additional plots could help resolve scientific controversies. Thus explicit acknowledgement of plots can yield direct scientific benefits. Consideration of plots and storytelling devices may also assist in the interpretation of published work, and can help scientists improve their own storytelling.

  8. Determination of the particulate extinction-coefficient profile and the column-integrated lidar ratios using the backscatter-coefficient and optical-depth profiles

    Science.gov (United States)

    Vladimir A Kovalev; Wei Min Hao; Cyle Wold

    2007-01-01

    A new method is considered that can be used for inverting data obtained from a combined elastic-inelastic lidar or a high spectral resolution lidar operating in a one-directional mode, or an elastic lidar operating in a multiangle mode. The particulate extinction coefficient is retrieved from the simultaneously measured profiles of the particulate backscatter...

  9. Some algorithmic problems of plotting codes for unstructured grids

    Science.gov (United States)

    Loehner, Rainald; Parikh, Paresh; Gumbert, Clyde

    1989-01-01

    Some algorithmic problems encountered during the development of unstructured grid plotting codes are described. Chief among them are the interpolation of three-dimensional data on planes, the plotting of a three-dimensional surface with a constant value for a given unknown, and the calculation of particle and oil-flow paths. Some special features of the unstructured grid plotting code, FEPLOT3D, are also described.

  10. Cross plotting of Rock Properties for Fluid and Lithology ...

    African Journals Online (AJOL)

    Cross plotting of Rock Properties for Fluid and Lithology Discrimination using Well Data in a Niger Delta Oil Field. ... Cross plotting was carried out and the plots with most outstanding results were Vp/Vs versus AI, λρ Versus Vp/Vs, μρ against Density and λρ versus μρ. For the two wells considered, two reservoirs were ...

  11. Integrated community profiling indicates long-term temporal stability of the predominant faecal microbiota in captive cheetahs.

    Directory of Open Access Journals (Sweden)

    Anne A M J Becker

    Full Text Available Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus, this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (P<0.05, and by Lactobacillaceae. Moving window analysis of DGGE profiles revealed 23.3-25.6% change between consecutive samples for four of the cheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%. This observation may reflect the temporary impact of perturbations such as the animal's compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five

  12. Optimizing variable radius plot size and LiDAR resolution to model standing volume in conifer forests

    Science.gov (United States)

    Ram Kumar Deo; Robert E. Froese; Michael J. Falkowski; Andrew T. Hudak

    2016-01-01

    The conventional approach to LiDAR-based forest inventory modeling depends on field sample data from fixed-radius plots (FRP). Because FRP sampling is cost intensive, combining variable-radius plot (VRP) sampling and LiDAR data has the potential to improve inventory efficiency. The overarching goal of this study was to evaluate the integration of LiDAR and VRP data....

  13. OPUS/PlotOPUS: An ORIGEN-S Post-Processing Utility and Plotting Program for SCALE

    Energy Technology Data Exchange (ETDEWEB)

    Gauld, I.C.

    2001-03-08

    The OPUS utility program produces an output file that can be used for making a variety of plots from output produced by the ORIGEN-S code that computes reactor fuel depletion, activation and fission- product buildup, and the corresponding photon and neutron source spectra. Tables containing individual and total nuclide or element concentrations, in 14 different units, may be generated as a function of time. Three classes of plot data may be produced by OPUS: (1) dominant or selected isotopes or elements, (2) photon and neutron source spectra, and (3) comparisons of selected quantities (totals or individual nuclides) between different ORIGEN-S cases. The input is designed for ease of use with self-explanatory parameter names, free-form input, and commonly used default values. The formatted output data produced by OPUS is designed to be used directly by the PlotOPUS graphics-plotting program. PlotOPUS is an interactive Visual Basic program designed for Windows 9x, 2000, and NT computers. PlotOPUS reads the formatted output data file produced by OPUS, plots the data, and will generate Windows metafile (WMF), JPEG bitmap (JPG), or Windows bitmap (BMP) files for saving the plot images. Even though it is designed to interface with PlotOPUS, the formatted OPUS output file can be easily read by other graphics packages for data visualization.

  14. Deletion of the LTR enhancer/promoter has no impact on the integration profile of MLV vectors in human hematopoietic progenitors.

    Directory of Open Access Journals (Sweden)

    Arianna Moiani

    Full Text Available Moloney murine leukemia virus (MLV-derived gamma-retroviral vectors integrate preferentially near transcriptional regulatory regions in the human genome, and are associated with a significant risk of insertional gene deregulation. Self-inactivating (SIN vectors carry a deletion of the U3 enhancer and promoter in the long terminal repeat (LTR, and show reduced genotoxicity in pre-clinical assays. We report a high-definition analysis of the integration preferences of a SIN MLV vector compared to a wild-type-LTR MLV vector in the genome of CD34(+ human hematopoietic stem/progenitor cells (HSPCs. We sequenced 13,011 unique SIN-MLV integration sites and compared them to 32,574 previously generated MLV sites in human HSPCs. The SIN-MLV vector recapitulates the integration pattern observed for MLV, with the characteristic clustering of integrations around enhancer and promoter regions associated to H3K4me3 and H3K4me1 histone modifications, specialized chromatin configurations (presence of the H2A.Z histone variant and binding of RNA Pol II. SIN-MLV and MLV integration clusters and hot spots overlap in most cases and are generated at a comparable frequency, indicating that the reduced genotoxicity of SIN-MLV vectors in hematopoietic cells is not due to a modified integration profile.

  15. Estimating mapped-plot forest attributes with ratios of means

    Science.gov (United States)

    S.J. Zarnoch; W.A. Bechtold

    2000-01-01

    The mapped-plot design utilized by the U.S. Department of Agriculture (USDA) Forest Inventory and Analysis and the National Forest Health Monitoring Programs is described. Data from 2458 forested mapped plots systematically spread across 25 States reveal that 35 percent straddle multiple conditions. The ratio-of-means estimator is developed as a method to obtain...

  16. Precise FIA plot registration using field and dense LIDAR data

    Science.gov (United States)

    Demetrios Gatziolis

    2009-01-01

    Precise registration of forest inventory and analysis (FIA) plots is a prerequisite for an effective fusion of field data with ancillary spatial information, which is an approach commonly employed in the mapping of various forest parameters. Although the adoption of Global Positioning System technology has improved the precision of plot coordinates obtained during...

  17. A Guided Inquiry on Hubble Plots and the Big Bang

    Science.gov (United States)

    Forringer, Ted

    2014-01-01

    In our science for non-science majors course "21st Century Physics," we investigate modern "Hubble plots" (plots of velocity versus distance for deep space objects) in order to discuss the Big Bang, dark matter, and dark energy. There are two potential challenges that our students face when encountering these topics for the…

  18. Designing fractional factorial split-plot experiments using integer programming

    DEFF Research Database (Denmark)

    Capehart, Shay R.; Keha, Ahmet; Kulahci, Murat

    2011-01-01

    Split-plot designs are commonly used in industrial experiments when there are hard-to-change and easy-to-change factors. Due to the number of factors and resource limitations, it is more practical to run a fractional factorial split-plot (FFSP) design. These designs are variations of the fraction...

  19. Plotting Rates of Photosynthesis as a Function of Light Quantity.

    Science.gov (United States)

    Dean, Rob L.

    1996-01-01

    Discusses methods for plotting rates of photosynthesis as a function of light quantity. Presents evidence that suggests that empirically derived conversion factors, which are used to convert foot candles to photon fluence rates, should be used with extreme caution. Suggests how rate data are best plotted when any kind of light meter is not…

  20. Probability plots based on student’s t-distribution

    NARCIS (Netherlands)

    Hooft, R.W.W.|info:eu-repo/dai/nl/109722213; Straver, L.H.; Spek, A.L.|info:eu-repo/dai/nl/156517566

    2009-01-01

    The validity of the normal distribution as an error model is commonly tested with a (half) normal probability plot. Real data often contain outliers. The use of t-distributions in a probability plot to model such data more realistically is described. It is shown how a suitable value of the parameter

  1. Development of gnuplot plotting package for MAD-X

    CERN Document Server

    Romero Leiro, Freddy Jose

    2015-01-01

    MAD-X is a general purpose software for charged-particle optics design and it needs a visualisation tool to be able to show the data in a more manageable way, this visualisation tools being already in MAD-X are the PLOT and SETPLOT commands. Nonetheless issues like compatibility and the desire of having alternative ways to show the plots in a more portable way have lead to explore the use of open source available software to reproduce the same results. The purpose of this project is to create a package compatible with the MAD-X output format, capable of generating publication quality plots, mainly lattice beamline plots and scatter plots by using the Gnuplot for creating plots. This software must support the same options as the PLOT and SETPLOT commands from MAD-X but additions or improvement over the present version are more than welcome. The main purpose of the program is to pre-process the data in order to be ready for Gnuplot to read it and plot it .This report is mostly a description of the development o...

  2. Estimation of Optimal Size of Plots for Experiments with Radiometer ...

    African Journals Online (AJOL)

    An experimental error can lead to rework and, consequently, to the loss of financial and human resources. One way to reduce this problem is the estimation of the optimum size of experimental plot to carry out the treatments. The objective of this study was to estimate the optimal size of plots for reflectance measurements in ...

  3. Instrumentation for full-year plot-scale runoff monitoring

    Science.gov (United States)

    Replicated 0.34 ha cropping systems plots have been in place since 1991 at the USDA-ARS Goodwater Creek Experimental Watershed in central Missouri. Recently, instrumentation has been installed at 18 of those plots for continuous runoff water quality and quantity monitoring. That installation require...

  4. Effects of plot size on forest-type algorithm accuracy

    Science.gov (United States)

    James A. Westfall

    2009-01-01

    The Forest Inventory and Analysis (FIA) program utilizes an algorithm to consistently determine the forest type for forested conditions on sample plots. Forest type is determined from tree size and species information. Thus, the accuracy of results is often dependent on the number of trees present, which is highly correlated with plot area. This research examines the...

  5. Split-plot fractional designs: Is minimum aberration enough?

    DEFF Research Database (Denmark)

    Kulahci, Murat; Ramirez, Jose; Tobias, Randy

    2006-01-01

    Split-plot experiments are commonly used in industry for product and process improvement. Recent articles on designing split-plot experiments concentrate on minimum aberration as the design criterion. Minimum aberration has been criticized as a design criterion for completely randomized fractional...... factorial design and alternative criteria, such as the maximum number of clear two-factor interactions, are suggested (Wu and Hamada (2000)). The need for alternatives to minimum aberration is even more acute for split-plot designs. In a standard split-plot design, there are several types of two...... for completely randomized designs. Consequently, we provide a modified version of the maximum number of clear two-factor interactions design criterion to be used for split-plot designs....

  6. Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism

    DEFF Research Database (Denmark)

    Hu, Zheng; Zhu, Da; Wang, Wei

    2015-01-01

    Human papillomavirus (HPV) integration is a key genetic event in cervical carcinogenesis1. By conducting whole-genome sequencing and high-throughput viral integration detection, we identified 3,667 HPV integration breakpoints in 26 cervical intraepithelial neoplasias, 104 cervical carcinomas and ...... that fusion between viral and human DNA may have occurred by microhomology-mediated DNA repair pathways2. Our data provide insights into HPV integration-driven cervical carcinogenesis....... and five cell lines. Beyond recalculating frequencies for the previously reported frequent integration sites POU5F1B (9.7%), FHIT (8.7%), KLF12 (7.8%), KLF5 (6.8%), LRP1B (5.8%) and LEPREL1 (4.9%), we discovered new hot spots HMGA2 (7.8%), DLG2 (4.9%) and SEMA3D (4.9%). Protein expression from FHIT and LRP......1B was downregulated when HPV integrated in their introns. Protein expression from MYC and HMGA2 was elevated when HPV integrated into flanking regions. Moreover, microhomologous sequence between the human and HPV genomes was significantly enriched near integration breakpoints, indicating...

  7. Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis.

    Science.gov (United States)

    Chen, Wei; Zhao, Wenshan; Yang, Aiting; Xu, Anjian; Wang, Huan; Cong, Min; Liu, Tianhui; Wang, Ping; You, Hong

    2017-12-15

    -receptor interaction" were remarked significant (adjusted pGenes enriched in these pathways coupled with their regulatory miRNAs formed a functional miRNA-gene regulatory module that contains 7 miRNAs, 22 genes and 42 miRNA-gene connections. Gene interaction analysis based on String database revealed that 8 out of 22 genes were highly clustered. Finally, we experimentally confirmed a functional regulatory module containing 5 miRNAs (miR-130b-3p, miR-148a-3p, miR-345-5p, miR-378a-3p, and miR-422a) and 6 genes (COL6A1, COL6A2, COL6A3, PIK3R3, COL1A1, CCND2) associated with liver fibrosis. Our integrated analysis of miRNA and gene expression profiles highlighted a functional miRNA-gene regulatory module associated with liver fibrosis, which, to some extent, may provide important clues to better understand the underlying pathogenesis of liver fibrosis. Copyright © 2017. Published by Elsevier B.V.

  8. Methodical modeling of the investment value of land plots for housing development

    Directory of Open Access Journals (Sweden)

    Kulakov Kirill

    2017-01-01

    Full Text Available Analysis of housing construction in the Russian Federation showed that the development and regulation of the segment of the housing market for the integrated development of territories for residential development, is a priority national socio-economic task. Currently in the construction complex of the country it can provide a maximum supply of affordable housing from major developers that in the context of the turbulent economy it is especially important. In this regard great scientific and practical interest is the modeling of the investment value of land plots for housing development. The article presents the results of research on the development of the main stages of the method of calculation of the investment cost of land plots for integrated residential development areas, and give an algorithm of its application.

  9. Scaling from Surface Satellite Measurements of PIC to Integrated Euphotic Estimates over the Global Ocean: Do Vertical Profiles of Coccolithophores Look Like Vertical Profiles of Chlorophyll?

    Science.gov (United States)

    Balch, W. M.; Drapeau, D.; Bowler, B.; Lyczkowski, E.; Lubelczyk, L.

    2016-02-01

    We have participated in a number of cruises throughout the world ocean, observing the vertical and horizontal distributions of coccolithophores, their particulate inorganic carbon (PIC) and associated optical properties. We will provide a synthesis of our observations in support of the NASA ocean color algorithm for PIC, highlighting how the integrated concentration of these plants can be interpreted from surface satellite measurements. Our work has shown consistencies in the vertical distributions of coccolithophores that allow us to extrapolate surface PIC observations (from the top optical depth observed by satellite) to the integrated euphotic zone on depth scales of 100m. Such results are a function of the degree of eutrophy and are critical for understanding the global consequences of this phytoplankton functional group, their associated biogeochemistry and implications to the alkalinity pump. We will end by showing whether the vertical distributions of PIC differ from those of diatom biogenic silica.

  10. Using volcano plots and regularized-chi statistics in genetic association studies.

    Science.gov (United States)

    Li, Wentian; Freudenberg, Jan; Suh, Young Ju; Yang, Yaning

    2014-02-01

    Labor intensive experiments are typically required to identify the causal disease variants from a list of disease associated variants in the genome. For designing such experiments, candidate variants are ranked by their strength of genetic association with the disease. However, the two commonly used measures of genetic association, the odds-ratio (OR) and p-value may rank variants in different order. To integrate these two measures into a single analysis, here we transfer the volcano plot methodology from gene expression analysis to genetic association studies. In its original setting, volcano plots are scatter plots of fold-change and t-test statistic (or -log of the p-value), with the latter being more sensitive to sample size. In genetic association studies, the OR and Pearson's chi-square statistic (or equivalently its square root, chi; or the standardized log(OR)) can be analogously used in a volcano plot, allowing for their visual inspection. Moreover, the geometric interpretation of these plots leads to an intuitive method for filtering results by a combination of both OR and chi-square statistic, which we term "regularized-chi". This method selects associated markers by a smooth curve in the volcano plot instead of the right-angled lines which corresponds to independent cutoffs for OR and chi-square statistic. The regularized-chi incorporates relatively more signals from variants with lower minor-allele-frequencies than chi-square test statistic. As rare variants tend to have stronger functional effects, regularized-chi is better suited to the task of prioritization of candidate genes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia

    NARCIS (Netherlands)

    Taskesen, E.; Babaei, S.; Reinders, M.J.M.; De Ridder, J.

    2015-01-01

    Background Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and

  12. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    Directory of Open Access Journals (Sweden)

    Pin Cui

    2016-03-01

    Full Text Available Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV is currently invading the germline of the koala (Phascolarctos cinereus and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

  13. Evaluation of a Smartphone App for Forest Sample Plot Measurements

    Directory of Open Access Journals (Sweden)

    Mikko Vastaranta

    2015-04-01

    Full Text Available We evaluated a smartphone app (TRESTIMATM for forest sample plot measurements. The app interprets imagery collected from the sample plots using the camera in the smartphone and then estimates forest inventory attributes, including species-specific basal areas (G as well as the diameter (DgM and height (HgM of basal area median trees. The estimates from the smartphone app were compared to forest inventory attributes derived from tree-wise measurements using calipers and a Vertex height measurement device. The data consist of 2169 measured trees from 25 sample plots (32 m × 32 m, dominated by Scots pine and Norway spruce from southern Finland. The root-mean-square errors (RMSEs in the basal area varied from 19.7% to 29.3% and the biases from 11.4% to 18.4% depending on the number of images per sample plot and image shooting location. DgM measurement bias varied from −1.4% to 3.1% and RMSE from 5.2% to 11.6% depending on the tree species. Respectively, HgM bias varied from 5.0% to 8.3% and RMSE 10.0% to 13.6%. In general, four images captured toward the center of the plot provided more accurate results than four images captured away from the plot center. Increasing the number of captured images per plot to the analyses yielded only marginal improvement to the results.

  14. CFD Extraction Tool for TecPlot From DPLR Solutions

    Science.gov (United States)

    Norman, David

    2013-01-01

    This invention is a TecPlot macro of a computer program in the TecPlot programming language that processes data from DPLR solutions in TecPlot format. DPLR (Data-Parallel Line Relaxation) is a NASA computational fluid dynamics (CFD) code, and TecPlot is a commercial CFD post-processing tool. The Tec- Plot data is in SI units (same as DPLR output). The invention converts the SI units into British units. The macro modifies the TecPlot data with unit conversions, and adds some extra calculations. After unit conversions, the macro cuts a slice, and adds vectors on the current plot for output format. The macro can also process surface solutions. Existing solutions use manual conversion and superposition. The conversion is complicated because it must be applied to a range of inter-related scalars and vectors to describe a 2D or 3D flow field. It processes the CFD solution to create superposition/comparison of scalars and vectors. The existing manual solution is cumbersome, open to errors, slow, and cannot be inserted into an automated process. This invention is quick and easy to use, and can be inserted into an automated data-processing algorithm.

  15. Implementation of Integrated Service Networks under the Quebec Mental Health Reform: Facilitators and Barriers associated with Different Territorial Profiles

    Science.gov (United States)

    Grenier, Guy; Vallée, Catherine; Aubé, Denise; Farand, Lambert

    2017-01-01

    Introduction: This study evaluates implementation of the Quebec Mental Health Reform (2005–2015), which promoted the development of integrated service networks, in 11 local service networks organized into four territorial groups according to socio-demographic characteristics and mental health services offered. Methods: Data were collected from documents concerning networks; structured questionnaires completed by 90 managers and by 16 respondent-psychiatrists; and semi-structured interviews with 102 network stakeholders. Factors associated with implementation and integration were organized according to: 1) reform characteristics; 2) implementation context; 3) organizational characteristics; and 4) integration strategies. Results: While local networks were in a process of development and expansion, none were fully integrated at the time of the study. Facilitators and barriers to implementation and integration were primarily associated with organizational characteristics. Integration was best achieved in larger networks including a general hospital with a psychiatric department, followed by networks with a psychiatric hospital. Formalized integration strategies such as service agreements, liaison officers, and joint training reduced some barriers to implementation in networks experiencing less favourable conditions. Conclusion: Strategies for the implementation of healthcare reform and integrated service networks should include sustained support and training in best-practices, adequate performance indicators and resources, formalized integration strategies to improve network coordination and suitable initiatives to promote staff retention. PMID:29042845

  16. Implementation of Integrated Service Networks under the Quebec Mental Health Reform: Facilitators and Barriers associated with Different Territorial Profiles.

    Science.gov (United States)

    Fleury, Marie-Josée; Grenier, Guy; Vallée, Catherine; Aubé, Denise; Farand, Lambert

    2017-03-10

    This study evaluates implementation of the Quebec Mental Health Reform (2005-2015), which promoted the development of integrated service networks, in 11 local service networks organized into four territorial groups according to socio-demographic characteristics and mental health services offered. Data were collected from documents concerning networks; structured questionnaires completed by 90 managers and by 16 respondent-psychiatrists; and semi-structured interviews with 102 network stakeholders. Factors associated with implementation and integration were organized according to: 1) reform characteristics; 2) implementation context; 3) organizational characteristics; and 4) integration strategies. While local networks were in a process of development and expansion, none were fully integrated at the time of the study. Facilitators and barriers to implementation and integration were primarily associated with organizational characteristics. Integration was best achieved in larger networks including a general hospital with a psychiatric department, followed by networks with a psychiatric hospital. Formalized integration strategies such as service agreements, liaison officers, and joint training reduced some barriers to implementation in networks experiencing less favourable conditions. Strategies for the implementation of healthcare reform and integrated service networks should include sustained support and training in best-practices, adequate performance indicators and resources, formalized integration strategies to improve network coordination and suitable initiatives to promote staff retention.

  17. Implementation of Integrated Service Networks under the Quebec Mental Health Reform: Facilitators and Barriers associated with Different Territorial Profiles

    Directory of Open Access Journals (Sweden)

    Marie-Josée Fleury

    2017-03-01

    Full Text Available Introduction: This study evaluates implementation of the Quebec Mental Health Reform (2005–2015, which promoted the development of integrated service networks, in 11 local service networks organized into four territorial groups according to socio-demographic characteristics and mental health services offered. Methods: Data were collected from documents concerning networks; structured questionnaires completed by 90 managers and by 16 respondent-psychiatrists; and semi-structured interviews with 102 network stakeholders. Factors associated with implementation and integration were organized according to: 1 reform characteristics; 2 implementation context; 3 organizational characteristics; and 4 integration strategies. Results: While local networks were in a process of development and expansion, none were fully integrated at the time of the study. Facilitators and barriers to implementation and integration were primarily associated with organizational characteristics. Integration was best achieved in larger networks including a general hospital with a psychiatric department, followed by networks with a psychiatric hospital. Formalized integration strategies such as service agreements, liaison officers, and joint training reduced some barriers to implementation in networks experiencing less favourable conditions. Conclusion: Strategies for the implementation of healthcare reform and integrated service networks should include sustained support and training in best-practices, adequate performance indicators and resources, formalized integration strategies to improve network coordination and suitable initiatives to promote staff retention.

  18. Superplot: a graphical interface for plotting and analysing MultiNest output

    Science.gov (United States)

    Fowlie, Andrew; Bardsley, Michael Hugh

    2016-11-01

    We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by, e.g., MultiNest. A simple graphical interface allows one to browse a chain of many variables quickly, and make publication quality plots of, inter alia, one- and two-dimensional profile likelihood, posterior pdf (with kernel density estimation), confidence intervals and credible regions. In this short manual, we document installation and basic usage, and define all statistical quantities and conventions. The code is fully compatible with Linux and Windows. All functionality is available on Mac OSX, though it must be invoked by the command line rather than a graphical interface.

  19. Integrative analysis of the transcriptome profiles observed in type 1, type 2 and gestational diabetes mellitus reveals the role of inflammation.

    Science.gov (United States)

    Evangelista, Adriane F; Collares, Cristhianna V A; Xavier, Danilo J; Macedo, Claudia; Manoel-Caetano, Fernanda S; Rassi, Diane M; Foss-Freitas, Maria C; Foss, Milton C; Sakamoto-Hojo, Elza T; Nguyen, Catherine; Puthier, Denis; Passos, Geraldo A; Donadi, Eduardo A

    2014-05-23

    Type 1 diabetes (T1D) is an autoimmune disease, while type 2 (T2D) and gestational diabetes (GDM) are considered metabolic disturbances. In a previous study evaluating the transcript profiling of peripheral mononuclear blood cells obtained from T1D, T2D and GDM patients we showed that the gene profile of T1D patients was closer to GDM than to T2D. To understand the influence of demographical, clinical, laboratory, pathogenetic and treatment features on the diabetes transcript profiling, we performed an analysis integrating these features with the gene expression profiles of the annotated genes included in databases containing information regarding GWAS and immune cell expression signatures. Samples from 56 (19 T1D, 20 T2D, and 17 GDM) patients were hybridized to whole genome one-color Agilent 4x44k microarrays. Non-informative genes were filtered by partitioning, and differentially expressed genes were obtained by rank product analysis. Functional analyses were carried out using the DAVID database, and module maps were constructed using the Genomica tool. The functional analyses were able to discriminate between T1D and GDM patients based on genes involved in inflammation. Module maps of differentially expressed genes revealed that modulated genes: i) exhibited transcription profiles typical of macrophage and dendritic cells; ii) had been previously associated with diabetic complications by association and by meta-analysis studies, and iii) were influenced by disease duration, obesity, number of gestations, glucose serum levels and the use of medications, such as metformin. This is the first module map study to show the influence of epidemiological, clinical, laboratory, immunopathogenic and treatment features on the transcription profiles of T1D, T2D and GDM patients.

  20. Integrated inertial sensors and mobile computing for real-time cycling performance guidance via pedaling profile classification.

    Science.gov (United States)

    Xu, James Y; Nan, Xiaomeng; Ebken, Victor; Wang, Yan; Pottie, Greg J; Kaiser, William J

    2015-03-01

    Today, the bicycle is utilized as a daily commute tool, a physical rehabilitation asset, and sporting equipment, prompting studies into the biomechanics of cycling. Of the number of important parameters that affect cycling efficiency, the foot angle profile is one of the most important as it correlates directly with the effective force applied to the bike. However, there has been no compact and portable solution for measuring the foot angle and for providing the cyclist with real-time feedback due to a number of difficulties of the current tracking and sensing technologies and the myriad types of bikes available. This paper presents a novel sensing and mobile computing system for classifying the foot angle profiles during cycling and for providing real-time guidance to the user to achieve the correct profile. Continuous foot angle tracking is firstly converted into a discrete problem requiring only recognition of acceleration profiles of the foot using a single shoe mounted tri-axial accelerometer during each pedaling cycle. A classification method is then applied to identify the pedaling profile. Finally, a mobile solution is presented to provide real-time signal processing and guidance.

  1. POMO--Plotting Omics analysis results for Multiple Organisms.

    Science.gov (United States)

    Lin, Jake; Kreisberg, Richard; Kallio, Aleksi; Dudley, Aimée M; Nykter, Matti; Shmulevich, Ilya; May, Patrick; Autio, Reija

    2013-12-24

    Systems biology experiments studying different topics and organisms produce thousands of data values across different types of genomic data. Further, data mining analyses are yielding ranked and heterogeneous results and association networks distributed over the entire genome. The visualization of these results is often difficult and standalone web tools allowing for custom inputs and dynamic filtering are limited. We have developed POMO (http://pomo.cs.tut.fi), an interactive web-based application to visually explore omics data analysis results and associations in circular, network and grid views. The circular graph represents the chromosome lengths as perimeter segments, as a reference outer ring, such as cytoband for human. The inner arcs between nodes represent the uploaded network. Further, multiple annotation rings, for example depiction of gene copy number changes, can be uploaded as text files and represented as bar, histogram or heatmap rings. POMO has built-in references for human, mouse, nematode, fly, yeast, zebrafish, rice, tomato, Arabidopsis, and Escherichia coli. In addition, POMO provides custom options that allow integrated plotting of unsupported strains or closely related species associations, such as human and mouse orthologs or two yeast wild types, studied together within a single analysis. The web application also supports interactive label and weight filtering. Every iterative filtered result in POMO can be exported as image file and text file for sharing or direct future input. The POMO web application is a unique tool for omics data analysis, which can be used to visualize and filter the genome-wide networks in the context of chromosomal locations as well as multiple network layouts. With the several illustration and filtering options the tool supports the analysis and visualization of any heterogeneous omics data analysis association results for many organisms. POMO is freely available and does not require any installation or

  2. In-situ polymerization PLOT columns I: divinylbenzene

    Science.gov (United States)

    Shen, T. C.

    1992-01-01

    A novel method for preparation of porous-layer open-tubular (PLOT) columns is described. The method involves a simple and reproducible, straight-forward in-situ polymerization of monomer directly on the metal tube.

  3. A framework for plot control in interactive story systems

    Energy Technology Data Exchange (ETDEWEB)

    Sgouros, N.M.; Papakonstantinou, G.; Tsanakas, P. [National Technical Univ. of Athens, Zographou Campus (Greece)

    1996-12-31

    This paper presents a framework for plot control in interactive story systems. In this framework, the user takes the place of the main character of the story, the protagonist. The rest of the cast consists of discrete characters, each playing a specific role in the story. A separate module in this system, the plot manager, controls the behavior of the cast and specifies what the protagonist can do. The story plot is dynamically shaped by the interference between cast members and their social interactions. The system accepts as input a story map which provides the main metaphor for organizing the plot and localizes the interaction of the protagonist with the rest of the cast. We are implementing this framework in PEGASUS, an interactive travel story environment for Greek mythology.

  4. Experts’ Misinterpretation of Box Plots – a Dual Processing Approach

    National Research Council Canada - National Science Library

    Stephanie Lem; Patrick Onghena; Lieven Verschaffel; Wim Van Dooren

    2014-01-01

    Recent studies have shown that students often misinterpret the area of the box in box plots as representing the frequency or proportion of observations in that interval, while it actually represents density...

  5. Generalized box-plot for root growth ensembles

    National Research Council Canada - National Science Library

    Vad, Viktor; Cedrim, Douglas; Busch, Wolfgang; Filzmoser, Peter; Viola, Ivan

    2017-01-01

    .... We use the generalized box plot concept with a new formulation of data depth. In addition to spatial distributions, we created a visual representation to encode temporal distributions associated with the development of root individuals...

  6. Field Plot Points for Voyageurs National Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — A total of 191 vegetation field plot samples were collected at Voyageurs National Park and environs to support vegetation classification development. Teams of...

  7. Graphical interpretation of confidence curves in rankit plots

    DEFF Research Database (Denmark)

    Hyltoft Petersen, Per; Blaabjerg, Ole; Andersen, Marianne

    2004-01-01

    A well-known transformation from the bell-shaped Gaussian (normal) curve to a straight line in the rankit plot is investigated, and a tool for evaluation of the distribution of reference groups is presented. It is based on the confidence intervals for percentiles of the calculated Gaussian...... distribution and the percentage of cumulative points exceeding these limits. The process is to rank the reference values and plot the cumulative frequency points in a rankit plot with a logarithmic (In=log(e)) transformed abscissa. If the distribution is close to In-Gaussian the cumulative frequency points...... presentation, however, makes it easy to disclose deviations from In-Gaussianity, and to make other interpretations of the distributions, e.g., comparison to non-Gaussian distributions in the same plot, where the cumulative frequency percentage can be read from the ordinate. A long list of examples of In...

  8. Field Plot Points for Wupatki National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This spatial dataset in ESRI Coverage format maps field releve plot locations for the vegetation classification and descriptions of the vegetation map at Wupatki...

  9. The master plot in the audiovisual narrative. The western case.

    Directory of Open Access Journals (Sweden)

    José Félix GONZÁLEZ SÁNCHEZ

    2015-05-01

    Full Text Available A plot provides us the story that it offers a hyphen and later a film. Plots are limited, however possibilities, argument them that these offer music infinite. At the same time, we can say that all cultures avail themselves of some plots and similar arguments to structure their mythical stories. In addition, United States is the modern nation where better a dialectic relation between the myth and story keeps. At this nation, the significance of the event has been shown and you have gotten free through the myth. We will see through this article how the western is the kind of American cinema what else and better answer for the folkloric traditional story to the cánones, because your plots have been taken directly of the classical legends.

  10. Vegetation-plot data and databases in Europe: an overview

    NARCIS (Netherlands)

    Schaminée, J.H.J.; Hennekens, S.M.; Chytrý, M.; Rodwell, J.S.

    2009-01-01

    During the last decade many electronic databases of vegetation plots, mainly phytosociological relevés, were established in different European countries. These databases contain information which is extremely valuable for both testing various macroecological hypotheses and for nature conservation

  11. Casa Grande Ruins National Monument Vegetation Mapping Project - Plot Locations

    Data.gov (United States)

    National Park Service, Department of the Interior — This layer contains spatial information for 25 plots sampled during vegetation mapping and classification efforts at Casa Grande Ruins NM, AZ. Data was collected by...

  12. The Effect of Plot Size on Some Pratylenchus Penetrans ...

    African Journals Online (AJOL)

    Pratylenchus penetrans counts obtained from a rose field, sampled sequentially by decreasing the plot sizes were computed to obtain the respective sample means, variance and k-value of the negative binomial distribution. Plots 21 m x 80 m, 3.6 m x 3.6 m and 0.6 m x 0.6 m were sampled for the nematode. It is reported ...

  13. Oriented Spatial Box Plot, a New Pattern for Points Clusters

    OpenAIRE

    Etienne, Laurent; Devogele, Thomas; McArdle, Gavin

    2014-01-01

    Nowadays, an abundance of sensors are used to collect very large datasets containing spatial points which can be mined and analyzed to extract meaningful patterns and information. This article examines patterns which describe the dispersion of 2D data around a central tendency. Several state of the art patterns for point cluster analysis are presented and critiqued before a new pattern, the Oriented Spatial Box Plot, is defined. The Oriented Spatial Box Plot extends the clas...

  14. Tracking Changes in Cardiac Output: Statistical Considerations on the 4-Quadrant Plot and the Polar Plot Methodology

    National Research Council Canada - National Science Library

    Saugel, Bernd; Grothe, Oliver; Wagner, Julia Y

    2015-01-01

    When comparing 2 technologies for measuring hemodynamic parameters with regard to their ability to track changes, 2 graphical tools are omnipresent in the literaturethe 4-quadrant plot and the polar...

  15. Summarizing the incidence of adverse events using volcano plots and time intervals.

    Science.gov (United States)

    Zink, Richard C; Wolfinger, Russell D; Mann, Geoffrey

    2013-01-01

    Adverse event incidence analyses are a critical component for describing the safety profile of any new intervention. The results typically are presented in lengthy summary tables. For therapeutic areas where patients have frequent adverse events, analysis and interpretation are made more difficult by the sheer number and variety of events that occur. Understanding the risk in these instances becomes even more crucial. We describe a space-saving graphical summary that overcomes the limitations of traditional presentations of adverse events and improves interpretability of the safety profile. We present incidence analyses of adverse events graphically using volcano plots to highlight treatment differences. Data from a clinical trial of patients experiencing an aneurysmal subarachnoid hemorrhage are used for illustration. Adjustments for multiplicity are illustrated. Color is used to indicate the treatment with higher incidence; bubble size represents the total number of events that occur in the treatment arms combined. Adjustments for multiple comparisons are displayed in a manner to indicate clearly those events for which the difference between treatment arms is statistically significant. Furthermore, adverse events can be displayed by time intervals, with multiple volcano plots or animation to appreciate changes in adverse event risk over time. Such presentations can emphasize early differences across treatments that may resolve later or highlight events for which treatment differences may become more substantial with longer follow-up. Treatment arms are compared in a pairwise fashion. Volcano plots are space-saving tools that emphasize important differences between the adverse event profiles of two treatment arms. They can incorporate multiplicity adjustments in a manner that is straightforward to interpret and, by using time intervals, can illustrate how adverse event risk changes over the course of a clinical trial.

  16. Grid Integration of Aggregated Demand Response, Part 1: Load Availability Profiles and Constraints for the Western Interconnection

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Daniel J.; Matson, Nance; Sohn, Michael D.; Rose, Cody; Dudley, Junqiao; Goli, Sasank; Kiliccote, Sila; Hummon, Marissa; Palchak, David; Denholm, Paul; Jorgenson, Jennie

    2013-09-09

    Demand response (DR) has the potential to improve electric grid reliability and reduce system operation costs. However, including DR in grid modeling can be difficult due to its variable and non-traditional response characteristics, compared to traditional generation. Therefore, efforts to value the participation of DR in procurement of grid services have been limited. In this report, we present methods and tools for predicting demand response availability profiles, representing their capability to participate in capacity, energy, and ancillary services. With the addition of response characteristics mimicking those of generation, the resulting profiles will help in the valuation of the participation of demand response through production cost modeling, which informs infrastructure and investment planning.

  17. Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancers

    Science.gov (United States)

    Yan, Zhenyu; Shah, Parantu K.; Amin, Samir B.; Samur, Mehmet K.; Huang, Norman; Wang, Xujun; Misra, Vikas; Ji, Hongbin; Gabuzda, Dana; Li, Cheng

    2012-01-01

    We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted FFLs by their explanatory power to account for differential gene and miRNA expression between two biological conditions such as normal and cancer. GemiNI integrates not only gene and miRNA expression data but also computationally derived information about TF–target gene and miRNA–mRNA interactions. Literature validation shows that the integrated modeling of expression data and FFLs better identifies cancer-related TFs and miRNAs compared to existing approaches. We have utilized GemiNI for analyzing six data sets of solid cancers (liver, kidney, prostate, lung and germ cell) and found that top-ranked FFLs account for ∼20% of transcriptome changes between normal and cancer. We have identified common FFL regulators across multiple cancer types, such as known FFLs consisting of MYC and miR-15/miR-17 families, and novel FFLs consisting of ARNT, CREB1 and their miRNA partners. The results and analysis web server are available at http://www.canevolve.org/dChip-GemiNi. PMID:22645320

  18. Atrial fibrillation detection by heart rate variability in Poincare plot

    Directory of Open Access Journals (Sweden)

    Jeon Moongu

    2009-12-01

    Full Text Available Abstract Background Atrial fibrillation (AFib is one of the prominent causes of stroke, and its risk increases with age. We need to detect AFib correctly as early as possible to avoid medical disaster because it is likely to proceed into a more serious form in short time. If we can make a portable AFib monitoring system, it will be helpful to many old people because we cannot predict when a patient will have a spasm of AFib. Methods We analyzed heart beat variability from inter-beat intervals obtained by a wavelet-based detector. We made a Poincare plot using the inter-beat intervals. By analyzing the plot, we extracted three feature measures characterizing AFib and non-AFib: the number of clusters, mean stepping increment of inter-beat intervals, and dispersion of the points around a diagonal line in the plot. We divided distribution of the number of clusters into two and calculated mean value of the lower part by k-means clustering method. We classified data whose number of clusters is more than one and less than this mean value as non-AFib data. In the other case, we tried to discriminate AFib from non-AFib using support vector machine with the other feature measures: the mean stepping increment and dispersion of the points in the Poincare plot. Results We found that Poincare plot from non-AFib data showed some pattern, while the plot from AFib data showed irregularly irregular shape. In case of non-AFib data, the definite pattern in the plot manifested itself with some limited number of clusters or closely packed one cluster. In case of AFib data, the number of clusters in the plot was one or too many. We evaluated the accuracy using leave-one-out cross-validation. Mean sensitivity and mean specificity were 91.4% and 92.9% respectively. Conclusions Because pulse beats of ventricles are less likely to be influenced by baseline wandering and noise, we used the inter-beat intervals to diagnose AFib. We visually displayed regularity of the inter

  19. Atrial fibrillation detection by heart rate variability in Poincare plot.

    Science.gov (United States)

    Park, Jinho; Lee, Sangwook; Jeon, Moongu

    2009-12-11

    Atrial fibrillation (AFib) is one of the prominent causes of stroke, and its risk increases with age. We need to detect AFib correctly as early as possible to avoid medical disaster because it is likely to proceed into a more serious form in short time. If we can make a portable AFib monitoring system, it will be helpful to many old people because we cannot predict when a patient will have a spasm of AFib. We analyzed heart beat variability from inter-beat intervals obtained by a wavelet-based detector. We made a Poincare plot using the inter-beat intervals. By analyzing the plot, we extracted three feature measures characterizing AFib and non-AFib: the number of clusters, mean stepping increment of inter-beat intervals, and dispersion of the points around a diagonal line in the plot. We divided distribution of the number of clusters into two and calculated mean value of the lower part by k-means clustering method. We classified data whose number of clusters is more than one and less than this mean value as non-AFib data. In the other case, we tried to discriminate AFib from non-AFib using support vector machine with the other feature measures: the mean stepping increment and dispersion of the points in the Poincare plot. We found that Poincare plot from non-AFib data showed some pattern, while the plot from AFib data showed irregularly irregular shape. In case of non-AFib data, the definite pattern in the plot manifested itself with some limited number of clusters or closely packed one cluster. In case of AFib data, the number of clusters in the plot was one or too many. We evaluated the accuracy using leave-one-out cross-validation. Mean sensitivity and mean specificity were 91.4% and 92.9% respectively. Because pulse beats of ventricles are less likely to be influenced by baseline wandering and noise, we used the inter-beat intervals to diagnose AFib. We visually displayed regularity of the inter-beat intervals by way of Poincare plot. We tried to design an

  20. Demographic inference through approximate-Bayesian-computation skyline plots.

    Science.gov (United States)

    Navascués, Miguel; Leblois, Raphaël; Burgarella, Concetta

    2017-01-01

    The skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of the demographic trajectory. Because of this flexibility in shape, skyline plots can, in principle, provide realistic descriptions of the complex demographic scenarios that occur in natural populations. Currently, demographic estimates needed for skyline plots are estimated using coalescent samplers or a composite likelihood approach. Here, we provide a way to estimate historical effective population sizes using an Approximate Bayesian Computation (ABC) framework. We assess its performance using simulated and actual microsatellite datasets. Our method correctly retrieves the signal of contracting, constant and expanding populations, although the graphical shape of the plot is not always an accurate representation of the true demographic trajectory, particularly for recent changes in size and contracting populations. Because of the flexibility of ABC, similar approaches can be extended to other types of data, to multiple populations, or to other parameters that can change through time, such as the migration rate.

  1. sPlot: a statistical tool to unfold data distributions

    CERN Document Server

    Pivk, Muriel

    2005-01-01

    A novel method called sPlot, painless to implement, is presented. It projects out the signal and background distributions from a data sample for a variable that is used or not in the original likelihood fit. In each bin of that variable, optimal use is made of the existing information present in the whole event sample, in contrast to the case of the usual likelihood-ratio-cut projection plots. The thus reduced uncertainties in the low statistics bins, for the variable under consideration, makes it possible to detect small size biases such as pdf/data mismatches for a given species, and/or presence of an unexpected background contamination, that was not taken into account in the fit and therefore was biasing it. After presenting pedagogical examples, a brief application to Dalitz plots and measurements of branching ratios is given. A comparison with the projection plots shows the interest of the method. Finally are given the differents steps to implement the sPlot tool in an analysis.

  2. Study of the Dalitz plot of the $\\eta \\rightarrow \\pi^+ \\pi^- \\pi^0$ decay with the KLOE detector

    CERN Document Server

    Balkeståhl, L Caldeira

    2015-01-01

    The decay $\\eta \\rightarrow \\pi^+ \\pi^- \\pi^0$ is studied with the KLOE detector, at the DA$\\phi$NE e$^+$e$^-$ collider. Using a data sample corresponding to an integrated luminosity of $1.6$ fb$^{-1}$ a new study of the Dalitz plot is presented.

  3. A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites.

    Science.gov (United States)

    Koch, Alexander; Gawron, Daria; Steyaert, Sandra; Ndah, Elvis; Crappé, Jeroen; De Keulenaer, Sarah; De Meester, Ellen; Ma, Ming; Shen, Ben; Gevaert, Kris; Van Criekinge, Wim; Van Damme, Petra; Menschaert, Gerben

    2014-12-01

    Next-generation transcriptome sequencing is increasingly integrated with MS to enhance MS-based protein and peptide identification. Recently, a breakthrough in transcriptome analysis was achieved with the development of ribosome profiling (ribo-seq). This technology is based on the deep sequencing of ribosome-protected mRNA fragments, thereby enabling the direct observation of in vivo protein synthesis at the transcript level. In order to explore the impact of a ribo-seq-derived protein sequence search space on MS/MS spectrum identification, we performed a comprehensive proteome study on a human cancer cell line, using both shotgun and N-terminal proteomics, next to ribosome profiling, which was used to delineate (alternative) translational reading frames. By including protein-level evidence of sample-specific genetic variation and alternative translation, this strategy improved the identification score of 69 proteins and identified 22 new proteins in the shotgun experiment. Furthermore, we discovered 18 new alternative translation start sites in the N-terminal proteomics data and observed a correlation between the quantitative measures of ribo-seq and shotgun proteomics with a Pearson correlation coefficient ranging from 0.483 to 0.664. Overall, this study demonstrated the benefits of ribosome profiling for MS-based protein and peptide identification and we believe this approach could develop into a common practice for next-generation proteomics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Split-plot Experiments with Unusual Numbers of Subplot Runs

    DEFF Research Database (Denmark)

    Kulahci, Murat

    2007-01-01

    In many experimental situations, it may not be feasible or even possible to run experiments in a completely randomized fashion as usually recommended. Under these circumstances, split-plot experiments in which certain factors are changed less frequently than the others are often used. Most...... of the literature on split-plot designs is based on 2-level factorials. For those designs, the number of subplots is a power of 2. There may however be some situations where for cost purposes or physical constraints, we may need to have unusual number of subplots such as 3, 5, 6, etc. In this article, we explore...... this issue and provide some examples based on the Plackett and Burman designs. Also algorithmically constructed D-optimal split-plot designs are compared to those based on Plackett and Burman designs....

  5. When are bacteria dead? A step towards interpreting flow cytometry profiles after chlorine disinfection and membrane integrity staining.

    Science.gov (United States)

    Nocker, Andreas; Cheswick, Ryan; Dutheil de la Rochere, Pierre-Marie; Denis, Matthieu; Léziart, Tangui; Jarvis, Peter

    2017-04-01

    Flow cytometry is increasingly employed by drinking water providers. Its use with appropriate fluorescent stains allows the distinction between intact and membrane-damaged bacteria, which makes it ideally suited for assessment of disinfection efficiency. In contrast to plate counting, the technology allows the visualization of the gradual loss of membrane integrity. Although this sensitivity per se is very positive, it creates the problem of how this detailed viability information compares with binary plate counts where a colony is either formed or not. Guidelines are therefore needed to facilitate interpretation of flow cytometry results and to determine a degree of membrane damage where bacteria can be considered 'dead'. In this study we subjected Escherichia coli and environmental microorganisms in real water to increasing chlorine concentrations. Resulting flow cytometric patterns after membrane integrity staining were compared with culturability and in part with redox activity. For laboratory-grown bacteria, culturability was lost at lower disinfectant concentrations than membrane integrity making the latter a conservative viability parameter. No recovery from chlorine was observed for four days. For real water, loss of membrane integrity had to be much more substantial to completely suppress colony formation, probably due to the heterogenic composition of the natural microbial community with different members having different susceptibilities to the disinfectant.

  6. Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways.

    Science.gov (United States)

    Cogburn, L A; Wang, X; Carre, W; Rejto, L; Aggrey, S E; Duclos, M J; Simon, J; Porter, T E

    2004-01-01

    The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation-fasting and re-feeding-in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

  7. Comparison of combinations of sighting devices and target objects for establishing circular plots in the field

    Science.gov (United States)

    Sylvio Mannel; Mark A. Rumble; Maribeth Price; Thomas M. Juntti; Dong Hua

    2006-01-01

    Many aspects of ecological research require measurement of characteristics within plots. Often, the time spent establishing plots is small relative to the time spent collecting and recording data. However, some studies require larger numbers of plots, where the time spent establishing the plot is consequential to the field effort. In open habitats, circular plots are...

  8. Sediment distribution and dynamics inferred by integrated electromagnetic, optical and acoustic benthic profiling in the western Bay of Plenty (New Zealand)

    Science.gov (United States)

    Kulgemeyer, T.; von Dobeneck, T. F.; Müller, H.; Bryan, K. R.; de Lange, W. P.; Battershill, C.

    2015-12-01

    In October 2011, New Zealand experienced a marine pollution disaster after the MV RENA ran aground in the western Bay of Plenty. To estimate the transport and burial potential of contaminants, local sediment distribution and dynamics had to be assessed quickly. Our study made use of the benthic profiler NERIDIS III of the University of Bremen. 33 cross-shore profiles, each ca. 8 km long, have been surveyed. The main instrument is a controlled-source electromagnetic (CSEM) sensor, which is measuring the electric conductivity and magnetic susceptibility of the seafloor. High-resolution, overlapping seafloor photos have been taken by a bow-mounted digital camera. An on-board CTD with turbidity sensor complete the sensor arrangement. From the EM data, porosity and magnetite concentrations have been calculated and interpolated. The resulting maps show specific zones of magnetite enrichment, higher concentrations are correlated to low porosity. Photos have been used along with acoustic backscatter measured by a sidescan sonar to sketch out a preliminary map of sediment facies. Based on this, sides for grab sampling were selected. By taking grain size and mineralogy into account, a detailed map of the regional lithofacies could be created. Local sediment dynamics have been inferred by the observation of bedforms, the turbidity of bottom water and lithofacies. The results show two anti-parallel longshore transport paths dependent on differing weather conditions and water depths. The longshore magnetite distribution indicates that the heavy mineral fraction is mainly affected by storm-induced sediment transport. Our study demonstrates how integrated benthic profiling adds to the interpretability of data obtained by established methods. By bridging the gap between area-covering, but indirect data from hydroacoustics and precise, but punctual data from samples, benthic profiling enables fast and detailed assessment of sediment distribution and dynamics on a large scale.

  9. The Archetype-enabled EHR system ZK-ARCHE - integrating the ISO/EN 13606 standard and IHE XDS profile.

    Science.gov (United States)

    Kohler, Michael; Rinner, Christoph; Hübner-Bloder, Gudrun; Saboor, Samrend; Ammenwerth, Elske; Duftschmid, Georg

    2011-01-01

    The EHR system ZK-ARCHE automatically generates forms from ISO/EN 13606 archetypes. For this purpose the archetypes are augmented with components of the reference model to achieve so-called "comprehensive archetypes". Data collected via the forms are stored in a list which associates each value with the path of the corresponding comprehensive archetype node coded as W3C XPath. From this list archetype-conformant EHR extracts can be created. The system is embedded with the IHE XDS profile to allow direct data exchange in an environment of distributed data storage.

  10. Integrated transcriptomics and proteomics analysis of storage protein composition in developing barley grain to improve nutritional profile

    DEFF Research Database (Denmark)

    Kaczmarczyk, Agnieszka Ewa; Dionisio, Giuseppe; Renaut, Jenny

    2012-01-01

    The aim of the study was to understand the molecular and biochemical mechanisms underpinning the effect of nitrogen (N) on barley (Hordeum vulgare) storage protein production (hordeins) during grain filling. Using a combination of advanced biochemistry methods, we could comprehensively describe......-regimes caused significant differences in both quantity and quality of the storage proteins transcripts. Principal Component Analysis of the amino acid (AA) profiles also indicated dissimilarity in individual AA percentages, correlated to hordein content. The abundance values of proteins of interest confirmed...

  11. Volcano plots in hydrogen electrocatalysis – uses and abuses

    OpenAIRE

    Paola Quaino; Fernanda Juarez; Elizabeth Santos; Wolfgang Schmickler

    2014-01-01

    Summary Sabatier’s principle suggests, that for hydrogen evolution a plot of the rate constant versus the hydrogen adsorption energy should result in a volcano, and several such plots have been presented in the literature. A thorough examination of the data shows, that there is no volcano once the oxide-covered metals are left out. We examine the factors that govern the reaction rate in the light of our own theory and conclude, that Sabatier’s principle is only one of several factors that det...

  12. On the Nature of Earth-Mars Porkchop Plots

    Science.gov (United States)

    Woolley, Ryan C.; Whetsel, Charles W.

    2013-01-01

    Porkchop plots are a quick and convenient tool to help mission designers plan ballistic trajectories between two bodies. Parameter contours give rise to the familiar 'porkchop' shape. Each synodic period the pattern repeats, but not exactly, primarily due to differences in inclination and non-zero eccentricity. In this paper we examine the morphological features of Earth-to-Mars porkchop plots and the orbital characteristics that create them. These results are compared to idealistic and optimized transfers. Conclusions are drawn about 'good' opportunities versus 'bad' opportunities for different mission applications.

  13. Probability plots based on Student's t-distribution.

    Science.gov (United States)

    Hooft, Rob W W; Straver, Leo H; Spek, Anthony L

    2009-07-01

    The validity of the normal distribution as an error model is commonly tested with a (half) normal probability plot. Real data often contain outliers. The use of t-distributions in a probability plot to model such data more realistically is described. It is shown how a suitable value of the parameter nu of the t-distribution can be determined from the data. The results suggest that even data that seem to be modeled well using a normal distribution can be better modeled using a t-distribution.

  14. Geopolitical location and plot in The Night Manager

    DEFF Research Database (Denmark)

    Agger, Gunhild

    2017-01-01

    The primary aim of the article is to contribute to developing concepts for the analysis of location and plot in visual fiction. The secondary aim is to assess which strategies the Danish director Susanne Bier uses in her approach to an international production such as the British-American TV serial...... The Night Manager. Three perspectives are tested in combining the analysis of location with the development of the plot: the general concepts of universal and real geography; the idea of being located inside or outside a given context; and the associated notion of centre-periphery opposition. A geopolitical...

  15. PlotXY: A High Quality Plotting System for the Herschel Interactive Processing Environment (HIPE) and the Astronomical Community

    Science.gov (United States)

    Panuzzo, P.; Li, J.; Caux, E.

    2012-09-01

    The Herschel Interactive Processing Environment (HIPE) was developed by the European Space Agency (ESA) in collaboration with NASA and the Herschel Instrument Control Centres, to provide the astronomical community a complete environment to process and analyze the data gathered by the Herschel Space Observatory. One of the most important components of HIPE is the plotting system (named PlotXY) that we present here. With PlotXY it is possible to produce easily high quality publication-ready 2D plots. It provides a long list of features, with fully configurable components, and interactive zooming. The entire code of HIPE is written in Java and is open source released under the GNU Lesser General Public License version 3. A new version of PlotXY is being developed to be independent from the HIPE code base; it is available to the software development community for the inclusion in other projects at the URL google.com/p/jplot2d/'>http://code.google.com/p/jplot2d/.

  16. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach.

    Directory of Open Access Journals (Sweden)

    Luz A Betancur

    Full Text Available Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities.

  17. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach

    Science.gov (United States)

    Betancur, Luz A.; Naranjo-Gaybor, Sandra J.; Vinchira-Villarraga, Diana M.; Moreno-Sarmiento, Nubia C.; Maldonado, Luis A.; Suarez-Moreno, Zulma R.; Acosta-González, Alejandro; Padilla-Gonzalez, Gillermo F.; Puyana, Mónica; Castellanos, Leonardo; Ramos, Freddy A.

    2017-01-01

    Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities. PMID:28225766

  18. Profiling and sorting Mangifera Indica morphology for quality attributes and grade standards using integrated image processing algorithms

    Science.gov (United States)

    Balbin, Jessie R.; Fausto, Janette C.; Janabajab, John Michael M.; Malicdem, Daryl James L.; Marcelo, Reginald N.; Santos, Jan Jeffrey Z.

    2017-06-01

    Mango production is highly vital in the Philippines. It is very essential in the food industry as it is being used in markets and restaurants daily. The quality of mangoes can affect the income of a mango farmer, thus incorrect time of harvesting will result to loss of quality mangoes and income. Scientific farming is much needed nowadays together with new gadgets because wastage of mangoes increase annually due to uncouth quality. This research paper focuses on profiling and sorting of Mangifera Indica using image processing techniques and pattern recognition. The image of a mango is captured on a weekly basis from its early stage. In this study, the researchers monitor the growth and color transition of a mango for profiling purposes. Actual dimensions of the mango are determined through image conversion and determination of pixel and RGB values covered through MATLAB. A program is developed to determine the range of the maximum size of a standard ripe mango. Hue, light, saturation (HSL) correction is used in the filtering process to assure the exactness of RGB values of a mango subject. By pattern recognition technique, the program can determine if a mango is standard and ready to be exported.

  19. The discovery of putative urine markers for the specific detection of prostate tumor by integrative mining of public genomic profiles.

    Directory of Open Access Journals (Sweden)

    Min Chen

    Full Text Available Urine has emerged as an attractive biofluid for the noninvasive detection of prostate cancer (PCa. There is a strong imperative to discover candidate urinary markers for the clinical diagnosis and prognosis of PCa. The rising flood of various omics profiles presents immense opportunities for the identification of prospective biomarkers. Here we present a simple and efficient strategy to derive candidate urine markers for prostate tumor by mining cancer genomic profiles from public databases. Prostate, bladder and kidney are three major tissues from which cellular matters could be released into urine. To identify urinary markers specific for PCa, upregulated entities that might be shed in exosomes of bladder cancer and kidney cancer are first excluded. Through the ontology-based filtering and further assessment, a reduced list of 19 entities encoding urinary proteins was derived as putative PCa markers. Among them, we have found 10 entities closely associated with the process of tumor cell growth and development by pathway enrichment analysis. Further, using the 10 entities as seeds, we have constructed a protein-protein interaction (PPI subnetwork and suggested a few urine markers as preferred prognostic markers to monitor the invasion and progression of PCa. Our approach is amenable to discover and prioritize potential markers present in a variety of body fluids for a spectrum of human diseases.

  20. Integrated Analysis of DNA Methylation and mRNA Expression Profiles to Identify Key Genes in Severe Oligozoospermia

    Directory of Open Access Journals (Sweden)

    Zhiming Li

    2017-05-01

    Full Text Available Severe oligozoospermia (SO is a complex disorder, whose etiology is the combined effect of genetic factors and epigenetic conditions. In this study, we examined DNA methylation and mRNA expression status in a set of testicular tissues of SO patients (n = 3, and compared methylated data with those derived from obstructive azoospermia (OA patients (n = 3 with normal spermatogenesis phenotype. We identified 1,960 differentially methylated CpG sites showing significant alterations in SO vs. OA using the Illumina Infinium HumanMethylation450 bead array. By integrating above DNA methylation data and mRNA expression results, we totally identified 72 methylated CpG sites located in 65 genes with anti-correlation between DNA methylation and mRNA expression. Integrated pathways analysis indicates that these genes are involved in response to hormone stimulus, activation of protein kinase activity, and apoptotic process, among others. We also observed some genes with inversely correlated difference is novel in male infertility field, including PTPRN2, EPHX1, SERPINB9, SLIT3, etc. Our results lay a groundwork for further biological study of SO. Moreover, we generated a workflow for integrated analysis of DNA methylation and mRNA expression, which is expandable to other study types.

  1. Tracking forest resource condition through Permanent sample plots ...

    African Journals Online (AJOL)

    This paper presents efforts by Tanzania Forestry Research Institute (TAFORI) to establish Permanent Sample Plots (PSPs) as a means of setting baseline information on forest resources condition and eventual assessment of the impact of decentralization policy for Bukombe- Mbogwe Local Authority Forest Reserve ...

  2. Developing Box Plots While Navigating the Maze of Data Representations

    Science.gov (United States)

    Duncan, Bruce; Fitzallen, Noleine

    2013-01-01

    The learning sequence described in this article was developed to provide students with a demonstration of the development of box plots from authentic data as an illustration of the advantages gained from using multiple forms of data representation. The sequence follows an authentic process that starts with a problem to which data representations…

  3. Box-and-Whisker Plots Applied to Food Chemistry

    Science.gov (United States)

    Ferreira, Joao E. V.; Miranda, Ricardo M.; Figueiredo, Antonio F.; Barbosa, Jardel P.; Brasil, Edykarlos M.

    2016-01-01

    Box-and-whisker plots or simply boxplots are powerful graphical representations that give an overview of a data set. In this work five different examples illustrate the applications of boxplots in food chemistry. The examples involve relative sweetness of sugars and sugar alcohols with respect to sucrose, the potassium content of fruits and…

  4. Omitted Variable Sensitivity Analysis with the Annotated Love Plot

    Science.gov (United States)

    Hansen, Ben B.; Fredrickson, Mark M.

    2014-01-01

    The goal of this research is to make sensitivity analysis accessible not only to empirical researchers but also to the various stakeholders for whom educational evaluations are conducted. To do this it derives anchors for the omitted variable (OV)-program participation association intrinsically, using the Love plot to present a wide range of…

  5. Temporal MDS Plots for Analysis of Multivariate Data.

    Science.gov (United States)

    Jäckle, Dominik; Fischer, Fabian; Schreck, Tobias; Keim, Daniel A

    2016-01-01

    Multivariate time series data can be found in many application domains. Examples include data from computer networks, healthcare, social networks, or financial markets. Often, patterns in such data evolve over time among multiple dimensions and are hard to detect. Dimensionality reduction methods such as PCA and MDS allow analysis and visualization of multivariate data, but per se do not provide means to explore multivariate patterns over time. We propose Temporal Multidimensional Scaling (TMDS), a novel visualization technique that computes temporal one-dimensional MDS plots for multivariate data which evolve over time. Using a sliding window approach, MDS is computed for each data window separately, and the results are plotted sequentially along the time axis, taking care of plot alignment. Our TMDS plots enable visual identification of patterns based on multidimensional similarity of the data evolving over time. We demonstrate the usefulness of our approach in the field of network security and show in two case studies how users can iteratively explore the data to identify previously unknown, temporally evolving patterns.

  6. Surveillance of Site A and Plot M, Report for 2009.

    Energy Technology Data Exchange (ETDEWEB)

    Golchert, N. W.

    2010-04-21

    The results of the environmental surveillance program conducted at Site A/Plot M in the Palos Forest Preserve area for Calendar Year 2009 are presented. Based on the results of the 1976-1978 radiological characterization of the site, a determination was made that a surveillance program be established. The characterization study determined that very low levels of hydrogen-3 (as tritiated water) had migrated from the burial ground and were present in two nearby hand-pumped picnic wells. The current surveillance program began in 1980 and consists of sample collection and analysis of surface and subsurface water. The results of the analyses are used to monitor the migration pathway of hydrogen-3 contaminated water from the burial ground (Plot M) to the hand-pumped picnic wells and monitor for the presence of radioactive materials in the environment of the area. Hydrogen-3 in the Red Gate Woods picnic wells was still detected this year, but the average and maximum concentrations were significantly less than found earlier. Hydrogen-3 continues to be detected in a number of wells, boreholes, dolomite holes, and a surface stream. Analyses since 1984 have indicated the presence of low levels of strontium-90 in water from a number of boreholes next to Plot M. The results of the surveillance program continue to indicate that the radioactivity remaining at Site A/Plot M does not endanger the health or safety of the public visiting the site, using the picnic area, or living in the vicinity.

  7. Surveillance of Site A and Plot M report for 2010.

    Energy Technology Data Exchange (ETDEWEB)

    Golchert, N. W. (ESQ)

    2011-05-31

    The results of the environmental surveillance program conducted at Site A/Plot M in the Palos Forest Preserve area for Calendar Year 2010 are presented. Based on the results of the 1976-1978 radiological characterization of the site, a determination was made that a surveillance program be established. The characterization study determined that very low levels of hydrogen-3 (as tritiated water) had migrated from the burial ground and were present in two nearby hand-pumped picnic wells. The current surveillance program began in 1980 and consists of sample collection and analysis of surface and subsurface water. The results of the analyses are used to monitor the migration pathway of hydrogen-3 contaminated water from the burial ground (Plot M) to the hand-pumped picnic wells and monitor for the presence of radioactive materials in the environment of the area. Hydrogen-3 in the Red Gate Woods picnic wells was still detected this year, but the average and maximum concentrations were significantly less than found earlier. Hydrogen-3 continues to be detected in a number of wells, boreholes, dolomite holes, and a surface stream. Analyses since 1984 have indicated the presence of low levels of strontium-90 in water from a number of boreholes next to Plot M. The results of the surveillance program continue to indicate that the radioactivity remaining at Site A/Plot M does not endanger the health or safety of the public visiting the site, using the picnic area, or living in the vicinity.

  8. The Brazilian national system of forest permanent plots

    Science.gov (United States)

    Yeda Maria Malheiros de Oliveira; Maria Augusta Doetzer Rosot; Patricia Povoa de Mottos; Joberto Veloso de Freitas; Guilherme Luis Augusto Gomide; < i> et al< /i>

    2009-01-01

    The Brazilian National System of Forest Permanent Plots (SisPP) is a governmental initiative designed and being implemented in partnership by the Ministry of Environment (MMA), represented by the National Forest Programme (PNF) and the Brazilian Forest Service (SFB) and the Embrapa Forestry (a research center of the Brazilian Agricultural Research Corporation - Embrapa...

  9. A precision nutrient variability study of an experimental plot in ...

    African Journals Online (AJOL)

    The spatial soil fertility status of a 2.5 ha experimental plot was generated by mapping the soil nutrient concentration and fertility status using GIS kriging technique. The research was conducted in Mukono Zonal Agricultural Research and Development Institute, Mukono, Uganda in October 2013. Soil samples across the ...

  10. Estimation of optimum plot dimensions and replication number for ...

    African Journals Online (AJOL)

    Resultant basic unit grain yields were combined to simulate different plot sizes and shapes, and Smith's empirical model and subsequent derivations were used to estimate soil heterogeneity. The broadcast sown trials generally resulted in lower estimates of soil heterogeneity, higher coefficients of variation, and higher ...

  11. Constructing General Orthogonal Fractional Factorial Split-Plot Designs

    NARCIS (Netherlands)

    Sartono, B.; Goos, P.; Schoen, E.

    2015-01-01

    While the orthogonal design of split-plot fractional factorial experiments has received much attention already, there are still major voids in the literature. First, designs with one or more factors acting at more than two levels have not yet been considered. Second, published work on nonregular

  12. metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data

    DEFF Research Database (Denmark)

    Louvel, Guillaume; Der Sarkissian, Clio; Hanghøj, Kristian Ebbesen

    2016-01-01

    Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high......-throughput DNA sequencing (HTS). Here, we develop metaBIT, an open-source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy-based assignment and relative abundance calculation of microbial taxa......, as well as cross-sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present...

  13. Problems of Comparative Plotting of The Ship's Position

    Science.gov (United States)

    Stateczny, Andrzej

    In recent years the problem of position plotting in navigation has been dominated by satellite systems, the GPS in particular. These systems are used both at sea (maritime navigation) and in the air (aerial navigation) as well as on land (terrestrial navigation). With the application of satellite systems the position can be plotted within very short spaces of time, in the range of a few or a dozen seconds. Relying exclusively on satellite systems, however, exposes to the danger of losing information in case of average, intentional switch-off, disturbance and possible encoding of informat ion reaching the user. This results in the necessity of having yet another, autonomous system at one's disposal (independent of external information sources) making possible the plotting of position in an autonomous way. These requirements are met by methods of comparative navigation. The object of interest of comparative navigation is plotting the ship's position by comparing a dynamically registered image with a pattern image. The pattern images can be numeric radar charts, sonar or aerial, suitably prepared for comparison with respectively radar, sonar or aerial images. Yet the most frequently registered images at sea will be radar images; the pattern, on the other hand, will be a numeric radar chart generated on the basis of topographic and hydrometeorological data or previous radar observation. The following elements go to make up the process of plotting the ship's position by comparative methods based on radar observation: -transforming the radar image into a shape comparable with the chart, -adapting the sea chart for comparison with the radar image. This aim can be attained by generating a radar chart, -the application of a suitable matching algorithm. The aim of matching algorithms is the designation of the best fitting of the images, in this case of the numeric navigational sea chart and the radar image, -suitable plotting of the ship's position so as to ensure maximum

  14. Aquifer test interpretation using derivative analysis and diagnostic plots

    Science.gov (United States)

    Hernández-Espriú, Antonio; Real-Rangel, Roberto; Cortés-Salazar, Iván; Castro-Herrera, Israel; Luna-Izazaga, Gabriela; Sánchez-León, Emilio

    2017-04-01

    Pumping tests remain a method of choice to deduce fundamental aquifer properties and to assess well condition. In the oil and gas (O&G) industry, well testing has been the core technique in examining reservoir behavior over the last 50 years. The pressure derivative by Bourdet, it is perhaps, the most significant single development in the history of well test analysis. Recently, the so-called diagnostics plots (e.g. drawdown and drawdown derivative in a log-log plot) have been successfully tested in aquifers. However, this procedure is still underutilized by groundwater professionals. This research illustrates the applicability range, advantages and drawbacks (e.g. smoothing procedures) of diagnostic plots using field examples from a wide spectrum of tests (short/long tests, constant/variable flow rates, drawdown/buildup stages, pumping well/observation well) in dissimilar geological conditions. We analyze new and pre-existent aquifer tests in Mexico, USA, Canada, Germany, France and Saudi Arabia. In constant flow rate tests, our results show that derivative analysis is an easy, robust and powerful tool to assess near-borehole damage effects, formation heterogeneity, boundaries, flow regimes, infinite-acting radial stages, i.e., valid Theisian framework, and fracture-driven flow. In step tests, the effectiveness relies on high-frequency drawdown measurements. Moreover, we adapt O&G analytical solutions to cater for the conditions in groundwater systems. In this context, further parameters can be computed analytically from the plots, such as skin factor, head losses, wellbore storage, distance to the boundary, channel-aquifer and/or fracture zone width, among others. Therefore, diagnostic plots should be considered a mandatory tool for pumping tests analysis among hydrogeologists. This project has been supported by DGAPA (UNAM) under the research project PAPIIT IN-112815.

  15. 3D plotting of growth factor loaded calcium phosphate cement scaffolds.

    Science.gov (United States)

    Akkineni, Ashwini Rahul; Luo, Yongxiang; Schumacher, Matthias; Nies, Berthold; Lode, Anja; Gelinsky, Michael

    2015-11-01

    Additive manufacturing allows to widely control the geometrical features of implants. Recently, we described the fabrication of calcium phosphate cement (CPC) scaffolds by 3D plotting of a storable CPC paste based on water-immiscible carrier liquid. Plotting and hardening is conducted under mild conditions allowing the (precise and local) integration of biological components. In this study, we have developed a procedure for efficient loading of growth factors in the CPC scaffolds during plotting and demonstrated the feasibility of this approach. Bovine serum albumin (BSA) or vascular endothelial growth factor (VEGF), used as model proteins, were encapsulated in chitosan/dextran sulphate microparticles which could be easily mixed into the CPC paste in freeze-dried state. In order to prevent leaching of the proteins during cement setting, usually carried out by immersion in aqueous solutions, the plotted scaffolds were aged in water-saturated atmosphere (humidity). Setting in humidity avoided early loss of loaded proteins but provided sufficient amount of water to allow cement setting, as indicated by XRD analysis and mechanical testing in comparison to scaffolds set in water. Moreover, humidity-set scaffolds were characterised by altered, even improved properties: no swelling or crack formation was observed and accordingly, surface topography, total porosity and compressive modulus of the humidity-set scaffolds differed from those of the water-set counterparts. Direct cultivation of mesenchymal stem cells on the humidity-set scaffolds over 21days revealed their cytocompatibility. Maintenance of the bioactivity of VEGF during the fabrication procedure was proven in indirect and direct culture experiments with endothelial cells. Additive manufacturing techniques allow the fabrication of implants with defined architecture (inner pore structure and outer shape). Especially printing technologies conducted under mild conditions allow additionally the (spatially controlled

  16. Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress.

    Science.gov (United States)

    Wilmes, Anja; Limonciel, Alice; Aschauer, Lydia; Moenks, Konrad; Bielow, Chris; Leonard, Martin O; Hamon, Jeremy; Carpi, Donatella; Ruzek, Silke; Handler, Andreas; Schmal, Olga; Herrgen, Karin; Bellwon, Patricia; Burek, Christof; Truisi, Germaine L; Hewitt, Philip; Di Consiglio, Emma; Testai, Emanuela; Blaauboer, Bas J; Guillou, Claude; Huber, Christian G; Lukas, Arno; Pfaller, Walter; Mueller, Stefan O; Bois, Frederic Y; Dekant, Wolfgang; Jennings, Paul

    2013-02-21

    High content omic techniques in combination with stable human in vitro cell culture systems have the potential to improve on current pre-clinical safety regimes by providing detailed mechanistic information of altered cellular processes. Here we investigated the added benefit of integrating transcriptomics, proteomics and metabolomics together with pharmacokinetics for drug testing regimes. Cultured human renal epithelial cells (RPTEC/TERT1) were exposed to the nephrotoxin Cyclosporine A (CsA) at therapeutic and supratherapeutic concentrations for 14days. CsA was quantified in supernatants and cellular lysates by LC-MS/MS for kinetic modeling. There was a rapid cellular uptake and accumulation of CsA, with a non-linear relationship between intracellular and applied concentrations. CsA at 15μM induced mitochondrial disturbances and activation of the Nrf2-oxidative-damage and the unfolded protein-response pathways. All three omic streams provided complementary information, especially pertaining to Nrf2 and ATF4 activation. No stress induction was detected with 5μM CsA; however, both concentrations resulted in a maximal secretion of cyclophilin B. The study demonstrates for the first time that CsA-induced stress is not directly linked to its primary pharmacology. In addition we demonstrate the power of integrated omics for the elucidation of signaling cascades brought about by compound induced cell stress. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Scaling wood volume estimates from inventory plots to landscapes with airborne LiDAR in temperate deciduous forest

    Directory of Open Access Journals (Sweden)

    Shaun R. Levick

    2016-05-01

    Full Text Available Abstract Background Monitoring and managing carbon stocks in forested ecosystems requires accurate and repeatable quantification of the spatial distribution of wood volume at landscape to regional scales. Grid-based forest inventory networks have provided valuable records of forest structure and dynamics at individual plot scales, but in isolation they may not represent the carbon dynamics of heterogeneous landscapes encompassing diverse land-management strategies and site conditions. Airborne LiDAR has greatly enhanced forest structural characterisation and, in conjunction with field-based inventories, it provides avenues for monitoring carbon over broader spatial scales. Here we aim to enhance the integration of airborne LiDAR surveying with field-based inventories by exploring the effect of inventory plot size and number on the relationship between field-estimated and LiDAR-predicted wood volume in deciduous broad-leafed forest in central Germany. Results Estimation of wood volume from airborne LiDAR was most robust (R2 = 0.92, RMSE = 50.57 m3 ha−1 ~14.13 Mg C ha−1 when trained and tested with 1 ha experimental plot data (n = 50. Predictions based on a more extensive (n = 1100 plot network with considerably smaller (0.05 ha plots were inferior (R2 = 0.68, RMSE = 101.01 ~28.09 Mg C ha−1. Differences between the 1 and 0.05 ha volume models from LiDAR were negligible however at the scale of individual land-management units. Sample size permutation tests showed that increasing the number of inventory plots above 350 for the 0.05 ha plots returned no improvement in R2 and RMSE variability of the LiDAR-predicted wood volume model. Conclusions Our results from this study confirm the utility of LiDAR for estimating wood volume in deciduous broad-leafed forest, but highlight the challenges associated with field plot size and number in establishing robust relationships between airborne LiDAR and field derived wood volume. We

  18. Scaling wood volume estimates from inventory plots to landscapes with airborne LiDAR in temperate deciduous forest.

    Science.gov (United States)

    Levick, Shaun R; Hessenmöller, Dominik; Schulze, E-Detlef

    2016-12-01

    Monitoring and managing carbon stocks in forested ecosystems requires accurate and repeatable quantification of the spatial distribution of wood volume at landscape to regional scales. Grid-based forest inventory networks have provided valuable records of forest structure and dynamics at individual plot scales, but in isolation they may not represent the carbon dynamics of heterogeneous landscapes encompassing diverse land-management strategies and site conditions. Airborne LiDAR has greatly enhanced forest structural characterisation and, in conjunction with field-based inventories, it provides avenues for monitoring carbon over broader spatial scales. Here we aim to enhance the integration of airborne LiDAR surveying with field-based inventories by exploring the effect of inventory plot size and number on the relationship between field-estimated and LiDAR-predicted wood volume in deciduous broad-leafed forest in central Germany. Estimation of wood volume from airborne LiDAR was most robust (R2 = 0.92, RMSE = 50.57 m3 ha-1 ~14.13 Mg C ha-1) when trained and tested with 1 ha experimental plot data (n = 50). Predictions based on a more extensive (n = 1100) plot network with considerably smaller (0.05 ha) plots were inferior (R2 = 0.68, RMSE = 101.01 ~28.09 Mg C ha-1). Differences between the 1 and 0.05 ha volume models from LiDAR were negligible however at the scale of individual land-management units. Sample size permutation tests showed that increasing the number of inventory plots above 350 for the 0.05 ha plots returned no improvement in R2 and RMSE variability of the LiDAR-predicted wood volume model. Our results from this study confirm the utility of LiDAR for estimating wood volume in deciduous broad-leafed forest, but highlight the challenges associated with field plot size and number in establishing robust relationships between airborne LiDAR and field derived wood volume. We are moving into a forest management era where field

  19. A tool to determine crown and plot canopy transparency for forest inventory and analysis phase 3 plots using digital photographs

    Science.gov (United States)

    Matthew F. Winn; Philip A. Araman

    2012-01-01

    The USDA Forest Service Forest Inventory and Analysis (FIA) program collects crown foliage transparency estimates for individual trees on Phase 3 (P3) inventory plots. The FIA crown foliage estimate is obtained from a pair of perpendicular side views of the tree. Researchers with the USDA Forest Service Southern Research Station have developed a computer program that...

  20. Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network.

    Science.gov (United States)

    Xu, Ke; Xiong, Wei; Zhou, Ming; Wang, Heran; Yang, Jing; Li, Xiayu; Chen, Pan; Liao, Qianjin; Deng, Hao; Li, Xiaoling; Li, Guiyuan; Zeng, Zhaoyang

    2016-01-01

    BRD7 is a single bromodomain-containing protein that functions as a subunit of the SWI/SNF chromatin-remodeling complex to regulate transcription. It also interacts with the well-known tumor suppressor protein p53 to trans-activate genes involved in cell cycle arrest. In this paper, we report an integrative analysis of genome-wide chromatin occupancy of BRD7 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and digital gene expression (DGE) profiling by RNA-sequencing upon the overexpression of BRD7 in human cells. We localized 156 BRD7-binding peaks representing 184 genes by ChIP-sequencing, and most of these peaks were co-localized with histone modification sites. Four novel motifs were significantly represented in these BRD7-enriched regions. Ingenuity pathway analysis revealed that 22 of these BRD7 target genes were involved in a network regulating cell death and survival. DGE profiling identified 560 up-regulated genes and 1088 down-regulated genes regulated by BRD7. Using Gene Ontology and pathway analysis, we found significant enrichment of the cell cycle and apoptosis pathway genes. For the integrative analysis of the ChIP-seq and DEG data, we constructed a regulating network of BRD7 downstream genes, and this network suggests multiple feedback regulations of the pathways. Furthermore, we validated BIRC2, BIRC3, TXN2, and NOTCH1 genes as direct, functional BRD7 targets, which were involved in the cell cycle and apoptosis pathways. These results provide a genome-wide view of chromatin occupancy and the gene regulation network of the BRD7 signaling pathway.

  1. Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling

    Directory of Open Access Journals (Sweden)

    Dongguo Li

    2015-01-01

    Full Text Available Breast cancer is a heterogeneous disease with well-defined molecular subtypes. Currently, comparative genomic hybridization arrays (aCGH techniques have been developed rapidly, and recent evidences in studies of breast cancer suggest that tumors within gene expression subtypes share similar DNA copy number aberrations (CNA which can be used to further subdivide subtypes. Moreover, subtype-specific miRNA expression profiles are also proposed as novel signatures for breast cancer classification. The identification of mRNA or miRNA expression-based breast cancer subtypes is considered an instructive means of prognosis. Here, we conducted an integrated analysis based on copy number aberrations data and miRNA-mRNA dual expression profiling data to identify breast cancer subtype-specific biomarkers. Interestingly, we found a group of genes residing in subtype-specific CNA regions that also display the corresponding changes in mRNAs levels and their target miRNAs’ expression. Among them, the predicted direct correlation of BRCA1-miR-143-miR-145 pairs was selected for experimental validation. The study results indicated that BRCA1 positively regulates miR-143-miR-145 expression and miR-143-miR-145 can serve as promising novel biomarkers for breast cancer subtyping. In our integrated genomics analysis and experimental validation, a new frame to predict candidate biomarkers of breast cancer subtype is provided and offers assistance in order to understand the potential disease etiology of the breast cancer subtypes.

  2. Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis

    Directory of Open Access Journals (Sweden)

    Barker Jeffery L

    2009-08-01

    Full Text Available Abstract Background Cortical development is a complex process that includes sequential generation of neuronal progenitors, which proliferate and migrate to form the stratified layers of the developing cortex. To identify the individual microRNAs (miRNAs and mRNAs that may regulate the genetic network guiding the earliest phase of cortical development, the expression profiles of rat neuronal progenitors obtained at embryonic day 11 (E11, E12 and E13 were analyzed. Results Neuronal progenitors were purified from telencephalic dissociates by a positive-selection strategy featuring surface labeling with tetanus-toxin and cholera-toxin followed by fluorescence-activated cell sorting. Microarray analyses revealed the fractions of miRNAs and mRNAs that were up-regulated or down-regulated in these neuronal progenitors at the beginning of cortical development. Nearly half of the dynamically expressed miRNAs were negatively correlated with the expression of their predicted target mRNAs. Conclusion These data support a regulatory role for miRNAs during the transition from neuronal progenitors into the earliest differentiating cortical neurons. In addition, by supplying a robust data set in which miRNA and mRNA profiles originate from the same purified cell type, this empirical study may facilitate the development of new algorithms to integrate various "-omics" data sets.

  3. Integrated genomic profiling identifies candidate genes implicated in glioma-genesis and a novel LEO1-SLC12A1 fusion gene.

    Science.gov (United States)

    Bralten, Linda B C; Kloosterhof, Nanne K; Gravendeel, Lonneke A M; Sacchetti, Andrea; Duijm, Elza J; Kros, Johan M; van den Bent, Martin J; Hoogenraad, Casper C; Sillevis Smitt, Peter A E; French, Pim J

    2010-06-01

    We performed genotyping and exon-level expression profiling on 21 glioblastomas (GBMs) and 19 oligodendrogliomas (ODs) to identify genes involved in glioma initiation and/or progression. Low-copy number amplifications (2.5 7) were more frequently observed in GBMs; ODs generally have more heterozygous deletions per tumor. Four high-copy amplicons were identified in more than one sample and resulted in overexpression of the known oncogenes EGFR, MDM2, and CDK4. In the fourth amplicon, RBBP5, a member of the RB pathway, may act as a novel oncogene in GBMs. Not all hCNAs contain known genes, which may suggest that other transcriptional and/or regulatory elements are the target for amplification. Regions with most frequent allelic loss, both in ODs and GBMs, resulted in a reduced expression of known tumor suppressor genes. We identified a homozygous deletion spanning the Pragmin gene in one sample, but direct sequencing of all coding exons in 20 other glioma samples failed to detect additional genetic changes. Finally, we screened for fusion genes by identifying aberrant 5'-3' expression of genes that lie over regions of a copy number change. A fusion gene between exon 11 of LEO1 and exon 10 of SLC12A1 was identified. Our data show that integrated genomic profiling can identify genes involved in tumor initiation, and/or progression and can be used as an approach to identify novel fusion genes. (c) 2010 Wiley-Liss, Inc.

  4. A systematic integrated analysis of brain expression profiles reveals YAP1 and other prioritized hub genes as important upstream regulators in Alzheimer's disease.

    Science.gov (United States)

    Xu, Min; Zhang, Deng-Feng; Luo, Rongcan; Wu, Yong; Zhou, Hejiang; Kong, Li-Li; Bi, Rui; Yao, Yong-Gang

    2018-02-01

    Profiling the spatial-temporal expression pattern and characterizing the regulatory networks of brain tissues are vital for understanding the pathophysiology of Alzheimer's disease (AD). We performed a systematic integrated analysis of expression profiles of AD-affected brain tissues (684 AD and 562 controls). A network-based convergent functional genomic approach was used to prioritize possible regulator genes during AD development, followed by functional characterization. We generated a complete list of differentially expressed genes and hub genes of the transcriptomic network in AD brain and constructed a Web server (www.alzdata.org) for public access. Seventeen hub genes active at the early stages, especially YAP1, were recognized as upstream regulators of the AD network. Cellular assays proved that early alteration of YAP1 could promote AD by influencing the whole transcriptional network. Early expression disturbance of hub genes is an important feature of AD development, and interfering with this process may reverse the disease progression. Copyright © 2017 the Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  5. Social-economic profile of asthmatic patients assisted at a Nucleus of Integrated Medical Assistance - doi:10.5020/18061230.2008.p180

    Directory of Open Access Journals (Sweden)

    Anisia Torquilho Praxedes

    2012-01-01

    Full Text Available Objective: To determine the social-economic profile of asthmatic patients who use the health services rendered by the Nucleus of Integrated Medical Assistance (NAMI, in Fortaleza- Ce. Methods: This descriptive, retrospective and cross-sectional study, of a quantitative approach, had a sample comprised by 40 asthmatic patients assisted at NAMI during the period of April to May, 2006. The data collection was accomplished by means of a standard semi-structured interview, with open and closed questions. Results: The age range between 0 to 5 years old represented the greater percentage of patients, thus obtaining 60.0% of the answered questionnaires. According to social-economic conditions, 55.0% were illiterate or were learning to read, 75.0% were using some drug prescribed at NAMI, 72.5% fully ignored the disease, 52.5% recognized the factors that triggered the asthmatic crisis and 55.0% said having often crisis. Seventy per cent (70.0% of the interviewed showed some difficulty related to the use of the drugs; 47.5% referred having different problems related to the access to the medications. Conclusion: By the analysis of the determined social-economic profile of asthmatics patients assisted at NAMI, it is concluded that great part of them are people with little instruction, due to the social exclusion in which they are found; being the majority of them children of female gender. NCT00722657

  6. Integration of gene expression and DNA methylation profiles provides a molecular subtype for risk assessment in atherosclerosis.

    Science.gov (United States)

    Ma, Sheng-Chao; Zhang, Hui-Ping; Kong, Fan-Qi; Zhang, Hui; Yang, Cheng; He, Yang-Yang; Wang, Yan-Hua; Yang, An-Ning; Tian, Ju; Yang, Xiao-Ling; Zhang, Ming-Hao; Xu, Hua; Jiang, Yi-Deng; Yu, Zheng

    2016-06-01

    The aim of the present study was to identify an effective method for detecting early‑phase atherosclerosis (AS), as well as to provide useful DNA methylation profiles to serve as biomarkers for the detection of AS. A total of 300 individuals (150 AS patients and 150 healthy subjects) were recruited for peripheral blood DNA methylation analyses at 12 gene promoter loci using nested methylation‑specific polymerase chain reaction in a test set. Based on the test set, the promoter methylation of TIMP metallopeptidase inhibitor 1 (TIMP1), ATP binding cassette subfamily A member 1 (ABCA1), and acetyl-CoA acetyltransferase 1 (ACAT1) were determined to be candidate biomarkers; demonstrating the highest sensitivity (88%) and specificity (90%). The biomarkers that were candidates for early AS detection were validated in an independent validation set (n=100). In the validation set, the combination of TIMP1, ABCA1 and ACAT1 methylation achieved sensitivity, specificity and coincidence rate values of 88, 70 and 79%, respectively. In the current pilot study, the patterns of DNA methylation of AS‑associated genes were observed to be significantly altered in the peripheral blood of AS patients. Thus, the AS-specific methylation of the three‑gene panel (TIMP1, ABCA1, and ACAT1) may serve as a valuable biomarker for the early detection of AS.

  7. Integrating milk metabolite profile information for the prediction of traditional milk traits based on SNP information for Holstein cows.

    Directory of Open Access Journals (Sweden)

    Nina Melzer

    Full Text Available In this study the benefit of metabolome level analysis for the prediction of genetic value of three traditional milk traits was investigated. Our proposed approach consists of three steps: First, milk metabolite profiles are used to predict three traditional milk traits of 1,305 Holstein cows. Two regression methods, both enabling variable selection, are applied to identify important milk metabolites in this step. Second, the prediction of these important milk metabolite from single nucleotide polymorphisms (SNPs enables the detection of SNPs with significant genetic effects. Finally, these SNPs are used to predict milk traits. The observed precision of predicted genetic values was compared to the results observed for the classical genotype-phenotype prediction using all SNPs or a reduced SNP subset (reduced classical approach. To enable a comparison between SNP subsets, a special invariable evaluation design was implemented. SNPs close to or within known quantitative trait loci (QTL were determined. This enabled us to determine if detected important SNP subsets were enriched in these regions. The results show that our approach can lead to genetic value prediction, but requires less than 1% of the total amount of (40,317 SNPs., significantly more important SNPs in known QTL regions were detected using our approach compared to the reduced classical approach. Concluding, our approach allows a deeper insight into the associations between the different levels of the genotype-phenotype map (genotype-metabolome, metabolome-phenotype, genotype-phenotype.

  8. Functional annotation of rheumatoid arthritis and osteoarthritis associated genes by integrative genome-wide gene expression profiling analysis.

    Directory of Open Access Journals (Sweden)

    Zhan-Chun Li

    Full Text Available BACKGROUND: Rheumatoid arthritis (RA and osteoarthritis (OA are two major types of joint diseases that share multiple common symptoms. However, their pathological mechanism remains largely unknown. The aim of our study is to identify RA and OA related-genes and gain an insight into the underlying genetic basis of these diseases. METHODS: We collected 11 whole genome-wide expression profiling datasets from RA and OA cohorts and performed a meta-analysis to comprehensively investigate their expression signatures. This method can avoid some pitfalls of single dataset analyses. RESULTS AND CONCLUSION: We found that several biological pathways (i.e., the immunity, inflammation and apoptosis related pathways are commonly involved in the development of both RA and OA. Whereas several other pathways (i.e., vasopressin-related pathway, regulation of autophagy, endocytosis, calcium transport and endoplasmic reticulum stress related pathways present significant difference between RA and OA. This study provides novel insights into the molecular mechanisms underlying this disease, thereby aiding the diagnosis and treatment of the disease.

  9. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

    DEFF Research Database (Denmark)

    Do, Duy Ngoc; Ostersen, Tage; Strathe, Anders Bjerring

    2013-01-01

    . Residual feed intake is a feed efficiency measure and is highly economically important in animal production. In our study, a total of 596 Yorkshire boars had phenotypic and genotypic records. After quality control, 37,915 SNPs were available for GWAS which was implemented in the DMU software package....... Genome wide association analysis detected 3,450 SNPs (P 7,169 nearby genes were found in 0.5 Mb flanking the SNP positions for all 3,450 SNPs. Among them, 2,934 genes were functionally recognized in pigs and were used as input...... in Database for Annotation, Visualization and Integrated Discovery (DAVID). Neuroactive ligand-receptor interaction, SNARE interactions in vesicular transport, pyruvate metabolism and Wnt signaling pathway were detected by using KEGG tools, growth hormone and phospholipase C signaling pathway were detected...

  10. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

    DEFF Research Database (Denmark)

    Do, Duy Ngoc; Ostersen, Tage; Strathe, Anders Bjerring

    . Residual feed intake is a feed efficiency measure and is highly economically important in animal production. In our study, a total of 596 Yorkshire boars had phenotypic and genotypic records. After quality control, 37,915 SNPs were available for GWAS which was implemented in the DMU software package....... Genome wide association analysis detected 3,450 SNPs (P 7,169 nearby genes were found in 0.5 Mb flanking the SNP positions for all 3,450 SNPs. Among them, 2,934 genes were functionally recognized in pigs and were used as input...... in Database for Annotation, Visualization and Integrated Discovery (DAVID). Neuroactive ligand-receptor interaction, SNARE interactions in vesicular transport, pyruvate metabolism and Wnt signaling pathway were detected by using KEGG tools, growth hormone and phospholipase C signaling pathway were detected...

  11. Longitudinal assessment in an undergraduate longitudinal integrated clerkship: the mini Clinical Evaluation Exercise (mCEX) profile.

    Science.gov (United States)

    Playford, Denese; Kirke, Andrew; Maley, Moira; Worthington, Rhonda

    2013-08-01

    Student and assessor performance were examined over three academic years using the mini Clinical Evaluation Exercise (mCEX) as a continuous feedback tool across all disciplines, in all learning contexts, for an entire integrated undergraduate year. Students could complete any number of mCEX, but had to submit a minimum number per discipline. Students were free to choose assessors. Assessors were not trained. Data were collected in a customised database, and analysed in SPSS ver 18.0.0. 5686 mCEX were submitted during 2008-2010 (Cronbach's α = 0.80). Marks were affected by doctor grade (F = 146.6, p educational/feedback value. Assessors mark consistent with a framework of encouraging student performance. Over an entire longitudinal clerkship, students complete mCEX in excess of course requirements. This study confirms the impact of the longitudinal context on assessor and student behaviour.

  12. Mayday - integrative analytics for expression data

    Directory of Open Access Journals (Sweden)

    Nieselt Kay

    2010-03-01

    Full Text Available Abstract Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well

  13. Mayday--integrative analytics for expression data.

    Science.gov (United States)

    Battke, Florian; Symons, Stephan; Nieselt, Kay

    2010-03-09

    DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad

  14. Insights into plant cell wall structure, architecture, and integrity using glycome profiling of native and AFEXTM-pre-treated biomass.

    Science.gov (United States)

    Pattathil, Sivakumar; Hahn, Michael G; Dale, Bruce E; Chundawat, Shishir P S

    2015-07-01

    Cell walls, which constitute the bulk of plant biomass, vary considerably in their structure, composition, and architecture. Studies on plant cell walls can be conducted on both native and pre-treated plant biomass samples, allowing an enhanced understanding of these structural and compositional variations. Here glycome profiling was employed to determine the relative abundance of matrix polysaccharides in several phylogenetically distinct native and pre-treated plant biomasses. Eight distinct biomass types belonging to four different subgroups (i.e. monocot grasses, woody dicots, herbaceous dicots, and softwoods) were subjected to various regimes of AFEX™ (ammonia fiber expansion) pre-treatment [AFEX is a trademark of MBI, Lansing (http://www.mbi.org]. This approach allowed detailed analysis of close to 200 cell wall glycan epitopes and their relative extractability using a high-throughput platform. In general, irrespective of the phylogenetic origin, AFEX™ pre-treatment appeared to cause loosening and improved accessibility of various xylan epitope subclasses in most plant biomass materials studied. For most biomass types analysed, such loosening was also evident for other major non-cellulosic components including subclasses of pectin and xyloglucan epitopes. The studies also demonstrate that AFEX™ pre-treatment significantly reduced cell wall recalcitrance among diverse phylogenies (except softwoods) by inducing structural modifications to polysaccharides that were not detectable by conventional gross composition analyses. It was found that monitoring changes in cell wall glycan compositions and their relative extractability for untreated and pre-treated plant biomass can provide an improved understanding of variations in structure and composition of plant cell walls and delineate the role(s) of matrix polysaccharides in cell wall recalcitrance. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  15. Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma.

    Directory of Open Access Journals (Sweden)

    Yuexin Liu

    Full Text Available Small sample sizes used in previous studies result in a lack of overlap between the reported gene signatures for prediction of chemotherapy response. Although morphologic features, especially tumor nuclear morphology, are important for cancer grading, little research has been reported on quantitatively correlating cellular morphology with chemotherapy response, especially in a large data set. In this study, we have used a large population of patients to identify molecular and morphologic signatures associated with chemotherapy response in serous ovarian carcinoma.A gene expression model that predicts response to chemotherapy is developed and validated using a large-scale data set consisting of 493 samples from The Cancer Genome Atlas (TCGA and 244 samples from an Australian report. An identified 227-gene signature achieves an overall predictive accuracy of greater than 85% with a sensitivity of approximately 95% and specificity of approximately 70%. The gene signature significantly distinguishes between patients with unfavorable versus favorable prognosis, when applied to either an independent data set (P = 0.04 or an external validation set (P<0.0001. In parallel, we present the production of a tumor nuclear image profile generated from 253 sample slides by characterizing patients with nuclear features (such as size, elongation, and roundness in incremental bins, and we identify a morphologic signature that demonstrates a strong association with chemotherapy response in serous ovarian carcinoma.A gene signature discovered on a large data set provides robustness in accurately predicting chemotherapy response in serous ovarian carcinoma. The combination of the molecular and morphologic signatures yields a new understanding of potential mechanisms involved in drug resistance.

  16. Volcano plots in hydrogen electrocatalysis - uses and abuses.

    Science.gov (United States)

    Quaino, Paola; Juarez, Fernanda; Santos, Elizabeth; Schmickler, Wolfgang

    2014-01-01

    Sabatier's principle suggests, that for hydrogen evolution a plot of the rate constant versus the hydrogen adsorption energy should result in a volcano, and several such plots have been presented in the literature. A thorough examination of the data shows, that there is no volcano once the oxide-covered metals are left out. We examine the factors that govern the reaction rate in the light of our own theory and conclude, that Sabatier's principle is only one of several factors that determine the rate. With the exception of nickel and cobalt, the reaction rate does not decrease for highly exothermic hydrogen adsorption as predicted, because the reaction passes through more suitable intermediate states. The case of nickel is given special attention; since it is a 3d metal, its orbitals are compact and the overlap with hydrogen is too low to make it a good catalyst.

  17. Volcano plots in hydrogen electrocatalysis – uses and abuses

    Science.gov (United States)

    Quaino, Paola; Juarez, Fernanda; Santos, Elizabeth

    2014-01-01

    Summary Sabatier’s principle suggests, that for hydrogen evolution a plot of the rate constant versus the hydrogen adsorption energy should result in a volcano, and several such plots have been presented in the literature. A thorough examination of the data shows, that there is no volcano once the oxide-covered metals are left out. We examine the factors that govern the reaction rate in the light of our own theory and conclude, that Sabatier’s principle is only one of several factors that determine the rate. With the exception of nickel and cobalt, the reaction rate does not decrease for highly exothermic hydrogen adsorption as predicted, because the reaction passes through more suitable intermediate states. The case of nickel is given special attention; since it is a 3d metal, its orbitals are compact and the overlap with hydrogen is too low to make it a good catalyst. PMID:24991521

  18. Volcano plots in hydrogen electrocatalysis – uses and abuses

    Directory of Open Access Journals (Sweden)

    Paola Quaino

    2014-06-01

    Full Text Available Sabatier’s principle suggests, that for hydrogen evolution a plot of the rate constant versus the hydrogen adsorption energy should result in a volcano, and several such plots have been presented in the literature. A thorough examination of the data shows, that there is no volcano once the oxide-covered metals are left out. We examine the factors that govern the reaction rate in the light of our own theory and conclude, that Sabatier’s principle is only one of several factors that determine the rate. With the exception of nickel and cobalt, the reaction rate does not decrease for highly exothermic hydrogen adsorption as predicted, because the reaction passes through more suitable intermediate states. The case of nickel is given special attention; since it is a 3d metal, its orbitals are compact and the overlap with hydrogen is too low to make it a good catalyst.

  19. CADASTRAL CLASSIFICATION OF THE LAND PLOTS IN UKRAINE

    Directory of Open Access Journals (Sweden)

    KIRICHEK Yu. O.

    2016-04-01

    Full Text Available Summary. Work concerns development of national system of classification of the land plots. The developed classification will allow to solve correctly a number of the corresponding cadastral, land management, estimated and other tasks. The analysis of classifications of lands, improvements and real estate in general is made. The created offers concerning creation of a new classification of the land plots in Ukraine. Today the Ukrainian real estate market has no single system that separates the system property groups, classes and types. This significantly complicates the work and can not fully be aware of the specific situation of real estate market. This task is designed to solve classification properties, it is used to transition from a diversity of individual properties to a limited number of classes of evaluation objects. The classification is different functional purpose (use facilities assessment, which determines the difference in value.

  20. [Eugenics, an element of the literary plots of dystopia].

    Science.gov (United States)

    Baum, Ewa; Musielak, Michał

    2007-01-01

    The work presents the ideas and assumptions of eugenics, a social philosophy established in 1883 by Francis Galton, which affected the social policies of numerous European countries in the first half of the 20th century. The work shows the effect of eugenics on the literary standards of European prose in the previous century. Two outstanding dystopian novels of the 20th century, The Brave New World by Aldous Huxley and 1984 by George Orwell, situate eugenics as a permanent element of the literary plot of dystopia. Apart from the typical features of this type of novel, for example: personal narration with a trace of irony, a totalitarian state and Newspeak, eugenics is an important element of the literary plot with is aim to exclude and marginalise certain social groups. Eugenics is also one of the main social ideas criticised by both the writers.

  1. D.3.3 PLOT Persuasive Learning Design Framework

    DEFF Research Database (Denmark)

    Gram-Hansen, Sandra Burri

    2012-01-01

    In this third and final deliverable of WP3: Persuasive Learning Designs, the theoretical cross field between persuasion and learning and the practical analysis of the technological learning tools and products which are currently related to the PLOT project, namely the GLOMaker and the 3ET tool......, are linked together as persuasive learning designs are defined and exemplified through the four e-PLOT cases. Based on the literary study of D.3.1 as well as the subsequent discussions and reflections regarding the theoretical foundation and practical application of persuasive learning technologies......, this report presents a novel perspective on the definition of persuasive design, and in continuation, an applicable definition of persuasive learning designs. D.3.3 is formally described as: “A set of Persuasive Learning Designs (PLDs) appropriately described in terms of theoretical background and expected...

  2. Anthropometric Profile of Children Attending Anganwadi Centers under Integrated Child Development Sevices (ICDS Scheme in Doiwala Block

    Directory of Open Access Journals (Sweden)

    Gagan Deep Kaur

    2014-12-01

    Full Text Available Introduction In any community, Mothers and Children constitutes not only priority group, but they are also a “Vulnerable” or “Special-risk Group”. Similarly in India our biggest problem is malnutrition among under five year old children. To break the vicious cycle of malnutrition, morbidity reduced learning capacity and mortality India launched the Integrated Child Development Services (ICDS Scheme in 1975. It is the foremost symbol of India’s commitment to her children Rationale: Forty percent of the world's severely under-nourished under-five children live in India so the present study was conducted to assess the nutritional status of children availing the services under Integrated Child Development Service Scheme in Uttarakhand. Objective: To estimate the level of nutrition in children attending Anganwadi centers of Doiwala block. Methods: Out of these Seven ICDS project areas, Doiwala Block was chosen for the study purpose since it is also the field practice area of Department of Community Medicine, HIMS. 19 AWC was selected by using Simple Random Sampling technique in Doiwala block. All the children aged between 3- 6years attending Anganwadi centers were included in community based, cross sectional study. Predesigned pretested anthropometric survey tool with local adaptability and minor modification for local suitability was adopted to collect information pertaining to growth monitoring of the children [Adopted from WHO child growth standard 2006]. Children were weighed, and their height and MUAC were recorded. Weight for age, height for age and MUAC for age was calculated using WHO growth references .Nutritional status according to the WHO Child Growth Standards was analysed using WHO Anthro statistical software. Results: 200 children were surveyed. From the total population 110 are males and 90 are females. After the analysis of weight for age with anthro software it was found that 20.9% of children lie within -2 SD with a mean

  3. Fisher.py: Fisher Matrix Manipulation and Confidence Contour Plotting

    Science.gov (United States)

    Coe, Dan

    2010-10-01

    Fisher.py allows you to combine constraints from multiple experiments (e.g., weak lensing + supernovae) and add priors (e.g., a flat universe) simply and easily. Calculate parameter uncertainties and plot confidence ellipses. Fisher matrix expectations for several experiments are included as calculated by myself (time delays) and the Dark Energy Task Force (WL/SN/BAO/CL/CMB), or provide your own.

  4. Using SAS Generate Trial Designs and Plot Maps

    OpenAIRE

    Edzard van Santen

    2012-01-01

    Previous contribution in this series on SAS tips and tricks introduced the basic aspects of macro variables (van Santen, 2009a,b) and PROC SQL introduced as time saving tools of the SAS/BASE installation (van Santen, 2010). In this contribution I demonstrate how these tools might be combined and used in conjunction with an EXCEL spreadsheet to generate field trial designs and plot plans

  5. Roles of microRNAs in immunopathogenesis of non-alcoholic fatty liver disease revealed by integrated analysis of microRNA and mRNA expression profiles.

    Science.gov (United States)

    Zhang, Yu-Jun; Hu, Ying; Li, Jing; Chi, Yu-Jing; Jiang, Wei-Wei; Zhang, Feng; Liu, Yu-Lan

    2017-02-01

    The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease (NAFLD). We analyzed differentially expressed microRNA and mRNA expression profiles of CD4+ T lymphocytes from the liver and mesenteric lymph nodes (MLNs) of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR. Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4+ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly de-regulated in CD4+ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR-206-3p, miR-181a-5p, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways. The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.

  6. Looking at large data sets using binned data plots

    Energy Technology Data Exchange (ETDEWEB)

    Carr, D.B.

    1990-04-01

    This report addresses the monumental challenge of developing exploratory analysis methods for large data sets. The goals of the report are to increase awareness of large data sets problems and to contribute simple graphical methods that address some of the problems. The graphical methods focus on two- and three-dimensional data and common task such as finding outliers and tail structure, assessing central structure and comparing central structures. The methods handle large sample size problems through binning, incorporate information from statistical models and adapt image processing algorithms. Examples demonstrate the application of methods to a variety of publicly available large data sets. The most novel application addresses the too many plots to examine'' problem by using cognostics, computer guiding diagnostics, to prioritize plots. The particular application prioritizes views of computational fluid dynamics solution sets on the fly. That is, as each time step of a solution set is generated on a parallel processor the cognostics algorithms assess virtual plots based on the previous time step. Work in such areas is in its infancy and the examples suggest numerous challenges that remain. 35 refs., 15 figs.

  7. The value of building plots in Italy - pdf

    Directory of Open Access Journals (Sweden)

    Paolo Rosato

    2014-12-01

    Full Text Available This paper suggests some analysis on dynamics of building plots value in Italy. This is an important subject, since the study of changes in plots value in space and time enables the evaluation of urban rent, which is essential for a fair and effective planning. The analysis confirm past hypothesis which are well known to real estate market operators. The first resulting fact is that the changes in building plots value are concurrent to those in real estate value and the increase occurring in the last years is in relative terms higher than the past one. This seems to confirm that, during real estate market expansion, most of the increase of buildings’ value is attributable to the land rent. The second observation is about value dynamics over time: it has been observed that, during an expansion in demand, the value significantly increases in central areas, much more than in peripheral ones; this means that absolute rent arising from shortage in urban areas is higher than the differential rent created through urban expansion in peripheral areas. Finally, it was highlighted that the factors affecting the value in building areas play different roles, depending on their location relative to the urban centre, identifying differently structured market segments.

  8. Are Sport-Specific Profiles of Tendon Stiffness and Cross-Sectional Area Determined by Structural or Functional Integrity?

    Directory of Open Access Journals (Sweden)

    Hans-Peter Wiesinger

    Full Text Available The present study aimed to determine whether distinct sets of tendon properties are seen in athletes engaged in sports with contrasting requirements for tendon function and structural integrity. Patellar and Achilles tendon morphology and force-deformation relation were measured by combining ultrasonography, electromyography and dynamometry in elite ski jumpers, distance runners, water polo players and sedentary individuals. Tendon cross-sectional area normalized to body mass2/3 was smaller in water polo players than in other athletes (patellar and Achilles tendon; -28 to -24% or controls (patellar tendon only; -9%. In contrast, the normalized cross-sectional area was larger in runners (patellar tendon only; +26% and ski jumpers (patellar and Achilles tendon; +21% and +13%, respectively than in controls. Tendon stiffness normalized to body mass2/3 only differed in ski jumpers, compared to controls (patellar and Achilles tendon; +11% and +27%, respectively and to water polo players (Achilles tendon only; +23%. Tendon size appears as an adjusting variable to changes in loading volume and/or intensity, possibly to preserve ultimate strength or fatigue resistance. However, uncoupled morphological and mechanical properties indicate that functional requirements may also influence tendon adaptations.

  9. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor.

    Directory of Open Access Journals (Sweden)

    Biaoyang Lin

    2009-08-01

    Full Text Available The androgen receptor (AR plays important roles in the development of male phenotype and in different human diseases including prostate cancers. The AR can act either as a promoter or a tumor suppressor depending on cell types. The AR proliferative response program has been well studied, but its prohibitive response program has not yet been thoroughly studied.Previous studies found that PC3 cells expressing the wild-type AR inhibit growth and suppress invasion. We applied expression profiling to identify the response program of PC3 cells expressing the AR (PC3-AR under different growth conditions (i.e. with or without androgens and at different concentration of androgens and then applied the newly developed ChIP-seq technology to identify the AR binding regions in the PC3 cancer genome. A surprising finding was that the comparison of MOCK-transfected PC3 cells with AR-transfected cells identified 3,452 differentially expressed genes (two fold cutoff even without the addition of androgens (i.e. in ethanol control, suggesting that a ligand independent activation or extremely low-level androgen activation of the AR. ChIP-Seq analysis revealed 6,629 AR binding regions in the cancer genome of PC3 cells with an FDR (false discovery rate cut off of 0.05. About 22.4% (638 of 2,849 can be mapped to within 2 kb of the transcription start site (TSS. Three novel AR binding motifs were identified in the AR binding regions of PC3-AR cells, and two of them share a core consensus sequence CGAGCTCTTC, which together mapped to 27.3% of AR binding regions (1,808/6,629. In contrast, only about 2.9% (190/6,629 of AR binding sites contains the canonical AR matrix M00481, M00447 and M00962 (from the Transfac database, which is derived mostly from AR proliferative responsive genes in androgen dependent cells. In addition, we identified four top ranking co-occupancy transcription factors in the AR binding regions, which include TEF1 (Transcriptional enhancer factor

  10. Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine.

    Directory of Open Access Journals (Sweden)

    Jeremy J Jay

    Full Text Available Concise visualization is critical to present large amounts of information in a minimal space that can be interpreted quickly. Clinical applications in precision medicine present an important use case due to the time dependent nature of the interpretations, although visualization is increasingly necessary across the life sciences. In this paper we describe the Lollipops software for the presentation of panel or exome sequencing results. Source code and binaries are freely available at https://github.com/pbnjay/lollipops. Although other software and web resources exist to produce lollipop diagrams, these packages are less suited to clinical applications. The demands of precision medicine require the ability to easily fit into a workflow and incorporate external information without manual intervention.The Lollipops software provides a simple command line interface that only requires an official gene symbol and mutation list making it easily scriptable. External information is integrated using the publicly available Uniprot and Pfam resources. Heuristics are used to select the most informative components and condense them for a concise plot. The output is a flexible Scalable Vector Graphic (SVG diagram that can be displayed in a web page or graphic illustration tool.The Lollipops software creates information-dense, publication-quality mutation plots for automated pipelines and high-throughput workflows in precision medicine. The automatic data integration enables clinical data security, and visualization heuristics concisely present knowledge with minimal user configuration.

  11. Integrative analysis of transcriptomic and metabolomic profiling of ascites syndrome in broiler chickens induced by low temperature.

    Science.gov (United States)

    Shi, Shourong; Shen, Yiru; Zhao, Zhenhua; Hou, Zhuocheng; Yang, Ying; Zhou, Huaijun; Zou, Jianmin; Guo, Yuming

    2014-11-01

    Ascites syndrome (AS) still has an unacceptably high incidence rate in both humans and animals although there have been many studies on AS. To continue our previous pathological and biochemical investigation on the underlying mechanisms of AS incidence in broiler chickens, cutting-edge technologies including RNA-seq and metabolimics were used by directly comparing AS chickens and healthy controls. The RNA-seq analysis in the liver identified 390 differentially expressed genes (DEGs), among which 212 genes were up-regulated and 178 genes were down-regulated in the AS group compared to the control. For the down-regulated DEGs, further gene ontology (GO) analysis suggested that lipid metabolism, cell differentiation, enzyme linked receptor protein signaling pathway and steroid biosynthesis pathway were significantly enriched. For up-regulated DEGs, the cholesterol metabolic process has the lowest p value (0.000966) of fold enrichment while the cholesterol biosynthetic process has the highest fold enrichment (46.67). The metabolomic analysis of serum revealed statistically significant changes in the concentrations of LysoPC(20 : 4), LysoPC(16 : 0), LysoPC(18 : 0), LysoPC(18 : 1), LysoPC(18 : 2), PC(14 : 1/20 : 1), PC(20 : 4/18 : 0), PC(14 : 1/22 : 1), dihydroxyacetone, indoleacrylic acid, ursodeoxycholic acid, l-valine, and l-tryptophan. The integrative analysis of transcriptome and metabolome indicated that two biological pathways of tryptophan biosynthesis and metabolism, and glycerophospholipid metabolism may contribute to the induction of AS in broilers. These findings have provided novel insights into our understanding of molecular mechanisms of AS incidence in broilers.

  12. Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

    Directory of Open Access Journals (Sweden)

    Elodie Caboux

    Full Text Available The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as "warm ischemia". Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC and 3 lung carcinomas (LC cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of -3.5%/hr (95% CI: -7.0%/hr to 0.1%/hr; p = 0.054. In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5 and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1 was identified (FDR <0.05. Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.

  13. Considerations in Forest Growth Estimation Between Two Measurements of Mapped Forest Inventory Plots

    Science.gov (United States)

    Michael T. Thompson

    2006-01-01

    Several aspects of the enhanced Forest Inventory and Analysis (FIA) program?s national plot design complicate change estimation. The design incorporates up to three separate plot sizes (microplot, subplot, and macroplot) to sample trees of different sizes. Because multiple plot sizes are involved, change estimators designed for polyareal plot sampling, such as those...

  14. A narratological analysis of Mark 12:1-12: The plot of the Gospel of ...

    African Journals Online (AJOL)

    The purpose of this article is an attempt to read Mark 12: 1-12 in terms of the plot of the Gospel. Firstly a brief survey is given of the development of the term plot from Aristotle to the present, thereafter an own methodological point of departure concerning plot is formulated in order to study the plot of Mark. The conclusions ...

  15. Plot and Personification in “Tehran-e- Makhuf“

    Directory of Open Access Journals (Sweden)

    M. Pashaei

    Full Text Available Story is one of the important and influential literary genres that deserves to research on its structure and content .By study and analysis of a story, the reader could comprehend the textual messages and change his attitude toward life and different issues .After defining of the social novel, the author tries to analyze plot and personification in novel of “Tehran-e- Makhuf” and respond to the questions on the method employed for plot and personification and analyze it from plot and its components such as conflict, suspension and resolution and compare the differences and similarities between old tales and modern novels.The plot of “Tehran-e- Makhuf” is not so complex due to its subject and content and natural order of events dominates on artificial discipline and it lacks open plot. Of main elements of plot, conflict is more outstanding here. This novel is full of emotional and moral conflicts and there is no similarity with historical novels that describe good and bad conflicts. Cause and effect relationship is main element of plot that shadows on the story events .In “Tehrna-e- Makhuf”, the author tries to violate the principles and cause to imbalance in natural events sequences with discomposing rational and experiential relationship and take action toward artificiality and unnatural suspension. In creating suspension by emphasis on incidences in some extremist cases, Kazemi tries to found the story based on the considerable sequence of events and this conduct reduces quality of the story significantly and leads to imbalance in rational and acceptable discipline.Kazemi employs direct or reporting personification mostly. This novel lacks diversity in personage considerably .All characters speak in similar style and there is no particular speech style. The personification of Kazemi in “Tehran-e-Makhuf” is continuous and interdependent in style of old tales and novel in European account. In some cases, he approaches to story

  16. Contemplation on Plot and Personification in Tehran Makhuf

    Directory of Open Access Journals (Sweden)

    Mohammad Pashaei

    2013-10-01

    Full Text Available  Abstract Story is one of the important and influential literary genres that deserves to research on its structure and content .By study and analysis of a story, the reader could comprehend the textual messages and change his attitude toward life and different issues .After defining of the social novel, the author tries to analyze plot and personification in novel of “Tehran-e- Makhuf” and respond to the questions on the method employed for plot and personification and analyze it from plot and its components such as conflict, suspension and resolution and compare the differences and similarities between old tales and modern novels.  The plot of “Tehran-e- Makhuf” is not so complex due to its subject and content and natural order of events dominates on artificial discipline and it lacks open plot. Of main elements of plot, conflict is more outstanding here. This novel is full of emotional and moral conflicts and there is no similarity with historical novels that describe good and bad conflicts. Cause and effect relationship is main element of plot that shadows on the story events .In “Tehrna-e- Makhuf”, the author tries to violate the principles and cause to imbalance in natural events sequences with discomposing rational and experiential relationship and take action toward artificiality and unnatural suspension. In creating suspension by emphasis on incidences in some extremist cases, Kazemi tries to found the story based on the considerable sequence of events and this conduct reduces quality of the story significantly and leads to imbalance in rational and acceptable discipline.  Kazemi employs direct or reporting personification mostly. This novel lacks diversity in personage considerably .All characters speak in similar style and there is no particular speech style. The personification of Kazemi in “Tehran-e-Makhuf” is continuous and interdependent in style of old tales and novel in European

  17. Contemplation on Plot and Personification in Tehran Makhuf

    Directory of Open Access Journals (Sweden)

    Mirjalil Akrami

    2013-11-01

    Full Text Available Abstract Story is one of the important and influential literary genres that deserves to research on its structure and content .By study and analysis of a story, the reader could comprehend the textual messages and change his attitude toward life and different issues .After defining of the social novel, the author tries to analyze plot and personification in novel of “Tehran-e- Makhuf” and respond to the questions on the method employed for plot and personification and analyze it from plot and its components such as conflict, suspension and resolution and compare the differences and similarities between old tales and modern novels.  The plot of “Tehran-e- Makhuf” is not so complex due to its subject and content and natural order of events dominates on artificial discipline and it lacks open plot. Of main elements of plot, conflict is more outstanding here. This novel is full of emotional and moral conflicts and there is no similarity with historical novels that describe good and bad conflicts. Cause and effect relationship is main element of plot that shadows on the story events .In “Tehrna-e- Makhuf”, the author tries to violate the principles and cause to imbalance in natural events sequences with discomposing rational and experiential relationship and take action toward artificiality and unnatural suspension. In creating suspension by emphasis on incidences in some extremist cases, Kazemi tries to found the story based on the considerable sequence of events and this conduct reduces quality of the story significantly and leads to imbalance in rational and acceptable discipline.  Kazemi employs direct or reporting personification mostly. This novel lacks diversity in personage considerably .All characters speak in similar style and there is no particular speech style. The personification of Kazemi in “Tehran-e-Makhuf” is continuous and interdependent in style of old tales and novel in European account. In some cases, he

  18. Carbon dioxide balance of subarctic tundra from plot to regional scales

    Directory of Open Access Journals (Sweden)

    M. E. Marushchak

    2013-01-01

    Full Text Available We report here the carbon dioxide (CO2 budget of a 98.6 km2 subarctic tundra area in northeast European Russia based on measurements at two different scales and two independent upscaling approaches. Plot-scale measurements (chambers on terrestrial surfaces, gas gradient method and bubble collectors on lakes were carried out from July 2007 to October 2008. The landscape-scale eddy covariance (EC measurements covered the snow-free period of 2008. The annual net ecosystem exchange (NEE of different land cover types ranged from −251 to 84 g C m−2. Leaf area index (LAI was an excellent predictor of the spatial variability in gross photosynthesis (GP, NEE and ecosystem respiration (ER. The plot-scale CO2 fluxes were first scaled up to the EC source area and then to the whole study area using two data sets: a land cover classification and a LAI map, both based on field data and a 2.4 m pixel-sized QuickBird satellite image. The good agreement of the CO2 balances for the EC footprint based on the different measuring techniques (−105 to −81 g C m−2 vs. −79 g C m−2; growing season 2008 justified the integration of the plot-scale measurements over the larger area. The regional CO2 balance based on area-integrated plot-scale measurements was −41 or −79 g C m−2 yr−1 according to the two upscaling methods, the land cover classification and the LAI map, respectively. Due to the heterogeneity of tundra, the effect of climate change on CO2 uptake will vary strongly according to the land cover type and, moreover, likely changes in their relative coverage in the future will have great impact on the regional CO2 balance.

  19. Clinical and angiographic outcomes following first-in-man implantation of a novel thin-strut low-profile fixed-wire stent: The Svelte Coronary Stent Integrated Delivery System first-in-man trial

    NARCIS (Netherlands)

    R. Diletti (Roberto); H.M. Garcia-Garcia (Hector); C.V. Bourantas (Christos); R.J.M. van Geuns (Robert Jan); N.M. van Mieghem (Nicolas); P. Agostoni (Pierfrancesco); T. Muramatsu (Takashi); V. Farooq (Vasim); R. Spencer (Richard); J. de Schepper; M. Pomeranz (Mark); P.R. Stella (Pieter); P.W.J.C. Serruys (Patrick)

    2013-01-01

    textabstractAims: The Svelte Stent Integrated Delivery System (IDS) is a novel fixed-wire thin-strut cobalt-chromium stent characterised by a very low entry profile. The aim of the present study is to evaluate the safety and the feasibility of the Svelte stent IDS implantation in humans. Methods and

  20. Correlation analysis of respiratory signals by using parallel coordinate plots.

    Science.gov (United States)

    Saatci, Esra

    2018-01-01

    The understanding of the bonds and the relationships between the respiratory signals, i.e. the airflow, the mouth pressure, the relative temperature and the relative humidity during breathing may provide the improvement on the measurement methods of respiratory mechanics and sensor designs or the exploration of the several possible applications in the analysis of respiratory disorders. Therefore, the main objective of this study was to propose a new combination of methods in order to determine the relationship between respiratory signals as a multidimensional data. In order to reveal the coupling between the processes two very different methods were used: the well-known statistical correlation analysis (i.e. Pearson's correlation and cross-correlation coefficient) and parallel coordinate plots (PCPs). Curve bundling with the number intersections for the correlation analysis, Least Mean Square Time Delay Estimator (LMS-TDE) for the point delay detection and visual metrics for the recognition of the visual structures were proposed and utilized in PCP. The number of intersections was increased when the correlation coefficient changed from high positive to high negative correlation between the respiratory signals, especially if whole breath was processed. LMS-TDE coefficients plotted in PCP indicated well-matched point delay results to the findings in the correlation analysis. Visual inspection of PCB by visual metrics showed range, dispersions, entropy comparisons and linear and sinusoidal-like relationships between the respiratory signals. It is demonstrated that the basic correlation analysis together with the parallel coordinate plots perceptually motivates the visual metrics in the display and thus can be considered as an aid to the user analysis by providing meaningful views of the data. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Manual transportation within the plot and physical damages to bananas

    Directory of Open Access Journals (Sweden)

    Magalhães Mário Jorge Maia de

    2004-01-01

    Full Text Available The manual transportation of banana bunches within plots provokes physical damages to fruits compromising their quality. To assess the influence of the distance banana bunches travel on the shoulders of harvesters within the plot, on the incidence of physical damages present on the peel of fruits of the Nanicão cultivar, two experiments were carried out in the Vale do Ribeira region (SP, in sites with slope < 1%. Each experiment divided the plot in different distance bands, two of which were included in this study: one located far away from the collection roads (30-50 m and 80-100 m distance bands and another in an intermediate position (70-80 m and 130-150 m distance bands. For each distance band, six banana bunches of 36 mm gauged fruits were randomly sampled. Four banana hands were cut from the middle region of each bunch and ten fruits were assessed per hand, totaling 240 fruits per treatment. Bunches were harvested at the same maturity degree and those served as control were not transported. A total of 1440 fruits was assessed in the two experiments. The physical damages on the fruit surface were graded on a scale with 6 divisions: 0-0.25 cm²; 0.25-0.5 cm²; 0.5-1.0 cm²; 1.0-1.5 cm²; 1.5-2.0 cm²; 2.0-2.5 cm². The bunches transported on the shoulders of harvesters on distances over 70 m suffered increased (P < 0.01 damaged area. Most damages presented areas up to 0.5 cm².

  2. WASP (Write a Scientific Paper) using Excel - 3: Plotting data.

    Science.gov (United States)

    Grech, Victor

    2018-02-13

    The plotting of data into graphs should be a mandatory step in all data analysis as part of a descriptive statistics exercise, since it gives the researcher an overview of the shape and nature of the data. Moreover, outlier values may be identified, which may be incorrect data, or true outliers, from which important findings (and publications) may arise. This exercise should always precede inferential statistics, when possible, and this paper in the Early Human Development WASP series provides some pointers for doing so in Microsoft Excel™. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. How to Create and Manipulate Radar Range-Doppler Plots

    Science.gov (United States)

    2014-12-01

    TYPE OF REPORT Technical Note 7. DOCUMENT DATE December 2014 8. FILE NUMBER 2012/1057198/1 9. TASK NUMBER 07/139 10. TASK SPONSOR DMO/MEWSPO 11. No. OF...not straightforward. But there is some latitude in the definition of a spectrum’s bandwidth, given that technically each plot in Figure 11 has infinite... localised near its peak at −102 m/s. 46 UNCLASSIFIED UNCLASSIFIED DSTO–TN–1386 10.2 Series of Chirped Rectangular Pulses with Doppler Windowing The

  4. Selection of a Representative Subset of Global Climate Models that Captures the Profile of Regional Changes for Integrated Climate Impacts Assessment

    Science.gov (United States)

    Ruane, Alex C.; Mcdermid, Sonali P.

    2017-01-01

    We present the Representative Temperature and Precipitation (T&P) GCM Subsetting Approach developed within the Agricultural Model Intercomparison and Improvement Project (AgMIP) to select a practical subset of global climate models (GCMs) for regional integrated assessment of climate impacts when resource limitations do not permit the full ensemble of GCMs to be evaluated given the need to also focus on impacts sector and economics models. Subsetting inherently leads to a loss of information but can free up resources to explore important uncertainties in the integrated assessment that would otherwise be prohibitive. The Representative T&P GCM Subsetting Approach identifies five individual GCMs that capture a profile of the full ensemble of temperature and precipitation change within the growing season while maintaining information about the probability that basic classes of climate changes (relatively cool/wet, cool/dry, middle, hot/wet, and hot/dry) are projected in the full GCM ensemble. We demonstrate the selection methodology for maize impacts in Ames, Iowa, and discuss limitations and situations when additional information may be required to select representative GCMs. We then classify 29 GCMs over all land areas to identify regions and seasons with characteristic diagonal skewness related to surface moisture as well as extreme skewness connected to snow-albedo feedbacks and GCM uncertainty. Finally, we employ this basic approach to recognize that GCM projections demonstrate coherence across space, time, and greenhouse gas concentration pathway. The Representative T&P GCM Subsetting Approach provides a quantitative basis for the determination of useful GCM subsets, provides a practical and coherent approach where previous assessments selected solely on availability of scenarios, and may be extended for application to a range of scales and sectoral impacts.

  5. Selection of a representative subset of global climate models that captures the profile of regional changes for integrated climate impacts assessment

    Directory of Open Access Journals (Sweden)

    Alex C. Ruane

    2017-03-01

    Full Text Available Abstract We present the Representative Temperature and Precipitation (T&P GCM Subsetting Approach developed within the Agricultural Model Intercomparison and Improvement Project (AgMIP to select a practical subset of global climate models (GCMs for regional integrated assessment of climate impacts when resource limitations do not permit the full ensemble of GCMs to be evaluated given the need to also focus on impacts sector and economics models. Subsetting inherently leads to a loss of information but can free up resources to explore important uncertainties in the integrated assessment that would otherwise be prohibitive. The Representative T&P GCM Subsetting Approach identifies five individual GCMs that capture a profile of the full ensemble of temperature and precipitation change within the growing season while maintaining information about the probability that basic classes of climate changes (relatively cool/wet, cool/dry, middle, hot/wet, and hot/dry are projected in the full GCM ensemble. We demonstrate the selection methodology for maize impacts in Ames, Iowa, and discuss limitations and situations when additional information may be required to select representative GCMs. We then classify 29 GCMs over all land areas to identify regions and seasons with characteristic diagonal skewness related to surface moisture as well as extreme skewness connected to snow-albedo feedbacks and GCM uncertainty. Finally, we employ this basic approach to recognize that GCM projections demonstrate coherence across space, time, and greenhouse gas concentration pathway. The Representative T&P GCM Subsetting Approach provides a quantitative basis for the determination of useful GCM subsets, provides a practical and coherent approach where previous assessments selected solely on availability of scenarios, and may be extended for application to a range of scales and sectoral impacts.

  6. Recurrence plot for parameters analysing of internal combustion engine

    Science.gov (United States)

    Alexa, O.; Ilie, C. O.; Marinescu, M.; Vilau, R.; Grosu, D.

    2015-11-01

    In many technical disciplines modem data analysis techniques has been successfully applied to understand the complexity of the system. The growing volume of theoretical knowledge about systems dynamic's offered researchers the opportunity to look for non-linear dynamics in data whose evolution linear models are unable to explain in a satisfactory manner. One approach in this respect is Recurrence Analysis - RA which is a graphical method designed to locate hidden recurring patterns, nonstationarity and structural changes. RA approach arose in natural sciences like physics and biology but quickly was adopted in economics and engineering. Meanwhile. The fast development of computer resources has provided powerful tools to perform this new and complex model. One free software which was used to perform our analysis is Visual Recurrence Analysis - VRA developed by Eugene Kononov. As is presented in this paper, the recurrence plot investigation for the analyzing of the internal combustion engine shows some of the RPA capabilities in this domain. We chose two specific engine parameters measured in two different tests to perform the RPA. These parameters are injection impulse width and engine angular speed and the tests are I11n and I51n. There were computed graphs for each of them. Graphs were analyzed and compared to obtain a conclusion. This work is an incipient research, being one of the first attempts of using recurrence plot for analyzing automotive dynamics. It opens a wide field of action for future research programs.

  7. Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci

    Directory of Open Access Journals (Sweden)

    Merok Marianne A

    2010-05-01

    Full Text Available Abstract Background Estimates suggest that up to 30% of colorectal cancers (CRC may develop due to an increased genetic risk. The mean age at diagnosis for CRC is about 70 years. Time of disease onset 20 years younger than the mean age is assumed to be indicative of genetic susceptibility. We have compared high resolution tumor genome copy number variation (CNV (Roche NimbleGen, 385 000 oligo CGH array in microsatellite stable (MSS tumors from two age groups, including 23 young at onset patients without known hereditary syndromes and with a median age of 44 years (range: 28-53 and 17 elderly patients with median age 79 years (range: 69-87. Our aim was to identify differences in the tumor genomes between these groups and pinpoint potential susceptibility loci. Integration analysis of CNV and genome wide mRNA expression data, available for the same tumors, was performed to identify a restricted candidate gene list. Results The total fraction of the genome with aberrant copy number, the overall genomic profile and the TP53 mutation spectrum were similar between the two age groups. However, both the number of chromosomal aberrations and the number of breakpoints differed significantly between the groups. Gains of 2q35, 10q21.3-22.1, 10q22.3 and 19q13.2-13.31 and losses from 1p31.3, 1q21.1, 2q21.2, 4p16.1-q28.3, 10p11.1 and 19p12, positions that in total contain more than 500 genes, were found significantly more often in the early onset group as compared to the late onset group. Integration analysis revealed a covariation of DNA copy number at these sites and mRNA expression for 107 of the genes. Seven of these genes, CLC, EIF4E, LTBP4, PLA2G12A, PPAT, RG9MTD2, and ZNF574, had significantly different mRNA expression comparing median expression levels across the transcriptome between the two groups. Conclusions Ten genomic loci, containing more than 500 protein coding genes, are identified as more often altered in tumors from early onset versus late

  8. Dalitz plot analysis of $B^0 \\to \\overline{D}^0 \\pi^+\\pi^-$ decays

    CERN Document Server

    Aaij, Roel; Adinolfi, Marco; Affolder, Anthony; Ajaltouni, Ziad; Akar, Simon; Albrecht, Johannes; Alessio, Federico; Alexander, Michael; Ali, Suvayu; Alkhazov, Georgy; Alvarez Cartelle, Paula; Alves Jr, Antonio Augusto; Amato, Sandra; Amerio, Silvia; Amhis, Yasmine; An, Liupan; Anderlini, Lucio; Anderson, Jonathan; Andreassen, Rolf; Andreotti, Mirco; Andrews, Jason; Appleby, Robert; Aquines Gutierrez, Osvaldo; Archilli, Flavio; d'Argent, Philippe; Artamonov, Alexander; Artuso, Marina; Aslanides, Elie; Auriemma, Giulio; Baalouch, Marouen; Bachmann, Sebastian; Back, John; Badalov, Alexey; Baesso, Clarissa; Baldini, Wander; Barlow, Roger; Barschel, Colin; Barsuk, Sergey; Barter, William; Batozskaya, Varvara; Battista, Vincenzo; Bay, Aurelio; Beaucourt, Leo; Beddow, John; Bedeschi, Franco; Bediaga, Ignacio; Bel, Lennaert; Belogurov, Sergey; Belyaev, Ivan; Ben-Haim, Eli; Bencivenni, Giovanni; Benson, Sean; Benton, Jack; Berezhnoy, Alexander; Bernet, Roland; Bertolin, Alessandro; Bettler, Marc-Olivier; van Beuzekom, Martinus; Bien, Alexander; Bifani, Simone; Bird, Thomas; Birnkraut, Alex; Bizzeti, Andrea; Blake, Thomas; Blanc, Frédéric; Blouw, Johan; Blusk, Steven; Bocci, Valerio; Bondar, Alexander; Bondar, Nikolay; Bonivento, Walter; Borghi, Silvia; Borgia, Alessandra; Borsato, Martino; Bowcock, Themistocles; Bowen, Espen Eie; Bozzi, Concezio; Brett, David; Britsch, Markward; Britton, Thomas; Brodzicka, Jolanta; Brook, Nicholas; Bursche, Albert; Buytaert, Jan; Cadeddu, Sandro; Calabrese, Roberto; Calvi, Marta; Calvo Gomez, Miriam; Campana, Pierluigi; Campora Perez, Daniel; Capriotti, Lorenzo; Carbone, Angelo; Carboni, Giovanni; Cardinale, Roberta; Cardini, Alessandro; Carniti, Paolo; Carson, Laurence; Carvalho Akiba, Kazuyoshi; Casanova Mohr, Raimon; Casse, Gianluigi; Cassina, Lorenzo; Castillo Garcia, Lucia; Cattaneo, Marco; Cauet, Christophe; Cavallero, Giovanni; Cenci, Riccardo; Charles, Matthew; Charpentier, Philippe; Chefdeville, Maximilien; Chen, Shanzhen; Cheung, Shu-Faye; Chiapolini, Nicola; Chrzaszcz, Marcin; Cid Vidal, Xabier; Ciezarek, Gregory; Clarke, Peter; Clemencic, Marco; Cliff, Harry; Closier, Joel; Coco, Victor; Cogan, Julien; Cogneras, Eric; Cogoni, Violetta; Cojocariu, Lucian; Collazuol, Gianmaria; Collins, Paula; Comerma-Montells, Albert; Contu, Andrea; Cook, Andrew; Coombes, Matthew; Coquereau, Samuel; Corti, Gloria; Corvo, Marco; Counts, Ian; Couturier, Benjamin; Cowan, Greig; Craik, Daniel Charles; Crocombe, Andrew; Cruz Torres, Melissa Maria; Cunliffe, Samuel; Currie, Robert; D'Ambrosio, Carmelo; Dalseno, Jeremy; David, Pascal; David, Pieter; Davis, Adam; De Bruyn, Kristof; De Capua, Stefano; De Cian, Michel; De Miranda, Jussara; De Paula, Leandro; De Silva, Weeraddana; De Simone, Patrizia; Dean, Cameron Thomas; Decamp, Daniel; Deckenhoff, Mirko; Del Buono, Luigi; Déléage, Nicolas; Derkach, Denis; Deschamps, Olivier; Dettori, Francesco; Dey, Biplab; Di Canto, Angelo; Di Ruscio, Francesco; Dijkstra, Hans; Donleavy, Stephanie; Dordei, Francesca; Dorigo, Mirco; Dosil Suárez, Alvaro; Dossett, David; Dovbnya, Anatoliy; Dreimanis, Karlis; Dujany, Giulio; Dupertuis, Frederic; Durante, Paolo; Dzhelyadin, Rustem; Dziurda, Agnieszka; Dzyuba, Alexey; Easo, Sajan; Egede, Ulrik; Egorychev, Victor; Eidelman, Semen; Eisenhardt, Stephan; Eitschberger, Ulrich; Ekelhof, Robert; Eklund, Lars; El Rifai, Ibrahim; Elsasser, Christian; Ely, Scott; Esen, Sevda; Evans, Hannah Mary; Evans, Timothy; Falabella, Antonio; Färber, Christian; Farinelli, Chiara; Farley, Nathanael; Farry, Stephen; Fay, Robert; Ferguson, Dianne; Fernandez Albor, Victor; Ferrari, Fabio; Ferreira Rodrigues, Fernando; Ferro-Luzzi, Massimiliano; Filippov, Sergey; Fiore, Marco; Fiorini, Massimiliano; Firlej, Miroslaw; Fitzpatrick, Conor; Fiutowski, Tomasz; Fol, Philip; Fontana, Marianna; Fontanelli, Flavio; Forty, Roger; Francisco, Oscar; Frank, Markus; Frei, Christoph; Frosini, Maddalena; Fu, Jinlin; Furfaro, Emiliano; Gallas Torreira, Abraham; Galli, Domenico; Gallorini, Stefano; Gambetta, Silvia; Gandelman, Miriam; Gandini, Paolo; Gao, Yuanning; García Pardiñas, Julián; Garofoli, Justin; Garra Tico, Jordi; Garrido, Lluis; Gascon, David; Gaspar, Clara; Gastaldi, Ugo; Gauld, Rhorry; Gavardi, Laura; Gazzoni, Giulio; Geraci, Angelo; Gerick, David; Gersabeck, Evelina; Gersabeck, Marco; Gershon, Timothy; Ghez, Philippe; Gianelle, Alessio; Gianì, Sebastiana; Gibson, Valerie; Giubega, Lavinia-Helena; Gligorov, V.V.; Göbel, Carla; Golubkov, Dmitry; Golutvin, Andrey; Gomes, Alvaro; Gotti, Claudio; Grabalosa Gándara, Marc; Graciani Diaz, Ricardo; Granado Cardoso, Luis Alberto; Graugés, Eugeni; Graverini, Elena; Graziani, Giacomo; Grecu, Alexandru; Greening, Edward; Gregson, Sam; Griffith, Peter; Grillo, Lucia; Grünberg, Oliver; Gui, Bin; Gushchin, Evgeny; Guz, Yury; Gys, Thierry; Hadjivasiliou, Christos; Haefeli, Guido; Haen, Christophe; Haines, Susan; Hall, Samuel; Hamilton, Brian; Hampson, Thomas; Han, Xiaoxue; Hansmann-Menzemer, Stephanie; Harnew, Neville; Harnew, Samuel; Harrison, Jonathan; He, Jibo; Head, Timothy; Heijne, Veerle; Hennessy, Karol; Henrard, Pierre; Henry, Louis; Hernando Morata, Jose Angel; van Herwijnen, Eric; Heß, Miriam; Hicheur, Adlène; Hill, Donal; Hoballah, Mostafa; Hombach, Christoph; Hulsbergen, Wouter; Humair, Thibaud; Hussain, Nazim; Hutchcroft, David; Hynds, Daniel; Idzik, Marek; Ilten, Philip; Jacobsson, Richard; Jaeger, Andreas; Jalocha, Pawel; Jans, Eddy; Jawahery, Abolhassan; Jing, Fanfan; John, Malcolm; Johnson, Daniel; Jones, Christopher; Joram, Christian; Jost, Beat; Jurik, Nathan; Kandybei, Sergii; Kanso, Walaa; Karacson, Matthias; Karbach, Moritz; Karodia, Sarah; Kelsey, Matthew; Kenyon, Ian; Kenzie, Matthew; Ketel, Tjeerd; Khanji, Basem; Khurewathanakul, Chitsanu; Klaver, Suzanne; Klimaszewski, Konrad; Kochebina, Olga; Kolpin, Michael; Komarov, Ilya; Koopman, Rose; Koppenburg, Patrick; Korolev, Mikhail; Kravchuk, Leonid; Kreplin, Katharina; Kreps, Michal; Krocker, Georg; Krokovny, Pavel; Kruse, Florian; Kucewicz, Wojciech; Kucharczyk, Marcin; Kudryavtsev, Vasily; Kurek, Krzysztof; Kvaratskheliya, Tengiz; La Thi, Viet Nga; Lacarrere, Daniel; Lafferty, George; Lai, Adriano; Lambert, Dean; Lambert, Robert W; Lanfranchi, Gaia; Langenbruch, Christoph; Langhans, Benedikt; Latham, Thomas; Lazzeroni, Cristina; Le Gac, Renaud; van Leerdam, Jeroen; Lees, Jean-Pierre; Lefèvre, Regis; Leflat, Alexander; Lefrançois, Jacques; Leroy, Olivier; Lesiak, Tadeusz; Leverington, Blake; Li, Yiming; Likhomanenko, Tatiana; Liles, Myfanwy; Lindner, Rolf; Linn, Christian; Lionetto, Federica; Liu, Bo; Lohn, Stefan; Longstaff, Iain; Lopes, Jose; Lucchesi, Donatella; Luo, Haofei; Lupato, Anna; Luppi, Eleonora; Lupton, Oliver; Machefert, Frederic; Machikhiliyan, Irina V; Maciuc, Florin; Maev, Oleg; Malde, Sneha; Malinin, Alexander; Manca, Giulia; Mancinelli, Giampiero; Manning, Peter Michael; Mapelli, Alessandro; Maratas, Jan; Marchand, Jean François; Marconi, Umberto; Marin Benito, Carla; Marino, Pietro; Märki, Raphael; Marks, Jörg; Martellotti, Giuseppe; Martinelli, Maurizio; Martinez Santos, Diego; Martinez Vidal, Fernando; Martins Tostes, Danielle; Massafferri, André; Matev, Rosen; Mathe, Zoltan; Matteuzzi, Clara; Mauri, Andrea; Maurin, Brice; Mazurov, Alexander; McCann, Michael; McCarthy, James; McNab, Andrew; McNulty, Ronan; McSkelly, Ben; Meadows, Brian; Meier, Frank; Meissner, Marco; Merk, Marcel; Milanes, Diego Alejandro; Minard, Marie-Noelle; Mitzel, Dominik Stefan; Molina Rodriguez, Josue; Monteil, Stephane; Morandin, Mauro; Morawski, Piotr; Mordà, Alessandro; Morello, Michael Joseph; Moron, Jakub; Morris, Adam Benjamin; Mountain, Raymond; Muheim, Franz; Müller, Janine; Müller, Katharina; Müller, Vanessa; Mussini, Manuel; Muster, Bastien; Naik, Paras; Nakada, Tatsuya; Nandakumar, Raja; Nasteva, Irina; Needham, Matthew; Neri, Nicola; Neubert, Sebastian; Neufeld, Niko; Neuner, Max; Nguyen, Anh Duc; Nguyen, Thi-Dung; Nguyen-Mau, Chung; Nicol, Michelle; Niess, Valentin; Niet, Ramon; Nikitin, Nikolay; Nikodem, Thomas; Novoselov, Alexey; O'Hanlon, Daniel Patrick; Oblakowska-Mucha, Agnieszka; Obraztsov, Vladimir; Ogilvy, Stephen; Okhrimenko, Oleksandr; Oldeman, Rudolf; Onderwater, Gerco; Osorio Rodrigues, Bruno; Otalora Goicochea, Juan Martin; Otto, Adam; Owen, Patrick; Oyanguren, Maria Aranzazu; Pal, Bilas Kanti; Palano, Antimo; Palombo, Fernando; Palutan, Matteo; Panman, Jacob; Papanestis, Antonios; Pappagallo, Marco; Pappalardo, Luciano; Parkes, Christopher; Parkinson, Christopher John; Passaleva, Giovanni; Patel, Girish; Patel, Mitesh; Patrignani, Claudia; Pearce, Alex; Pellegrino, Antonio; Penso, Gianni; Pepe Altarelli, Monica; Perazzini, Stefano; Perret, Pascal; Pescatore, Luca; Petridis, Konstantinos; Petrolini, Alessandro; Petruzzo, Marco; Picatoste Olloqui, Eduardo; Pietrzyk, Boleslaw; Pilař, Tomas; Pinci, Davide; Pistone, Alessandro; Playfer, Stephen; Plo Casasus, Maximo; Polci, Francesco; Poluektov, Anton; Polyakov, Ivan; Polycarpo, Erica; Popov, Alexander; Popov, Dmitry; Popovici, Bogdan; Potterat, Cédric; Price, Eugenia; Price, Joseph David; Prisciandaro, Jessica; Pritchard, Adrian; Prouve, Claire; Pugatch, Valery; Puig Navarro, Albert; Punzi, Giovanni; Qian, Wenbin; Quagliani, Renato; Rachwal, Bartolomiej; Rademacker, Jonas; Rakotomiaramanana, Barinjaka; Rama, Matteo; Rangel, Murilo; Raniuk, Iurii; Rauschmayr, Nathalie; Raven, Gerhard; Redi, Federico; Reichert, Stefanie; Reid, Matthew; dos Reis, Alberto; Ricciardi, Stefania; Richards, Sophie; Rihl, Mariana; Rinnert, Kurt; Rives Molina, Vincente; Robbe, Patrick; Rodrigues, Ana Barbara; Rodrigues, Eduardo; Rodriguez Perez, Pablo; Roiser, Stefan; Romanovsky, Vladimir; Romero Vidal, Antonio; Rotondo, Marcello; Rouvinet, Julien; Ruf, Thomas; Ruiz, Hugo; Ruiz Valls, Pablo; Saborido Silva, Juan Jose; Sagidova, Naylya; Sail, Paul; Saitta, Biagio; Salustino Guimaraes, Valdir; Sanchez Mayordomo, Carlos; Sanmartin Sedes, Brais; Santacesaria, Roberta; Santamarina Rios, Cibran; Santovetti, Emanuele; Sarti, Alessio; Satriano, Celestina; Satta, Alessia; Saunders, Daniel Martin; Savrina, Darya; Schiller, Manuel; Schindler, Heinrich; Schlupp, Maximilian; Schmelling, Michael; Schmelzer, Timon; Schmidt, Burkhard; Schneider, Olivier; Schopper, Andreas; Schune, Marie Helene; Schwemmer, Rainer; Sciascia, Barbara; Sciubba, Adalberto; Semennikov, Alexander; Sepp, Indrek; Serra, Nicola; Serrano, Justine; Sestini, Lorenzo; Seyfert, Paul; Shapkin, Mikhail; Shapoval, Illya; Shcheglov, Yury; Shears, Tara; Shekhtman, Lev; Shevchenko, Vladimir; Shires, Alexander; Silva Coutinho, Rafael; Simi, Gabriele; Sirendi, Marek; Skidmore, Nicola; Skillicorn, Ian; Skwarnicki, Tomasz; Smith, Edmund; Smith, Eluned; Smith, Jackson; Smith, Mark; Snoek, Hella; Sokoloff, Michael; Soler, Paul; Soomro, Fatima; Souza, Daniel; Souza De Paula, Bruno; Spaan, Bernhard; Spradlin, Patrick; Sridharan, Srikanth; Stagni, Federico; Stahl, Marian; Stahl, Sascha; Steinkamp, Olaf; Stenyakin, Oleg; Sterpka, Christopher Francis; Stevenson, Scott; Stoica, Sabin; Stone, Sheldon; Storaci, Barbara; Stracka, Simone; Straticiuc, Mihai; Straumann, Ulrich; Stroili, Roberto; Sun, Liang; Sutcliffe, William; Swientek, Krzysztof; Swientek, Stefan; Syropoulos, Vasileios; Szczekowski, Marek; Szczypka, Paul; Szumlak, Tomasz; T'Jampens, Stephane; Tekampe, Tobias; Teklishyn, Maksym; Tellarini, Giulia; Teubert, Frederic; Thomas, Christopher; Thomas, Eric; van Tilburg, Jeroen; Tisserand, Vincent; Tobin, Mark; Todd, Jacob; Tolk, Siim; Tomassetti, Luca; Tonelli, Diego; Topp-Joergensen, Stig; Torr, Nicholas; Tournefier, Edwige; Tourneur, Stephane; Trabelsi, Karim; Tran, Minh Tâm; Tresch, Marco; Trisovic, Ana; Tsaregorodtsev, Andrei; Tsopelas, Panagiotis; Tuning, Niels; Ubeda Garcia, Mario; Ukleja, Artur; Ustyuzhanin, Andrey; Uwer, Ulrich; Vacca, Claudia; Vagnoni, Vincenzo; Valenti, Giovanni; Vallier, Alexis; Vazquez Gomez, Ricardo; Vazquez Regueiro, Pablo; Vázquez Sierra, Carlos; Vecchi, Stefania; Velthuis, Jaap; Veltri, Michele; Veneziano, Giovanni; Vesterinen, Mika; Viaud, Benoit; Vieira, Daniel; Vieites Diaz, Maria; Vilasis-Cardona, Xavier; Vollhardt, Achim; Volyanskyy, Dmytro; Voong, David; Vorobyev, Alexey; Vorobyev, Vitaly; Voß, Christian; de Vries, Jacco; Waldi, Roland; Wallace, Charlotte; Wallace, Ronan; Walsh, John; Wandernoth, Sebastian; Wang, Jianchun; Ward, David; Watson, Nigel; Websdale, David; Whitehead, Mark; Wiedner, Dirk; Wilkinson, Guy; Wilkinson, Michael; Williams, Matthew; Williams, Mike; Wilson, Fergus; Wimberley, Jack; Wishahi, Julian; Wislicki, Wojciech; Witek, Mariusz; Wormser, Guy; Wotton, Stephen; Wright, Simon; Wyllie, Kenneth; Xie, Yuehong; Xing, Zhou; Xu, Zhirui; Yang, Zhenwei; Yuan, Xuhao; Yushchenko, Oleg; Zangoli, Maria; Zavertyaev, Mikhail; Zhang, Liming; Zhang, Wen Chao; Zhang, Yanxi; Zhelezov, Alexey; Zhokhov, Anatoly; Zhong, Liang

    2015-01-01

    The resonant substructures of $B^0 \\to \\overline{D}^0 \\pi^+\\pi^-$ decays are studied with the Dalitz plot technique. In this study a data sample corresponding to an integrated luminosity of 3.0 fb$^{-1}$ of $pp$ collisions collected by the LHCb detector is used. The branching fraction of the $B^0 \\to \\overline{D}^0 \\pi^+\\pi^-$ decay in the region $m(\\overline{D}^0\\pi^{\\pm})>2.1$ GeV$/c^2$ is measured to be $(8.46 \\pm 0.14 \\pm 0.29 \\pm 0.40) \\times 10^{-4}$, where the first uncertainty is statistical, the second is systematic and the last arises from the normalisation channel $B^0 \\to D^*(2010)^-\\pi^+$. The $\\pi^+\\pi^-$ S-wave components are modelled with the Isobar and K-matrix formalisms. Results of the Dalitz plot analyses using both models are presented. A resonant structure at $m(\\overline{D}^0\\pi^-) \\approx 2.8$ GeV$/c^{2}$ is confirmed and its spin-parity is determined for the first time as $J^P = 3^-$. The branching fraction, mass and width of this structure are determined together with those of the $D...

  9. Open Plot Project: an open-source toolkit for 3-D structural data analysis

    Directory of Open Access Journals (Sweden)

    S. Tavani

    2011-05-01

    Full Text Available In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis.

    The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies (complementary to the User Manual, and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

  10. Incomplete split-plot designs based on alpha-designs: a compromise between traditional split-plot designs and randomised complete block design

    DEFF Research Database (Denmark)

    Kristensen, Kristian

    2012-01-01

    to traditional split-plots in most cases—and the increase in efficiency of the designs can be quite large—especially for comparisons involving the whole-plot treatment. The efficiency for the comparison of the main effect of the whole-plot treatment was in most cases larger for randomized complete block design...... than for the incomplete split-plot design, but for other comparisons the proposed designs were in most cases more efficient than a randomized complete block design. The efficiency of the designs was compared to traditional split-plot designs and randomized complete block designs using three types......The paper shows how the α-design (also known as generalised lattice) may be used for constructing incomplete split-plot designs and describes four different methods (A, B, C and D) of construction. Intra-block efficiency factors and theoretical considerations are used to compare the methods. Based...

  11. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.

    Directory of Open Access Journals (Sweden)

    Yi-Hsiang Hsu

    2010-06-01

    Full Text Available Osteoporosis is a complex disorder and commonly leads to fractures in elderly persons. Genome-wide association studies (GWAS have become an unbiased approach to identify variations in the genome that potentially affect health. However, the genetic variants identified so far only explain a small proportion of the heritability for complex traits. Due to the modest genetic effect size and inadequate power, true association signals may not be revealed based on a stringent genome-wide significance threshold. Here, we take advantage of SNP and transcript arrays and integrate GWAS and expression signature profiling relevant to the skeletal system in cellular and animal models to prioritize the discovery of novel candidate genes for osteoporosis-related traits, including bone mineral density (BMD at the lumbar spine (LS and femoral neck (FN, as well as geometric indices of the hip (femoral neck-shaft angle, NSA; femoral neck length, NL; and narrow-neck width, NW. A two-stage meta-analysis of GWAS from 7,633 Caucasian women and 3,657 men, revealed three novel loci associated with osteoporosis-related traits, including chromosome 1p13.2 (RAP1A, p = 3.6x10(-8, 2q11.2 (TBC1D8, and 18q11.2 (OSBPL1A, and confirmed a previously reported region near TNFRSF11B/OPG gene. We also prioritized 16 suggestive genome-wide significant candidate genes based on their potential involvement in skeletal metabolism. Among them, 3 candidate genes were associated with BMD in women. Notably, 2 out of these 3 genes (GPR177, p = 2.6x10(-13; SOX6, p = 6.4x10(-10 associated with BMD in women have been successfully replicated in a large-scale meta-analysis of BMD, but none of the non-prioritized candidates (associated with BMD did. Our results support the concept of our prioritization strategy. In the absence of direct biological support for identified genes, we highlighted the efficiency of subsequent functional characterization using publicly available expression profiling relevant

  12. Function plot response: A scalable system for teaching kinematics graphs

    Science.gov (United States)

    Laverty, James; Kortemeyer, Gerd

    2012-08-01

    Understanding and interpreting graphs are essential skills in all sciences. While students are mostly proficient in plotting given functions and reading values off graphs, they frequently lack the ability to construct and interpret graphs in a meaningful way. Students can use graphs as representations of value pairs, but often fail to interpret them as the representation of functions, and mostly fail to use them as representations of physical reality. Working with graphs in classroom settings has been shown to improve student abilities with graphs, particularly when the students can interact with them. We introduce a novel problem type in an online homework system, which requires students to construct the graphs themselves in free form, and requires no hand-grading by instructors. Initial experiences using the new problem type in an introductory physics course are reported.

  13. Multiscale recurrence quantification analysis of order recurrence plots

    Science.gov (United States)

    Xu, Mengjia; Shang, Pengjian; Lin, Aijing

    2017-03-01

    In this paper, we propose a new method of multiscale recurrence quantification analysis (MSRQA) to analyze the structure of order recurrence plots. The MSRQA is based on order patterns over a range of time scales. Compared with conventional recurrence quantification analysis (RQA), the MSRQA can show richer and more recognizable information on the local characteristics of diverse systems which successfully describes their recurrence properties. Both synthetic series and stock market indexes exhibit their properties of recurrence at large time scales that quite differ from those at a single time scale. Some systems present more accurate recurrence patterns under large time scales. It demonstrates that the new approach is effective for distinguishing three similar stock market systems and showing some inherent differences.

  14. Finding the plot in South African reading education

    Directory of Open Access Journals (Sweden)

    Peter Rule

    2017-01-01

    Full Text Available This article argues that we have lost the plot in South African reading education. To find it, we need to move beyond the predominant mode of reading as oral performance, where the emphasis is on accuracy and pronunciation, to reading as comprehension of meaning in text. While reading research in South Africa has been conducted mainly in school contexts, this case study is of a school and Adult Basic Education and Training Centre in a rural KwaZulu-Natal community near Pietermaritzburg. It found that an oratorical approach to reading dominated in both settings. It suggests that developing the way in which teachers understand the teaching of reading and transforming the teaching practices of those who teach as they were taught in the education system of the apartheid era are key to improving the teaching of reading.

  15. D.3.2 PLOT Persuasive Learning Design Framework

    DEFF Research Database (Denmark)

    Gram-Hansen, Sandra Burri; Schärfe, Henrik; Winther-Nielsen, Nicolai

    2011-01-01

    This deliverable is the second of three deliverables in WP3: Persuasive Learning Design Framework, and draws upon the theoretical foundation presented in the first deliverable D.3.1, as the persuasive potential of existing systems are explored, analysed and discussed. D.3.2. is formally described...... of the technological learning tools and products which are currently related to the PLOT project, namely the GLOMaker and the 3ET tool, and a selection of GLOs and learning exercises. The primary focus of the analysis is to explore how the theoretical perspectives presented in D.3.1 are represented in these tools...... as an: ‚Internal report for project use containing an empirically-based assessment of existing systems and their potential in terms of learning and persuasion. This will be used as a discussion document by the consortium.‛ To meet the requirements of this deliverable, this documents presents analysis...

  16. Dalitz plot analysis of $B_s^0 \\rightarrow \\overline{D}^0 K^- \\pi^+$ decays

    CERN Document Server

    Aaij, Roel; Adinolfi, Marco; Affolder, Anthony; Ajaltouni, Ziad; Akar, Simon; Albrecht, Johannes; Alessio, Federico; Alexander, Michael; Ali, Suvayu; Alkhazov, Georgy; Alvarez Cartelle, Paula; Alves Jr, Antonio Augusto; Amato, Sandra; Amerio, Silvia; Amhis, Yasmine; An, Liupan; Anderlini, Lucio; Anderson, Jonathan; Andreassen, Rolf; Andreotti, Mirco; Andrews, Jason; Appleby, Robert; Aquines Gutierrez, Osvaldo; Archilli, Flavio; Artamonov, Alexander; Artuso, Marina; Aslanides, Elie; Auriemma, Giulio; Baalouch, Marouen; Bachmann, Sebastian; Back, John; Badalov, Alexey; Baesso, Clarissa; Baldini, Wander; Barlow, Roger; Barschel, Colin; Barsuk, Sergey; Barter, William; Batozskaya, Varvara; Battista, Vincenzo; Bay, Aurelio; Beaucourt, Leo; Beddow, John; Bedeschi, Franco; Bediaga, Ignacio; Belogurov, Sergey; Belous, Konstantin; Belyaev, Ivan; Ben-Haim, Eli; Bencivenni, Giovanni; Benson, Sean; Benton, Jack; Berezhnoy, Alexander; Bernet, Roland; Bettler, Marc-Olivier; van Beuzekom, Martinus; Bien, Alexander; Bifani, Simone; Bird, Thomas; Bizzeti, Andrea; Bjørnstad, Pål Marius; Blake, Thomas; Blanc, Frédéric; Blouw, Johan; Blusk, Steven; Bocci, Valerio; Bondar, Alexander; Bondar, Nikolay; Bonivento, Walter; Borghi, Silvia; Borgia, Alessandra; Borsato, Martino; Bowcock, Themistocles; Bowen, Espen Eie; Bozzi, Concezio; Brambach, Tobias; van den Brand, Johannes; Bressieux, Joël; Brett, David; Britsch, Markward; Britton, Thomas; Brodzicka, Jolanta; Brook, Nicholas; Brown, Henry; Bursche, Albert; Busetto, Giovanni; Buytaert, Jan; Cadeddu, Sandro; Calabrese, Roberto; Calvi, Marta; Calvo Gomez, Miriam; Campana, Pierluigi; Campora Perez, Daniel; Carbone, Angelo; Carboni, Giovanni; Cardinale, Roberta; Cardini, Alessandro; Carson, Laurence; Carvalho Akiba, Kazuyoshi; Casse, Gianluigi; Cassina, Lorenzo; Castillo Garcia, Lucia; Cattaneo, Marco; Cauet, Christophe; Cenci, Riccardo; Charles, Matthew; Charpentier, Philippe; Chefdeville, Maximilien; Chen, Shanzhen; Cheung, Shu-Faye; Chiapolini, Nicola; Chrzaszcz, Marcin; Ciba, Krzystof; Cid Vidal, Xabier; Ciezarek, Gregory; Clarke, Peter; Clemencic, Marco; Cliff, Harry; Closier, Joel; Coco, Victor; Cogan, Julien; Cogneras, Eric; Collins, Paula; Comerma-Montells, Albert; Contu, Andrea; Cook, Andrew; Coombes, Matthew; Coquereau, Samuel; Corti, Gloria; Corvo, Marco; Counts, Ian; Couturier, Benjamin; Cowan, Greig; Craik, Daniel Charles; Cruz Torres, Melissa Maria; Cunliffe, Samuel; Currie, Robert; D'Ambrosio, Carmelo; Dalseno, Jeremy; David, Pascal; David, Pieter; Davis, Adam; De Bruyn, Kristof; De Capua, Stefano; De Cian, Michel; De Miranda, Jussara; De Paula, Leandro; De Silva, Weeraddana; De Simone, Patrizia; Decamp, Daniel; Deckenhoff, Mirko; Del Buono, Luigi; Déléage, Nicolas; Derkach, Denis; Deschamps, Olivier; Dettori, Francesco; Di Canto, Angelo; Dijkstra, Hans; Donleavy, Stephanie; Dordei, Francesca; Dorigo, Mirco; Dosil Suárez, Alvaro; Dossett, David; Dovbnya, Anatoliy; Dreimanis, Karlis; Dujany, Giulio; Dupertuis, Frederic; Durante, Paolo; Dzhelyadin, Rustem; Dziurda, Agnieszka; Dzyuba, Alexey; Easo, Sajan; Egede, Ulrik; Egorychev, Victor; Eidelman, Semen; Eisenhardt, Stephan; Eitschberger, Ulrich; Ekelhof, Robert; Eklund, Lars; El Rifai, Ibrahim; Elsasser, Christian; Ely, Scott; Esen, Sevda; Evans, Hannah Mary; Evans, Timothy; Falabella, Antonio; Färber, Christian; Farinelli, Chiara; Farley, Nathanael; Farry, Stephen; Fay, Robert; Ferguson, Dianne; Fernandez Albor, Victor; Ferreira Rodrigues, Fernando; Ferro-Luzzi, Massimiliano; Filippov, Sergey; Fiore, Marco; Fiorini, Massimiliano; Firlej, Miroslaw; Fitzpatrick, Conor; Fiutowski, Tomasz; Fontana, Marianna; Fontanelli, Flavio; Forty, Roger; Francisco, Oscar; Frank, Markus; Frei, Christoph; Frosini, Maddalena; Fu, Jinlin; Furfaro, Emiliano; Gallas Torreira, Abraham; Galli, Domenico; Gallorini, Stefano; Gambetta, Silvia; Gandelman, Miriam; Gandini, Paolo; Gao, Yuanning; García Pardiñas, Julián; Garofoli, Justin; Garra Tico, Jordi; Garrido, Lluis; Gaspar, Clara; Gauld, Rhorry; Gavardi, Laura; Gavrilov, Gennadii; Geraci, Angelo; Gersabeck, Evelina; Gersabeck, Marco; Gershon, Timothy; Ghez, Philippe; Gianelle, Alessio; Gianì, Sebastiana; Gibson, Valerie; Giubega, Lavinia-Helena; Gligorov, Vladimir; Göbel, Carla; Golubkov, Dmitry; Golutvin, Andrey; Gomes, Alvaro; Gotti, Claudio; Grabalosa Gándara, Marc; Graciani Diaz, Ricardo; Granado Cardoso, Luis Alberto; Graugés, Eugeni; Graziani, Giacomo; Grecu, Alexandru; Greening, Edward; Gregson, Sam; Griffith, Peter; Grillo, Lucia; Grünberg, Oliver; Gui, Bin; Gushchin, Evgeny; Guz, Yury; Gys, Thierry; Hadjivasiliou, Christos; Haefeli, Guido; Haen, Christophe; Haines, Susan; Hall, Samuel; Hamilton, Brian; Hampson, Thomas; Han, Xiaoxue; Hansmann-Menzemer, Stephanie; Harnew, Neville; Harnew, Samuel; Harrison, Jonathan; He, Jibo; Head, Timothy; Heijne, Veerle; Hennessy, Karol; Henrard, Pierre; Henry, Louis; Hernando Morata, Jose Angel; van Herwijnen, Eric; Heß, Miriam; Hicheur, Adlène; Hill, Donal; Hoballah, Mostafa; Hombach, Christoph; Hulsbergen, Wouter; Hunt, Philip; Hussain, Nazim; Hutchcroft, David; Hynds, Daniel; Idzik, Marek; Ilten, Philip; Jacobsson, Richard; Jaeger, Andreas; Jalocha, Pawel; Jans, Eddy; Jaton, Pierre; Jawahery, Abolhassan; Jing, Fanfan; John, Malcolm; Johnson, Daniel; Jones, Christopher; Joram, Christian; Jost, Beat; Jurik, Nathan; Kaballo, Michael; Kandybei, Sergii; Kanso, Walaa; Karacson, Matthias; Karbach, Moritz; Karodia, Sarah; Kelsey, Matthew; Kenyon, Ian; Ketel, Tjeerd; Khanji, Basem; Khurewathanakul, Chitsanu; Klaver, Suzanne; Klimaszewski, Konrad; Kochebina, Olga; Kolpin, Michael; Komarov, Ilya; Koopman, Rose; Koppenburg, Patrick; Korolev, Mikhail; Kozlinskiy, Alexandr; Kravchuk, Leonid; Kreplin, Katharina; Kreps, Michal; Krocker, Georg; Krokovny, Pavel; Kruse, Florian; Kucewicz, Wojciech; Kucharczyk, Marcin; Kudryavtsev, Vasily; Kurek, Krzysztof; Kvaratskheliya, Tengiz; La Thi, Viet Nga; Lacarrere, Daniel; Lafferty, George; Lai, Adriano; Lambert, Dean; Lambert, Robert W; Lanfranchi, Gaia; Langenbruch, Christoph; Langhans, Benedikt; Latham, Thomas; Lazzeroni, Cristina; Le Gac, Renaud; van Leerdam, Jeroen; Lees, Jean-Pierre; Lefèvre, Regis; Leflat, Alexander; Lefrançois, Jacques; Leo, Sabato; Leroy, Olivier; Lesiak, Tadeusz; Leverington, Blake; Li, Yiming; Likhomanenko, Tatiana; Liles, Myfanwy; Lindner, Rolf; Linn, Christian; Lionetto, Federica; Liu, Bo; Lohn, Stefan; Longstaff, Iain; Lopes, Jose; Lopez-March, Neus; Lowdon, Peter; Lu, Haiting; Lucchesi, Donatella; Luo, Haofei; Lupato, Anna; Luppi, Eleonora; Lupton, Oliver; Machefert, Frederic; Machikhiliyan, Irina V; Maciuc, Florin; Maev, Oleg; Malde, Sneha; Malinin, Alexander; Manca, Giulia; Mancinelli, Giampiero; Mapelli, Alessandro; Maratas, Jan; Marchand, Jean François; Marconi, Umberto; Marin Benito, Carla; Marino, Pietro; Märki, Raphael; Marks, Jörg; Martellotti, Giuseppe; Martens, Aurelien; Martín Sánchez, Alexandra; Martinelli, Maurizio; Martinez Santos, Diego; Martinez Vidal, Fernando; Martins Tostes, Danielle; Massafferri, André; Matev, Rosen; Mathe, Zoltan; Matteuzzi, Clara; Mazurov, Alexander; McCann, Michael; McCarthy, James; McNab, Andrew; McNulty, Ronan; McSkelly, Ben; Meadows, Brian; Meier, Frank; Meissner, Marco; Merk, Marcel; Milanes, Diego Alejandro; Minard, Marie-Noelle; Moggi, Niccolò; Molina Rodriguez, Josue; Monteil, Stephane; Morandin, Mauro; Morawski, Piotr; Mordà, Alessandro; Morello, Michael Joseph; Moron, Jakub; Morris, Adam Benjamin; Mountain, Raymond; Muheim, Franz; Müller, Katharina; Mussini, Manuel; Muster, Bastien; Naik, Paras; Nakada, Tatsuya; Nandakumar, Raja; Nasteva, Irina; Needham, Matthew; Neri, Nicola; Neubert, Sebastian; Neufeld, Niko; Neuner, Max; Nguyen, Anh Duc; Nguyen, Thi-Dung; Nguyen-Mau, Chung; Nicol, Michelle; Niess, Valentin; Niet, Ramon; Nikitin, Nikolay; Nikodem, Thomas; Novoselov, Alexey; O'Hanlon, Daniel Patrick; Oblakowska-Mucha, Agnieszka; Obraztsov, Vladimir; Oggero, Serena; Ogilvy, Stephen; Okhrimenko, Oleksandr; Oldeman, Rudolf; Onderwater, Gerco; Orlandea, Marius; Otalora Goicochea, Juan Martin; Owen, Patrick; Oyanguren, Maria Arantza; Pal, Bilas Kanti; Palano, Antimo; Palombo, Fernando; Palutan, Matteo; Panman, Jacob; Papanestis, Antonios; Pappagallo, Marco; Pappalardo, Luciano; Parkes, Christopher; Parkinson, Christopher John; Passaleva, Giovanni; Patel, Girish; Patel, Mitesh; Patrignani, Claudia; Pazos Alvarez, Antonio; Pearce, Alex; Pellegrino, Antonio; Pepe Altarelli, Monica; Perazzini, Stefano; Perez Trigo, Eliseo; Perret, Pascal; Perrin-Terrin, Mathieu; Pescatore, Luca; Pesen, Erhan; Petridis, Konstantin; Petrolini, Alessandro; Picatoste Olloqui, Eduardo; Pietrzyk, Boleslaw; Pilař, Tomas; Pinci, Davide; Pistone, Alessandro; Playfer, Stephen; Plo Casasus, Maximo; Polci, Francesco; Poluektov, Anton; Polycarpo, Erica; Popov, Alexander; Popov, Dmitry; Popovici, Bogdan; Potterat, Cédric; Price, Eugenia; Prisciandaro, Jessica; Pritchard, Adrian; Prouve, Claire; Pugatch, Valery; Puig Navarro, Albert; Punzi, Giovanni; Qian, Wenbin; Rachwal, Bartolomiej; Rademacker, Jonas; Rakotomiaramanana, Barinjaka; Rama, Matteo; Rangel, Murilo; Raniuk, Iurii; Rauschmayr, Nathalie; Raven, Gerhard; Reichert, Stefanie; Reid, Matthew; dos Reis, Alberto; Ricciardi, Stefania; Richards, Sophie; Rihl, Mariana; Rinnert, Kurt; Rives Molina, Vincente; Roa Romero, Diego; Robbe, Patrick; Rodrigues, Ana Barbara; Rodrigues, Eduardo; Rodriguez Perez, Pablo; Roiser, Stefan; Romanovsky, Vladimir; Romero Vidal, Antonio; Rotondo, Marcello; Rouvinet, Julien; Ruf, Thomas; Ruffini, Fabrizio; Ruiz, Hugo; Ruiz Valls, Pablo; Saborido Silva, Juan Jose; Sagidova, Naylya; Sail, Paul; Saitta, Biagio; Salustino Guimaraes, Valdir; Sanchez Mayordomo, Carlos; Sanmartin Sedes, Brais; Santacesaria, Roberta; Santamarina Rios, Cibran; Santovetti, Emanuele; Sarti, Alessio; Satriano, Celestina; Satta, Alessia; Saunders, Daniel Martin; Savrie, Mauro; Savrina, Darya; Schiller, Manuel; Schindler, Heinrich; Schlupp, Maximilian; Schmelling, Michael; Schmidt, Burkhard; Schneider, Olivier; Schopper, Andreas; Schune, Marie Helene; Schwemmer, Rainer; Sciascia, Barbara; Sciubba, Adalberto; Seco, Marcos; Semennikov, Alexander; Sepp, Indrek; Serra, Nicola; Serrano, Justine; Sestini, Lorenzo; Seyfert, Paul; Shapkin, Mikhail; Shapoval, Illya; Shcheglov, Yury; Shears, Tara; Shekhtman, Lev; Shevchenko, Vladimir; Shires, Alexander; Silva Coutinho, Rafael; Simi, Gabriele; Sirendi, Marek; Skidmore, Nicola; Skwarnicki, Tomasz; Smith, Anthony; Smith, Edmund; Smith, Eluned; Smith, Jackson; Smith, Mark; Snoek, Hella; Sokoloff, Michael; Soler, Paul; Soomro, Fatima; Souza, Daniel; Souza De Paula, Bruno; Spaan, Bernhard; Sparkes, Ailsa; Spradlin, Patrick; Sridharan, Srikanth; Stagni, Federico; Stahl, Marian; Stahl, Sascha; Steinkamp, Olaf; Stenyakin, Oleg; Stevenson, Scott; Stoica, Sabin; Stone, Sheldon; Storaci, Barbara; Stracka, Simone; Straticiuc, Mihai; Straumann, Ulrich; Stroili, Roberto; Subbiah, Vijay Kartik; Sun, Liang; Sutcliffe, William; Swientek, Krzysztof; Swientek, Stefan; Syropoulos, Vasileios; Szczekowski, Marek; Szczypka, Paul; Szilard, Daniela; Szumlak, Tomasz; T'Jampens, Stephane; Teklishyn, Maksym; Tellarini, Giulia; Teubert, Frederic; Thomas, Christopher; Thomas, Eric; van Tilburg, Jeroen; Tisserand, Vincent; Tobin, Mark; Tolk, Siim; Tomassetti, Luca; Tonelli, Diego; Topp-Joergensen, Stig; Torr, Nicholas; Tournefier, Edwige; Tourneur, Stephane; Tran, Minh Tâm; Tresch, Marco; Tsaregorodtsev, Andrei; Tsopelas, Panagiotis; Tuning, Niels; Ubeda Garcia, Mario; Ukleja, Artur; Ustyuzhanin, Andrey; Uwer, Ulrich; Vagnoni, Vincenzo; Valenti, Giovanni; Vallier, Alexis; Vazquez Gomez, Ricardo; Vazquez Regueiro, Pablo; Vázquez Sierra, Carlos; Vecchi, Stefania; Velthuis, Jaap; Veltri, Michele; Veneziano, Giovanni; Vesterinen, Mika; Viaud, Benoit; Vieira, Daniel; Vieites Diaz, Maria; Vilasis-Cardona, Xavier; Vollhardt, Achim; Volyanskyy, Dmytro; Voong, David; Vorobyev, Alexey; Vorobyev, Vitaly; Voß, Christian; Voss, Helge; de Vries, Jacco; Waldi, Roland; Wallace, Charlotte; Wallace, Ronan; Walsh, John; Wandernoth, Sebastian; Wang, Jianchun; Ward, David; Watson, Nigel; Websdale, David; Whitehead, Mark; Wicht, Jean; Wiedner, Dirk; Wilkinson, Guy; Williams, Matthew; Williams, Mike; Wilson, Fergus; Wimberley, Jack; Wishahi, Julian; Wislicki, Wojciech; Witek, Mariusz; Wormser, Guy; Wotton, Stephen; Wright, Simon; Wu, Suzhi; Wyllie, Kenneth; Xie, Yuehong; Xing, Zhou; Xu, Zhirui; Yang, Zhenwei; Yuan, Xuhao; Yushchenko, Oleg; Zangoli, Maria; Zavertyaev, Mikhail; Zhang, Liming; Zhang, Wen Chao; Zhang, Yanxi; Zhelezov, Alexey; Zhokhov, Anatoly; Zhong, Liang; Zvyagin, Alexander

    2014-01-01

    The resonant substructure of $B_s^0 \\rightarrow \\overline{D}^0 K^- \\pi^+$ decays is studied with the Dalitz plot analysis technique. The study is based on a data sample corresponding to an integrated luminosity of $3.0\\,{\\rm fb}^{-1}$ of $pp$ collision data recorded by LHCb. A structure at $m(\\overline{D}^0 K^-) \\approx 2.86 {\\rm GeV}/c^2$ is found to be an admixture of spin-1 and spin-3 resonances. The masses and widths of these states and of the $D^*_{s2}(2573)^-$ meson are measured, as are the complex amplitudes and fit fractions for all the $\\overline{D}^0 K^-$ and $K^-\\pi^+$ components included in the amplitude model. In addition, the $D^*_{s2}(2573)^-$ resonance is confirmed to be spin-2.

  17. Plant mycorrhizal traits and carbon fates from plot to globe

    Science.gov (United States)

    Soudzilovskaia, N.; Cornelissen, H. H. C.

    2016-12-01

    Evidence is accumulating that plant traits related to mycorrhizal symbiosis, i.e. mycorrhizal type and the degree of plant root colonization by mycorrhizal fungi have important consequences for carbon pools and allocation in plants and soil. How plant and soil carbon pools vary among vegetation dominated by plants of different mycorrhizal types is a new and exciting research challenge. Absence of global databases on abundance of mycorrhizal fungi in soil and plant roots retards research aimed to understand involvement of mycorrhizas into soil carbon transformation processes. Using own data and published studies we have assembled currently world-largest database of plant species-per-site degrees root colonization by two most common types of mycorrhizal fungi, arbuscular mycorrhizal (AM) and ectomycorrhizal (EM). The database features records for plant root colonization degrees by AM and EM (above 8000 records in total). Using this database, we demonstrate that the degree of mycorrhizal fungal colonization has globally consistent patterns across plant species. This suggests that the level of plant species-specific root colonization can be used as a plant trait. I will discuss how combining plot-level field data, literature data and mycorrhizal infection trait data may help us to quantify the carbon consequences of relative dominance by arbuscular versus ectomycorrhizal symbiosis in vegetation from plot to global scale. To exemplify this method, I will present an assessment of the impacts of EM shrub encroachment on carbon stocks in sub-arctic tundra, and show how the plant trait data (root, leaf, stem and mycorrhizal colonization traits) could predict (1) impacts of AM and EM vegetation on soil carbon budget and (2) changes in soil carbon budget due to increase of EM plants in an AM-dominated ecosystem and visa versa. This approach may help to predict how global change-mediated vegetation shifts, via mycorrhizal carbon pools and dynamics, may affect terrestric and

  18. Long Term Effects of Poultry Litter on Soil Physical and Chemical Properties in Cotton Plots

    Science.gov (United States)

    Surrency, J.; Tsegaye, T.; Coleman, T.; Fahsi, A.; Reddy, C.

    1998-01-01

    Poultry litter and compost can alter the moisture holding capacity of a soil. These organic materials can also increase the nutrient status of a soil during the decomposition process by microbial actions. The objective of this study was to evaluate the effect of poultry litter and compost on the dielectric constant and moisture holding capacity of soil. The Delta-T theta-probe was used to measure volumetric soil water content and the apparent dielectric constant of the upper 6-cm of the soil profile. Soil texture, pH, and organic matter were also determined for each plot. Results of these analyses indicated that the pH of the soil ranged from 6.4 to 7.7 and the volumetric soil moisture content ranged from 0.06 to 0.18 cu m/cu m for the upper 6-cm of the soil profile. The effect of poultry litter and compost on soil properties resulted in an increase in the volumetric moisture content and dielectric constant of the soil due to the improvement of the soil structure.

  19. Field Plot and Accuracy Assessment Points for Padre Island National Seashore Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — Accuracy Assessment, Observation and Plot Points. Currently there are NO DATA in this feature class. As of December 2009, a plots database has not been developed and...

  20. Field Plot and Accuracy Assessment Points for Bent's Old Fort National Historic Site Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — Accuracy Assessment, Observation and Plot Points. Plots within the park were identified and sampled in the summer of 2005. In the summer of 2006, randomly selected...

  1. Pre-ABoVE: Poplar Vegetation Plots, Arctic and Interior Alaska and Yukon, 2003-2005

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides vegetation cover and environmental plot data collected from 32 balsam poplar (Populus balsamifera L., Salicaceae) vegetation plots located on...

  2. Field Plot Points Modified for Fort Necessity National Battlefield Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — Locations of vegetation classification sampling plots at Fort Necessity National Battlefield. In this data set, the X, Y coordinates for three plots have been...

  3. Field Plot and Observation Points for Dinosaur National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This point file displays the 727 vegetation plots and 217 observation points visited in 2002, 2003 and 2004 as part of the vegetation mapping project. Plots and...

  4. An Integrated Analysis of MicroRNA and mRNA Expression Profiles to Identify RNA Expression Signatures in Lambskin Hair Follicles in Hu Sheep.

    Directory of Open Access Journals (Sweden)

    Xiaoyang Lv

    Full Text Available Wave patterns in lambskin hair follicles are an important factor determining the quality of sheep's wool. Hair follicles in lambskin from Hu sheep, a breed unique to China, have 3 types of waves, designated as large, medium, and small. The quality of wool from small wave follicles is excellent, while the quality of large waves is considered poor. Because no molecular and biological studies on hair follicles of these sheep have been conducted to date, the molecular mechanisms underlying the formation of different wave patterns is currently unknown. The aim of this article was to screen the candidate microRNAs (miRNA and genes for the development of hair follicles in Hu sheep. Two-day-old Hu lambs were selected from full-sib individuals that showed large, medium, and small waves. Integrated analysis of microRNA and mRNA expression profiles employed high-throughout sequencing technology. Approximately 13, 24, and 18 differentially expressed miRNAs were found between small and large waves, small and medium waves, and medium and large waves, respectively. A total of 54, 190, and 81 differentially expressed genes were found between small and large waves, small and medium waves, and medium and large waves, respectively, by RNA sequencing (RNA-seq analysis. Differentially expressed genes were classified using gene ontology and pathway analyses. They were found to be mainly involved in cell differentiation, proliferation, apoptosis, growth, immune response, and ion transport, and were associated with MAPK and the Notch signaling pathway. Reverse transcription-polymerase chain reaction (RT-PCR analyses of differentially-expressed miRNA and genes were consistent with sequencing results. Integrated analysis of miRNA and mRNA expression indicated that, compared to small waves, large waves included 4 downregulated miRNAs that had regulatory effects on 8 upregulated genes and 3 upregulated miRNAs, which in turn influenced 13 downregulated genes. Compared to

  5. Trends in the Evolution of Snake Toxins Underscored by an Integrative Omics Approach to Profile the Venom of the Colubrid Phalotris mertensi.

    Science.gov (United States)

    Campos, Pollyanna Fernandes; Andrade-Silva, Débora; Zelanis, André; Paes Leme, Adriana Franco; Rocha, Marisa Maria Teixeira; Menezes, Milene Cristina; Serrano, Solange M T; Junqueira-de-Azevedo, Inácio de Loiola Meirelles

    2016-08-16

    Only few studies on snake venoms were dedicated to deeply characterize the toxin secretion of animals from the Colubridae family, despite the fact that they represent the majority of snake diversity. As a consequence, some evolutionary trends observed in venom proteins that underpinned the evolutionary histories of snake toxins were based on data from a minor parcel of the clade. Here, we investigated the proteins of the totally unknown venom from Phalotris mertensi (Dipsadinae subfamily), in order to obtain a detailed profile of its toxins and to appreciate evolutionary tendencies occurring in colubrid venoms. By means of integrated omics and functional approaches, including RNAseq, Sanger sequencing, high-resolution proteomics, recombinant protein production, and enzymatic tests, we verified an active toxic secretion containing up to 21 types of proteins. A high content of Kunitz-type proteins and C-type lectins were observed, although several enzymatic components such as metalloproteinases and an L-amino acid oxidase were also present in the venom. Interestingly, an arguable venom component of other species was demonstrated as a true venom protein and named svLIPA (snake venom acid lipase). This finding indicates the importance of checking the actual protein occurrence across species before rejecting genes suggested to code for toxins, which are relevant for the discussion about the early evolution of reptile venoms. Moreover, trends in the evolution of some toxin classes, such as simplification of metalloproteinases and rearrangements of Kunitz and Wap domains, parallel similar phenomena observed in other venomous snake families and provide a broader picture of toxin evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity.

    Directory of Open Access Journals (Sweden)

    Montserrat Torres-Oliva

    2018-01-01

    Full Text Available Drosophila melanogaster head development represents a valuable process to study the developmental control of various organs, such as the antennae, the dorsal ocelli and the compound eyes from a common precursor, the eye-antennal imaginal disc. While the gene regulatory network underlying compound eye development has been extensively studied, the key transcription factors regulating the formation of other head structures from the same imaginal disc are largely unknown. We obtained the developmental transcriptome of the eye-antennal discs covering late patterning processes at the late 2nd larval instar stage to the onset and progression of differentiation at the end of larval development. We revealed the expression profiles of all genes expressed during eye-antennal disc development and we determined temporally co-expressed genes by hierarchical clustering. Since co-expressed genes may be regulated by common transcriptional regulators, we combined our transcriptome dataset with publicly available ChIP-seq data to identify central transcription factors that co-regulate genes during head development. Besides the identification of already known and well-described transcription factors, we show that the transcription factor Hunchback (Hb regulates a significant number of genes that are expressed during late differentiation stages. We confirm that hb is expressed in two polyploid subperineurial glia cells (carpet cells and a thorough functional analysis shows that loss of Hb function results in a loss of carpet cells in the eye-antennal disc. Additionally, we provide for the first time functional data indicating that carpet cells are an integral part of the blood-brain barrier. Eventually, we combined our expression data with a de novo Hb motif search to reveal stage specific putative target genes of which we find a significant number indeed expressed in carpet cells.

  7. Evaluating uncertainty in 7Be-based soil erosion estimates: an experimental plot approach

    Science.gov (United States)

    Blake, Will; Taylor, Alex; Abdelli, Wahid; Gaspar, Leticia; Barri, Bashar Al; Ryken, Nick; Mabit, Lionel

    2014-05-01

    a perforated pipe which fed into a collection bin for overland flow and associated sediment capture. At the same time, a flat area at the top of the slope was ploughed and tilled to create a reference site with same inventory baseline as the slope. Rain gauges were set up at the reference and slope site. The tilled surface had a low bulk density and high permeability at the start of the experiment (ksat > 100 mm hr-1). Hence, despite high rainfall in December 2013 (200 mm), notable runoff was observed only after intense rain storms during late 2013 and early January 2014 when the soil profile was saturated. Captured eroded sediment was analysed for 7Be and particle size. Subsequently, the plot soil surface was intensively sampled to quantify 7Be inventory patterns and develop a tracer budget. Preliminary results are discussed in the context of the above potential sources of uncertainty.

  8. 9 CFR 108.7 - Filing of plot plans, blueprints, and legends.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Filing of plot plans, blueprints, and... REQUIREMENTS FOR LICENSED ESTABLISHMENTS § 108.7 Filing of plot plans, blueprints, and legends. Three copies of all plot plans, blueprints, and legends, including revisions, shall be submitted to Animal and Plant...

  9. Procedures to handle inventory cluster plots that straddle two or more conditions

    Science.gov (United States)

    Jerold T. Hahn; Colin D. MacLean; Stanford L. Arner; William A. Bechtold

    1995-01-01

    We review the relative merits and field procedures for four basic plot designs to handle forest inventory plots that straddle two or more conditions, given that subplots will not be moved. A cluster design is recommended that combines fixed-area subplots and variable-radius plot (VRP) sampling. Each subplot in a cluster consists of a large fixed-area subplot for...

  10. The influence of fipronil on Reticulitermes flavipes (Isoptera: Rhinotermitidae) feeding beyond treated plots

    Science.gov (United States)

    Thomas Shelton

    2013-01-01

    A small-plot field trial was conducted to examine the area of influence of fipronil at incremental distances away from treated plots on the Harrison Experimental Forest near Saucier, MS. Small treated (water and fipronil) plots were surrounded by untreated wooden boards in an eight-point radial pattern, and examined for evidence of termite feeding every 60 d for 1 yr...

  11. An ecoinformatics application for forest dynamics plot data management and sharing

    Science.gov (United States)

    Chau-Chin Lin; Abd Rahman Kassim; Kristin Vanderbilt; Donald Henshaw; Eda C. Melendez-Colom; John H. Porter; Kaoru Niiyama; Tsutomu Yagihashi; Sek Aun Tan; Sheng-Shan Lu; Chi-Wen Hsiao; Li-Wan Chang; Meei-Ru. Jeng

    2011-01-01

    Several forest dynamics plot research projects in the East-Asia Pacific region of the International Long-Term Ecological Research network actively collect long-term data, and some of these large plots are members of the Center for Tropical Forest Science network. The wealth of forest plot data presents challenges in information management to researchers. In order to...

  12. multilocational evaluation of white yam genotypes using gge bi-plot ...

    African Journals Online (AJOL)

    PROF EKWUEME

    The GGE bi-plot generated several graphic bi-plots which showed Umudike, Nsukka, Ubiaja and Katsina-Ala as belonging to one mega – environment while Abuja and Ubiaja belong to another. The GGE bi-plot also showed the discriminating and non-discriminating environments. Katsina-Ala was the most discriminating ...

  13. Multilocational evaluation of white yam genotypes using GGE bi-plot ...

    African Journals Online (AJOL)

    The GGE bi-plot generated several graphic bi-plots which showed Umudike, Nsukka, Ubiaja and Katsina-Ala as belonging to one mega – environment while Abuja and Ubiaja belong to another. The GGE bi-plot also showed the discriminating and non-discriminating environments. Katsina-Ala was the most discriminating ...

  14. Classification of calorimetric titration plots for alkyltrimethylammonium and alkylpyridinium cationic surfactants in aqueous solutions

    NARCIS (Netherlands)

    Bijma, K; Engberts, J.B.F.N.; Blandamer, M.J; Cullis, P.M.; Last, P.M.; Irlam, K.D.; Soldi, L.G.

    1997-01-01

    Calorimetric titration plots for deaggregation of micelles formed by alkylpyridinium and alkyltrimethylammonium surfactants are classified into three types, A, B and C, depending on the shape of the plot of the enthalpy of dilution as a function of surfactant concentration. For Type A plots the

  15. Maintaining a permanent plot data base for growth and yield research: Solutions to some recurring problems

    Science.gov (United States)

    John C. Byrne

    1993-01-01

    Methods for solving some recurring problems of maintaining a permanent plot data base for growth and yield reseuch are described. These methods include documenting data from diverse sampling designs, changing sampling designs, changing field procedures, and coordinating activities in the plots with the land management agency. Managing a permanent plot data base (...

  16. Immigration of the barley mildew pathogen into field plots of barley

    DEFF Research Database (Denmark)

    O'Hara, R.B.; Brown, J.K.M.

    1996-01-01

    Immigration of the barley powdery mildew pathogen (Erysiphe graminis f.sp. hordei) into field plots of the spring barley variety Tyra (carrying the resistance allele Mla1) was investigated. Spores were trapped from the top of the plot canopies, as well as from control plots of wheat with no barley...

  17. Influence of tree spatial pattern and sample plot type and size on inventory

    Science.gov (United States)

    John-Pascall Berrill; Kevin L. O' Hara

    2012-01-01

    Sampling with different plot types and sizes was simulated using tree location maps and data collected in three even-aged coast redwood (Sequoia sempervirens) stands selected to represent uniform, random, and clumped spatial patterns of tree locations. Fixed-radius circular plots, belt transects, and variable-radius plots were installed by...

  18. A K-sample Homogeneity Test based on the Quantification of the p-p Plot

    NARCIS (Netherlands)

    Hinloopen, Jeroen; Wagenvoort, Rien; Marrewijk, van Charles

    2008-01-01

    We propose a quantification of the p-p plot that assigns equal weight to all distances between the respective distributions: the surface between the p-p plot and the diagonal. This surface is labelled the Harmonic Weighted Mass (HWM) index. We introduce the diagonal-deviation (d-d) plot that allows

  19. Profiling application potential for alkali treated sisal fiber ...

    African Journals Online (AJOL)

    Profiling application potential for alkali treated sisal fiber-polypropylene composite in Ashby material-property plots. ... International Journal of Engineering, Science and Technology. Journal Home · ABOUT · Advanced Search · Current Issue ...

  20. Farmers' awareness on landslide susceptibility on their plots: a first step towards household resilience in the Rwenzori region, Western Uganda

    Science.gov (United States)

    Mertens, Kewan; Jacobs, Lies; Maes, Jan; Kervyn, Matthieu; Vranken, Liesbet

    2016-04-01

    with a lower education level, lower trust, social capital and networks and with a recent migration history are less able to estimate landslide susceptibility on their plots. Literature on other disasters has demonstrated that human capital, social networks and past experience are crucial factors in determining risk perception. To our knowledge this is the first study to specifically investigate landslide risk awareness in a developing country, integrating both detailed socio-economic and geographical data. While estimating the awareness of landslide susceptibility is not sufficient to come to an estimation of a household's coping capacity, we consider it to be a first and necessary step towards a full estimation of household resilience.

  1. The physical model of a terraced plot: first results

    Science.gov (United States)

    Perlotto, Chiara; D'Agostino, Vincenzo; Buzzanca, Giacomo

    2017-04-01

    Terrace building have been expanded in the 19th century because of the increased demographic pressure and the need to crop additional areas at steeper slopes. Terraces are also important to regulate the hydrological behavior of the hillslope. Few studies are available in literature on rainfall-runoff processes and flood risk mitigation in terraced areas. Bench terraces, reducing the terrain slope and the length of the overland flow, quantitatively control the runoff flow velocity, facilitating the drainage and thus leading to a reduction of soil erosion. The study of the hydrologic-hydraulic function of terraced slopes is essential in order to evaluate their possible use to cooperate for flood-risk mitigation also preserving the landscape value. This research aims to better focus the times of the hydrological response, which are determined by a hillslope plot bounded by a dry-stone wall, considering both the overland flow and the groundwater. A physical model, characterized by a quasi-real scale, has been built to reproduce the behavior of a 3% outward sloped terrace at bare soil condition. The model consists of a steel metal box (1 m large, 3.3 m long, 2 m high) containing the hillslope terrain. The terrain is equipped with two piezometers, 9 TDR sensors measuring the volumetric water content, a surface spillway at the head releasing the steady discharge under test, a scale at the wall base to measure the outflowing discharge. The experiments deal with different initial moisture condition (non-saturated and saturated), and discharges of 19.5, 12.0 and 5.0 l/min. Each experiment has been replicated, conducting a total number of 12 tests. The volumetric water content analysis produced by the 9 TDR sensors was able to provide a quite satisfactory representation of the soil moisture during the runs. Then, different lag times at the outlet since the inflow initiation were measured both for runoff and groundwater. Moreover, the time of depletion and the piezometer

  2. Integrated permanent plot and aerial monitoring for the spruce budworm decision support system

    Science.gov (United States)

    David A. MacLean

    2000-01-01

    Spruce budworm (Choristoneura fumiferana Clem.) outbreaks cause severe mortality and growth loss of spruce and fir forest over ranch of eastern North America. The Spruce Budworm Decision Support System (DSS) links prediction and interpretation models to the ARC/1NFO GIS, under an ArcView graphical user interface. It helps forest managers predict...

  3. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  4. Integrating P3 Data Into P2 Analyses: What is the Added Value

    Science.gov (United States)

    James R. Steinman

    2001-01-01

    The Forest Inventory and Analysis and Forest Health Monitoring Programs of the USDA Forest Service are integrating field procedures for measuring their networks of plots throughout the United States. These plots are now referred to as Phase 2 (P2) and Phase 3 (P3) plots, respectively, and 1 out of every 16 P2 plots will also be a P3 plot. Mensurational methods will be...

  5. Advances in validating SALTIRSOIL at plot scale: first results.

    Science.gov (United States)

    Visconti, Fernando; de Paz, José Miguel; Molina, María José; Sánchez, Juan

    2012-03-01

    SALTIRSOIL (SALTs in IRrigated SOILs) is a model for the medium to long term simulation of soil salinity in irrigated, well-drained lands. Once the algorithms were verified, the objective of our study was to validate SALTIRSOIL under one of several water quality and management scenarios in Mediterranean agriculture. Because drip and surface are the most common irrigation systems in irrigated agriculture in Valencia (Spain), the validation was performed with climate, soil, irrigation water (composition and management) and crop (species and management) information from an experimental plot surface irrigated with well water and planted with watermelon that has been monitored since the late spring of 2007. To carry out the validation, first we performed a global sensitivity analysis (GSA). Second, we compared simulated soil saturation extract composition against measured data. According to the GSA, SALTIRSOIL calculations of soil salinity seem to be most affected by climate (rainfall and evapotranspiration) with 60% of explained soil salinity variance, water salinity with 26% of explained variance, and then irrigation with 4%. According to the closeness of the first comparisons between predictions and measurements, SALTIRSOIL does not seem to be affected by any systematic error, and as a consequence, neither inclusion of new parameters nor calibration of the others already included would be needed at least for surface irrigation. The validation of SALTIRSOIL continues under other water quality and irrigation management scenarios. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. The imprint of exile through the plot of the narratives

    Directory of Open Access Journals (Sweden)

    Silvia Dutrénit Bielous

    2010-06-01

    Full Text Available Exile is a circumstance different from other migrations, although it resembles them in the possible insertion or alienation from the receiving society. It is with no a doubt a forced migration process which is always accompanied by an idea and an imaginary: the disappearrance of the conditions that forced to exile and thus, the return.Although it is not possible to generalize, because there is no one single experience of exile and the subjectivities that compose it are diverse, it undoubtedly produces a sensation of alienation, which can lead to the rejection of the cultural norms of society; it is part of a process of “being in one place, but thinking about another.” However, as exile is prolonged, the experience of adaptation for the different generations involved becomes diversified, communication vessels develop, feelings of inclusion, of adaptation, of attachment with the social and cultural environment that the place of refuge offered.The present text builds on testimonies of Uruguayans exiled in Mexico who have returned to their country. In their narrative, the meanings that relate to the subjective perspective that provoked the “return” to their country of origin as being viable and a palpable event are perceived. In summary, an incursion through the testimonial plot explains to what extent the return is a recovery of the space of identity longed for and the subsequent abandonment of the foreign space, in other words, it adds to the perspective of identity as a dynamic and relational construction.

  7. SplicePlot: a utility for visualizing splicing quantitative trait loci.

    Science.gov (United States)

    Wu, Eric; Nance, Tracy; Montgomery, Stephen B

    2014-04-01

    RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure. Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available.

  8. Alternative Analytical Method Used in Plotting the Shear Force and Bending Moment Diagrams, Displacements and Rotations Distributions for Beams Subjected to Bending

    Science.gov (United States)

    Marin, Cornel; Filip, Vivian; Marin, Alexandru

    2009-01-01

    The actual graphical methods used by engineers when plotting the stress distributions are based on integrating the differential equations of stresses for each beam segment. The resulting integration constants are obtained by imposing boundary conditions for each beam segment. Using MathCAD, this alternative proposed analytical method uses the step function Φ(x-a) which introduces a compact form of the stresses, strain and displacements expressions. The constructive optimization is thus easier to be performed.

  9. Simulations and field observations of root water uptake in plots with different soil water availability.

    Science.gov (United States)

    Cai, Gaochao; Vanderborght, Jan; Couvreur, Valentin; Javaux, Mathieu; Vereecken, Harry

    2015-04-01

    Root water uptake is a main process in the hydrological cycle and vital for water management in agronomy. In most models of root water uptake, the spatial and temporal soil water status and plant root distributions are required for water flow simulations. However, dynamic root growth and root distributions are not easy and time consuming to measure by normal approaches. Furthermore, root water uptake cannot be measured directly in the field. Therefore, it is necessary to incorporate monitoring data of soil water content and potential and root distributions within a modeling framework to explore the interaction between soil water availability and root water uptake. But, most models are lacking a physically based concept to describe water uptake from soil profiles with vertical variations in soil water availability. In this contribution, we present an experimental setup in which root development, soil water content and soil water potential are monitored non-invasively in two field plots with different soil texture and for three treatments with different soil water availability: natural rain, sheltered and irrigated treatment. Root development is monitored using 7-m long horizontally installed minirhizotubes at six depths with three replicates per treatment. The monitoring data are interpreted using a model that is a one-dimensional upscaled version of root water uptake model that describes flow in the coupled soil-root architecture considering water potential gradients in the system and hydraulic conductances of the soil and root system (Couvreur et al., 2012). This model approach links the total root water uptake to an effective soil water potential in the root zone. The local root water uptake is a function of the difference between the local soil water potential and effective root zone water potential so that compensatory uptake in heterogeneous soil water potential profiles is simulated. The root system conductance is derived from inverse modelling using

  10. Integrated "omics" profiling indicates that miRNAs are modulators of the ontogenetic venom composition shift in the Central American rattlesnake, Crotalus simus simus.

    Science.gov (United States)

    Durban, Jordi; Pérez, Alicia; Sanz, Libia; Gómez, Aarón; Bonilla, Fabián; Rodríguez, Santos; Chacón, Danilo; Sasa, Mahmood; Angulo, Yamileth; Gutiérrez, José M; Calvete, Juan J

    2013-04-10

    Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom composition are genetically controlled rather than environmentally induced. However, the molecular mechanisms underlying these changes remain elusive. Here we have explored the basis and level of regulation of the ontogenetic shift in the venom composition of the Central American rattlesnake, Crotalus s. simus using a combined proteomics and transcriptomics approach. Proteomic analysis showed that the ontogenetic shift in the venom composition of C. s. simus is essentially characterized by a gradual reduction in the expression of serine proteinases and PLA2 molecules, particularly crotoxin, a β-neurotoxic heterodimeric PLA2, concominantly with an increment of PI and PIII metalloproteinases at age 9-18 months. Comparison of the transcriptional activity of the venom glands of neonate and adult C. s. simus specimens indicated that their transcriptomes exhibit indistinguisable toxin family profiles, suggesting that the elusive mechanism by which shared transcriptomes generate divergent venom phenotypes may operate post-transcriptionally. Specifically, miRNAs with frequency count of 1000 or greater exhibited an uneven distribution between the newborn and adult datasets. Of note, 590 copies of a miRNA targeting crotoxin B-subunit was exclusively found in the transcriptome of the adult snake, whereas 1185 copies of a miRNA complementary to a PIII-SVMP mRNA was uniquely present in the newborn dataset. These results support the view that age-dependent changes in the concentration of miRNA modulating the transition from a crotoxin-rich to a SVMP-rich venom from birth through adulthood can potentially explain what is observed in the proteomic analysis of the ontogenetic changes in the venom composition of C. s. simus. Existing snake venom toxins are the result of early

  11. Integrated “omics” profiling indicates that miRNAs are modulators of the ontogenetic venom composition shift in the Central American rattlesnake, Crotalus simus simus

    Science.gov (United States)

    2013-01-01

    Background Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom composition are genetically controlled rather than environmentally induced. However, the molecular mechanisms underlying these changes remain elusive. Here we have explored the basis and level of regulation of the ontogenetic shift in the venom composition of the Central American rattlesnake, Crotalus s. simus using a combined proteomics and transcriptomics approach. Results Proteomic analysis showed that the ontogenetic shift in the venom composition of C. s. simus is essentially characterized by a gradual reduction in the expression of serine proteinases and PLA2 molecules, particularly crotoxin, a β-neurotoxic heterodimeric PLA2, concominantly with an increment of PI and PIII metalloproteinases at age 9–18 months. Comparison of the transcriptional activity of the venom glands of neonate and adult C. s. simus specimens indicated that their transcriptomes exhibit indistinguisable toxin family profiles, suggesting that the elusive mechanism by which shared transcriptomes generate divergent venom phenotypes may operate post-transcriptionally. Specifically, miRNAs with frequency count of 1000 or greater exhibited an uneven distribution between the newborn and adult datasets. Of note, 590 copies of a miRNA targeting crotoxin B-subunit was exclusively found in the transcriptome of the adult snake, whereas 1185 copies of a miRNA complementary to a PIII-SVMP mRNA was uniquely present in the newborn dataset. These results support the view that age-dependent changes in the concentration of miRNA modulating the transition from a crotoxin-rich to a SVMP-rich venom from birth through adulhood can potentially explain what is observed in the proteomic analysis of the ontogenetic changes in the venom composition of C. s. simus. Conclusions Existing snake venom

  12. Litterfall and Leaf Area Index in the CONECOFOR Permanent Monitoring Plots

    Directory of Open Access Journals (Sweden)

    Andrea CUTINI

    2002-09-01

    Full Text Available Forest canopies are more sensitive and react more promptly to abiotic and biotic disturbances than other stand structural components. Monitoring crown and canopy characteristics is therefore a crucial issue for intensive and continuous monitoring programs of forest ecosystem status. These observations formed the basis for the measurement of annual litter production and leaf area index (LAI in the Italian permanent monitoring plots (CONECOFOR program established within the EC-UN/ECE program "Intensive Monitoring (Level II of Forest Ecosystems". Preliminary results after three years of observation are presented. The low value of within plot mean relative standard deviation (20.8 ± 1.9% of litter production, which in any case never exceeded 30%, accounted for the good sampling error and accuracy of the chosen method, which seems to be accurate enough to detect changes in litter production through the years. The higher inconsistency of the amount of woody and fruits fractions over the years demonstrated the greater reliability of leaf fraction or, on the other hand, of LAI compared to total litter. Mean values of annual leaf-litter and total litter production and LAI were rather high in comparison with data reported in literature for similar stands, and reflected both a medium-high productivity and a juvenile phase in the development of the selected stands on average. Focusing on changes in litter production through the years, statistical analysis on a sub-sample of plots showed the existence of significant differences both in leaf litter and total litter production. These findings seem to attribute to the "year" factor a driving role in determining changes in litter production and LAI. Temporal intermittence in data collection, together with the shortness of the monitoring period, make it difficult to speculate or arrive at definitive conclusions on changes in litter production due to time-dependent factors. The importance of having a complete

  13. Design and Fabrication of Complex Scaffolds for Bone Defect Healing: Combined 3D Plotting of a Calcium Phosphate Cement and a Growth Factor-Loaded Hydrogel.

    Science.gov (United States)

    Ahlfeld, Tilman; Akkineni, Ashwini Rahul; Förster, Yvonne; Köhler, Tino; Knaack, Sven; Gelinsky, Michael; Lode, Anja

    2017-01-01

    Additive manufacturing enables the fabrication of scaffolds with defined architecture. Versatile printing technologies such as extrusion-based 3D plotting allow in addition the incorporation of biological components increasing the capability to restore functional tissues. We have recently described the fabrication of calcium phosphate cement (CPC) scaffolds by 3D plotting of an oil-based CPC paste under mild conditions. In the present study, we have developed a strategy for growth factor loading based on multichannel plotting: a biphasic scaffold design was realised combining CPC with VEGF-laden, highly concentrated hydrogel strands. As hydrogel component, alginate and an alginate-gellan gum blend were evaluated; the blend exhibited a more favourable VEGF release profile and was chosen for biphasic scaffold fabrication. After plotting, two-step post-processing was performed for both, hydrogel crosslinking and CPC setting, which was shown to be compatible with both materials. Finally, a scaffold was designed and fabricated which can be applied for testing in a rat critical size femur defect. Optimization of CPC plotting enabled the fabrication of highly resolved structures with strand diameters of only 200 µm. Micro-computed tomography revealed a precise strand arrangement and an interconnected pore space within the biphasic scaffold even in swollen state of the hydrogel strands.

  14. Generation of Domestic Hot Water, Space Heating and Driving Pattern Profiles for Integration Analysis of Active Loads in Low Voltage Grids

    DEFF Research Database (Denmark)

    Diaz de Cerio Mendaza, Iker; Pigazo, Alberto; Bak-Jensen, Birgitte

    2013-01-01

    at household level. Despite of the well-known flexible service that this kind of loads can provide, their flexibility is highly dependent of the domestic hot water and space heating demand and the driving habits of each user. This paper presents two methodologies employed to randomly generate thermal power...... demand and electric vehicle driving profiles, to be used for power grid calculations. The generated thermal profiles relied on a statistical analysis made from real domestic hot water and space heating data from 25 households of a typical Danish residential area. The driving profiles instead were formed...

  15. Determination of the \\eta\\to\\pi^+\\pi^-\\pi^0 Dalitz Plot slopes and asymmetries with the KLOE detector

    CERN Document Server

    Ambrosino, F; Antonelli, M; Archilli, F; Bacci, C; Beltrame, P; Bencivenni, G; Bertolucci, S; Bini, C; Bloise, C; Bocchetta, S; Bocci, V; Bossi, F; Branchini, P; Caloi, R; Campana, P; Capon, G; Capussela, T; Ceradini, F; Chi, S; Chiefari, G; Ciambrone, P; De Lucia, E; De Santis, A; De Simone, P; De Zorzi, G; Denig, A; Di Domenico, A; Di Donato, C; Di Falco, S; Di Micco, B; Doria, A; Dreucci, M; Felici, G; Ferrari, A; Ferrer, M L; Finocchiaro, G; Fiore, S; Forti, C; Franzini, P; Gatti, C; Gauzzi, P; Giovannella, S; Gorini, E; Graziani, E; Incagli, M; Kluge, W; Kulikov, V; Lacava, F; Lanfranchi, G; Lee-Franzini, J; Leone, D; Martini, M; Massarotti, P; Mei, W; Meola, S; Miscetti, S; Moulson, M; Müller, S; Murtas, F; Napolitano, M; Nguyen, F; Palutan, M; Pasqualucci, E; Passeri, A; Patera, V; Perfetto{*}, F; Primavera, M; Santangelo, P; Saracino, G; Sciascia, B; Sciubba, A; Scuri, F; Sfiligoi, I; Spadaro, T; Testa, M; Tortora, L; Valente, P; Valeriani, B; Venanzoni, G; Versaci, R; Xu, G

    2007-01-01

    We have studied, with the KLOE detector at the DA$\\Phi$NE $\\Phi$-Factory, the dynamics of the decay $\\eta\\to\\pi^+\\pi^-\\pi^0$ using data from the radiative $\\phi\\to\\eta\\gamma$ decay for an integrated luminosity $L = 450 \\textrm{pb^{-1}}$. From a fit to the Dalitz plot density distribution we obtain a precise measurement of the slope parameters. This should allow to improve the knowledge of the decay amplitude which is sensitive to the u-d quark mass difference. We also present new best results on the C-violating asymmetries in the $\\eta\\to\\pi^+\\pi^-\\pi^0$ decay.

  16. User Guide for the Plotting Software for the Los Alamos National Laboratory Nuclear Weapons Analysis Tools Version 2.0

    Energy Technology Data Exchange (ETDEWEB)

    Cleland, Timothy James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2018-01-02

    The Los Alamos National Laboratory Plotting Software for the Nuclear Weapons Analysis Tools is a Java™ application based upon the open source library JFreeChart. The software provides a capability for plotting data on graphs with a rich variety of display options while allowing the viewer interaction via graph manipulation and scaling to best view the data. The graph types include XY plots, Date XY plots, Bar plots and Histogram plots.

  17. Using of Pickett’s plot in determining the reservoir characteristics in Abu Roash Formation, El-Razzak Oil Field, North Western Desert, Egypt

    Directory of Open Access Journals (Sweden)

    A.A. El-Khadragy

    2014-03-01

    A new technique has been applied through Pickett’s plot, to develop some of reservoir petrophysical parameters. These parameters include capillary pressure, pore throat aperture radii, height above the free water table and bulk volume of water. This technique depends on the use of log–log plots of effective porosity versus resistivity combined with empirical relationships for calculating the capillary pressure expressed as a function of permeability, porosity and water saturation. Also, this technique gave the values of petrophysical exponents (m, n and a which were used to calculate the accurate value of water saturation in both clean and shaly rocks and then adjust estimation of hydrocarbon saturation. The integration of these petrophysical parameters on a log–log graph of porosity versus resistivity gives the importance for Pickett plot to be used in reservoir interpretation.

  18. Mortality factors for dead trees from a subset of plots from the Sierra Nevada Forest Dynamics Plot Network from 1998 to 2010

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This dataset was used to summarize and analyze the mortality factors recorderd on dead trees in the Sierra Nevada Forest Dynamics Plot Network, which is managed by...

  19. Estimation of Missing Observations in Two-Level Split-Plot Designs

    DEFF Research Database (Denmark)

    Almimi, Ashraf A.; Kulahci, Murat; Montgomery, Douglas C.

    2008-01-01

    . If the smaller effects do not point at the origin, then different contrast columns to some or all of the initial ones should be discarded and the plots re-examined for bias. Using examples, we show how the method provides estimates for the missing observations that are very close to their actual values......Inserting estimates for the missing observations from split-plot designs restores their balanced or orthogonal structure and alleviates the difficulties in the statistical analysis. In this article, we extend a method due to Draper and Stoneman to estimate the missing observations from unreplicated...... two-level factorial and fractional factorial split-plot (FSP and FFSP) designs. The missing observations, which can either be from the same whole plot, from different whole plots, or comprise entire whole plots, are estimated by equating to zero a number of specific contrast columns equal...

  20. Field Plot Points for Colonial National Historical Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile shows the location of vegetation sampling plots used for vegetation classification and mapping at Colonial National Historical Park.

  1. Field Plot Points for Richmond National Battlefield Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile shows the location of vegetation sampling plots used for vegetation classification and mapping at Richmond National Battlefield Park.

  2. Checking the Adequacy of Fit of Models from Split-Plot Designs

    DEFF Research Database (Denmark)

    Almini, A. A.; Kulahci, Murat; Montgomery, D. C.

    2009-01-01

    -plot models. In this article, we propose the computation of two R-2, R-2-adjusted, prediction error sums of squares (PRESS), and R-2-prediction statistics to measure the adequacy of fit for the WP and the SP submodels in a split-plot design. This is complemented with the graphical analysis of the two types...... of errors to check for any violation of the underlying assumptions and the adequacy of fit of split-plot models. Using examples, we show how computing two measures of model adequacy of fit for each split-plot design model is appropriate and useful as they reveal whether the correct WP and SP effects have...

  3. Porphyrins profile by high performance liquid chromatography ...

    African Journals Online (AJOL)

    E. Fateen

    2008-09-07

    Sep 7, 2008 ... Triple fragmentation mass spec- trometry (MS3) was done on the positive mode at collision en- ergy 45%. The masses of porphyrins and their MS3 fragments are shown in Table 1 [14]. 2.2.3. Quantitative determination of porphyrins profile. Calibration curve for each standard was plotted as a response.

  4. Fitting diameter distribution models to data from forest inventories with concentric plot design

    Energy Technology Data Exchange (ETDEWEB)

    Nanos, N.; Sjöstedt de Luna, S.

    2017-11-01

    Aim: Several national forest inventories use a complex plot design based on multiple concentric subplots where smaller diameter trees are inventoried when lying in the smaller-radius subplots and ignored otherwise. Data from these plots are truncated with threshold (truncation) diameters varying according to the distance from the plot centre. In this paper we designed a maximum likelihood method to fit the Weibull diameter distribution to data from concentric plots. Material and methods: Our method (M1) was based on multiple truncated probability density functions to build the likelihood. In addition, we used an alternative method (M2) presented recently. We used methods M1 and M2 as well as two other reference methods to estimate the Weibull parameters in 40000 simulated plots. The spatial tree pattern of the simulated plots was generated using four models of spatial point patterns. Two error indices were used to assess the relative performance of M1 and M2 in estimating relevant stand-level variables. In addition, we estimated the Quadratic Mean plot Diameter (QMD) using Expansion Factors (EFs). Main results: Methods M1 and M2 produced comparable estimation errors in random and cluster tree spatial patterns. Method M2 produced biased parameter estimates in plots with inhomogeneous Poisson patterns. Estimation of QMD using EFs produced biased results in plots within inhomogeneous intensity Poisson patterns. Research highlights:We designed a new method to fit the Weibull distribution to forest inventory data from concentric plots that achieves high accuracy and precision in parameter estimates regardless of the within-plot spatial tree pattern.

  5. Evaluation of Soft Tissue Landmark Reliability between Manual and Computerized Plotting Methods.

    Science.gov (United States)

    Kasinathan, Geetha; Kommi, Pradeep B; Kumar, Senthil M; Yashwant, Aniruddh; Arani, Nandakumar; Sabapathy, Senkutvan

    2017-04-01

    The aim of the study is to evaluate the reliability of soft tissue landmark identification between manual and digital plot-tings in both X and Y axes. A total of 50 pretreatment lateral cephalograms were selected from patients who reported for orthodontic treatment. The digital images of each cephalogram were imported directly into Dolphin software for onscreen digi-talization, while for manual tracing, images were printed using a compatible X-ray printer. After the images were standardized, and 10 commonly used soft tissue landmarks were plotted on each cephalogram by six different professional observers, the values obtained were plotted in X and Y axes. Intraclass correlation coefficient was used to determine the intrarater reliability for repeated landmark plotting obtained by both the methods. The evaluation for reliability of soft tissue landmark plottings in both manual and digital methods after subjecting it to interclass correlation showed a good reliability, which was nearing complete homogeneity in both X and Y axes, except for Y axis of throat point in manual plotting, which showed moderate reliability as a cephalometric variable. Intraclass correlation of soft tissue nasion had a moderate reliability along X axis. Soft tissue pogonion shows moderate reliability in Y axis. Throat point exhibited moderate reliability in X axis. The interclass correlation in X and Y axes shows high reliability in both hard tissue and soft tissue except for throat point in Y axis, when plotted manually. The intraclass correlation is more consistent and highly reliable for soft tissue landmarks and the hard tissue landmark identification is also consistent. The results obtained for manual and digital methods were almost similar, but the digital landmark plotting has an added advantage in archiving, retrieval, transmission, and can be enhanced during plotting of lateral cephalograms. Hence, the digital method of landmark plotting could be preferred for both daily use and

  6. Moving Toward Integrating Gene Expression Profiling into High-throughput Testing:A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

    Science.gov (United States)

    Microarray profiling of chemical-induced effects is being increasingly used in medium and high-throughput formats. In this study, we describe computational methods to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), ...

  7. Box, Line, and Midgap Plots: Effects of Display Characteristics on the Accuracy and Bias of Estimates of Whisker Length.

    Science.gov (United States)

    Stock, William A.; Behrens, John T.

    1991-01-01

    The accuracy and bias of estimates of whisker length based on box, line, and midgap plots were examined. For each type of graph, 20 different undergraduates (n=60) viewed 48 single-plot graphs. Whisker-length estimates for box and line plots were more accurate and less biased than those for midgap plots. (TJH)

  8. Plot intensity and cycle-length effects on growth and removals estimates from forest inventories

    Science.gov (United States)

    Paul C. Van Deusen; Francis A. Roesch

    2015-01-01

    Continuous forest inventory planners can allocate the budget to more plots per acre or a shorter remeasurement cycle. A higher plot intensity benefits small area estimation and allows for more precision in current status estimates. Shorter cycles may provide better estimates of growth, removals and mortality. On a fixed budget, the planner can't have both greater...

  9. 9 CFR 108.2 - Plot plans, blueprints, and legends required.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Plot plans, blueprints, and legends... REQUIREMENTS FOR LICENSED ESTABLISHMENTS § 108.2 Plot plans, blueprints, and legends required. Each applicant... area, blueprints for each building used in the preparation of biological products and legends...

  10. 9 CFR 108.6 - Revision of plot plans, blueprints, and legends.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Revision of plot plans, blueprints... FACILITY REQUIREMENTS FOR LICENSED ESTABLISHMENTS § 108.6 Revision of plot plans, blueprints, and legends..., blueprints, or legends and submit to Animal and Plant Health Inspection Service for review and filing when...

  11. Forest Plots in Excel: Moving beyond a Clump of Trees to a Forest of Visual Information

    Science.gov (United States)

    Derzon, James H.; Alford, Aaron A.

    2013-01-01

    Forest plots provide an effective means of presenting a wealth of information in a single graphic. Whether used to illustrate multiple results in a single study or the cumulative knowledge of an entire field, forest plots have become an accepted and generally understood way of presenting many estimates simultaneously. This article explores…

  12. Using contour plots in elecgroproduction to examine regions in {epsilon}, Q{sup 2}, W space

    Energy Technology Data Exchange (ETDEWEB)

    Funsten, H. [College of William and Mary, Williamsburg, VA (United States)

    1994-04-01

    In determining incident CEBAF beam energies for CLAS electroproduction experiments that separate the longitudinal and transverse cross section components, contour plots of {epsilon} defined over a 2 dimensional Q{sup 2}, W space can be useful. This note describes an approximate method of constructing such plots.

  13. Determination of the Runoff and Suspended Sediment from Two Different Slope Length Using Field Plots

    Directory of Open Access Journals (Sweden)

    Hüseyin Şensoy

    2013-11-01

    Full Text Available In this study, the effect of slope length on runoff and suspended sediment yield has been investigated by using plots on uniform slopes under natural rainfall conditions. From September 2007 to September 2009, during two year-period, measurements were done in Dallıca village experimental area in Bartın province. In this study, six field plots with a width of 1.87 m were used. Three of them were 5.5 m long (short plots and remaining three were 11.05 m long (long plots. Plots were located on bare soil surface that has no conservative vegetation. During the period of experimentation, a total of 158 rainy days were registered and average annual rainfall amount was 1194.8 mm. Average annual runoff per square meter was 270.81 mm, and 311.27 mm in long and short plots, respectively. Average annual suspended sediment was 809.68 g m-2, and 766.53 g m-2 from long and short plots, respectively. While statistically significant differences were found in runoff amount from plots with different lengths, there were no statistically significant differences in terms of the amount of eroded sediment.

  14. The status of accurately locating forest inventory and analysis plots using the Global Positioning System

    Science.gov (United States)

    Michael Hoppus; Andrew Lister

    2007-01-01

    Historically, field crews used Global Positioning System (GPS) coordinates to establish and relocate plots, as well as document their general location. During the past 5 years, the increase in Geographic Information System (GIS) capabilities and in customer requests to use the spatial relationships between Forest Inventory and Analysis (FIA) plot data and other GIS...

  15. Follow-up Designs to Resolve Confounding in Split-Plot Experiments

    DEFF Research Database (Denmark)

    Almimi, Ashraf A.; Kulahci, Murat; Montgomery, Douglas C.

    2008-01-01

    Split-plot designs are effective in industry due to time and/or cost constraints, restriction on randomization of the treatment combinations of the hard-to-change factors, and different sizes of experimental units. Some of the results of fractional factorial split-plot experiments can be ambiguou...

  16. The Power of Refutational Text: Changing Intuitions about the Interpretation of Box Plots

    Science.gov (United States)

    Lem, Stephanie; Onghena, Patrick; Verschaffel, Lieven; Van Dooren, Wim

    2017-01-01

    Graphicacy is an important skill in today's society; however, the interpretation of graphs proofs to be more difficult than it might seem. In this study, we focus on one specific misinterpretation, the area misinterpretation of box plots, which is caused by incorrect heuristic processing of salient features of the box plot. In this study, we tried…

  17. Combining Multiple External Representations and Refutational Text: An Intervention on Learning to Interpret Box Plots

    Science.gov (United States)

    Lem, Stephanie; Kempen, Goya; Ceulemans, Eva; Onghena, Patrick; Verschaffel, Lieven; Van Dooren, Wim

    2015-01-01

    Box plots are frequently misinterpreted and educational attempts to correct these misinterpretations have not been successful. In this study, we used two instructional techniques that seemed powerful to change the misinterpretation of the area of the box in box plots, both separately and in combination, leading to three experimental conditions,…

  18. Governing in the space of the "Seam" : Airport security after the liquid bomb plot

    NARCIS (Netherlands)

    Hoijtink, M.

    This paper provides a detailed study of the liquid bomb plot from 2006, focusing on the ways in which the plot was constituted as “an event unlike others” (Adey, Anderson, and Lobo Guerrero 2011, 340). Engaging with a critical body of scholarship that examines how events are assembled and governed

  19. Dalitz Plot analysis for η → π+π-π0 at KLOE

    Directory of Open Access Journals (Sweden)

    Balkeståhl L. Caldeira

    2014-03-01

    Full Text Available We present the status of an ongoing analysis of the η → π+π−π0 Dalitz plot, as well as preliminary results for the Dalitz plot parameters. The analysis is based on data taken at the DAΦNE φ-factory with the KLOE detector.

  20. Amplitude analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot

    NARCIS (Netherlands)

    Ablikim, M.; Achasov, M. N.; Ai, X. C.; Albayrak, O.; Albrecht, M.; Ambrose, D. J.; An, F. F.; An, Q.; Bai, J. Z.; Ferroli, R. Baldini; Ban, Y.; Bennett, J. V.; Bertani, M.; Bian, J. M.; Boger, E.; Bondarenko, O.; Boyko, I.; Braun, S.; Briere, R. A.; Cai, H.; Cai, X.; Cakir, O.; Calcaterra, A.; Cao, G. F.; Cetin, S. A.; Chang, J. F.; Chelkov, G.; Chen, G.; Chen, H. S.; Chen, J. C.; Chen, M. L.; Chen, S. J.; Chen, X.; Chen, X. R.; Chen, Y. B.; Cheng, H. P.; Chu, X. K.; Chu, Y. P.; Cronin-Hennessy, D.; Dai, H. L.; Dai, J. P.; Dedovich, D.; Deng, Z. Y.; Denig, A.; Denysenko, I.; Destefanis, M.; Ding, W. M.; Ding, Y.; Dong, C.; Dong, J.; Dong, L. Y.; Dong, M. Y.; Du, S. X.; Fan, J. Z.; Fang, J.; Fang, S. S.; Fang, Y.; Fava, L.; Feng, C. Q.; Fu, C. D.; Fuks, O.; Gao, Q.; Gao, Y.; Geng, C.; Goetzen, K.; Gong, W. X.; Gradl, W.; Greco, M.; Gu, M. H.; Gu, Y. T.; Guan, Y. H.; Guo, A. Q.; Guo, L. B.; Guo, T.; Guo, Y. P.; Han, Y. L.; Harris, F. A.; He, K. L.; He, M.; He, Z. Y.; Held, T.; Heng, Y. K.; Hou, Z. L.; Hu, C.; Hu, H. M.; Hu, J. F.; Hu, T.; Huang, G. M.; Huang, G. S.; Huang, H. P.; Huang, J. S.; Huang, L.; Huang, X. T.; Huang, Y.; Hussain, T.; Ji, C. S.; Ji, Q.; Ji, Q. P.; Ji, X. B.; Ji, X. L.; Jiang, L. L.; Jiang, L. W.; Jiang, X. S.; Jiao, J. B.; Jiao, Z.; Jin, D. P.; Jin, S.; Johansson, T.; Kalantar-Nayestanaki, N.; Kang, X. L.; Kang, X. S.; Kavatsyuk, M.; Kloss, B.; Kopf, B.; Kornicer, M.; Kuehn, W.; Kupsc, A.; Lai, W.; Lange, J. S.; Lara, M.; Larin, P.; Leyhe, M.; Li, C. H.; Li, Cheng; Li, Cui; Li, D.; Li, D. M.; Li, F.; Li, G.; Li, H. B.; Li, J. C.; Li, K.; Li, K.; Li, Lei; Li, P. R.; Li, Q. J.; Li, T.; Li, W. D.; Li, W. G.; Li, X. L.; Li, X. N.; Li, X. Q.; Li, Z. B.; Liang, H.; Liang, Y. F.; Liang, Y. T.; Lin, D. X.; Liu, B. J.; Liu, C. L.; Liu, C. X.; Liu, F. H.; Liu, Fang; Liu, Feng; Liu, H. B.; Liu, H. H.; Liu, H. M.; Liu, J.; Liu, J. P.; Liu, K.; Liu, K. Y.; Liu, P. L.; Liu, Q.; Liu, S. B.; Liu, X.; Liu, Y. B.; Liu, Z. A.; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H.; Lou, X. C.; Lu, G. R.; Lu, H. J.; Lu, H. L.; Lu, J. G.; Lu, X. R.; Lu, Y.; Lu, Y. P.; Luo, C. L.; Luo, M. X.; Luo, T.; Luo, X. L.; Lv, M.; Ma, F. C.; Ma, H. L.; Ma, Q. M.; Ma, S.; Ma, T.; Ma, X. Y.; Maas, F. E.; Maggiora, M.; Malik, Q. A.; Mao, Y. J.; Mao, Z. P.; Messchendorp, J. G.; Min, J.; Min, T. J.; Mitchell, R. E.; Mo, X. H.; Mo, Y. J.; Moeini, H.; Morales, C. Morales; Moriya, K.; Muchnoi, N. Yu.; Muramatsu, H.; Nefedov, Y.; Nikolaev, I. B.; Ning, Z.; Nisar, S.; Niu, X. Y.; Olsen, S. L.; Ouyang, Q.; Pacetti, S.; Pelizaeus, M.; Peng, H. P.; Peters, K.; Ping, J. L.; Ping, R. G.; Poling, R.; Qin, N.; Qi, M.; Qian, S.; Qiao, C. F.; Qin, L. Q.; Qin, X. S.; Qin, Y.; Qin, Z. H.; Qiu, J. F.; Rashid, K. H.; Redmer, C. F.; Ripka, M.; Rong, G.; Ruan, X. D.; Sarantsev, A.; Schoenning, K.; Schumann, S.; Shan, W.; Shao, M.; Shen, C. P.; Shen, X. Y.; Sheng, H. Y.; Shepherd, M. R.; Song, W. M.; Song, X. Y.; Spataro, S.; Spruck, B.; Sun, G. X.; Sun, J. F.; Sun, S. S.; Sun, Y. J.; Sun, Y. Z.; Sun, Z. J.; Sun, Z. T.; Tang, C. J.; Tang, X.; Tapan, I.; Thorndike, E. H.; Toth, D.; Ullrich, M.; Uman, I.; Varner, G. S.; Wang, B.; Wang, D.; Wang, D. Y.; Wang, K.; Wang, L. L.; Wang, L. S.; Wang, M.; Wang, P.; Wang, P. L.; Wang, Q. J.; Wang, S. G.; Wang, W.; Wang, X. F.; Wang, Y. D.; Wang, Y. F.; Wang, Y. Q.; Wang, Z.; Wang, Z. G.; Wang, Z. H.; Wang, Z. Y.; Wei, D. H.; Wei, J. B.; Weidenkaff, P.; Wen, S. P.; Werner, M.; Wiedner, U.; Wolke, M.; Wu, L. H.; Wu, N.; Wu, Z.; Xia, L. G.; Xia, Y.; Xiao, D.; Xiao, Z. J.; Xie, Y. G.; Xiu, Q. L.; Xu, G. F.; Xu, L.; Xu, Q. J.; Xu, Q. N.; Xu, X. P.; Xue, Z.; Yan, L.; Yan, W. B.; Yan, W. C.; Yan, Y. H.; Yang, H. X.; Yang, L.; Yang, Y.; Yang, Y. X.; Ye, H.; Ye, M.; Ye, M. H.; Yu, B. X.; Yu, C. X.; Yu, H. W.; Yu, J. S.; Yu, S. P.; Yuan, C. Z.; Yuan, W. L.; Yuan, Y.; Zafar, A. A.; Zallo, A.; Zang, S. L.; Zeng, Y.; Zhang, B. X.; Zhang, B. Y.; Zhang, C.; Zhang, C. B.; Zhang, C. C.; Zhang, D. H.; Zhang, H. H.; Zhang, H. Y.; Zhang, J. J.; Zhang, J. Q.; Zhang, J. W.; Zhang, J. Y.; Zhang, J. Z.; Zhang, S. H.; Zhang, X. J.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Z. H.; Zhang, Z. P.; Zhang, Z. Y.; Zhao, G.; Zhao, J. W.; Zhao, Lei; Zhao, Ling; Zhao, M. G.; Zhao, Q.; Zhao, Q. W.; Zhao, S. J.; Zhao, T. C.; Zhao, X. H.; Zhao, Y. B.; Zhao, Z. G.; Zhemchugov, A.; Zheng, B.; Zheng, J. P.; Zheng, Y. H.; Zhong, B.; Zhou, L.; Zhou, Li; Zhou, X.; Zhou, X. K.; Zhou, X. R.; Zhou, X. Y.; Zhu, K.; Zhu, K. J.; Zhu, X. L.; Zhu, Y. C.; Zhu, Y. S.; Zhu, Z. A.; Zhuang, J.; Zou, B. S.; Zou, J. H.

    2014-01-01

    We perform an analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot using a data set of 2.92 fb(-1) of e(+) e(-) collisions at the (3770) mass accumulated by the BESIII experiment, in which 166694 candidate events are selected with a background of 15.1%. The Dalitz plot is found to be well

  1. In loco parentis: The adoption plot in Dutch-language colonial ...

    African Journals Online (AJOL)

    The enduring relevance of the adoption plot is not to be underestimated. We still tend to conceive of Third World children as essentially parentless and as such, up for adoption by First World citizens, as the imagery of international relief demonstrates. Keywords: postcolonialism, children's literature, adoption plot, childhood

  2. The importance of Ljubljana’s plot gardening for individuals, the environment and the city

    Directory of Open Access Journals (Sweden)

    Karmen Bukvič

    2010-01-01

    Full Text Available This article examines the importance of Ljubljana’s plot gardening in relation to three aspects: social, ecological and spatial. Plot gardening in a city, as a common urban practice, is comprised of several aspects, not only food supply, as is stressed in this text. As an informal social activity, it satisfies many individual needs and is related to the quality of life and living environment. It is also important when considering spatial values and preferences because in the process of studying plot gardening as a social phenomenon the cultural specifics and social importance of this activity for Ljubljana residents is being identified. Thus, with favourable conditions and management as well as monitoring of the activity, plot gardening is positive in numerous regards, not only for the plot users but also for the city and the environment as well because the green city system and a positive city image are important. Disagreements that arose due to issues of cleaning up plot gardens in Ljubljana required a suitable solution to the problems of plot gardening. Considering the facts and in order to prevent the problems that can arise from this activity, the importance of and justification for plot gardening is stressed, particularly concentrating on the advantages of the practice.

  3. Polygonal plot method for estimating the canopy-spread cover of ...

    African Journals Online (AJOL)

    An optical method for measuring canopy-spread cover of shrubs is described by means of an illustrated example. Boundaries of plots are hypothetical lines joining the centres of wholly visible shrubs or groups of shrubs surrounding the observation point. Plots are subdivided into triangular subplots to allow calculation of ...

  4. A standardized data structure for describing and exchanging data from remeasured growth and yield plots

    Science.gov (United States)

    Michael D. Sweet; John C. Byrne

    1990-01-01

    Proposes standard data definitions and format to facilitate the sharing of growth and yield permanent plot data for the development, testing, and improvement of tree or stand growth models. The data structure presented provides standards for documenting sampling design, plot location and summary descriptors, measurement dates, treatments, site attributes, and...

  5. SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes

    DEFF Research Database (Denmark)

    Sidiropoulos, Nikos; Sohi, Sina Hadi; Pedersen, Thomas Lin

    2017-01-01

    the representation of data sets with differing sample size we have developed a new type of plot overcoming limitations of current standard visualization charts. SinaPlot is inspired by the strip chart and the violin plot and operates by letting the normalized density of points restrict the jitter along the x......-axis. The plot displays the same contour as a violin plot but resembles a simple strip chart for a small number of data points. By normalizing jitter over all classes the plot provides a fair representation for comparison between classes with a varying number of samples. In this way, the plot conveys information...

  6. Linear scaling relationships and volcano plots in homogeneous catalysis - revisiting the Suzuki reaction.

    Science.gov (United States)

    Busch, Michael; Wodrich, Matthew D; Corminboeuf, Clémence

    2015-12-01

    Linear free energy scaling relationships and volcano plots are common tools used to identify potential heterogeneous catalysts for myriad applications. Despite the striking simplicity and predictive power of volcano plots, they remain unknown in homogeneous catalysis. Here, we construct volcano plots to analyze a prototypical reaction from homogeneous catalysis, the Suzuki cross-coupling of olefins. Volcano plots succeed both in discriminating amongst different catalysts and reproducing experimentally known trends, which serves as validation of the model for this proof-of-principle example. These findings indicate that the combination of linear scaling relationships and volcano plots could serve as a valuable methodology for identifying homogeneous catalysts possessing a desired activity through a priori computational screening.

  7. PETRO.CALC.PLOT, Microsoft Excel macros to aid petrologic interpretation

    Science.gov (United States)

    Sidder, Gary B.

    1994-07-01

    PETRO.CALC.PLOT is a package of macros which normalizes whole-rock oxide data to 100%, calculates the cation percentages and molecular proportions used for normative mineral calculations, computes the apices for ternary diagrams, determines sums and ratios of specific elements of petrologic interest, and plots 33 X-Y graphs and five ternary diagrams. PETRO.CALC.PLOT also may be used to create other diagrams as desired by the user. The macros run in Microsoft Excel 3.0 and 4.0 for Macintosh computers and in Microsoft Excel 3.0 and 4.0 for Windows. Macros provided in PETRO.CALC.PLOT minimize repetition and time required to recalculate and plot whole-rock oxide data for petrologic analysis.

  8. Master plot analysis of microcracking in graphite/epoxy and graphite/PEEK laminates

    Science.gov (United States)

    Nairn, John A.; Hu, Shoufeng; Bark, Jong Song

    1993-01-01

    We used a variational stress analysis and an energy release rate failure criterion to construct a master plot analysis of matrix microcracking. In the master plot, the results for all laminates of a single material are predicted to fall on a single line whose slope gives the microcracking toughness of the material. Experimental results from 18 different layups of AS4/3501-6 laminates show that the master plot analysis can explain all observations. In particular, it can explain the differences between microcracking of central 90 deg plies and of free-surface 90 deg plies. Experimental results from two different AS4/PEEK laminates tested at different temperatures can be explained by a modified master plot that accounts for changes in the residual thermal stresses. Finally, we constructed similar master plot analyses for previous literature microcracking models. All microcracking theories that ignore the thickness dependence of the stresses gave poor results.

  9. Visual coherence for large-scale line-plot visualizations

    KAUST Repository

    Muigg, Philipp

    2011-06-01

    Displaying a large number of lines within a limited amount of screen space is a task that is common to many different classes of visualization techniques such as time-series visualizations, parallel coordinates, link-node diagrams, and phase-space diagrams. This paper addresses the challenging problems of cluttering and overdraw inherent to such visualizations. We generate a 2x2 tensor field during line rasterization that encodes the distribution of line orientations through each image pixel. Anisotropic diffusion of a noise texture is then used to generate a dense, coherent visualization of line orientation. In order to represent features of different scales, we employ a multi-resolution representation of the tensor field. The resulting technique can easily be applied to a wide variety of line-based visualizations. We demonstrate this for parallel coordinates, a time-series visualization, and a phase-space diagram. Furthermore, we demonstrate how to integrate a focus+context approach by incorporating a second tensor field. Our approach achieves interactive rendering performance for large data sets containing millions of data items, due to its image-based nature and ease of implementation on GPUs. Simulation results from computational fluid dynamics are used to evaluate the performance and usefulness of the proposed method. © 2011 The Author(s).

  10. Plot - level stem volume estimation and tree species discrimination with CASI remote sensing

    Energy Technology Data Exchange (ETDEWEB)

    Holmgren, Johan; Wallerman, J.; Olsson, Haakan

    1999-10-01

    Spectral data from the Compact Airborne Spectrographic Imager (CASI), with four bands (460-495 nm, 550-580 nm, 660-682 nm, 740-762 nm) acquired from a forest test area (Lat. 60 deg 00` N, Long. 17 deg 18` E), the Kaettboele estate near Uppsala, was analysed together with forest data from a number of field plots. Data from two flight lines, one towards and the other perpendicular to the sun was used. Information about stem volume and species composition from plots with 10-m radius, 138 in the first and 120 in the second flight line, was available. There was a positive correlation (R{sup 2} 0.51-0.53) between stem volume and the inverted radiance for all four bands on plot level. The strong correlation between stem volume and a shadow density measure indicates that shadows explain much of the correlation. For the flight line perpendicular to the sun, the correlation was stronger for the side towards the sun compared to the side away from the sun. In the first flight line, plots with a stem volume > 120 m{sup 3}ha{sup -1} were classified according to the tree species composition (pine, spruce, deciduous trees). Groups were formed based on the classification, and the hypothesis that there was no difference in spectral radiance between these groups was tested. It was possible to separate pine dominated plots from spruce dominated plots. It was also possible to separate spruce dominated plots from spruce dominated plots with a minor portion of pine, but not pine dominated plots from pine dominated plots with a minor portion of spruce. The near-infrared band was the best band for discrimination of tree species 16 refs, 2 figs, 8 tabs

  11. Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.

    KAUST Repository

    Baumgarten, Sebastian

    2013-10-12

    Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.

  12. Data Profiling

    OpenAIRE

    Hladíková, Radka

    2010-01-01

    Title: Data Profiling Author: Radka Hladíková Department: Department of Software Engineering Supervisor: Ing. Vladimír Kyjonka Supervisor's e-mail address: Abstract: This thesis puts mind on problems with data quality and data profiling. This Work analyses and summarizes problems of data quality, data defects, process of data quality, data quality assessment and data profiling. The main topic is data profiling as a process of researching data available in existing...

  13. Ground ice and hydrothermal ground motions on aufeis plots of river valleys

    Directory of Open Access Journals (Sweden)

    V. R. Alekseev

    2015-01-01

    Full Text Available Localized groundwater outflow and layered freezing of them in forms of large ice clusters on the surface creates specific conditions for energy and mass exchange in the «atmosphere–soil–lithosphere» system. In winter, the soil temperature profile is essentially deformed due to heat emission by the aufeis layer of water at its freezing that forms a specific thermocline layer. Deformation of the temperature profile, gradually decreasing, moves down the cross-section and disappearing at the interface between frozen and thawed rocks. Magnitude and number of the temperature deviations from a «normal» state depends on the heat storage of the aufeis-forming waters and on the number of outflows at a given point. The thermocline formation changes conditions of freezing for underlying ground layers together with mechanism of ice saturation of them, and that results in formation of two-layer ice-ground complexes (IGC which differ drastically from cryogenic features in adjacent parts of the valley. Analysis of genetic characteristics and relation of components of the surface and subsurface layers allowed identification of seven types of the aufeis IGC: massive-segregation, cement-basal, layered-segregation, basal-segregation, vacuum-filtration, pressureinjection, and fissure-vein. Yearly formation and destruction of aufeises and subsurface ices is accompanied by a sequence of particularly hazardous geodynamical phenomena, among which the most important are winter flooding of territories, layered freezing of water, ground heaving, thermokarst, and thermoerosion. Combination of these processes may cause a rapid (often unexpected reconfiguration of channels of both surface and subsurface runoff, abrupt uplifts and subsidences of the surface, and decompaction and «shaking-up» of seasonally thawing and seasonally freezing rocks, which may create exceptionally unfavorable conditions for construction and operation of engineering structures. Aufeis plots

  14. Integration of miRNA and mRNA expression profiles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia

    DEFF Research Database (Denmark)

    Moraes, Leonardo N; Fernandez, Geysson J; Vechetti-Júnior, Ivan J

    2017-01-01

    Cardiac cachexia (CC) is a common complication of heart failure (HF) associated with muscle wasting and poor patient prognosis. Although different mechanisms have been proposed to explain muscle wasting during CC, its pathogenesis is still not understood. Here, we described an integrative analysis...

  15. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  16. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  17. Construction of an experimental plot seeder of wheat planting and compare it by imported one

    Directory of Open Access Journals (Sweden)

    I Eskandari

    2016-09-01

    Full Text Available Introduction Researchers frequently include multiple cultivars and fertility levels in field experiments. Therefore, the experiments sowing operation must represent a considerable saving in time and labor, compared to hand sowing. Greater flexibility in experimental design and setup could be achieved by equipment that enables quick changes in the cultivar and fertilizer rates from one plot to the next. A satisfactory seed drill must distribute a given quantity of seed evenly over a predetermined length of coulter row, the coulters must be spaced at exact intervals and depth of sowing must be uniform. In a self-propelled type of plot seeder, no coulter should run in a wheel track as the compaction of the soil can cause observable differences in vigor between plants in such a row and those in un-compacted rows. The machine should sow in succession from a try in which a series of seed pocket separated clearly and must be put into distributer funnel by an assistant operator. The length of gap being varied according to the nature and purpose of the plot. The objectives of this experiment were 1- to design and construct a local self-propelled plot seeder and 2- To compare it with the imported (Wintersteiger plot seeder in cereal breeding programs. Materials and Methods A small-plot seeder was designed and constructed to meet this objective. The unit consists of the following basic components: a toolbar for pulling a set of six blade coulter, an air compressor for lifting and putting down the openers and metering transmission drive wheel, an operators chair and work rack, one belt seed distribution. A cone-celled and rotor seed distributor is used for seed distribution to the openers. The cone system is connected to the gearbox and allows for great flexibility in changing cultivars, crop species, and plot length. This is driven by the separate drive wheel. The cone-celled distributor sows all the seed of the sample in making one complete turn. The

  18. PLOT SIZE IN THE EVALUATION OF PAPAYA SEEDLINGS 'BAIXINHO DE SANTA AMÁLIA' IN TUBES

    Directory of Open Access Journals (Sweden)

    HUMBERTO FELIPE CELANTI

    Full Text Available ABSTRACT Were evaluated three characters in papaya seedlings 'Baixinho de Santa Amália' to estimate the optimum plot size and the number of replications in a completely randomized experiment, a randomized block and Latin square. The characters were seedling height, leaf number and length of roots from uniformity test with 240 seedlings. The determination of the optimum plot size was done by applying the method of Hatheway (1961. The number of seedlings per plot for seedling production is variable depending on the number of treatments and replications assumed precision, the character in question and the experimental design. Comparing designs, the plot size is greater in the Latin square, followed by a randomized block design and completely randomized, and this difference is more pronounced the lower the number of treatments and replicates used. For the same number of treatments and the same precision, the most efficient use of the experimental area is given using smaller plot, with more replications, which require less space in the nursery than larger plots with fewer replications. For experiments completely randomized and randomized blocks with five or more treatments, four replications, and precision of 15% around the mean, it is recommended to use nine seedlings per plot.

  19. visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.

    Directory of Open Access Journals (Sweden)

    Matthew Scales

    Full Text Available We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk, a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV. Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…. It also allows annotation of genes and other custom features in the plotted region(s. Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3.

  20. visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.

    Science.gov (United States)

    Scales, Matthew; Jäger, Roland; Migliorini, Gabriele; Houlston, Richard S; Henrion, Marc Y R

    2014-01-01

    We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV). Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).

  1. Monitoring soil erosion processes: The erosion plots at the Geocampus, University of Trier

    Science.gov (United States)

    Lassu, Tamas; Rodrigo Comino, Jesús; Seeger, Manuel; Ries, Johannes B.

    2015-04-01

    Long term monitoring on erosion plots is one of the most reliable methods to quantify the actual soil erosion rates. Although the direct extrapolation of the measured data to regional scale is problematic, due to the high spatial and temporal variability of the soil erosion processes, they provide indispensable experimental data for soil erosion model conception, calibration and validation. At the University Trier in 2013 four test plots were put into practice on colluvial loess loam soil with dimension 3 x 10 m and similar properties. They are representative for the regional conditions. The plots are located 265 m above sea level and they have a general inclination of 12-13°. In 2012 on two plots subsoiling was applied in order to reduce the compaction caused by the heavy machinery used during the construction of the plots. The two other plots were not disturbed and no melioration measures were applied. In the first year of the experiment after the preparation of the parcels, they were left for a spontaneous revegetation. Total runoff and sediment removal data was collected weekly, additionally a meteorological station provides continuously data about climate conditions. The data evaluation of the first year 2013/14 revealed big difference between the single plots. Total runoff was measured between 0 and 4.76 l m-2 (m=0.8 l m-2), total eroded sediment between 0 and 3.86 g m-2 (m=0.21 g m-2) weekly. The higher rates were recorded on the plots without subsoiling. After the first year, total eroded soil was calculated. The results were between 0.03 and 0.17 t ha-1a-1. With the help of the erosion plots at the University of Trier, the impact of the different soil use management concepts and cultivation techniques on runoff and erosion dynamics can be evaluated, additionally reliable data for modeling soil erosion can be generated as well.

  2. Variability of snow depth at the plot scale: implications for mean depth estimation and sampling strategies

    Directory of Open Access Journals (Sweden)

    J. I. López-Moreno

    2011-08-01

    Full Text Available Snow depth variability over small distances can affect the representativeness of depth samples taken at the local scale, which are often used to assess the spatial distribution of snow at regional and basin scales. To assess spatial variability at the plot scale, intensive snow depth sampling was conducted during January and April 2009 in 15 plots in the Rio Ésera Valley, central Spanish Pyrenees Mountains. Each plot (10 × 10 m; 100 m2 was subdivided into a grid of 1 m2 squares; sampling at the corners of each square yielded a set of 121 data points that provided an accurate measure of snow depth in the plot (considered as ground truth. The spatial variability of snow depth was then assessed using sampling locations randomly selected within each plot. The plots were highly variable, with coefficients of variation up to 0.25. This indicates that to improve the representativeness of snow depth sampling in a given plot the snow depth measurements should be increased in number and averaged when spatial heterogeneity is substantial.

    Snow depth distributions were simulated at the same plot scale under varying levels of standard deviation and spatial autocorrelation, to enable the effect of each factor on snowpack representativeness to be established. The results showed that the snow depth estimation error increased markedly as the standard deviation increased. The results indicated that in general at least five snow depth measurements should be taken in each plot to ensure that the estimation error is <10 %; this applied even under highly heterogeneous conditions. In terms of the spatial configuration of the measurements, the sampling strategy did not impact on the snow depth estimate under lack of spatial autocorrelation. However, with a high spatial autocorrelation a smaller error was obtained when the distance between measurements was greater.

  3. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies

    Directory of Open Access Journals (Sweden)

    Specht Günther

    2010-03-01

    Full Text Available Abstract Background Mitochondrial DNA (mtDNA is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. Description eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle, security aspects (by using database technology and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs. It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. Conclusions The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

  4. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies.

    Science.gov (United States)

    Weissensteiner, Hansi; Schönherr, Sebastian; Specht, Günther; Kronenberg, Florian; Brandstätter, Anita

    2010-03-09

    Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle), security aspects (by using database technology) and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs). It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

  5. Micrometry combined with profile mapping for the absolute measurement of Integrated Column Density (ICD) and for accurate X-ray mass attenuation coefficients using XERT

    Energy Technology Data Exchange (ETDEWEB)

    Islam, M. Tauhidul; Rae, Nicholas A.; Glover, Jack L.; Barnea, Zwi [School of Physics, University of Melbourne, Victoria 3010 (Australia); Chantler, Christopher T., E-mail: chantler@physics.unimelb.edu.a [School of Physics, University of Melbourne, Victoria 3010 (Australia)

    2010-07-21

    Absolute values of the column densities [{rho}t]{sub c} of four gold foils were measured using micrometry combined with the 2D X-ray attenuation profile. The absolute calibration of [{rho}t]{sub c} was made with a reference foil and the [{rho}t]{sub c} of other foils were determined following the thickness transfer method. By this method, we obtain absolute calibration to 0.1% or better which was not possible using only the X-ray map of a single foil over its central region.

  6. On the unique reconstruction of a signal from its unthresholded recurrence plot

    Science.gov (United States)

    Sipers, Aloys; Borm, Paul; Peeters, Ralf

    2011-06-01

    We address the information content of unthresholded recurrence plots, generated by the time-delay embedding method from scalar signals admitting a Fourier series representation (including periodic and sampled signals). This is important for making valid inferences from unthresholded recurrence plots. A graph theoretic framework is developed to give a complete analysis of the impact of the choice of time-delay and embedding dimension on information content. A distance measure for unthresholded recurrence plots is introduced to approach signal reconstruction and approximation by minimization, robust to inaccuracies and noise. Examples and an application from EEG analysis clarify the theoretical results and demonstrate their practical potential.

  7. Teaching: the role of active manipulation of three-dimensional scatter plots in understanding the concept of confounding

    Science.gov (United States)

    Busstra, Cora MC; Hartog, Rob; van 't Veer, Pieter

    2005-01-01

    In teaching epidemiology, confounding is a difficult topic. The authors designed active learning objects (LO) based on manipulable three-dimensional (3D) plots to facilitate understanding of confounding. The 3D LOs help illustrate of how confounding can occur, how it generates bias and how to adjust for it. For the development of the LOs, guidelines were formulated based on epidemiology and theories of instructional design. These included integrating the conceptual and empirical aspects: the causal relationships believed to be operating in the study population (conceptual aspect) and data-oriented associations (empirical aspect). Other guidelines based on theories of instructional design included: actively engage the students, use visual methods when possible, and motivate the students about the importance of the topic. Students gave the method strong positive evaluations. Experts in epidemiology agreed that the 3D LOs apply generally accepted scientific views on confounding. Based on their experiences, the authors think that the 3D plots can be useful addition in the teaching of confounding. The article includes links and a downloadable file that provide a demonstration of the 3D LO-based teaching materials. PMID:15953393

  8. Using UAV data for soil surface change detection at a loess field plot

    Science.gov (United States)

    Eltner, Anette; Baumgart, Philipp

    2014-05-01

    Application of unmanned aerial vehicles (UAV) denotes an increasing interest in geosciences due to major developments within the last years. Today, UAV are economical, reliable and flexible in usage. They provide a non-invasive method to measure the soil surface and its changes - e.g. due to erosion - with high resolution. Advances in digital photogrammetry and computer vision allow for fast and dense digital surface reconstruction from overlapping images. The study site is located in the Saxonian loess (Germany). The area is fragile due to erodible soils and intense agricultural utilisation. Hence, detectable soil surface changes are expected. The size of the field plot is 20 x 30 meters and the period of investigation lasts from October 2012 till July 2013 at which four surveys were performed. The UAV deployed in this study is equipped with a compact camera which is attached to an active stabilising camera mount. In addition, the micro drone integrates GPS and IMU that enables autonomous surveys with programmed flight patterns. About 100 photos are needed to cover the study site at a minimal flying height of eight metres and 65%/80% image overlap. For multi-temporal comparison a stable local reference system is established. Total station control of the signalised ground control points confirms two mm accuracy for the study period. To estimate the accuracy of the digital surface models (DSM) derived from the UAV images a comparison to DSM from terrestrial laser scanning (TLS) is conducted. The standard deviation of differences amounts five millimetres. To analyse surface changes methods from image processing are applied to the DSM. Erosion rills could be extracted for quantitative and qualitative consideration. Furthermore, volumetric changes are measured. First results indicate levelling processes during the winter season and reveal rill and inter-rill erosion during spring and summer season.

  9. Field Plot and Observation Points for Colorado National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This point file displays the 525 field plot and observation locations visited in 2003 and 2004 as part of the vegetation mapping project for Colorado National...

  10. Ionospheric Values (Daily Work Sheets), F-Plots, Tabulations, Booklets, Catalogs, and Log Books

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These ionospheric data consist of scaling notes, equipment usage logs, and ionospheric values in the form of daily work sheets, F-Plots, tabulations, and booklets....

  11. Field Plot Points for Bluestone National Scenic River Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This feature class contains point features which represent locations of vegetation sampling plots in Bluestone National Scenic River. Location coordinates for most...

  12. Field Plot Points for George Washington Birthplace National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile shows the location of vegetation sampling plots used for vegetation classification and mapping at George Washington Birthplace National Monument.

  13. Field Plot Points for Booker T. Washington National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile shows the location of vegetation sampling plots used for vegetation classification and mapping at Booker T. Washington National Monument

  14. Field Plot Points for Appomattox Court House National Historical Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile shows the location of vegetation sampling plots used for vegetation classification and mapping at Appomottox Court House National Historical Park

  15. Field Plot Points for Fredericksburg and Spotsylvania National Military Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile shows the location of vegetation sampling plots used for vegetation classification and mapping at Fredericksburg and Spotsylvania National Military Park

  16. Volcano plots in analyzing differential expressions with mRNA microarrays.

    Science.gov (United States)

    Li, Wentian

    2012-12-01

    A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.

  17. Technical note: A significance test for data-sparse zones in scatter plots

    Science.gov (United States)

    Vetrova, V. V.; Bardsley, W. E.

    2012-04-01

    Data-sparse zones in scatter plots of hydrological variables can be of interest in various contexts. For example, a well-defined data-sparse zone may indicate inhibition of one variable by another. It is of interest therefore to determine whether data-sparse regions in scatter plots are of sufficient extent to be beyond random chance. We consider the specific situation of data-sparse regions defined by a linear internal boundary within a scatter plot defined over a rectangular region. An Excel VBA macro is provided for carrying out a randomisation-based significance test of the data-sparse region, taking into account both the within-region number of data points and the extent of the region. Example applications are given with respect to a rainfall time series from Israel and also to validation scatter plots from a seasonal forecasting model for lake inflows in New Zealand.

  18. Quilt plots: a simple tool for the visualisation of large epidemiological data.

    Directory of Open Access Journals (Sweden)

    Handan Wand

    Full Text Available Graphical representation of data is one of the most easily comprehended forms of explanation. The current study describes a simple visualization tool which may allow greater understanding of medical and epidemiological data.We propose a simple use of an existing tool for visualization of data, known as a ''quilt plot'' (also defined as "heat maps", that provides an alternative to presenting large volumes of data as frequency tables [corrected]. Data from the Australian Needle and Syringe Program survey are used to illustrate "quilt plots".Visualization of large volumes of data using "quilt plots" enhances interpretation of medical and epidemiological data. Such intuitive presentations are particularly useful for the rapid assessment of problems in the data which cannot be readily identified by manual review. We recommend that, where possible, "quilt plots" be used along with traditional quantitative assessments of the data as an explanatory data analysis tool.

  19. Census of permanent study plots for marine birds at Nunivak Island in 1982

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — In 1978, cliff-nesting seabirds at Nunivak Island were surveyed, and five permanent study plots were delineated for future evaluations of population changes (Ritchie...

  20. Field Plot Points for Guilford Courthouse National Military Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This is a vector file showing the location of NatureServe plots at Guilford Courthouse National Military Park. The coordinates of this dataset were collected using a...

  1. Optimal plot size in the evaluation of papaya scions: proposal and comparison of methods

    Directory of Open Access Journals (Sweden)

    Humberto Felipe Celanti

    Full Text Available ABSTRACT Evaluating the quality of scions is extremely important and it can be done by characteristics of shoots and roots. This experiment evaluated height of the aerial part, stem diameter, number of leaves, petiole length and length of roots of papaya seedlings. Analyses were performed from a blank trial with 240 seedlings of "Golden Pecíolo Curto". The determination of the optimum plot size was done by applying the methods of maximum curvature, maximum curvature of coefficient of variation and a new proposed method, which incorporates the bootstrap resampling simulation to the maximum curvature method. According to the results obtained, five is the optimal number of seedlings of papaya "Golden Pecíolo Curto" per plot. The proposed method of bootstrap simulation with replacement provides optimal plot sizes equal or higher than the maximum curvature method and provides same plot size than maximum curvature method of the coefficient of variation.

  2. Methodical modeling of the investment value of land plots for housing development

    National Research Council Canada - National Science Library

    Kulakov Kirill; Baronin Sergey

    2017-01-01

    ... from major developers that in the context of the turbulent economy it is especially important. In this regard great scientific and practical interest is the modeling of the investment value of land plots for housing development...

  3. Behavior of QQ-plots and genomic control in studies of gene-environment interaction.

    Directory of Open Access Journals (Sweden)

    Arend Voorman

    2011-05-01

    Full Text Available Genome-wide association studies of gene-environment interaction (GxE GWAS are becoming popular. As with main effects GWAS, quantile-quantile plots (QQ-plots and Genomic Control are being used to assess and correct for population substructure. However, in G x E work these approaches can be seriously misleading, as we illustrate; QQ-plots may give strong indications of substructure when absolutely none is present. Using simulation and theory, we show how and why spurious QQ-plot inflation occurs in G x E GWAS, and how this differs from main-effects analyses. We also explain how simple adjustments to standard regression-based methods used in G x E GWAS can alleviate this problem.

  4. Pre-ABoVE: Arctic Vegetation Plots at Happy Valley, Alaska, 1994

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides environmental, soil, and vegetation data collected in July 1994 from 56 study plots at the Happy Valley research site, located along the...

  5. Pre-ABoVE: Arctic Vegetation Plots at Imnavait Creek, Alaska, 1984-1985

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides environmental, soil, and vegetation data collected during the periods of August 1984 and August-September 1985 from 84 study plots at the...

  6. Pre-ABoVE: Arctic Vegetation Plots at Toolik Lake, Alaska, 1989

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides environmental, soil, and vegetation data collected in August 1989 from 81 study plots at the Toolik Lake research site, located in the...

  7. Cedar Breaks National Monument Vegetation Mapping Project - Field Plot, Observation Points and Accuracy Assessment Points

    Data.gov (United States)

    National Park Service, Department of the Interior — This point file contains 282 point locations of field plot and observation data used by, and collected for, the vegetation mapping project for Cedar Breaks National...

  8. Field Plot Points for Sunset Crater Volcano National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This spatial dataset in ESRI Coverage format maps field releve plot locations for the vegetation classification and descriptions of the vegetation map at Sunset...

  9. Pre-ABoVE: Arctic Vegetation Plots, Willow Communities, North Slope, Alaska, 1997

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides environmental, soil, and vegetation data collected in July and August 1997 from 85 study plots in willow shrub communities located along a...

  10. Simkin et al. 2016 PNAS data on herbaceous species richness and associated plot and covariate information

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset includes the geographic location (lat/lon) for 15,136 plots, as well as the herbaceous species richness, climate, soil pH, and other variables related...

  11. Technical note: A significance test for data-sparse zones in scatter plots

    Directory of Open Access Journals (Sweden)

    V. V. Vetrova

    2012-04-01

    Full Text Available Data-sparse zones in scatter plots of hydrological variables can be of interest in various contexts. For example, a well-defined data-sparse zone may indicate inhibition of one variable by another. It is of interest therefore to determine whether data-sparse regions in scatter plots are of sufficient extent to be beyond random chance. We consider the specific situation of data-sparse regions defined by a linear internal boundary within a scatter plot defined over a rectangular region. An Excel VBA macro is provided for carrying out a randomisation-based significance test of the data-sparse region, taking into account both the within-region number of data points and the extent of the region. Example applications are given with respect to a rainfall time series from Israel and also to validation scatter plots from a seasonal forecasting model for lake inflows in New Zealand.

  12. Accuracy Assessment Plots for Chickasaw National Recreation Area Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This file represents the accuracy assessment plots used to characterize the vegetation at Chickasaw National Recreation Area for the purposes of assessing the...

  13. Field Plot Points for Devils Tower National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — Vegetation field plots at Devils Tower NM were visited, described, and documented in a digital database. The database consists of 2 parts - (1) Physical Descriptive...

  14. Field Plot Points for Washita Battlefield National Historic Site Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This metadata is for the 2005 vegetation data points (spatial database) created from the sample vegetation plots collected at Washita Battlefield National Historic...

  15. Field Plot Points for Fort Larned National Historic Site Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This metadata is for the 2005 vegetation data points (spatial database) created from the sample vegetation plots collected at Fort Larned National Historic Site.

  16. Field Plot Points for Wind Cave National Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — Vegetation field plots at Wind Cave NP were visited, described, and documented in a digital database. The database consists of 2 parts - (1) Physical Descriptive...

  17. Field Plot Points for Lyndon B. Johnson National Historical Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This metadata is for the 2005 vegetation data points (spatial database) created from the sample vegetation plots collected at Lyndon B. Johnson National Historical...

  18. shinyCircos: an R/Shiny application for interactive creation of Circos plot.

    Science.gov (United States)

    Yu, Yiming; Ouyang, Yidan; Yao, Wen

    2017-11-24

    Creation of Circos plot is one of the most efficient approaches to visualize genomic data. However, the installation and use of existing tools to make Circos plot are challenging for users lacking of coding experiences. To address this issue, we developed an R/Shiny application shinyCircos, a graphical user interface for interactive creation of Circos plot. shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community. Furthermore, various types of Circos plots could be easily generated and decorated with simple mouse-click. shinyCircos and its manual are freely available at https://github.com/venyao/shinyCircos. shinyCircos is deployed at https://yimingyu.shinyapps.io/shinycircos/ and http://shinycircos.ncpgr.cn/for online use. yaowen@henau.edu.cn, diana1983941@mail.hzau.edu.cn.

  19. Pre-ABoVE: Arctic Vegetation Plots at Barrow, Alaska, 2012

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides vegetation cover and environmental plot data collected on the Barrow Environmental Observatory (BEO), Barrow, Alaska in 2012. Forty-eight 1 x...

  20. Pre-ABoVE: Arctic Vegetation Plots, Oumalik, Alaska, 1983-1985

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides environmental, soil, and vegetation data collected between 1983 and 1985 from 87 study plots near an abandoned test oil well in Oumalik,...

  1. Field Plot Points for Buck Island Reef National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile represents all the field plots visited on Buck Island. To fully comprehend this feature class, please refer to the full "Buck Island Reef National...

  2. NOTE - Minimum number of common bean plants per plot to assess field resistance to white mold

    Directory of Open Access Journals (Sweden)

    uliana Andrade Dias

    2011-01-01

    Full Text Available This study aimed to determine the minimum number of plants per plot to assess the field resistance in common beanto white mold. Thirteen cultivars were inoculated with six isolates of Sclerotinia sclerotiorum and evaluated in a randomized blockdesign with three replications and plots consisting of 1-m rows with 15 plants. Plants were inoculated by the straw test as proposedby Petzoldt and Dickson (1996, to evaluate partial resistance in a greenhouse. Eight days after inoculation the disease severity wasevaluated on a 1-9 diagrammatic scale, where 1 = asymptomatic plants to 9 = plant death. To determine the minimum number ofplants per plot, the following methods were used: maximum curvature, segmented linear model, quadratic segmented model and therelative CV model. There were significant differences among cultivars and isolates and no significant cultivar - isolate interaction.It was observed that eight plants per plot is an adequate number to assess the reaction of common bean to white mold.

  3. Field Plot Points Modified for Valley Forge National Historical Park Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This shapefile includes the locations of vegetation classification sampling plots used to develop an association-level vegetation classification of Valley Forge...

  4. Field Plot and Observation Points for Pipe Spring National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This point feature class contains points representing field sample data (3 plots points and 4 observations points, collected August 2007 and September 2008) for the...

  5. Kaloko-Honokohau National Historical Park Vegetation Mapping Project - Field Plots, Observation and Accuracy Assessment Points

    Data.gov (United States)

    National Park Service, Department of the Interior — This metadata is for the 2008 vegetation (classification) field plots (spatial database) and 2010 accuracy assessment points (spatial database) created from the...

  6. Summary of Cackling Canada goose nesting plot data for the 1984 Yukon Delta NWR Flyway report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Forty sample plots ranging in size from 81-311 acres (total:7041 acres) were located throughout the Yukon Delta CacklingCanada Goose (CCG) nesting range in areas...

  7. Field Plot Points for Walnut Canyon National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This spatial dataset in ESRI Coverage format maps field releve plot locations for the vegetation classification and descriptions of the vegetation map at Walnut...

  8. User's manual for THPLOT, A FORTRAN 77 Computer program for time history plotting

    Science.gov (United States)

    Murray, J. E.

    1982-01-01

    A general purpose FORTRAN 77 computer program (THPLOT) for plotting time histories using Calcomp pen plotters is described. The program is designed to read a time history data file and to generate time history plots for selected time intervals and/or selected data channels. The capabilities of the program are described. The card input required to define the plotting operation is described and examples of card input and the resulting plotted output are given. The examples are followed by a description of the printed output, including both normal output and error messages. Lastly, implementation of the program is described. A complete listing of the program with reference maps produced by the CDC FTN 5.0 compiler is included.

  9. Evaluation of the improvement in sensitivity of nested frequency plots to vegetational change by summation

    Science.gov (United States)

    Smith, Stuart D.; Bunting, Stephen C.; Hironaka, M.

    1987-01-01

    At four sites in Idaho, frequency was measured separately with three different-sized plots (10 x 25, 15 x 33.5, and 20 x 50 cm) arranged in a nested configuration. These individual frequency values were added together to create a summed “frequency.” This summed value was compared to the original frequency values generated by each individual plot size in respect to its ability to detect range trend. The summation procedure consistently detected smaller changes in frequency than any individual plot size. In addition, the summed values detected a significant change in more species at each site. Summing the frequency values usually detected changes at a lower alpha level than did any single plot (0.10 vs. 0.20).

  10. Comparison of three methods for drawing line in the Rutland-Patlak plot of renography

    DEFF Research Database (Denmark)

    Jødal, Lars; Eskild-Jensen, Anni; Brøchner-Mortensen, Jens

    BACKGROUND: When individual kidney function is determined by renography, the Rutland-Patlak plot is used in the calculations. In the so-called uptake phase the plot is a straight line, but the duration of this phase may differ from patient to patient. A good method for drawing the correct line...... in the Rutland-Patlak plot should take into account that data may show unusual behaviour or be noisy. AIM: To find a method for the line-drawing that gives reliable results on all groups of data. MATERIAL AND METHODS: Data were collected from 63 consecutive renographies routinely made at the department...... of Nuclear Medicine in Aalborg. Furthermore, 10 renographies were selected where at least one kidney had a renogram with irregular behaviour or noisy data ("problematic" data). Rutland-Patlak plots were calculated, and three methods were used for line-drawing: Manual drawing on hardcopies by three...

  11. Calibration of an electronic counter and pulse height analyzer for plotting erythrocyte volume spectra.

    Science.gov (United States)

    1963-03-01

    A simple technique is presented for calibrating an electronic system used in the plotting of erythrocyte volume spectra. The calibration factors, once obtained, apparently remain applicable for some time. Precise estimates of calibration factors appe...

  12. Field Plot and Observation Points for Fossil Butte National Monument Vegetation Mapping Project

    Data.gov (United States)

    National Park Service, Department of the Interior — This point file contains 255 point locations of field plot and observation data used by, and collected for, the vegetation mapping project for Fossil Butte National...

  13. Optothermal profile of an ablation catheter with integrated microcoil for MR-thermometry during Nd:YAG laser interstitial thermal therapies of the liver—an in-vitro experimental and theoretical study.

    Science.gov (United States)

    Kardoulaki, Evdokia M; Syms, Richard R A; Young, Ian R; Choonee, Kaushal; Rea, Marc; Gedroyc, Wladyslaw M W

    2015-03-01

    Flexible microcoils integrated with ablation catheters can improve the temperature accuracy during local MR-thermometry in Nd:YAG laser interstitial thermal therapies. Here, the authors are concerned with obtaining a preliminary confirmation of the clinical utility of the modified catheter. They investigate whether the thin-film substrate and copper tracks of the printed coil inductor affect the symmetry of the thermal profile, and hence of the lesion produced. Transmission spectroscopy in the near infrared was performed to test for the attenuation at 1064 nm through the 25 μm thick Kapton substrate of the microcoil. The radial transmission profile of an infrared high-power, light emitting diode with >80% normalized power at 1064 nm was measured through a cross section of the modified applicator to assess the impact of the copper inductor on the optical profile. The measurements were performed in air, as well as with the applicator surrounded by two types of scattering media; crystals of NaCl and a layer of liver-mimicking gel phantom. A numerical model based on Huygens-Fresnel principle and finite element simulations, using a commercially available package (COMSOL Multiphysics), were employed to compare with the optical measurements. The impact of the modified optical profile on the thermal symmetry was assessed by examining the high resolution microcoil derived thermal maps from a Nd:YAG laser ablation performed on a liver-mimicking gel phantom. Less than 30% attenuation through the Kapton film was verified. Shadowing behind the copper tracks was observed in air and the measured radial irradiation correlated well with the diffraction pattern calculated numerically using the Huygens-Fresnel principle. Both optical experiments and simulations, demonstrate that shadowing is mitigated by the scattering properties of a turbid medium. The microcoil derived thermal maps at the end of a Nd:YAG laser ablation performed on a gel phantom in a 3 T scanner confirm that the

  14. Multiscale Poincar? plots for visualizing the structure of heartbeat time series

    OpenAIRE

    Henriques, Teresa S.; Mariani, Sara; Burykin, Anton; Rodrigues, Filipa; Silva, Tiago F.; Goldberger, Ary L.

    2016-01-01

    Background Poincar? delay maps are widely used in the analysis of cardiac interbeat interval (RR) dynamics. To facilitate visualization of the structure of these time series, we introduce multiscale Poincar? (MSP) plots. Methods Starting with the original RR time series, the method employs a coarse-graining procedure to create a family of time series, each of which represents the system?s dynamics in a different time scale. Next, the Poincar? plots are constructed for the original and the coa...

  15. Change of soils agrochemical properties at industrial plots polluted by fluorides

    Directory of Open Access Journals (Sweden)

    N. F. Pavlyukova

    2006-11-01

    Full Text Available The changes of some agrochemical properties of soils of model plots closed to industrial enterprises with fluoride atmospheric emissions were studied. The alkalescence of soils at the plots was found. The reduction of content of the mobile forms of phosphorus, nitrite and nitrate forms of nitrogen and humus level in soil is caused by the increasing amount of nitrogen of ammonium compounds.

  16. Homolog-focused profiling of ginsenosides based on the integration of step-wise formate anion-to-deprotonated ion transition screening and scheduled multiple reaction monitoring.

    Science.gov (United States)

    Song, Yuelin; Zhang, Na; Shi, Shepo; Li, Jun; Zhao, Yunfang; Zhang, Qian; Jiang, Yong; Tu, Pengfei

    2015-08-07

    Homolog-focused profiling is a favored option to bridge targeted metabolomics toward non-targeted metabolomics. In current study, an attempt was made for the large-scale ginsenoside-specific analysis in ginseng (G) and American ginseng (AG). When formic acid (0.1%, v/v) was introduced as the mobile phase additive, formate anion-to-deprotonated ion transitions ([M+HCOO](-)>[M-H](-)) with an optimal collision energy (-32eV) could result in satisfactory responses for ginsenosides. Therefore, a step-wise multiple reaction monitoring (MRM)-based method employing [M+HCOO](-)>[M-H](-) ion pairs was constructed to screen ginsenosides among 501-1250u (for Q1) with a step-size of 2u, and MRM also served as a survey experiment to trigger enhanced product ion scans for MS(2) spectrum acquisition on a hybrid triple quadrupole-linear ion trap mass spectrometer; then, the identification of those observed ginsenosides was achieved on the basis of the well-defined mass cracking patterns for ginsenosides; afterwards, scheduled MRM was introduced for large-scale relatively quantitative analysis of all detected ginsenosides. Finally, comparative metabolomics were performed to differentiate G, AG, and their processed products. Method validation was carried out using thirteen authentic compounds. A total of 221 ginsenosides, among which 185 ones were annotated, were observed and relatively quantitated. All crude materials were obviously classified into groups I-III. Above all, the MRM-based homolog-focused profiling of ginsenosides could be used as a reliable tool to gain an in-depth view for ginsenoside-enriched herbal products. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Expanding fatality estimates from the search plot to the entire site

    Energy Technology Data Exchange (ETDEWEB)

    Huso, Manuela; Wilson, Zac; Arnett, Ed

    2011-07-01

    Full text: Simple counts of carcasses found at wind farms do not reflect actual fatality because of detection bias. Two commonly recognized sources of bias are carcass removal by scavengers and imperfect detection of remaining carcasses by searchers. There are at least two other sources of imperfect detection: 1) the search plot does not comprise all of the fatalities associated with a turbine and 2) often only a portion of the designated area of the search plot is accessible. Ignoring the fatalities that land outside the search plots will lead to an underestimate of fatality. For carcasses landing within the limits of the search plots, adjusting fatality estimates by a simple measure of the proportion of the plot searched, without accounting for changes in carcass density throughout the plot will likely lead to overestimates of fatality. I propose a method of estimating the detection bias resulting from these two additional sources based on models of carcass density. I test these models at two sites: Locust Ridge, P A and Casselman, P A. Accurate, unbiased fatality estimates are critical to assessing curtailment and deterrent strategies and are fundamental to understanding acute and cumulative impacts of wind power on wildlife populations. Failing to properly correct for imperfect detection of carcasses will lead to biased estimates and inappropriate inference regarding fatality impacts. (Author)

  18. Runoff and soil erosion of field plots in a subtropical mountainous region of China

    Science.gov (United States)

    Fang, N. F.; Wang, L.; Shi, Z. H.

    2017-09-01

    Anthropogenic pressure coupled with strong precipitation events and a mountainous landscape have led to serious soil erosion and associated problems in the subtropical climate zone of China. This study analyzes 1576 rainfall-runoff-soil loss events at 36 experimental plots (a total of 148 plot-years of data) under a wide range of conditions in subtropical mountainous areas of China where slope farming is commonly practiced. The plots, which have standardized dimensions, represent five common types of land use and have four different slopes. Event-based analyses show that almost half of the total rainfall caused soil erosion in the study area. The dominant factor controlling the runoff coefficient is the slope gradient rather than the land use type. The maximum soil lossfor crop plots under steep tillage (35°) is 5004 t km-2 for a single event. Among the common local crops, the average soil loss values increase in the following order: buckwheat extreme events. The annual average soil loss of the 44 plots ranges from 19 to 4090 t km-2 year-1. The annual soil loss of plots of different land use types decrease in the following order: bare land (1533 t km-2 year-1) > cropland (1179 t km-2 year-1) > terraced cropland (1083 t km-2 year-1) > orchard land (1020 t km-2 year-1) > grassland (762 t km-2 year-1) > terraced orchard land (297 t km-2 year-1) > forest and grassland (281 t km-2 year-1).

  19. GPM GROUND VALIDATION ENVIRONMENT CANADA (EC) WIND PROFILER GCPEX V1

    Data.gov (United States)

    National Aeronautics and Space Administration — The GPM Ground Validation Environment Canada (EC) Wind Profiler GCPEx dataset provides post-processed consensus winds and daily quick look plots from the Vaisala...

  20. Determination of $\\eta\\to\\pi^+\\pi^-\\pi^0$ Dalitz plot slopes and asymmetries with the KLOE detector

    CERN Document Server

    Ambrosino, F; Antonelli, M; Archilli, F; Bacci, C; Beltrame, P; Bencivenni, G; Bertolucci, S; Bini, C; Bloise, C; Bocchetta, S; Bossi, F; Branchini, P; Caloi, R; Campana, P; Capon, G; Capussela, T; Ceradini, F; Cesario, F; Chi, S; Chiefari, G; Ciambrone, P; Crucianelli, F; De Lucia, E; De Santis, A; De Simone, P; De Zorzi, G; Denig, A; Di Domenico, A; Di Donato, C; Di Micco, B; Doria, A; Dreucci, M; Felici, G; Ferrari, A; Ferrer, M L; Fiore, S; Forti, C; Franzini, P; Gatti, C; Gauzzi, P; Giovannella, S; Gorini, E; Graziani, E; Kluge, W; Kulikov, V; Lacava, F; Lanfranchi, G; Lee-Franzini, J; Leone, D; Martini, M; Massarotti, P; Mei, W; Meola, S; Miscetti, S; Moulson, M; Müller, S; Murtas, F; Napolitano, M; Nguyen, F; Palutan, M; Pasqualucci, E; Passeri, A; Patera, V; Perfetto, F; Primavera, M; Santangelo, P; Saracino, G; Sciascia, B; Sciubba, A; Sibidanov, A; Spadaro, T; Testa, M; Tortora, L; Valente, P; Venanzoni, G; Versaci, R; Xu, G

    2008-01-01

    We have studied, with the KLOE detector at the DA$\\Phi$NE $\\Phi$-Factory, the dynamics of the decay $\\eta\\to\\pi^+\\pi^-\\pi^0$ using $\\eta$ mesons from the decay $\\phi\\to\\eta\\gamma$ for an integrated luminosity ${\\mathcal L}$ = 450 pb$^{-1}$. From a fit to the Dalitz plot density distribution we obtain a precise measurement of the slope parameters. An alternative parametrization relates the $\\pi^+\\pi^-\\pi^0$ slopes to that for $\\eta\\to 3\\pi^0$ showing the consistency of KLOE results for both channels. We also obtain the best confirmation of the $C$-invariance in the $\\eta\\to\\pi^+\\pi^-\\pi^0$ decay.

  1. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITH TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  2. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITHOUT TURB3D)

    Science.gov (United States)

    Buning, P. G.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  3. Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Liang Zhou

    2010-12-01

    Full Text Available With the advent of second-generation sequencing, the expression of gene transcripts can be digitally measured with high accuracy. The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC using massively parallel sequencing technology.The expression of mRNAs and miRNAs were analyzed in tumor tissues and matched normal adjacent tissues obtained from 10 ccRCC patients without distant metastases. In a prevalence screen, some of the most interesting results were validated in a large cohort of ccRCC patients.A total of 404 miRNAs and 9,799 mRNAs were detected to be differentially expressed in the 10 ccRCC patients. We also identified 56 novel miRNA candidates in at least two samples. In addition to confirming that canonical cancer genes and miRNAs (including VEGFA, DUSP9 and ERBB4; miR-210, miR-184 and miR-206 play pivotal roles in ccRCC development, promising novel candidates (such as PNCK and miR-122 without previous annotation in ccRCC carcinogenesis were also discovered in this study. Pathways controlling cell fates (e.g., cell cycle and apoptosis pathways and cell communication (e.g., focal adhesion and ECM-receptor interaction were found to be significantly more likely to be disrupted in ccRCC. Additionally, the results of the prevalence screen revealed that the expression of a miRNA gene cluster located on Xq27.3 was consistently downregulated in at least 76.7% of ∼50 ccRCC patients.Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC.

  4. Vegetation Plot Data of the Coastal Wetland Elevation Monitoring Sites on National Wildlife Refuges in the South Atlantic Geography.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Plot level raw datasets--including Cover, Woody Stem, Plot/Environmental, and Soil--from vegetation sampling on Coastal Wetland Elevation Monitoring Sites within the...

  5. The CD3 versus CD7 plot in multicolor flow cytometry reflects progression of disease stage in patients infected with HTLV-I.

    Directory of Open Access Journals (Sweden)

    Seiichiro Kobayashi

    Full Text Available PURPOSE: In a recent study to purify adult T-cell leukemia-lymphoma (ATL cells from acute-type patients by flow cytometry, three subpopulations were observed in a CD3 versus CD7 plot (H: CD3(highCD7(high; D: CD3(dimCD7(dim; L: CD3(dimCD7(low. The majority of leukemia cells were enriched in the L subpopulation and the same clone was included in the D and L subpopulations, suggesting clonal evolution. In this study, we analyzed patients with indolent-type ATL and human T-cell leukemia virus type I (HTLV-I asymptomatic carriers (ACs to see whether the CD3 versus CD7 profile reflected progression in the properties of HTLV-I-infected cells. EXPERIMENTAL DESIGN: Using peripheral blood mononuclear cells from patient samples, we performed multi-color flow cytometry. Cells that underwent fluorescence-activated cell sorting were subjected to molecular analyses, including inverse long PCR. RESULTS: In the D(% versus L(% plot, patient data could largely be categorized into three groups (Group 1: AC; Group 2: smoldering- and chronic-type ATL; and Group 3: acute-type ATL. Some exceptions, however, were noted (e.g., ACs in Group 2. In the follow-up of some patients, clinical disease progression correlated well with the CD3 versus CD7 profile. In clonality analysis, we clearly detected a major clone in the D and L subpopulations in ATL cases and, intriguingly, in some ACs in Group 2. CONCLUSION: We propose that the CD3 versus CD7 plot reflects progression of disease stage in patients infected with HTLV-I. The CD3 versus CD7 profile will be a new indicator, along with high proviral load, for HTLV-I ACs in forecasting disease progression.

  6. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITHOUT TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  7. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITH TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  8. Plot 4

    DEFF Research Database (Denmark)

    Lund, Inger-Lise; Hermansen, Anne-Mette; Ferdinand, Trine

    Her møder eleven både den klassiske litteratur og de helt nye tekster. Nye medieformer giver særlige oplevelsesmuligheder og har anderledes sprogformer. Eleverne møder det hele. De skal arbejde med tekster, som udfordrer dem både sprogligt og intellektuelt, og som rummer den store variation, der ...

  9. Plot 5

    DEFF Research Database (Denmark)

    Lund, Inger-Lise; Hermansen, Anne-Mette; Ferdinand, Trine

    Hvert kapitel har sin særlige vinkel. Der er fokus på gysergenren og dens særlige virkemidler, på evnen til at leve sig ind i digte og mærke det, der ikke står på linjerne, på elevernes kritiske analyse og fortolkning af reklamespots ved at zoome ind på genrens typiske virkemidler. Et kapitel har...

  10. Plot 6

    DEFF Research Database (Denmark)

    Lund, Inger-Lise; Ferdinand, Trine; Abildgaard, Stina

    Elevbogen indeholder 6 kapitler. Kapitlernes indhold kommer rundt i hele danskfaget med forskellige vinkler, og elevernes læring udspringer af kompetenceområderne: læsning, fremstilling, fortolkning og kommunikation...

  11. Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses

    Science.gov (United States)

    Malacarne, Giulia; Costantini, Laura; Coller, Emanuela; Battilana, Juri; Velasco, Riccardo; Vrhovsek, Urska; Grando, Maria Stella; Moser, Claudio

    2015-01-01

    Flavonols are a ubiquitous class of flavonoids that accumulate preferentially in flowers and mature berries. Besides their photo-protective function, they play a fundamental role during winemaking, stabilizing the colour by co-pigmentation with anthocyanins and contributing to organoleptic characteristics. Although the general flavonol pathway has been genetically and biochemically elucidated, the genetic control of flavonol content and composition at harvest is still not clear. To this purpose, the grapes of 170 segregating F1 individuals from a ‘Syrah’×’Pinot Noir’ population were evaluated at the mature stage for the content of six flavonol aglycons in four seasons. Metabolic data in combination with genetic data enabled the identification of 16 mQTLs (metabolic quantitative trait loci). For the first time, major genetic control by the linkage group 2 (LG 2)/MYBA region on flavonol variation, in particular of tri-hydroxylated flavonols, is demonstrated. Moreover, seven regions specifically associated with the fine control of flavonol biosynthesis are identified. Gene expression profiling of two groups of individuals significantly divergent for their skin flavonol content identified a large set of differentially modulated transcripts. Among these, the transcripts coding for MYB and bZIP transcription factors, methyltranferases, and glucosyltranferases specific for flavonols, proteins, and factors belonging to the UV-B signalling pathway and co-localizing with the QTL regions are proposed as candidate genes for the fine regulation of flavonol content and composition in mature grapes. PMID:26071529

  12. Integrative RNA- and miRNA-Profile Analysis Reveals a Likely Role of BR and Auxin Signaling in Branch Angle Regulation of B. napus

    Directory of Open Access Journals (Sweden)

    Hongtao Cheng

    2017-05-01

    Full Text Available Oilseed rape (Brassica napus L. is the second largest oilseed crop worldwide and one of the most important oil crops in China. As a component of plant architecture, branch angle plays an important role in yield performance, especially under high-density planting conditions. However, the mechanisms underlying the regulation of branch angle are still largely not understood. Two oilseed rape lines with significantly different branch angles were used to conduct RNA- and miRNA-profiling at two developmental stages, identifying differential expression of a large number of genes involved in auxin- and brassinosteroid (BR-related pathways. Many auxin response genes, including AUX1, IAA, GH3, and ARF, were enriched in the compact line. However, a number of genes involved in BR signaling transduction and biosynthesis were down-regulated. Differentially expressed miRNAs included those involved in auxin signaling transduction. Expression patterns of most target genes were fine-tuned by related miRNAs, such as miR156, miR172, and miR319. Some miRNAs were found to be differentially expressed at both developmental stages, including three miR827 members. Our results provide insight that auxin- and BR-signaling may play a pivotal role in branch angle regulation.

  13. Incomplete split-plots in designs with many entries – a compromise between split-plots and randomized complete block designs

    OpenAIRE

    Kristensen, Kristian

    2012-01-01

    The paper shows how the Alpha-design (also known as generalised lattice) may be used for constructing incomplete split-plot designs and describes 4 different methods (A, B, C and D) of construction. Intra-block efficiency factors and theoretical considerations are used to compare the methods. Based on those considerations method B was considered to be the most appropriate method for trials where tests for interaction between the two factors were important and thus this method was used and mos...

  14. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (WITH TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  15. PLOT3D/AMES, SGI IRIS VERSION (WITH TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  16. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (WITHOUT TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  17. PLOT3D/AMES, SGI IRIS VERSION (WITHOUT TURB3D)

    Science.gov (United States)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  18. (PLOT79): a comprehensive portable Fortran scientific line graphics system, as applied to biomedical research.

    Science.gov (United States)

    Beebe, N H; Rodgers, R P

    1989-01-01

    Scientific results are often most succinctly presented in graphical form. We describe a system for computer-generated scientific line graphics known as (PLOT79), named to commemorate the SIGGRAPH CORE graphics standard proposal of 1979. (PLOT79) is a widely used and actively evolving graphics system, written primarily in SFTRAN3, a structured procedural computer language which can be translated readily into Fortran. The package embodies concepts of sound software engineering, having been designed from the outset to be portable, maintainable and hardware-independent; much of the effort required to implement the system was directed toward the development of software engineering tools to ensure these goals. A modular design strategy has allowed a wide variety of graphics output devices to be supported. (PLOT79) has been installed under numerous operating systems, and software tools provided by UNIX have allowed particularly efficient installation and use of the system. Access to (PLOT79) is available through three avenues: (1) linking (PLOT79) routines with a user-written high-level program; (2) use of pre-written high-level applications programs which perform certain frequently-required tasks such as the plotting of simple two or three-dimensional data; or (3) the use of an interactive graphics command parser known as slides. (PLOT79) has proven popular among workers in the physical sciences and engineering both for its easy availability, openness (all source code is provided), and powerful capability. The system presents an equally important (though lesser known) resource for biomedical research, as demonstrated by examples from ongoing biomedical research projects. It also provides a focus for discussion of the practical limitations inherent in existing graphics standards and programming languages.

  19. Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research

    NARCIS (Netherlands)

    Graffelman, J.; Eeuwijk, van F.A.

    2005-01-01

    The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations between multiple variables, generalisations of the scatter plot are useful. We present an overview of multivariate scatter plots

  20. Maintaining the confidentiality of plot locations by exploiting the low sensitivity of forest structure models to different spectral extraction kernels

    Science.gov (United States)

    Sean P. Healey; Elizabeth Lapoint; Gretchen G. Moisen; Scott L. Powell

    2011-01-01

    The United States Forest Service Forest Inventory and Analysis (FIA) unit maintains a large national network of inventory plots.While the consistency and extent of this network make FIA data attractive for ecological modelling, the FIA is charged by statute not to publicly reveal inventory plot locations. However, use of FIA plot data by the remote sensing community...