WorldWideScience

Sample records for tools mapping targeted

  1. Mapping Medicare Disparities Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CMS Office of Minority Health has designed an interactive map, the Mapping Medicare Disparities Tool, to identify areas of disparities between subgroups of...

  2. Recovery Action Mapping Tool

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Recovery Action Mapping Tool is a web map that allows users to visually interact with and query actions that were developed to recover species listed under the...

  3. Tools for mapping ecosystem services

    Science.gov (United States)

    Palomo, Ignacio; Adamescu, Mihai; Bagstad, Kenneth J.; Cazacu, Constantin; Klug, Hermann; Nedkov, Stoyan; Burkhard, Benjamin; Maes, Joachim

    2017-01-01

    Mapping tools have evolved impressively in recent decades. From early computerised mapping techniques to current cloud-based mapping approaches, we have witnessed a technological evolution that has facilitated the democratisation of Geographic Information

  4. Neighborhood Mapping Tool

    Data.gov (United States)

    Department of Housing and Urban Development — This tool assists the public and Choice Neighborhoods applicants to prepare data to submit with their grant application by allowing applicants to draw the exact...

  5. Medicare Part D Opioid Drug Mapping Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Medicare Part D opioid prescribing mapping tool is an interactive tool that shows geographic comparisons, at the state, county, and ZIP code levels, of...

  6. a comparative survey on mind mapping tools

    Directory of Open Access Journals (Sweden)

    Avgoustos A. TSINAKOS

    2009-07-01

    Full Text Available Mind Mapping is an important technique that improves the way you takes notes, and enhances your creative problem solving. By using Mind Maps, you can quickly identify and understand the structure of a subject and the way that pieces of information fit together, as well as recording the raw facts contained in normal notes. It can also be used as complementary tools for knowledge construction and sharing. Their suitability as a pedagogical tool for education, e-learning and training, increases their importance. Also, in a world of information overload and businesses struggling to keep up with the place of change, knowledge workers need effective tools to organize, analyze, brainstorm and collaborate on ideas. In resent years, a wide variety of mind mapping software tools have been developed. An often question that comes up, due to this plethora of software tools, is “which is the best mind mapping software?” Anyone who gives you an immediate answer either knows you and your mind mapping activities very well or their answer in not worth a lot. The “best” depends so much on how you use mind maps. In this paper we are trying to investigate different user profiles and to identify various axes for comparison among mind mapping tools that are suitable for a specific user profile, describe each axis and then analyze each tool.

  7. Globes, Maps, Photographs: Geographic Tools.

    Science.gov (United States)

    McDermott, Paul D.; And Others

    This compilation of reprinted articles that originally appeared in the Journal of Geography from September 1969 through the May 1970 issues, is intended to help teachers use globes, maps, and photographs with skill and understanding. The articles were designed with several objectives in mind: 1) to provide information regarding the design,…

  8. Crime clocks and target performance maps

    CSIR Research Space (South Africa)

    Cooper, Antony K

    1999-12-01

    Full Text Available for the prevention and management of crime. This paper describes two innovative techniques that were developed by CSIR for analysing crime: "crime clocks" and "target performance maps"....

  9. Risk-targeted maps for Romania

    Science.gov (United States)

    Vacareanu, Radu; Pavel, Florin; Craciun, Ionut; Coliba, Veronica; Arion, Cristian; Aldea, Alexandru; Neagu, Cristian

    2018-03-01

    Romania has one of the highest seismic hazard levels in Europe. The seismic hazard is due to a combination of local crustal seismic sources, situated mainly in the western part of the country and the Vrancea intermediate-depth seismic source, which can be found at the bend of the Carpathian Mountains. Recent seismic hazard studies have shown that there are consistent differences between the slopes of the seismic hazard curves for sites situated in the fore-arc and back-arc of the Carpathian Mountains. Consequently, in this study we extend this finding to the evaluation of the probability of collapse of buildings and finally to the development of uniform risk-targeted maps. The main advantage of uniform risk approach is that the target probability of collapse will be uniform throughout the country. Finally, the results obtained are discussed in the light of a recent study with the same focus performed at European level using the hazard data from SHARE project. The analyses performed in this study have pointed out to a dominant influence of the quantile of peak ground acceleration used for anchoring the fragility function. This parameter basically alters the shape of the risk-targeted maps shifting the areas which have higher collapse probabilities from eastern Romania to western Romania, as its exceedance probability increases. Consequently, a uniform procedure for deriving risk-targeted maps appears as more than necessary.

  10. Infralittoral mapping around an oceanic archipelago using MERIS FR satellite imagery and deep kelp observations: A new tool for assessing MPA coverage targets

    Science.gov (United States)

    Amorim, Patrícia; Atchoi, Elizabeth; Berecibar, Estibaliz; Tempera, Fernando

    2015-06-01

    This work presents the first climatologic maps of diffuse attenuation of down-welling solar radiation (KdPAR and Kd490 coefficients) for the Azores derived from full resolution (FR) MERIS satellite imagery. Associating this information with a new mesoscale bathymetry compilation permits estimating the percentage of surface light reaching the seabed. A video annotation dataset derived from a deep kelp survey conducted on the Formigas Bank is subsequently used to estimate the light levels experienced by these bionomically-crucial frondose algae. Empirical light-based thresholds for the lower infralittoral boundary in the Azores are derived from the deepest kelp occurrences. This information is eventually used to map the geographical extent of this major marine biological zone in the archipelago, yielding an area estimate of 894.7 km2. The average depth of the infralittoral limit in the Azores is established at 69 m. It is determined that the present Azores marine protected area (MPA) network already covers 28.9% of the region's infralittoral grounds. However, island-specific values highlight that MPA percentage coverage varies between islands with values ranging from a marginal coverage of 7.3% (on Terceira Island) to 100% coverage around the island of Corvo and the Formigas Bank. These results suggest that conservation managers may make use of the current spatially-based protection framework of the archipelago to, on the whole and for this specific major habitat, surpass the goals suggested by international conventions and conservation fora for MPA coverage. However, an analysis of the statutory MPA regulations further reveals that measures in place are insufficient to provide a no-take and no-disturbance protection of infralittoral biotopes. In order to achieve the recommended strict protection of the currently protected infralittoral zones, conservation measures ought to be enhanced.

  11. The EPSA Project Finance Mapping Tool

    Energy Technology Data Exchange (ETDEWEB)

    Hadley, Stanton W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Chinthavali, Supriya [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-07-01

    The Energy Policy and Systems Analysis Office of DOE has requested a tool to compare the impact of various Federal policies on the financial viability of generation resources across the country. Policy options could include production tax credits, investment tax credits, solar renewable energy credits, tax abatement, accelerated depreciation, tax-free loans, and others. The tool would model the finances of projects in all fifty states, and possibly other geographic units like utility service territories and RTO/ISO territories. The tool would consider the facility s cost, financing, production, and revenues under different capital and market structures to determine things like levelized cost of energy, return on equity, and cost impacts on others (e.g., load-serving entities, society.) The tool would compare the cost and value of the facility to the local regional alternatives to determine how and where policy levers may provide sufficient incremental value to motivate investment. The results will be displayed through a purpose-built visualization that maps geographic variations and shows associated figures and tables.

  12. Stakeholder analysis and mapping as targeted communication strategy.

    Science.gov (United States)

    Shirey, Maria R

    2012-09-01

    This department highlights change management strategies that may be successful in strategically planning and executing organizational change initiatives. With the goal of presenting practical approaches helpful to nurse leaders advancing organizational change, content includes evidence-based projects, tools, and resources that mobilize and sustain organizational change initiatives. In this article, the author highlights the importance of stakeholder theory and discusses how to apply the theory to conduct a stakeholder analysis. This article also provides an explanation of how to use related stakeholder mapping techniques with targeted communication strategies.

  13. Mapping as a visual health communication tool: promises and dilemmas.

    Science.gov (United States)

    Parrott, Roxanne; Hopfer, Suellen; Ghetian, Christie; Lengerich, Eugene

    2007-01-01

    In the era of evidence-based public health promotion and planning, the use of maps as a form of evidence to communicate about the multiple determinants of cancer is on the rise. Geographic information systems and mapping technologies make future proliferation of this strategy likely. Yet disease maps as a communication form remain largely unexamined. This content analysis considers the presence of multivariate information, credibility cues, and the communication function of publicly accessible maps for cancer control activities. Thirty-six state comprehensive cancer control plans were publicly available in July 2005 and were reviewed for the presence of maps. Fourteen of the 36 state cancer plans (39%) contained map images (N = 59 static maps). A continuum of map inter activity was observed, with 10 states having interactive mapping tools available to query and map cancer information. Four states had both cancer plans with map images and interactive mapping tools available to the public on their Web sites. Of the 14 state cancer plans that depicted map images, two displayed multivariate data in a single map. Nine of the 10 states with interactive mapping capability offered the option to display multivariate health risk messages. The most frequent content category mapped was cancer incidence and mortality, with stage at diagnosis infrequently available. The most frequent communication function served by the maps reviewed was redundancy, as maps repeated information contained in textual forms. The social and ethical implications for communicating about cancer through the use of visual geographic representations are discussed.

  14. Concept Mapping Using Cmap Tools to Enhance Meaningful Learning

    Science.gov (United States)

    Cañas, Alberto J.; Novak, Joseph D.

    Concept maps are graphical tools that have been used in all facets of education and training for organizing and representing knowledge. When learners build concept maps, meaningful learning is facilitated. Computer-based concept mapping software such as CmapTools have further extended the use of concept mapping and greatly enhanced the potential of the tool, facilitating the implementation of a concept map-centered learning environment. In this chapter, we briefly present concept mapping and its theoretical foundation, and illustrate how it can lead to an improved learning environment when it is combined with CmapTools and the Internet. We present the nationwide “Proyecto Conéctate al Conocimiento” in Panama as an example of how concept mapping, together with technology, can be adopted by hundreds of schools as a means to enhance meaningful learning.

  15. Mind Maps as a Lifelong Learning Tool

    Science.gov (United States)

    Erdem, Aliye

    2017-01-01

    Mind map, which was developed by Tony Buzan as a note-taking technique, is an application which has the power of uncovering the thoughts which the brain has about a subject from different viewpoints and which activate the right and left lobes of the brain together as an alternative to linear thought. It is known that mind maps have benefits such…

  16. GOKaRT: Graphical Online Search Tool for Maps

    Directory of Open Access Journals (Sweden)

    Mechthild Schüler

    2008-09-01

    Full Text Available The map department of the Staats- und Universitätsbibliothek Göttingen together with the Berlin State Library propose a project to develop a web-based graphic cataloguing and search system for maps, to be funded by the German Research Foundation. This tool shall be made available to all map holdings in archives, libraries, university departments and museums in Germany as a comfortable means for the administration of map holdings and as a search tool. Sheets belonging to map series as well as single maps (old and new will be registered cooperatively by the participants with simple tools. This cooperation in data maintenance will facilitate the work especially for understaffed map holdings. Depending on the type of map there are four different mechanisms for map reference. For map series electronic index sheets are used which will show information regarding the various issues of the map sheets. Due to the intuitive graphic search entry GOKaRT-users will easily find the required maps of a certain region available in a chosen holding. User administration modules ensure comfortable handling. GOKaRT is being developed on the basis of licence-free open source programmes. In case financing is provided by the German Research Foundation, GOKaRT can be used free of charge internationally. This would require a contract stipulating data exchange between the partners as well as permanent storage and usability of the data.

  17. TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes

    Directory of Open Access Journals (Sweden)

    van der Spek Peter

    2006-03-01

    Full Text Available Abstract Background In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP allows the isolation of in vivo binding sites of transcription factors and provides a powerful tool for examining gene regulation. Crosslinked chromatin is immunoprecipitated with antibodies against specific transcription factors, thus enriching for sequences bound in vivo by these factors in the immunoprecipitated DNA. Cloning and sequencing the immunoprecipitated sequences allows identification of transcription factor target genes. Routinely, thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome and the genes located in the vicinity. These genes represent potential targets of the transcription factor of interest. Such bioinformatics analysis is very laborious if performed manually and for this reason there is a need for developing bioinformatic tools to automate and facilitate it. Results In order to facilitate this analysis we generated TF Target Mapper (Transcription Factor Target Mapper. TF Target Mapper is a BLAST search tool allowing rapid extraction of annotated information on genes around each hit. It combines sequence cleaning/filtering, pattern searching and BLAST searches with extraction of information on genes located around each BLAST hit and comparisons of the output list of genes or gene ontology IDs with user-implemented lists. We successfully applied and tested TF Target Mapper to analyse sequences bound in vivo by the transcription factor GATA-1. We show that TF Target Mapper efficiently extracted information on genes around ChIPed sequences, thus identifying known (e.g. α-globin and ζ-globin and potentially novel GATA-1 gene targets. Conclusion TF Target Mapper is a very efficient BLAST search tool that allows the rapid extraction of annotated information on the genes

  18. Concept mapping as learning tool in problem-oriented learning

    NARCIS (Netherlands)

    Fürstenau, B.; Kneppers, L.; Sánchez, J.; Cañas, A.J.; Novak, J.D.

    2010-01-01

    In two studies we investigated whether concept mapping or summary writing is more effective in supporting students’ learning from authentic problems in the field of business. We interpret concept mapping and summary writing as elaboration tools aiming at helping students to understand new

  19. Deriving optimal exploration target zones on mineral prospectivity maps

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2008-08-01

    Full Text Available This paper describes a quantitative methodology for deriving optimal exploration target zones based on a probabilistic mineral prospectivity map. The methodology is demonstrated in the Rodalquilar mineral district in Spain. A subset of known...

  20. Crime clocks and target performance maps

    CSIR Research Space (South Africa)

    Cooper, Anthony K

    1999-12-01

    Full Text Available View), spreadsheets (eg: Excel) and data bases (eg: Access). 2. Crime clocks A map of crime clocks displays the distribution of crime in time and space using scaled pie charts to show the relative crime rates for the selected period being analysed. Each... pie chart shows the total aggregated crime for an area (eg: CAS Block or precinct) and is positioned on the centroid of the relevant area. Hence, the size of each pie chart is proportional to the amount of crime that occurred in that area over...

  1. RISK COMMUNICATION IN ACTION: THE TOOLS OF MESSAGE MAPPING

    Science.gov (United States)

    Risk Communication in Action: The Tools of Message Mapping, is a workbook designed to guide risk communicators in crisis situations. The first part of this workbook will review general guidelines for risk communication. The second part will focus on one of the most robust tools o...

  2. Flow mapping for ESS horizontal target

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Y.; Kikura, H.; Taishi, T. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-09-01

    Flow behaviour for ESS horizontal target is studied experimentally using two dimensional water model. A velocity field of stationary flow in reaction zone has been obtained. Three dimensional effect was also studied as a spanwise flow structure. (author) 3 figs., 3 refs.

  3. Concept mapping: a tool for improving patient care.

    Science.gov (United States)

    Aberdeen, Suzanne

    2015-07-29

    This article reviews the use of concept mapping as a person-centred problem-solving aid to assessment, risk management, care evaluation and care planning for nurses. Concept maps are diagrams that are used to organise, represent and create knowledge, and provide a useful framework for critical analysis and problem solving. Concept mapping is discussed and demonstrated in relation to improving the quality of care for patients and as a tool for clinical leadership and teamwork. The benefits of concept mapping for patients' wellbeing and safety, staff satisfaction and team learning are evidenced.

  4. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB......) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure...... with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used...

  5. Performance Evaluation of Java Based Object Relational Mapping Tools

    Directory of Open Access Journals (Sweden)

    Shoaib Mahmood Bhatti

    2013-04-01

    Full Text Available Object persistency is the hot issue in the form of ORM (Object Relational Mapping tools in industry as developers use these tools during software development. This paper presents the performance evaluation of Java based ORM tools. For this purpose, Hibernate, Ebean and TopLinkhave been selected as the ORM tools which are popular and open source. Their performance has been measured from execution point of view. The results show that ORM tools are the good option for the developers considering the system throughput in shorter setbacks and they can be used efficiently and effectively for performing mapping of the objects into the relational dominated world of database, thus creating a hope for a better and well dominated future of this technology.

  6. Common features of microRNA target prediction tools

    Directory of Open Access Journals (Sweden)

    Sarah M. Peterson

    2014-02-01

    Full Text Available The human genome encodes for over 1800 microRNAs, which are short noncoding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one microRNA to target multiple gene transcripts, microRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of microRNA targets is a critical initial step in identifying microRNA:mRNA target interactions for experimental validation. The available tools for microRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to microRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all microRNA target prediction tools, four main aspects of the microRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MicroRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

  7. Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools

    Directory of Open Access Journals (Sweden)

    Hong Tran

    2014-01-01

    Full Text Available Background. Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. Aligning bisulfite short reads to a reference genome has been a challenging task. We compared five bisulfite short read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, and BRAT-BW, representing two classes of mapping algorithms (hash table and suffix/prefix tries. We examined their mapping efficiency (i.e., the percentage of reads that can be mapped to the genomes, usability, running time, and effects of changing default parameter settings using both real and simulated reads. We also investigated how preprocessing data might affect mapping efficiency. Conclusion. Among the five programs compared, in terms of mapping efficiency, Bismark performs the best on the real data, followed by BiSS, BSMAP, and finally BRAT-BW and BS-Seeker with very similar performance. If CPU time is not a constraint, Bismark is a good choice of program for mapping bisulfite treated short reads. Data quality impacts a great deal mapping efficiency. Although increasing the number of mismatches allowed can increase mapping efficiency, it not only significantly slows down the program, but also runs the risk of having increased false positives. Therefore, users should carefully set the related parameters depending on the quality of their sequencing data.

  8. Human MAP Tau Based Targeted Cytolytic Fusion Proteins

    Directory of Open Access Journals (Sweden)

    Olusiji A. Akinrinmade

    2017-06-01

    Full Text Available Some of the most promising small molecule toxins used to generate antibody drug conjugates (ADCs include anti-mitotic agents (e.g., auristatin and its derivatives which are designed to attack cancerous cells at their most vulnerable state during mitosis. We were interested in identifying a human cystostatic protein eventually showing comparable activities and allowing the generation of corresponding targeted fully human cytolytic fusion proteins. Recently, we identified the human microtubule associated protein tau (MAP tau, which binds specifically to tubulin and modulates the stability of microtubules, thereby blocking mitosis and presumably vesicular transport. By binding and stabilizing polymerized microtubule filaments, MAP tau-based fusion proteins skew microtubule dynamics towards cell cycle arrest and apoptosis. This biological activity makes rapidly proliferating cells (e.g., cancer and inflammatory cells an excellent target for MAP tau-based targeted treatments. Their superior selectivity for proliferating cells confers additional selectivity towards upregulated tumor-associated antigens at their surface, thereby preventing off-target related toxicity against normal cells bearing tumor-associated antigens at physiologically normal to low levels. In this review, we highlight recent findings on MAP tau-based targeted cytolytic fusion proteins reported in preclinical immunotherapeutic studies.

  9. Content Maps: A Teaching and Assessment Tool for Content Knowledge

    Science.gov (United States)

    Ward, Phillip; Lehwald, Harry; Lee, Yun Soo

    2015-01-01

    Developing content knowledge in teachers presents a constant challenge for teacher educators. This article introduces a teaching and assessment tool called a "content map," which allows teacher educators, teachers, and coaches to conceptualize the scope, sequence, and relational characteristics of the content being taught. Content maps…

  10. Mind Maps as Facilitative Tools in Science Education

    Science.gov (United States)

    Safar, Ammar H.; Jafer,Yaqoub J.; Alqadiri, Mohammad A.

    2014-01-01

    This study explored the perceptions, attitudes, and willingness of pre-service science teachers in the College of Education at Kuwait University about using concept/mind maps and its related application software as facilitative tools, for teaching and learning, in science education. The first level (i.e., reaction) of Kirkpatrick's/Phillips'…

  11. MIMOX: a web tool for phage display based epitope mapping

    Directory of Open Access Journals (Sweden)

    Honda Wataru

    2006-10-01

    Full Text Available Abstract Background Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them. Results We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results. Conclusion A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox.

  12. Concept Mapping as a Learning Tool in Occupational Therapy Education.

    Science.gov (United States)

    Grice, Kimatha

    2016-07-01

    This paper describes concept mapping and its use as a teaching and learning tool in an entry level occupational therapy program. In order for students to demonstrate their mastery of the concepts associated with a particular topic or body of knowledge, assignments involving concept maps were developed and used in two courses in an entry level occupational therapy program. Students were then surveyed about their perceptions and attitudes regarding the assignments. Students found the process of creating concept maps valuable to their learning of the content and the majority also enjoyed the process as a learning activity. The use of concept mapping as a way to encourage independent, individualized, and student-centered learning is discussed.

  13. SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

    Directory of Open Access Journals (Sweden)

    Santosh Kumar Upadhyay

    2014-01-01

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated protein (Cas system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

  14. Web mapping: tools and solutions for creating interactive maps of forestry interest

    Directory of Open Access Journals (Sweden)

    Notarangelo G

    2011-12-01

    Full Text Available The spread of geobrowsers as tools for displaying geographically referenced information provides insights and opportunities to those who, not being specialists in Geographic Information Systems, want to take advantage from exploration and communication power offered by these software. Through the use of web services such as Google Maps and the use of suitable markup languages, one can create interactive maps starting from highly heterogeneous data and information. These interactive maps can also be easily distributed and shared with Internet users, because they do not need to use proprietary software nor special skills but only a web browser. Unlike the maps created with GIS, whose output usually is a static image, the interactive maps retain all their features to users advantage. This paper describes a web application that, using the Keyhole Markup Language and the free service of Google Maps, produces choropleth maps relating to some forest indicators estimated by the last Italian National Forest Inventory. The creation of a map is done through a simple and intuitive interface. The maps created by users can be downloaded as KML file and can be viewed or modified via the freeware application Google Earth or free and open source GIS software like Quantum GIS. The web application is free and available at www.ricercaforestale.it.

  15. Geo-environmental mapping tool applied to pipeline design

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Karina de S.; Calle, Jose A.; Gil, Euzebio J. [Geomecanica S/A Tecnologia de Solo Rochas e Materiais, Rio de Janeiro, RJ (Brazil); Sare, Alexandre R. [Geomechanics International Inc., Houston, TX (United States); Soares, Ana Cecilia [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil)

    2009-07-01

    The Geo-Environmental Mapping is an improvement of the Geological-Geotechnical Mapping used for basic pipeline designs. The main purpose is to assembly the environmental, geotechnical and geological concepts in a methodological tool capable to predict constrains and reduce the pipeline impact to the environment. The Geo-Environmental mapping was built to stress the influence of soil/structure interaction, related to the physical effect that comes from the contact between structures and soil or rock. A Geological-Geotechnical-Environmental strip (chart) was presented to emphasize the pipeline operational constrains and its influence to the environment. The mapping was developed to clearly show the occurrence and properties of geological materials divided into geotechnical domain units (zones). The strips present construction natural properties, such as: excavability, stability of the excavation and soil re-use capability. Also, the environmental constrains were added to the geological-geotechnical mapping. The Geo-Environmental Mapping model helps the planning of the geotechnical and environmental inquiries to be carried out during executive design, the discussion on the types of equipment to be employed during construction and the analysis of the geological risks and environmental impacts to be faced during the built of the pipeline. (author)

  16. Poster: A modern Python interface for the Generic Mapping Tools

    OpenAIRE

    Uieda, Leonardo; Wessel, Paul

    2017-01-01

    Poster presentation at the AGU Fall Meeting 2017.Abstract: IN51B-0018Inkscape source files for the poster and a Jupyter notebook with the demo are on the Github repository: github.com/leouieda/agu2017 The demo notebook can be run online using the MyBinder service: agu2017demo.gmtpython.xyzAbstractFigures generated by The Generic Mapping Tools (GMT) are present in countless publications across the Earth sciences. The command-line interface of GMT lends the tool its flexibility bu...

  17. Glimpse: Sparsity based weak lensing mass-mapping tool

    Science.gov (United States)

    Lanusse, F.; Starck, J.-L.; Leonard, A.; Pires, S.

    2018-02-01

    Glimpse, also known as Glimpse2D, is a weak lensing mass-mapping tool that relies on a robust sparsity-based regularization scheme to recover high resolution convergence from either gravitational shear alone or from a combination of shear and flexion. Including flexion allows the supplementation of the shear on small scales in order to increase the sensitivity to substructures and the overall resolution of the convergence map. To preserve all available small scale information, Glimpse avoids any binning of the irregularly sampled input shear and flexion fields and treats the mass-mapping problem as a general ill-posed inverse problem, regularized using a multi-scale wavelet sparsity prior. The resulting algorithm incorporates redshift, reduced shear, and reduced flexion measurements for individual galaxies and is made highly efficient by the use of fast Fourier estimators.

  18. Geomorphic Unit Tool (GUT): Applications of Fluvial Mapping

    Science.gov (United States)

    Kramer, N.; Bangen, S. G.; Wheaton, J. M.; Bouwes, N.; Wall, E.; Saunders, C.; Bennett, S.; Fortney, S.

    2017-12-01

    Geomorphic units are the building blocks of rivers and represent distinct habitat patches for many fluvial organisms. We present the Geomorphic Unit Toolkit (GUT), a flexible GIS geomorphic unit mapping tool, to generate maps of fluvial landforms from topography. GUT applies attributes to landforms based on flow stage (Tier 1), topographic signatures (Tier 2), geomorphic characteristics (Tier 3) and patch characteristics (Tier 4) to derive attributed maps at the level of detail required by analysts. We hypothesize that if more rigorous and consistent geomorphic mapping is conducted, better correlations between physical habitat units and ecohydraulic model results will be obtained compared to past work. Using output from GUT for coarse bed tributary streams in the Columbia River Basin, we explore relationships between salmonid habitat and geomorphic spatial metrics. We also highlight case studies of how GUT can be used to showcase geomorphic impact from large wood restoration efforts. Provided high resolution topography exists, this tool can be used to quickly assess changes in fluvial geomorphology in watersheds impacted by human activities.

  19. Magnetic Multi-Scale Mapping to Characterize Anthropogenic Targets

    Science.gov (United States)

    Le Maire, P.; Munschy, M.

    2017-12-01

    The discovery of buried anthropic objects on construction sites can cause delays and/or dangers for workers and for the public. Indeed, every year 500 tons of Unexploded-ordnance are discovered in France. Magnetic measurements are useful to localize magnetized objects. Moreover, it is the cheapest geophysical method which does not impact environment and which is relatively fast to perform. Fluxgate magnetometers (three components) are used to measure magnetic properties bellow the ground. These magnetic sensors are not absolute, so they need to be calibrated before the onset of the measurements. The advantage is that they allow magnetic compensation of the equipment attached to the sensor. So the choice of this kind sensor gives the opportunity to install the equipment aboard different magnetized supports: boat, quad bike, unmanned aerial vehicle, aircraft,... Indeed, this methodology permits to perform magnetic mapping with different scale and different elevation above ground level. An old French aerial military plant was chosen to perform this multi-scale approach. The advantage of the site is that it contains a lot of different targets with variable sizes and depth, e.g. buildings, unexploded-ordnances of the two world wars, trenches, pipes,… By comparison between the different magnetic anomaly maps at different elevations some of the geometric parameters of the magnetic sources can be characterized. The comparison between measured maps at different elevations and the prolonged map highlights the maximum distance for the target's detection (figure).

  20. New "Risk-Targeted" Seismic Maps Introduced into Building Codes

    Science.gov (United States)

    Luco, Nicholas; Garrett, B.; Hayes, J.

    2012-01-01

    Throughout most municipalities of the United States, structural engineers design new buildings using the U.S.-focused International Building Code (IBC). Updated editions of the IBC are published every 3 years. The latest edition (2012) contains new "risk-targeted maximum considered earthquake" (MCER) ground motion maps, which are enabling engineers to incorporate a more consistent and better defined level of seismic safety into their building designs.

  1. Mapping pediatric injuries to target prevention, education, and outreach.

    Science.gov (United States)

    Stewart, Camille L; Acker, Shannon N; Pyle, Laura; Smith, Dwayne S; Bensard, Denis D; Moulton, Steven L

    2017-08-01

    Initiatives exist to prevent pediatric injuries, but targeting these interventions to specific populations is challenging. We hypothesized that mapping pediatric injuries by zip code could be used to identify regions requiring more interventions and resources. We queried the trauma registries of two level I trauma centers for children 0-17years of age injured between 2009 and 2013 with home zip codes in our state. Maps were created to identify outlier zip codes. Multivariate linear regression analysis identified predictors within these zip codes. There were 5380 children who resided in the state and were admitted for traumatic injuries during the study period, with hospital costs totaling more than 200 million dollars. Choropleth mapping of patient addresses identified outlier zip codes in our metro area with higher incidences of specific mechanisms of injury and greater hospital charges. Multivariate analysis identified demographic features associated with higher rates of pediatric injuries and hospital charges, to further target interventions. We identified outlier zip codes in our metro area with higher frequencies of pediatric injuries and higher costs for treatment. These data have helped obtain funding for prevention and education efforts. Techniques such as those presented here are becoming more important as evidence based public health initiatives expand. Type of Study: Cost Effectiveness, II. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. A proposal for combining mapping, localization and target recognition

    Science.gov (United States)

    Grönwall, Christina; Hendeby, Gustaf; Sinivaara, Kristian

    2015-10-01

    Simultaneous localization and mapping (SLAM) is a well-known positioning approach in GPS-denied environments such as urban canyons and inside buildings. Autonomous/aided target detection and recognition (ATR) is commonly used in military application to detect threats and targets in outdoor environments. This papers present approaches to combine SLAM with ATR in ways that compensate for the drawbacks in each method. The methods use physical objects that are recognizable by ATR as unambiguous features in SLAM, while SLAM provides the ATR with better position estimates. Landmarks in the form of 3D point features based on normal aligned radial features (NARF) are used in conjunction with identified objects and 3D object models that replace landmarks when possible. This leads to a more compact map representation with fewer landmarks, which partly compensates for the introduced cost of the ATR. We analyze three approaches to combine SLAM and 3D-data; point-point matching ignoring NARF features, point-point matching using the set of points that are selected by NARF feature analysis, and matching of NARF features using nearest neighbor analysis. The first two approaches are is similar to the common iterative closest point (ICP). We propose an algorithm that combines EKF-SLAM and ATR based on rectangle estimation. The intended application is to improve the positioning of a first responder moving through an indoor environment, where the map offers localization and simultaneously helps locate people, furniture and potentially dangerous objects such as gas canisters.

  3. 1:10000 scale mapping with GPS and free GIS tools – comparison with topographic map

    Directory of Open Access Journals (Sweden)

    Andor Rábay

    2011-06-01

    Full Text Available Reliability of the road system illustrated on topographic maps with 1:10000 scale is questionable due to their age, but surveying a territory with area over 100 hectares is expensive with classical geodetic tools, although there is no need of geodetic accuracy in most cases. GPS-based mapping method described in this paper is suitable in these situations. The main concept is to keep the costs of the survey as low as possible, therefore free GIS applications and databases were used with navigation purpose GPS receivers. The accuracy provided by these devices is good enough for those purposes where the accuracy of topographic map with 1:10000 scale is adequate. GPS-based mapping can be done to update the road system of existing map or create own detailed road databases. The result of the work is not just a database but a navigation capable digital map, which can aid further activities on the field, like geographic researches, environment protection, tourism, fire service etc.

  4. SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps

    KAUST Repository

    Falivene, Laura

    2016-06-27

    Developing more efficient catalysts remains one of the primary targets of organometallic chemists. To accelerate reaching this goal, effective molecular descriptors and visualization tools can represent a remarkable aid. Here, we present a Web application for analyzing the catalytic pocket of metal complexes using topographic steric maps as a general and unbiased descriptor that is suitable for every class of catalysts. To show the broad applicability of our approach, we first compared the steric map of a series of transition metal complexes presenting popular mono-, di-, and tetracoordinated ligands and three classic zirconocenes. This comparative analysis highlighted similarities and differences between totally unrelated ligands. Then, we focused on a recently developed Fe(II) catalyst that is active in the asymmetric transfer hydrogenation of ketones and imines. Finally, we expand the scope of these tools to rationalize the inversion of enantioselectivity in enzymatic catalysis, achieved by point mutation of three amino acids of mononuclear p-hydroxymandelate synthase.

  5. MIMO: an efficient tool for molecular interaction maps overlap

    Science.gov (United States)

    2013-01-01

    Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

  6. [Digital administrative maps - a tool for visualization of epidemiological data].

    Science.gov (United States)

    Niewiadomska, Ewa; Kowalska, Malgorzata; Czech, Elibieta; Skrzypek, Michal

    2013-01-01

    The aim of the study is to present the methods for visualization of epidemiological data using digital contour maps that take into account administrative division of Poland. The possibility of epidemiological data visualization in a geographical order, limited to the administrative level of the country, voivodeships and poviats (countics), are presented. They are crucial for the process of identifying and undertaking adequate prophylactic activities directed towards decreasing the risk and improving the population's health. This paper presents tools and techniques available in Geographic Information System ArcGIS and statistical software package R. The work includes our own data reflecting: 1) the values of specific mortality rates due to respiratory diseases, Poland, 2010, based on the Central Statistical Office data, using the R statistical software package; 2) the averaged registered incidence rates of sarcoidosis in 2006-2010 for the population aged 19+ in the Silesian voivodeship, using G(eographic Information System ArcGIS; and 3) the number of children with diagnosed respiratory diseases in the city of L.egnica in 2009, taking into account their place of residence, using layered maps in Geographic Information System ArcGIS. The tools presented and described in this paper make it possible to visualize the results of research, to increase attractiveness of courses for students, as well as to enhance the skills and competence of students and participants of courses.

  7. Reactor FaceMap Tool: A modern graphics tool for displaying reactor data

    International Nuclear Information System (INIS)

    Roberts, J.C.

    1991-01-01

    A prominent graphical user interface in reactor physics applications at the Savannah River Site is the reactor facemap display. This is a two dimensional view of a cross section of a reactor. In the past each application which needed a facemap implemented its own version. Thus, none of the code was reused, the facemap implementation was hardware dependent and the user interface was different for each facemap. The Reactor FaceMap Tool was built to solve these problems. Through the use of modern computing technologies such as X Windows, object-oriented programming and client/server technology the Reactor FaceMap Tool has the flexibility to work in many diverse applications and the portability to run on numerous types of hardware

  8. A modern Python interface for the Generic Mapping Tools

    Science.gov (United States)

    Uieda, L.; Wessel, P.

    2017-12-01

    Figures generated by The Generic Mapping Tools (GMT) are present in countless publications across the Earth sciences. The command-line interface of GMT lends the tool its flexibility but also creates a barrier to entry for begginers. Meanwhile, adoption of the Python programming language has grown across the scientific community. This growth is largely due to the simplicity and low barrier to entry of the language and its ecosystem of tools. Thus, it is not surprising that there have been at least three attempts to create Python interfaces for GMT: gmtpy (github.com/emolch/gmtpy), pygmt (github.com/ian-r-rose/pygmt), and PyGMT (github.com/glimmer-cism/PyGMT). None of these projects are currently active and, with the exception of pygmt, they do not use the GMT Application Programming Interface (API) introduced in GMT 5. The two main Python libraries for plotting data on maps are the matplotlib Basemap toolkit (matplotlib.org/basemap) and Cartopy (scitools.org.uk/cartopy), both of which rely on matplotlib (matplotlib.org) as the backend for generating the figures. Basemap is known to have limitations and is being discontinued. Cartopy is an improvement over Basemap but is still bound by the speed and memory constraints of matplotlib. We present a new Python interface for GMT (GMT/Python) that makes use of the GMT API and of new features being developed for the upcoming GMT 6 release. The GMT/Python library is designed according to the norms and styles of the Python community. The library integrates with the scientific Python ecosystem by using the "virtual files" from the GMT API to implement input and output of Python data types (numpy "ndarray" for tabular data and xarray "Dataset" for grids). Other features include an object-oriented interface for creating figures, the ability to display figures in the Jupyter notebook, and descriptive aliases for GMT arguments (e.g., "region" instead of "R" and "projection" instead of "J"). GMT/Python can also serve as a backend

  9. TARGET - TASK ANALYSIS REPORT GENERATION TOOL, VERSION 1.0

    Science.gov (United States)

    Ortiz, C. J.

    1994-01-01

    The Task Analysis Report Generation Tool, TARGET, is a graphical interface tool used to capture procedural knowledge and translate that knowledge into a hierarchical report. TARGET is based on VISTA, a knowledge acquisition tool developed by the Naval Systems Training Center. TARGET assists a programmer and/or task expert organize and understand the steps involved in accomplishing a task. The user can label individual steps in the task through a dialogue-box and get immediate graphical feedback for analysis. TARGET users can decompose tasks into basic action kernels or minimal steps to provide a clear picture of all basic actions needed to accomplish a job. This method allows the user to go back and critically examine the overall flow and makeup of the process. The user can switch between graphics (box flow diagrams) and text (task hierarchy) versions to more easily study the process being documented. As the practice of decomposition continues, tasks and their subtasks can be continually modified to more accurately reflect the user's procedures and rationale. This program is designed to help a programmer document an expert's task thus allowing the programmer to build an expert system which can help others perform the task. Flexibility is a key element of the system design and of the knowledge acquisition session. If the expert is not able to find time to work on the knowledge acquisition process with the program developer, the developer and subject matter expert may work in iterative sessions. TARGET is easy to use and is tailored to accommodate users ranging from the novice to the experienced expert systems builder. TARGET is written in C-language for IBM PC series and compatible computers running MS-DOS and Microsoft Windows version 3.0 or 3.1. No source code is supplied. The executable also requires 2Mb of RAM, a Microsoft compatible mouse, a VGA display and an 80286, 386 or 486 processor machine. The standard distribution medium for TARGET is one 5.25 inch 360K

  10. Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families.

    Science.gov (United States)

    Voloshanenko, Oksana; Gmach, Philipp; Winter, Jan; Kranz, Dominique; Boutros, Michael

    2017-11-01

    Signaling pathway modules are often encoded by several closely related paralogous genes that can have redundant roles and are therefore difficult to analyze by loss-of-function analysis. A typical example is the Wnt signaling pathway, which in mammals is mediated by 19 Wnt ligands that can bind to 10 Frizzled (FZD) receptors. Although significant progress in understanding Wnt-FZD receptor interactions has been made in recent years, tools to generate systematic interaction maps have been largely lacking. Here we generated cell lines with multiplex mutant alleles of FZD1 , FZD2 , and FZD7 and demonstrate that these cells are unresponsive to canonical Wnt ligands. Subsequently, we performed genetic rescue experiments with combinations of FZDs and canonical Wnts to create a functional ligand-receptor interaction map. These experiments showed that whereas several Wnt ligands, such as Wnt3a, induce signaling through a broad spectrum of FZD receptors, others, such as Wnt8a, act through a restricted set of FZD genes. Together, our results map functional interactions of FZDs and 10 Wnt ligands and demonstrate how multiplex targeting by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 can be used to systematically elucidate the functions of multigene families.-Voloshanenko, O., Gmach, P., Winter, J., Kranz, D., Boutros, M. Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families. © The Author(s).

  11. Mapping data through concept maps: an auxiliary tool for decision making regarding institutional projects

    Energy Technology Data Exchange (ETDEWEB)

    D’Avila, Adriana L., E-mail: adriana@ien.gov.br [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil). Divisão de Engenharia Nuclear

    2017-11-01

    This paper reports a data mapping construction aimed to subsidize the decision making process regarding institutional projects, at different levels of responsibility, at the Instituto de Engenharia Nuclear. The conception models a systemic and adaptive tool which is based on the concept mapping theory developed by Novak. The Instituto de Engenharia Nuclear (IEN) is a research center of the Comissão de Energia Nuclear (CNEN), an autarchy attached to Ministério da Ciência, Tecnologia, Inovações e Comunicações. The main focus of IEN is research and development of nuclear science and technology. The developed tool creates a more effective and accessible way of sharing information. However, beyond project data integration into a specific instrument, it also has the intent to compensate the consequences of the continued reduction of the number of workers at IEN over recent years. The recent CNEN management report, published in 2016, showed the problematic situation caused by the loss of workers, stressing the high number of pensions granted and to be granted in the near future. The loss of labor force, besides exposing the urgent need for optimizing knowledge management efforts, also sheds light into another problem: the need for grouping responsibilities among the remaining workers. In this respect, the tool developed helps to face this challenge, enhancing autonomy at different levels but preserving the institutional guidelines. To conclude the report, and in order to exemplify the method, the paper also describes the map construction relative an innovative project proposal in a joint development towards the nuclear area. (author)

  12. Mapping data through concept maps: an auxiliary tool for decision making regarding institutional projects

    International Nuclear Information System (INIS)

    D’Avila, Adriana L.

    2017-01-01

    This paper reports a data mapping construction aimed to subsidize the decision making process regarding institutional projects, at different levels of responsibility, at the Instituto de Engenharia Nuclear. The conception models a systemic and adaptive tool which is based on the concept mapping theory developed by Novak. The Instituto de Engenharia Nuclear (IEN) is a research center of the Comissão de Energia Nuclear (CNEN), an autarchy attached to Ministério da Ciência, Tecnologia, Inovações e Comunicações. The main focus of IEN is research and development of nuclear science and technology. The developed tool creates a more effective and accessible way of sharing information. However, beyond project data integration into a specific instrument, it also has the intent to compensate the consequences of the continued reduction of the number of workers at IEN over recent years. The recent CNEN management report, published in 2016, showed the problematic situation caused by the loss of workers, stressing the high number of pensions granted and to be granted in the near future. The loss of labor force, besides exposing the urgent need for optimizing knowledge management efforts, also sheds light into another problem: the need for grouping responsibilities among the remaining workers. In this respect, the tool developed helps to face this challenge, enhancing autonomy at different levels but preserving the institutional guidelines. To conclude the report, and in order to exemplify the method, the paper also describes the map construction relative an innovative project proposal in a joint development towards the nuclear area. (author)

  13. Risk maps for targeting exotic plant pest detection programs in the United States

    Science.gov (United States)

    R.D. Magarey; D.M. Borchert; J.S. Engle; M Garcia-Colunga; Frank H. Koch; et al

    2011-01-01

    In the United States, pest risk maps are used by the Cooperative Agricultural Pest Survey for spatial and temporal targeting of exotic plant pest detection programs. Methods are described to create standardized host distribution, climate and pathway risk maps for the top nationally ranked exotic pest targets. Two examples are provided to illustrate the risk mapping...

  14. AthaMap web tools for the analysis of transcriptional and posttranscriptional regulation of gene expression in Arabidopsis thaliana.

    Science.gov (United States)

    Hehl, Reinhard; Bülow, Lorenz

    2014-01-01

    The AthaMap database provides a map of verified and predicted transcription factor (TF) and small RNA-binding sites for the A. thaliana genome. The database can be used for bioinformatic predictions of putative regulatory sites. Several online web tools are available that address specific questions. Starting with the identification of transcription factor-binding sites (TFBS) in any gene of interest, colocalizing TFBS can be identified as well as common TFBS in a set of user-provided genes. Furthermore, genes can be identified that are potentially targeted by specific transcription factors or small inhibitory RNAs. This chapter provides detailed information on how each AthaMap web tool can be used online. Examples on how this database is used to address questions in circadian and diurnal regulation are given. Furthermore, complementary databases and databases that go beyond questions addressed with AthaMap are discussed.

  15. Study maps as a tool for the adaptive tests construction

    Directory of Open Access Journals (Sweden)

    Dita Dlabolová

    2013-01-01

    Full Text Available Measurement of students’ knowledge is an essential part of the educational process. Teachers on universities often use computer-based tests to testing a large number of students in a short time. The question is, what kind of information these tests provide, and if it is possible to classify students on this basis. Praxis shows that the scalar test results in the form of simple numbers cannot be plainly interpreted as the level of knowledge; moreover it is not easy to build such tests, which detect the necessary information. In the first part of the article we present the results of pedagogical experiment focused on the difference between information obtained through the computer-based test and a teacher’s interview with the same students. Possible starting point to improve information from computer-based tests in non-scalar form is a construction of an adaptive test, adapting test items to identify knowledge similar to a conversation with a teacher. As a tool for the design of the adaptive tests we use so called study maps, which are described in the second part of the article.

  16. An Experiment in Mind-Mapping and Argument-Mapping: Tools for Assessing Outcomes in the Business Curriculum

    Science.gov (United States)

    Gargouri, Chanaz; Naatus, Mary Kate

    2017-01-01

    Distinguished from other teaching-learning tools, such as mind and concept mapping in which students draw pictures and concepts and show relationships and correlation between them to demonstrate their own understanding of complex concepts, argument mapping is used to demonstrate clarity of reasoning, based on supporting evidence, and come to a…

  17. MRO CRISM MAP-PROJECTED TARGETED REDUCED DATA RECORD V1.0

    Data.gov (United States)

    National Aeronautics and Space Administration — This volume contains the CRISM Map-projected Targeted Reduced Data Record (MTRDR) archive, a collection of multiband image cubes derived from targeted (gimbaled)...

  18. Concept-Mapping Tools and the Development of Students' Critical-Thinking Skills

    Science.gov (United States)

    Tseng, Sheng-Shiang

    2015-01-01

    Developing students' critical-thinking skills has recently received attention at all levels of education. This article proposes the use of concept-mapping tools to improve students' critical-thinking skills. The article introduces a Web-based concept-mapping tool--Popplet--and demonstrates its application for teaching critical-thinking skills in…

  19. Teachers' Perceptions of Esri Story Maps as Effective Teaching Tools

    Science.gov (United States)

    Strachan, Caitlin; Mitchell, Jerry

    2014-01-01

    The current study explores teachers' perceptions of Esri Story Maps as effective teaching tools. Story Maps are a relatively new web application created using Esri's cloud-based GIS platform, ArcGIS Online. They combine digitized, dynamic web maps with other story elements to help the creator effectively convey a message. The relative ease…

  20. MicroRNA: an Emerging Therapeutic Target and Intervention Tool

    Directory of Open Access Journals (Sweden)

    Decheng Yang

    2008-06-01

    Full Text Available MicroRNAs (miRNAs are a class of short non-coding RNAs with posttranscriptional regulatory functions. To date, more than 600 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs. Accumulating evidence has linked the dysregulated expression patterns of miRNAs to a variety of diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases and viral infections. MiRNAs provide its particular layer of network for gene regulation, thus possessing the great potential both as a novel class of therapeutic targets and as a powerful intervention tool. In this regard, synthetic RNAs that contain the binding sites of miRNA have been shown to work as a “decoy” or “miRNA sponge” to inhibit the function of specific miRNAs. On the other hand, miRNA expression vectors have been used to restore or overexpress specific miRNAs to achieve a long-term effect. Further, double-stranded miRNA mimetics for transient replacement have been experimentally validated. Endogenous precursor miRNAs have also been used as scaffolds for the induction of RNA interference. This article reviews the recent progress on this emerging technology as a powerful tool for gene regulation studies and particularly as a rationale strategy for design of therapeutics.

  1. MESSI: metabolic engineering target selection and best strain identification tool.

    Science.gov (United States)

    Kang, Kang; Li, Jun; Lim, Boon Leong; Panagiotou, Gianni

    2015-01-01

    Metabolic engineering and synthetic biology are synergistically related fields for manipulating target pathways and designing microorganisms that can act as chemical factories. Saccharomyces cerevisiae's ideal bioprocessing traits make yeast a very attractive chemical factory for production of fuels, pharmaceuticals, nutraceuticals as well as a wide range of chemicals. However, future attempts of engineering S. cerevisiae's metabolism using synthetic biology need to move towards more integrative models that incorporate the high connectivity of metabolic pathways and regulatory processes and the interactions in genetic elements across those pathways and processes. To contribute in this direction, we have developed Metabolic Engineering target Selection and best Strain Identification tool (MESSI), a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms. Furthermore, through a genome-wide association study of the metabolic pathway activities with the strains' natural variation, MESSI prioritizes genes and small variants as potential regulatory points and promising metabolic engineering targets. Users can choose various parameters in the whole process such as (i) weight and expectation of each metabolic pathway activity in the final ranking of the strains, (ii) Weighted AddScore Fuse or Weighted Borda Fuse aggregation algorithm, (iii) type of variants to be included, (iv) variant sets in different biological levels.Database URL: http://sbb.hku.hk/MESSI/. © The Author(s) 2015. Published by Oxford University

  2. Waste To Biogas Mapping Tool | Pacific Southwest, Region 9 ...

    Science.gov (United States)

    2018-04-10

    Interactive map (California, Arizona, Hawaii, Nevada) showing the location and contact information to connect organic waste producers and potential users. Add your business, ensure your information is correct.

  3. Waste To Biogas Mapping Tool | Pacific Southwest, Region 9 ...

    Science.gov (United States)

    2016-02-23

    Interactive map (California, Arizona, Hawaii, Nevada) showing the location and contact information to connect organic waste producers and potential users. Add your business, ensure your information is correct.

  4. Using Concept Mapping as as Tool for Program Theory Development

    Science.gov (United States)

    Orsi, Rebecca

    2011-01-01

    The purpose of this methodological study is to explore how well a process called "concept mapping" (Trochim, 1989) can articulate the theory which underlies a social program. Articulation of a program's theory is a key step in completing a sound theory based evaluation (Weiss, 1997a). In this study, concept mapping is used to…

  5. Concept Mapping Strategies: Content, Tools and Assessment for Human Geography

    Science.gov (United States)

    Wehry, Stephanie; Monroe-Ossi, Heather; Cobb, Sharon; Fountain, Cheryl

    2012-01-01

    This article examines the use of concept mapping for formative and summative assessment of northeast Florida middle school students' knowledge of human geography. The students were participants in an afterschool, academic, college reach-out program that provided opportunities to test concept mapping strategies that support spatial thinking and…

  6. The Generic Mapping Tools 6: Classic versus Modern Mode

    Science.gov (United States)

    Wessel, P.; Uieda, L.; Luis, J. M. F.; Scharroo, R.; Smith, W. H. F.; Wobbe, F.

    2017-12-01

    The Generic Mapping Tools (GMT; gmt.soest.hawaii.edu) is a 25-year old, mature open-source software package for the analysis and display of geoscience data (e.g., interpolate, filter, manipulate, project and plot temporal and spatial data). The GMT "toolbox" includes about 80 core and 40 supplemental modules sharing a common set of command options, file structures, and documentation. GMT5, when released in 2013, introduced an application programming interface (API) to allow programmatic access to GMT from other computing environments. Since then, we have released a GMT/MATLAB toolbox, an experimental GMT/Julia package, and will soon introduce a GMT/Python module. In developing these extensions, we wanted to simplify the GMT learning curve but quickly realized the main stumbling blocks to GMT command-line mastery would be ported to the external environments unless we introduced major changes. With thousands of GMT scripts already in use by scientists around the world, we were acutely aware of the need for backwards compatibility. Our solution, to be released as GMT 6, was to add a modern run mode that complements the classic mode offered so far. Modern mode completely eliminates the top three obstacles for new (and not so new) GMT users: (1) The responsibility to properly stack PostScript layers manually (i.e., the -O -K dance), (2) the responsibility of handling output redirection of PostScript (create versus append), and (3) the need to provide commands with repeated information about regions (-R) and projections (-J). Thus, modern mode results in shorter, simpler scripts with fewer pitfalls, without interfering with classic scripts. Our implementation adds five new commands that begin and end a modern session, simplify figure management, automate the conversion of PostScript to more suitable formats, automate region detection, and offer a new automated subplot environment for multi-panel illustrations. Here, we highlight the GMT modern mode and the

  7. Concept maps as an assessment tool in a nursing course.

    Science.gov (United States)

    Hsu, Liling; Hsieh, Suh-Ing

    2005-01-01

    A concept map can be thought of as a scheme representing visual knowledge in the form of a hierarchical graphic network composed of nodes and links. In the complex health environment, it is very important for nursing educators to cultivate in nursing students thinking and judgment skills. Concept mapping is an instructional strategy that requires learners to identify, graphically display, and link key concepts by organizing and analyzing information. Concept maps can be successfully used to teach conceptual thinking, thus increasing students' competence in critical thinking in the modern paradigm. The purpose of this study was to implement concept mapping as a learning strategy in a nursing course and to evaluate students' learning progress through the construction of concept maps based on scenarios. Forty-three students, who had enrolled in a 2-year nursing program and took Nursing I in the fall semester of 2002, were invited to participate in this study, which was approved by the institutional research committee. Written informed consent was obtained from all the students. The class met for 4 hours, once a week, for 16 weeks. Participants were divided into seven groups, and during the course, they were required to complete six concept maps, five of which dealt with physical functions, including activity and rest, fluids and electrolytes, neuroendocrines, sensory-perception, and sexuality. The last map dealt with role functions. All the first drafts of the concept maps received low scores, but the third and following drafts made by all the teams showed improvement. The results of this study indicated that the students developed their concept maps from a linear sequence of concepts at the beginning into a highly integrated web of concepts in the final draft. In this study, despite complaints about the heavy workload and time consumption, the students acquired problem-solving and critical-thinking skills by organizing complex patient data, analyzing concept

  8. Use of concurrent mixed methods combining concept mapping and focus groups to adapt a health equity tool in Canada.

    Science.gov (United States)

    Guichard, Anne; Tardieu, Émilie; Dagenais, Christian; Nour, Kareen; Lafontaine, Ginette; Ridde, Valéry

    2017-04-01

    The aim of this project was to identify and prioritize a set of conditions to be considered for incorporating a health equity tool into public health practice. Concept mapping and focus groups were implemented as complementary methods to investigate the conditions of use of a health equity tool by public health organizations in Quebec. Using a hybrid integrated research design is a richer way to address the complexity of questions emerging from intervention and planning settings. This approach provides a deeper, operational, and contextualized understanding of research results involving different professional and organizational cultures, and thereby supports the decision-making process. Concept mapping served to identify and prioritize in a limited timeframe the conditions to be considered for incorporation into a health equity tool into public health practices. Focus groups then provided a more refined understanding of the barriers, issues, and facilitating factors surrounding the tools adoption, helped distinguish among participants' perspectives based on functional roles and organizational contexts, and clarified some apparently contradictory results from the concept map. The combined use of these two techniques brought the strengths of each approach to bear, thereby overcoming some of the respective limitations of concept mapping and focus groups. This design is appropriate for investigating targets with multiple levels of complexity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. ErgoVSM: A Tool for Integrating Value Stream Mapping and Ergonomics in Manufacturing

    DEFF Research Database (Denmark)

    Jarebrant, Caroline; Winkel, Jørgen; Johansson Hanse, Jan

    2016-01-01

    Value stream mapping (VSM) is a lean tool aiming at waste reduction. Previous research suggests that the use of VSM may result in work intensification and thus an increased risk for the workers of developing work-related musculoskeletal disorders (MSD). In the current study, VSM was developed...... to also consider physical exposure in the analyzed production system (ErgoVSM). As the VSM, ErgoVSM is based on a participatory approach. ErgoVSM was tested in a Swedish manufacturing company. The results suggest that ErgoVSM catalyzes change processes to include intervention proposals emphasizing...... ergonomics in addition to waste reduction. Thus, ErgoVSM appeared useful for the investigated target group of production engineers and experienced operators. The performance improvements suggested when using the ordinary VSM seemed not to be hampered by adding the ergonomics complement. However, the use...

  10. CONCEPT MAPS – IMPROVEMENT TOOL FOR ACCOUNTING INFORMATION

    Directory of Open Access Journals (Sweden)

    Oana DRĂGAN

    2014-12-01

    Full Text Available Concept maps, viewed as an innovative method for learning and evolution, are used to synthesize the knowledge of the participants to the learning process and are based on the main concepts and the relationship between them. They offer a visual representation of the information held by an individual, caught through his ability to synthesize the notions/the key concepts. The current study intends to show the importance and efficiency of using the concept maps in economics, especially in the accounting department, a method designed to settle the learning process and, also, to offer a sustainable value. The current empirical study is based on the manner in which the accounting knowledge is displayed by a sample group of 19 practitioners. The originality, the relevance of the concept maps method is underlined by the idea of the practitioners creating their own concept maps designed to point out the importance of the cognitive structure when describing the relationships between different accounting principles.

  11. Genetic Map of Mango: A Tool for Mango Breeding

    Directory of Open Access Journals (Sweden)

    David N. Kuhn

    2017-04-01

    Full Text Available Mango (Mangifera indica is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color.

  12. Digital Subtraction Angiography (DSA) "Road Map": An Angiographic Tool

    Science.gov (United States)

    Turski, P. A.; Stieghorst, M. F.; Strother, C. M.; Crummy, A. B.; Lieberman, R. P.; Mistretta, C. A.

    1982-12-01

    Continuous Digital subtraction combined with intraarterial injections of contrast medium permits the display of arterial structures during real time fluoroscopy. This DSA "road map" facilitates selective catheterization and has proved useful in interventional procedures.

  13. A Genome-Wide Map of AAV-Mediated Human Gene Targeting

    OpenAIRE

    Deyle, David R.; Hansen, R. Scott; Cornea, Anda M.; Li, Li B.; Burt, Amber A.; Alexander, Ian E.; Sandstrom, Richard S.; Stamatoyannopoulos, John A.; Wei, Chia-Lin; Russell, David W.

    2014-01-01

    To determine which genomic features promote homologous recombination, we created a genome-wide map of gene targeting sites. An adeno-associated virus vector was used to target identical loci introduced as transcriptionally active retroviral vector proviruses. A comparison of ~2,000 targeted and untargeted sites showed that targeting occurred throughout the human genome and was not influenced by the presence of nearby CpG islands, sequence repeats, or DNase I hypersensitive sites. Targeted sit...

  14. Construction of concept maps as tool for Biochemistry learning

    Directory of Open Access Journals (Sweden)

    Silvia Lopes de Menezes

    2006-07-01

    Full Text Available The use of concept maps on the teaching of sciences has been object of worldwide research with different purposes: to detect the previous knowledge of the students on certain topics or to evaluate learning, among others. Based on Ausubel´s cognitive psychology, concept maps assume that the learning is accomplished by assimilation of new concepts and propositions to the students´ cognitive structure, contributing to establish links between the previous and new knowledge. It is especially interesting on the approach of interdisciplinary issues, as many studied in Biochemistry.The relevance of the use of concept maps on biochemistry learning was evaluated on a thirty-hour undergraduation optional course, with interdisciplinary topics, which are not usually included on introductory Biochemistry courses. The course Biochemistry of Animal Venoms was structured in seven module where the biochemical action mechanisms of the venoms of Crotalus sp (south american rattlesnake, Bothrops sp (jararaca, Loxosceles sp (brown spider, Tityus sp (yellow scorpion, Phoneutria sp (armed spider, Apis mellifera (honey bee and Latrodectus sp (black widowwere discussed. The students worked in small groups and, at each module, there were (1 an oriented study, guided by questions, texts and schemes, supervised by the teachers, (2 the construction of individual concept maps, where the local and systemic effects of the venoms should be predicted by their biochemical composition and (3 the construction of a new map by the group, incorporating the information of the individual maps. The difficulty level of these tasks was gradually increased throughout the course, with lesser time to carry out the tasks, lesser assistance during the oriented study and even lesser information on the venom effects.The course assessment was given by the number, quality and correction of the concepts relationship present in the concept maps, through a questionnaire and by the

  15. Regional climatic mapping as a tool for sustainable development.

    Science.gov (United States)

    Katzschner, Lutz; Mülder, Jochen

    2008-04-01

    In the framework of an EU project on sustainable village development in China (SUCCESS), the natural climate resource was evaluated. Climate is seen as a potential for sustainability, an improvement of social life, agricultural production and reduction of air pollution problems. In this respect, thermal comfort conditions, microclimates and ventilation patterns were studied in seven Chinese villages and climate maps were drawn. Following planning recommendations, they can be transferred to decision-makers for their village development. In this framework, the paper presents a general methodology of urban climate mapping, carried out in China, applicable to all countries and climates.

  16. GPCR-targeting nanobodies: attractive research tools, diagnostics, and therapeutics.

    NARCIS (Netherlands)

    Mujić-Delić, A.; de Wit, R.H.; Verkaar, F.; Smit, M.J.

    2014-01-01

    G-protein-coupled receptors (GPCRs) represent a major therapeutic target class. A large proportion of marketed drugs exert their effect through modulation of GPCR function, and GPCRs have been successfully targeted with small molecules. Yet, the number of small new molecular entities targeting GPCRs

  17. A Java Based Human Computer Interface For a UAV Decision Support Tool Using Conformal Mapping

    National Research Council Canada - National Science Library

    Flood, Randy

    1999-01-01

    .... We solve the problem in two ways. First, we create a UAV Decision Support Tool (UAV DST) that uses a set of Java software objects to display maps and convert between latitude-longitude coordinates and x-y coordinates...

  18. U-Map and U-Multirank: profiling and ranking tools for higher education institutions

    NARCIS (Netherlands)

    Jongbloed, Benjamin W.A.; Kaiser, Franciscus; van Vught, Franciscus A.

    2013-01-01

    U-Map and U-Multirank are web-based transparency instruments, showing institutional diversity in higher education. Both tools are multidimensional, web-based and user-driven, and make use of indicators relating to individual higher education institutions (HEIs). U-Map shows what a HEI is doing and

  19. Best Practices in Educational Psychology: Using Evolving Concept Maps as Instructional and Assessment Tools

    Science.gov (United States)

    Buehl, Michelle M.; Fives, Helenrose

    2011-01-01

    We describe the implementation of evolving concept maps in two different graduate-level educational psychology courses: "The Adolescent Learner" and "Theories of Learning and Cognition." We provide an explicit description of how we used evolving concept maps as instructional and assessment tools in our respective classes, changes in the…

  20. iMindMap as an Innovative Tool in Teaching and Learning Accounting: An Exploratory Study

    Science.gov (United States)

    Wan Jusoh, Wan Noor Hazlina; Ahmad, Suraya

    2016-01-01

    Purpose: The purpose of this study is to explore the use of iMindMap software as an interactive tool in the teaching and learning method and also to be able to consider iMindMap as an alternative instrument in achieving the ultimate learning outcome. Design/Methodology/Approach: Out of 268 students of the management accounting at the University of…

  1. Concept mapping and text writing as learning tools in problem-oriented learning

    NARCIS (Netherlands)

    Fürstenau, B.; Kneppers, L.; Dekker, R.; Cañas, A.J.; Novak, J.D.; Vanhaer, J.

    2012-01-01

    In two studies we investigated whether concept mapping or summary writing better support students while learning from authentic problems in the field of business. We interpret concept mapping and summary writing as elaboration tools aiming at helping students to understand new information, and to

  2. Concept Mapping as a Learning Tool in Higher Education: A Critical Analysis of Recent Reviews

    Science.gov (United States)

    Kinchin, Ian M.

    2014-01-01

    This article aims to reexamine conclusions drawn by recent analyses of the literature on concept mapping as an educational tool by considering the wider literature on curriculum development. This is with the aim of enhancing the application of concept mapping to higher education. As part of an iterative review process, issues raised by previous…

  3. Principal tools for exploring the brain and mapping its activity

    International Nuclear Information System (INIS)

    Mazoyer, B.; Mashaal, M.

    1996-01-01

    The electro-encephalography (EEG), magneto-encephalography (MEG), scanner, positron computed tomography, single photon emission computed tomography (SPECT) and NMR imaging are the main methods used to explore human brain and to do a mapping of its activity. These methods are described into details (principle, visualization, uses, advantages, disadvantages). They can be useful to detect the possible anomalies of the human brain. (O.M.)

  4. Tools for Developing a Quality Management Program: Proactive Tools (Process Mapping, Value Stream Mapping, Fault Tree Analysis, and Failure Mode and Effects Analysis)

    International Nuclear Information System (INIS)

    Rath, Frank

    2008-01-01

    This article examines the concepts of quality management (QM) and quality assurance (QA), as well as the current state of QM and QA practices in radiotherapy. A systematic approach incorporating a series of industrial engineering-based tools is proposed, which can be applied in health care organizations proactively to improve process outcomes, reduce risk and/or improve patient safety, improve through-put, and reduce cost. This tool set includes process mapping and process flowcharting, failure modes and effects analysis (FMEA), value stream mapping, and fault tree analysis (FTA). Many health care organizations do not have experience in applying these tools and therefore do not understand how and when to use them. As a result there are many misconceptions about how to use these tools, and they are often incorrectly applied. This article describes these industrial engineering-based tools and also how to use them, when they should be used (and not used), and the intended purposes for their use. In addition the strengths and weaknesses of each of these tools are described, and examples are given to demonstrate the application of these tools in health care settings

  5. a Target Aware Texture Mapping for Sculpture Heritage Modeling

    Science.gov (United States)

    Yang, C.; Zhang, F.; Huang, X.; Li, D.; Zhu, Y.

    2017-08-01

    In this paper, we proposed a target aware image to model registration method using silhouette as the matching clues. The target sculpture object in natural environment can be automatically detected from image with complex background with assistant of 3D geometric data. Then the silhouette can be automatically extracted and applied in image to model matching. Due to the user don't need to deliberately draw target area, the time consumption for precisely image to model matching operation can be greatly reduced. To enhance the function of this method, we also improved the silhouette matching algorithm to support conditional silhouette matching. Two experiments using a stone lion sculpture of Ming Dynasty and a potable relic in museum are given to evaluate the method we proposed. The method we proposed in this paper is extended and developed into a mature software applied in many culture heritage documentation projects.

  6. Designing decision support tools for targeted N-regulation

    DEFF Research Database (Denmark)

    Christensen, Andreas Aagaard; Piil, Kristoffer; Andersen, Peter Stubkjær

    2017-01-01

    in Denmark to develop and improve a functioning decision support tool for landscape scale N-management. The aim of the study is to evaluate how a decision support tool can best be designed in order to enable landscape scale strategic N-management practices. Methods: A prototype GIS-tool for capturing......: (1) The formulation of an inclusive, socially acceptable common understanding of current land use patterns, conditions for production and effects on the environment among the stakeholders present; (2) Successful and appropriate handling of errors and imprecisions in the data being presented through...

  7. Star-Mapping Tools Enable Tracking of Endangered Animals

    Science.gov (United States)

    2009-01-01

    Software programmer Jason Holmberg of Portland, Oregon, partnered with a Goddard Space Flight Center astrophysicist to develop a method for tracking the elusive whale shark using the unique spot patterns on the fish s skin. Employing a star-mapping algorithm originally designed for the Hubble Space Telescope, Holmberg created the Shepherd Project, a photograph database and pattern-matching system that can identify whale sharks by their spots and match images contributed to the database by photographers from around the world. The system has been adapted for tracking other rare and endangered animals, including polar bears and ocean sunfish.

  8. Revealing targeted therapy for human cancer by gene module maps

    NARCIS (Netherlands)

    Wong, David J.; Nuyten, Dimitry S. A.; Regev, Aviv; Lin, Meihong; Adler, Adam S.; Segal, Eran; van de Vijver, Marc J.; Chang, Howard Y.

    2008-01-01

    A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new

  9. MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars

    Science.gov (United States)

    Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.

    2006-12-01

    Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its

  10. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

  11. Global mapping of miRNA-target interactions in cattle (Bos taurus)

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Moore, Michael J; Luna, Joseph M

    2017-01-01

    With roles in development, cell proliferation and disease, micro-RNA (miRNA) biology is of great importance and a potential therapeutic target. Here we used cross-linking immunoprecipitation (CLIP) and ligation of miRNA-target chimeras on the Argonaute (AGO) protein to globally map miRNA interact...

  12. Thermal inertia mapping - A promising new tool for mineral exploration

    Science.gov (United States)

    Short, N. M.

    1983-01-01

    The Heat Capacity Mapping Mission (HCMM) is a NASA-sponsored program designed to acquire day visible and day and night thermal IR imagery from a satellite launched on April 26, 1978 into a near polar orbit at 620 km altitude. The data are used to produce temperature difference (12 or 36 hour interval) and apparent thermal inertia (ATI) images or numerical data sets for selected areas within much of North America, Europe, North Africa, and Australia. These data are being applied to rock type discrimination, soil moisture detection, assessment of vegetation states, thermal current monitoring in water bodies, urban heat island analysis and other multidisciplinary studies. Key geological results include (1) groups of dissimilar rock materials and some individual rock types can be separated and sometimes identified by their satellite-determined thermal inertias (dependent on their albedos, densities, and conductivities), (2) large lineaments (including some faults) are often recognized by their thermal signatures (may relate to moisture content and/or reduced bulk density), and (3) visually striking expressions of geomorphic units (types) at a regional scale are especially enhanced in the night IR imagery.

  13. A GIS semiautomatic tool for classifying and mapping wetland soils

    Science.gov (United States)

    Moreno-Ramón, Héctor; Marqués-Mateu, Angel; Ibáñez-Asensio, Sara

    2016-04-01

    Wetlands are one of the most productive and biodiverse ecosystems in the world. Water is the main resource and controls the relationships between agents and factors that determine the quality of the wetland. However, vegetation, wildlife and soils are also essential factors to understand these environments. It is possible that soils have been the least studied resource due to their sampling problems. This feature has caused that sometimes wetland soils have been classified broadly. The traditional methodology states that homogeneous soil units should be based on the five soil forming-factors. The problem can appear when the variation of one soil-forming factor is too small to differentiate a change in soil units, or in case that there is another factor, which is not taken into account (e.g. fluctuating water table). This is the case of Albufera of Valencia, a coastal wetland located in the middle east of the Iberian Peninsula (Spain). The saline water table fluctuates throughout the year and it generates differences in soils. To solve this problem, the objectives of this study were to establish a reliable methodology to avoid that problems, and develop a GIS tool that would allow us to define homogeneous soil units in wetlands. This step is essential for the soil scientist, who has to decide the number of soil profiles in a study. The research was conducted with data from 133 soil pits of a previous study in the wetland. In that study, soil parameters of 401 samples (organic carbon, salinity, carbonates, n-value, etc.) were analysed. In a first stage, GIS layers were generated according to depth. The method employed was Bayesian Maxim Entropy. Subsequently, it was designed a program in GIS environment that was based on the decision tree algorithms. The goal of this tool was to create a single layer, for each soil variable, according to the different diagnostic criteria of Soil Taxonomy (properties, horizons and diagnostic epipedons). At the end, the program

  14. Using intervention mapping to develop a work-related guidance tool for those affected by cancer

    Directory of Open Access Journals (Sweden)

    Munir Fehmidah

    2013-01-01

    Full Text Available Abstract Background Working-aged individuals diagnosed and treated for cancer require support and assistance to make decisions regarding work. However, healthcare professionals do not consider the work-related needs of patients and employers do not understand the full impact cancer can have upon the employee and their work. We therefore developed a work-related guidance tool for those diagnosed with cancer that enables them to take the lead in stimulating discussion with a range of different healthcare professionals, employers, employment agencies and support services. The tool facilitates discussions through a set of questions individuals can utilise to find solutions and minimise the impact cancer diagnosis, prognosis and treatment may have on their employment, sick leave and return to work outcomes. The objective of the present article is to describe the systematic development and content of the tool using Intervention Mapping Protocol (IMP. Methods The study used the first five steps of the intervention mapping process to guide the development of the tool. A needs assessment identified the ‘gaps’ in information/advice received from healthcare professionals and other stakeholders. The intended outcomes and performance objectives for the tool were then identified followed by theory-based methods and an implementation plan. A draft of the tool was developed and subjected to a two-stage Delphi process with various stakeholders. The final tool was piloted with 38 individuals at various stages of the cancer journey. Results The tool was designed to be a self-led tool that can be used by any person with a cancer diagnosis and working for most types of employers. The pilot study indicated that the tool was relevant and much needed. Conclusions Intervention Mapping is a valuable protocol for designing complex guidance tools. The process and design of this particular tool can lend itself to other situations both occupational and more health

  15. Authoring Tool for Identifying Learning Styles, Using Self-Organizing Maps on Mobile Devices

    Directory of Open Access Journals (Sweden)

    Ramón Zatarain Cabada

    2011-05-01

    Full Text Available This work explores a methodological proposal whose main objective is the identification of learning styles using a method of self-organizing maps designed to work, for the most part, on mobile devices. These maps can work in real time and without direct student interaction, which implies the absence of prior information. The results generated are an authoring tool for adaptive courses in Web 2.0 environments.

  16. GIS-based interactive tool to map the advent of world conquerors

    Science.gov (United States)

    Lakkaraju, Mahesh

    The objective of this thesis is to show the scale and extent of some of the greatest empires the world has ever seen. This is a hybrid project between the GIS based interactive tool and the web-based JavaScript tool. This approach lets the students learn effectively about the emperors themselves while understanding how long and far their empires spread. In the GIS based tool, a map is displayed with various points on it, and when a user clicks on one point, the relevant information of what happened at that particular place is displayed. Apart from this information, users can also select the interactive animation button and can walk through a set of battles in chronological order. As mentioned, this uses Java as the main programming language, and MOJO (Map Objects Java Objects) provided by ESRI. MOJO is very effective as its GIS related features can be included in the application itself. This app. is a simple tool and has been developed for university or high school level students. D3.js is an interactive animation and visualization platform built on the Javascript framework. Though HTML5, CSS3, Javascript and SVG animations can be used to derive custom animations, this tool can help bring out results with less effort and more ease of use. Hence, it has become the most sought after visualization tool for multiple applications. D3.js has provided a map-based visualization feature so that we can easily display text-based data in a map-based interface. To draw the map and the points on it, D3.js uses data rendered in TOPO JSON format. The latitudes and longitudes can be provided, which are interpolated into the Map svg. One of the main advantages of doing it this way is that more information is retained when we use a visual medium.

  17. A Side Scan Sonar Image Target Detection Algorithm Based on a Neutrosophic Set and Diffusion Maps

    Directory of Open Access Journals (Sweden)

    Xiao Wang

    2018-02-01

    Full Text Available To accurately achieve side scan sonar (SSS image target detection, a novel target detection algorithm based on a neutrosophic set (NS and diffusion maps (DMs is proposed in this paper. Firstly, the neutrosophic subset images were obtained by transforming the input SSS image into the NS domain. Secondly, the shadowed areas of the SSS image were detected using the single gray value threshold method before the diffusion map was calculated. Lastly, based on the diffusion map, the target areas were detected using the improved target scoring equation defined by the diffusion distance and texture feature. The experiments using SSS images of single clear and unclear targets, with or without shadowed areas, showed that the algorithm accurately detects targets. Experiments using SSS images of multiple targets, with or without shadowed areas, showed that no false or missing detections occurred. The target areas were also accurately detected in SSS images with complex features such as sand wave terrain. The accuracy and effectiveness of the proposed algorithm were assessed.

  18. Map based multimedia tool on Pacific theatre in World War II

    Science.gov (United States)

    Pakala Venkata, Devi Prasada Reddy

    Maps have been used for depicting data of all kinds in the educational community for many years. A standout amongst the rapidly changing methods of teaching is through the development of interactive and dynamic maps. The emphasis of the thesis is to develop an intuitive map based multimedia tool, which provides a timeline of battles and events in the Pacific theatre of World War II. The tool contains summaries of major battles and commanders and has multimedia content embedded in it. The primary advantage of this Map tool is that one can quickly know about all the battles and campaigns of the Pacific Theatre by accessing Timeline of Battles in each region or Individual Battles in each region or Summary of each Battle in an interactive way. This tool can be accessed via any standard web browser and motivate the user to know more about the battles involved in the Pacific Theatre. It was made responsive using Google maps API, JavaScript, HTML5 and CSS.

  19. Credit analysis using cognitive maps as a tool to support decision making in a factoring company

    Directory of Open Access Journals (Sweden)

    Sergio Renato Ferreira Decker

    2014-08-01

    Full Text Available This study represents a case study conducted in a factoring company in the city of Pelotas, Rio Grande do Sul. In order to support company managers, the research aimed to develop a tool to support the decision to grant credit to new customers. Aiming to better understand the problem presented, with all its complexity, a Cognitive Map of the credit analysis process was developed in a constructive way along with the maker.. Through the resulting Cognitive Map, the decision maker now possesses an important tool to describe their decisions. Such research will proceed with the development of the remaining steps necessary to build a  multicriteria decision model.

  20. Targeting malnutrition. Isotopic tools for evaluating nutrition worldwide

    International Nuclear Information System (INIS)

    Kinley, D. III

    1996-07-01

    This booklet provides a brief description of pioneering IAEA-supported work to evaluate vitamin A and iron deficiencies, bone disease, undernutrition and obesity and the special nutritional requirements of pregnant and lactating women and their children. And while it shows that the role of the Agency remains highly specialized, to develop and transfer nuclear-based evaluation tools, each of these areas of applied research aims at improving the scientific foundations for broader national food and nutrition-related development policies and programmes

  1. Modifications to risk-targeted seismic design maps for subduction and near-fault hazards

    Science.gov (United States)

    Liel, Abbie B.; Luco, Nicolas; Raghunandan, Meera; Champion, C.; Haukaas, Terje

    2015-01-01

    ASCE 7-10 introduced new seismic design maps that define risk-targeted ground motions such that buildings designed according to these maps will have 1% chance of collapse in 50 years. These maps were developed by iterative risk calculation, wherein a generic building collapse fragility curve is convolved with the U.S. Geological Survey hazard curve until target risk criteria are met. Recent research shows that this current approach may be unconservative at locations where the tectonic environment is much different than that used to develop the generic fragility curve. This study illustrates how risk-targeted ground motions at selected sites would change if generic building fragility curve and hazard assessment were modified to account for seismic risk from subduction earthquakes and near-fault pulses. The paper also explores the difficulties in implementing these changes.

  2. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

    Directory of Open Access Journals (Sweden)

    Leslie Regad

    Full Text Available Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC, obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at

  3. Enhanced clinical pharmacy service targeting tools: risk-predictive algorithms.

    Science.gov (United States)

    El Hajji, Feras W D; Scullin, Claire; Scott, Michael G; McElnay, James C

    2015-04-01

    This study aimed to determine the value of using a mix of clinical pharmacy data and routine hospital admission spell data in the development of predictive algorithms. Exploration of risk factors in hospitalized patients, together with the targeting strategies devised, will enable the prioritization of clinical pharmacy services to optimize patient outcomes. Predictive algorithms were developed using a number of detailed steps using a 75% sample of integrated medicines management (IMM) patients, and validated using the remaining 25%. IMM patients receive targeted clinical pharmacy input throughout their hospital stay. The algorithms were applied to the validation sample, and predicted risk probability was generated for each patient from the coefficients. Risk threshold for the algorithms were determined by identifying the cut-off points of risk scores at which the algorithm would have the highest discriminative performance. Clinical pharmacy staffing levels were obtained from the pharmacy department staffing database. Numbers of previous emergency admissions and admission medicines together with age-adjusted co-morbidity and diuretic receipt formed a 12-month post-discharge and/or readmission risk algorithm. Age-adjusted co-morbidity proved to be the best index to predict mortality. Increased numbers of clinical pharmacy staff at ward level was correlated with a reduction in risk-adjusted mortality index (RAMI). Algorithms created were valid in predicting risk of in-hospital and post-discharge mortality and risk of hospital readmission 3, 6 and 12 months post-discharge. The provision of ward-based clinical pharmacy services is a key component to reducing RAMI and enabling the full benefits of pharmacy input to patient care to be realized. © 2014 John Wiley & Sons, Ltd.

  4. Using a concept map as a tool for strategic planning: The Healthy Brain Initiative.

    Science.gov (United States)

    Anderson, Lynda A; Day, Kristine L; Vandenberg, Anna E

    2011-09-01

    Concept mapping is a tool to assist in strategic planning that allows planners to work through a sequence of phases to produce a conceptual framework. Although several studies describe how concept mapping is applied to various public health problems, the flexibility of the methods used in each phase of the process is often overlooked. If practitioners were more aware of the flexibility, more public health endeavors could benefit from using concept mapping as a tool for strategic planning. The objective of this article is to describe how the 6 concept-mapping phases originally outlined by William Trochim guided our strategic planning process and how we adjusted the specific methods in the first 2 phases to meet the specialized needs and requirements to create The Healthy Brain Initiative: A National Public Health Road Map to Maintaining Cognitive Health. In the first stage (phases 1 and 2 of concept mapping), we formed a steering committee, convened 4 work groups over a period of 3 months, and generated an initial set of 42 action items grounded in science. In the second stage (phases 3 and 4), we engaged stakeholders in sorting and rating the action items and constructed a series of concept maps. In the third and final stage (phases 5 and 6), we examined and refined the action items and generated a final concept map consisting of 44 action items. We then selected the top 10 action items, and in 2007, we published The Healthy Brain Initiative: A National Public Health Road Map to Maintaining Cognitive Health, which represents the strategic plan for The Healthy Brain Initiative.

  5. Tools to Analyze Morphology and Spatially Mapped Molecular Data | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    This project is to develop, deploy, and disseminate a suite of open source tools and integrated informatics platform that will facilitate multi-scale, correlative analyses of high resolution whole slide tissue image data, spatially mapped genetics and molecular data for cancer research. This platform will play an essential role in supporting studies of tumor initiation, development, heterogeneity, invasion, and metastasis.

  6. Mapping, Awareness, and Virtualization Network Administrator Training Tool (MAVNATT) Architecture and Framework

    Science.gov (United States)

    2015-06-01

    capable of all network monitoring areas and can also perform integrated network discovery with SNMP, LDAP , ICMP, SSH, and other protocols [24], [27], [28...based Mapping Yes (ICMP, SNMP, WMI) Yes (Plugin Dependent) Yes (ICMP, SNMP, WMI, LDAP , SSH) 24 3. Virtualization Virtualization tools

  7. GeneRecon—A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, Thomas; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm

    2006-01-01

    GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case-control data from phased or unphased SNP and micro-satellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis Hastings sampling in the state space...

  8. Staff and Client Perspectives on the Journey Mapping Online Evaluation Tool in a Drug Court Program

    Science.gov (United States)

    Crunkilton, Dhira D.

    2009-01-01

    The purpose of this study was to assess staff and client perspectives on the Internet-based Journey Mapping program evaluation tool. A drug court program was chosen for a case study research design. Six staff and 10 clients participated in interviews and observations, and also responded to a questionnaire. A staff survey provided additional data.…

  9. Impact of targeted UPLC-MS/MS metabolomics on chemical and biochemical characterisation of MAPs

    Directory of Open Access Journals (Sweden)

    Martens, Stefan

    2016-07-01

    Full Text Available Analysis of natural product pattern (metabolites; metabolomics and its formation (pathway; biosynthesis in plants, especially in non-model or crop plants such as medicinal and aromatic plants (MAPs, is a research field with significant potential for breeders, growers and consumers. There is an increasing importance for constant and sustainable quality of MAPs final products. Polyphenols are one of the most important compounds for the antioxidant properties of MAPs and are often, if not identified as active principle, used as lead compounds in quality assessment of herbal drugs and related preparation (herbal tea, alcoholic extracts etc.. Therefore, offering an efficient, robust and reliable fast tool to determine these quality features of MAPs will guarantee the growers, industrial users and the consumers from possible frauds.

  10. Cost Based Value Stream Mapping as a Sustainable Construction Tool for Underground Pipeline Construction Projects

    Directory of Open Access Journals (Sweden)

    Murat Gunduz

    2017-11-01

    Full Text Available This paper deals with application of Value Stream Mapping (VSM as a sustainable construction tool on a real construction project of installation of underground pipelines. VSM was adapted to reduce the high percentage of non-value-added activities and time wastes during each construction stage and the paper searched for an effective way to consider the cost for studied construction of underground pipeline. This paper is unique in its way that it adopts cost implementation of VSM to improve the productivity in underground pipeline projects. The data was observed and collected from site during construction, indicating the cycle time, value added and non-value added of each construction stage. The current state was built based on these details. This was an eye-opening exercise and a process management tool as a trigger for improvement. After the current state assessment, a future state is attempted by Value Stream Mapping tool balancing the resources using a Line of Balance (LOB technique. Moreover, a sustainable cost estimation model was developed during current state and future state to calculate the cost of underground pipeline construction. The result shows a cost reduction of 20.8% between current and future states. This reflects the importance of the cost based Value Stream Mapping in construction as a sustainable measurement tool. This new tool could be utilized in construction industry to add the sustainability and effective cost management.

  11. Use of concept mapping as a facilitative tool to promote learning in pharmacology.

    Science.gov (United States)

    Qadir, Farida; Zehra, Tabassum; Khan, Imrana

    2011-08-01

    To assess whether students find concept mapping a useful learning methodology to conceptualize and organize topics studied in CNS module of Pharmacology; and to evaluate whether addition of concept mapping assignment could help to improve examination scores. An analytical study. College of Dentistry, Jinnah Medical and Dental College, Karachi, Pakistan, from March to May 2009. A class of 50 BDS students was recruited for the study. Two randomly selected groups of 12 students each, prepared concept maps in topics from CNS pharmacology which were displayed and discussed during tutorial sessions. The other two groups (n = 25) following the traditional teaching methodology, served as controls. Scores from best choice questions and short essay questions were compared between the investigational and control groups using the student's t-test with significance at p 0.05). However, feedback about concept mapping showed that the technique helped the students to conceptualize difficult topics in CNS pharmacology (86.36%). Concept mapping was particularly beneficial in preparing for exams as it provided a quick overview of the entire subject (68.68%). Students found concept mapping as a useful pedagogical tool which could potentially be used to acquire meaningful learning in Pharmacology as a supplement to traditional teaching techniques. It was not found beneficial in improving examination grades probably because standard examinations and concept mapping measure different cognitive domains.

  12. DMPD: Ubiquitin: tool and target for intracellular NF-kappaB inhibitors. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16982211 Ubiquitin: tool and target for intracellular NF-kappaB inhibitors. Wullaer...vg) (.html) (.csml) Show Ubiquitin: tool and target for intracellular NF-kappaB inhibitors. PubmedID 16982211 Title Ubiq

  13. Enhanced STEM Learning with the GeoMapApp Data Exploration Tool

    Science.gov (United States)

    Goodwillie, A. M.

    2014-12-01

    GeoMapApp (http://www.geomapapp.org), is a free, map-based data discovery and visualisation tool developed with NSF funding at Lamont-Doherty Earth Observatory. GeoMapApp provides casual and specialist users alike with access to hundreds of built-in geoscience data sets covering geology, geophysics, geochemistry, oceanography, climatology, cryospherics, and the environment. Users can also import their own data tables, spreadsheets, shapefiles, grids and images. Simple manipulation and analysis tools combined with layering capabilities and engaging visualisations provide a powerful platform with which to explore and interrogate geoscience data in its proper geospatial context thus helping users to more easily gain insight into the meaning of the data. A global elevation base map covering the oceans as well as continents forms the backbone of GeoMapApp. The multi-resolution base map is updated regularly and includes data sources ranging from Space Shuttle elevation data for land areas to ultra-high-resolution surveys of coral reefs and seafloor hydrothermal vent fields. Examples of built-in data sets that can be layered over the elevation model include interactive earthquake and volcano data, plate tectonic velocities, hurricane tracks, land and ocean temperature, water column properties, age of the ocean floor, and deep submersible bottom photos. A versatile profiling tool provides instant access to data cross-sections. Contouring and 3-D views are also offered - the attached image shows a 3-D view of East Africa's Ngorongoro Crater as an example. Tabular data - both imported and built-in - can be displayed in a variety of ways and a lasso tool enables users to quickly select data points directly from the map. A range of STEM-based education material based upon GeoMapApp is already available, including a number of self-contained modules for school- and college-level students (http://www.geomapapp.org/education/contributed_material.html). More learning modules are

  14. Evaluating gaze-based interface tools to facilitate point-and-select tasks with small targets

    DEFF Research Database (Denmark)

    Skovsgaard, Henrik; Mateo, Julio C.; Hansen, John Paulin

    2011-01-01

    Gaze interaction affords hands-free control of computers. Pointing to and selecting small targets using gaze alone is difficult because of the limited accuracy of gaze pointing. This is the first experimental comparison of gaze-based interface tools for small-target (e.g. <12 × 12 pixels) point-a...

  15. Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART).

    Science.gov (United States)

    Vance, Keith W

    2017-01-01

    Capture Hybridization Analysis of RNA Targets (CHART) has recently been developed to map the genome-wide binding profile of chromatin-associated RNAs. This protocol uses a small number of 22-28 nucleotide biotinylated antisense oligonucleotides, complementary to regions of the target RNA that are accessible for hybridization, to purify RNAs from a cross-linked chromatin extract. RNA-chromatin complexes are next immobilized on beads, washed, and specifically eluted using RNase H. Associated genomic DNA is then sequenced using high-throughput sequencing technologies and mapped to the genome to identify RNA-chromatin associations on a large scale. CHART-based strategies can be applied to determine the nature and extent of long noncoding RNA (long ncRNA) association with chromatin genome-wide and identify direct long ncRNA transcriptional targets.

  16. TF Target Mapper: a BLAST search tool for the identification of Transcription Factor target genes.

    NARCIS (Netherlands)

    S. Horsman (Sebastiaan); M.J. Moorhouse (Michael); V. de Jager (Victor); P.J. van der Spek (Peter); F.G. Grosveld (Frank); J. Strouboulis (John); E. Katsantoni (Eleni)

    2006-01-01

    textabstractBACKGROUND: In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and provides a

  17. Implementing Dementia Care Mapping as a practice development tool in dementia care services: a systematic review.

    Science.gov (United States)

    Surr, Claire A; Griffiths, Alys W; Kelley, Rachael

    2018-01-01

    Dementia Care Mapping (DCM) is an observational tool set within a practice development process. Following training in the method, DCM is implemented via a cyclic process of briefing staff, conducting mapping observations, data analysis and report preparation, feedback to staff and action planning. Recent controlled studies of DCM's efficacy have found heterogeneous results, and variability in DCM implementation has been indicated as a potential contributing factor. This review aimed to examine the primary research evidence on the processes and the barriers and facilitators to implementing DCM as a practice development method within formal dementia care settings. PUBMED, PsycINFO, CINAHL, The Cochrane Library-Cochrane reviews, HMIC (Ovid), Web of Science and Social Care Online were searched using the term "Dementia Care Mapping". Inclusion criterion was primary research studies in any formal dementia care settings where DCM was used as a practice development tool and which included discussion/critique of the implementation processes. Assessment of study quality was conducted using the Mixed Methods Appraisal Tool. Twelve papers were included in the review, representing nine research studies. The papers included discussion of various components of the DCM process, including mapper selection and preparation; mapping observations; data analysis, report writing and feedback; and action planning. However, robust evidence on requirements for successful implementation of these components was limited. Barriers and facilitators to mapping were also discussed. The review found some consensus that DCM is more likely to be successfully implemented if the right people are selected to be trained as mappers, with appropriate mapper preparation and ongoing support and with effective leadership for DCM within the implementing organization/unit and in organizations that already have a person-centered culture or ethos. Future development of the DCM tool should consider ways to save on

  18. Development of a Competency Mapping Tool for Undergraduate Professional Degree Programmes, Using Mechanical Engineering as a Case Study

    Science.gov (United States)

    Holmes, David W.; Sheehan, Madoc; Birks, Melanie; Smithson, John

    2018-01-01

    Mapping the curriculum of a professional degree to the associated competency standard ensures graduates have the competence to perform as professionals. Existing approaches to competence mapping vary greatly in depth, complexity, and effectiveness, and a standardised approach remains elusive. This paper describes a new mapping software tool that…

  19. What's in a Word? Concept mapping: a graphical tool to reinforce learning of epidemiological concepts.

    Science.gov (United States)

    Berglund, Anita

    2015-12-01

    Epidemiology is founded on central concepts and principles, essential for conducting, reporting and critically assessing epidemiological studies. Definitions of the many concepts used in the field can be found in textbooks and via the Dictionary of Epidemiology. However, central epidemiological concepts are labelled and used in multiple ways, leading to potential misunderstanding when communicating in different fora. The aim here is to describe collaborative concept mapping, and illustrate how it can be used in teaching and learning epidemiology. Concept mapping is a cognitive technique that is widely used in the education of medical and allied health professions as a tool for critical thinking, and to assimilate new knowledge, but it is still under-utilised in epidemiology. A specific concept map is defined by the aim and question in focus; it is thus framed by a context. The concept map is constructed using a set of concepts (nodes) that are linked with arrows or lines (links). Words and phrases (connective terms) are used to explain relationships between the concepts linked. Different domains can be interconnected by linking concepts in different areas (cross-links). The underlying structure of knowledge is often complex, and consequently concept maps can be constructed using different topological features. Here we provide an illustrative example of concept mapping, based on a set of 'basic' concepts introduced in a doctoral course in epidemiology. In summary, concept mapping is a compelling, active learning tool, which can promote shared deeper knowledge of concepts and their complex interconnections, thereby facilitating a better understanding of epidemiological research. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  20. Range-Doppler Mapping of Space-Based Targets Using the JRO 50 MHz Radar

    Science.gov (United States)

    Kesaraju, S.; Mathews, J. D.; Milla, M.; Vierinen, J.

    2017-12-01

    The Jicamarca Radio Observatory (JRO) two-dimensional square array radar system operating at 6-m wavelength was used to study the Moon and low Earth orbit satellites using the Range-Doppler inverse synthetic aperture radar technique also known as Delay-Doppler imaging. The radar data was collected on Oct 21, 2015. A circularly polarized coded pulse was transmitted from a quarter-array antenna segment during lunar transit over JRO. Dual-linear polarization receive systems were employed on two quarter-array segments and on two 1/64th array modules giving the longest possible baselines across the transit path. A Range-Doppler mapping technique that uses the rotational motion of the targets and an autofocusing motion and ionospheric delay compensation technique has been implemented to generate the two-dimensional maps of the point-target (Satellite) and range-spread target (Moon). A review of our technique and the maps obtained from these observations is presented herein. Range-Doppler maps of the Moon and satellites are instructive with regards to possible further improvement of the technique, especially regarding ionospheric compensation.

  1. Parametric tools over crowdsourced maps as means for participatory consideration of environmental issues in cities

    Science.gov (United States)

    Montoya, Paula; Ballesteros, José; Gervás, Pablo

    2015-04-01

    The increasing complexity of space use and resource cycles in cities, demands an understanding of the built environment as "ecological": enabling mutation while remaining balanced and biologically sustainable. Designing man`s environment is no longer a question of defining types, but rather an act of inserting changes within a complex system. Architecture and urban planning have become increasingly aware of their condition as system-oriented disciplines, and they are in the process of developing the necessary languages, design tools, and alliances. We will argue the relevance of parametric maps as one of the most powerful of those tools, in terms of their potential for adaptive prototype design, convergence of disciplines, and collaborative work. Cities need to change in order to survive. As the main human landscape (by 2050 75% of the world's population will live in urban areas) cities follow biological patterns of behaviour, constantly replacing their cells, renovating infrastructure systems and refining methods for energy provision and waste management. They need to adapt constantly. As responsive entities, they develop their own protocols for reaction to environmental change and challenge the increasing pressure of several issues related to scale: population, mobility, water and energy supply, pollution... The representation of these urban issues on maps becomes crucial for understanding and addressing them in design. Maps enhanced with parametric tools are relational and not only they register environmental dynamics but they allow adaptation of the system through interwoven parameters of mutation. Citizens are taking part in decisions and becoming aware of their role as urban experts in a bottom-up design process of the cities where they live. Modern tools for dynamic visualisation and collaborative edition of maps have an important role to play in this process. More and more people consult maps on hand-held devices as part of their daily routine. The advent

  2. Software project management tools in global software development: a systematic mapping study.

    Science.gov (United States)

    Chadli, Saad Yasser; Idri, Ali; Ros, Joaquín Nicolás; Fernández-Alemán, José Luis; de Gea, Juan M Carrillo; Toval, Ambrosio

    2016-01-01

    Global software development (GSD) which is a growing trend in the software industry is characterized by a highly distributed environment. Performing software project management (SPM) in such conditions implies the need to overcome new limitations resulting from cultural, temporal and geographic separation. The aim of this research is to discover and classify the various tools mentioned in literature that provide GSD project managers with support and to identify in what way they support group interaction. A systematic mapping study has been performed by means of automatic searches in five sources. We have then synthesized the data extracted and presented the results of this study. A total of 102 tools were identified as being used in SPM activities in GSD. We have classified these tools, according to the software life cycle process on which they focus and how they support the 3C collaboration model (communication, coordination and cooperation). The majority of the tools found are standalone tools (77%). A small number of platforms (8%) also offer a set of interacting tools that cover the software development lifecycle. Results also indicate that SPM areas in GSD are not adequately supported by corresponding tools and deserve more attention from tool builders.

  3. Evaluation and development of an ergonomic complement to the Value Stream Mapping tool

    DEFF Research Database (Denmark)

    Edwards, Kasper

    2009-01-01

    -out and physical work load problems are frequently described. Thus, the healthcare system needs to become more efficient and the principles of lean manufacturing are increasingly being selected by hospitals and wards as the methodology to becoming more efficient. Lean has been around for many years in the form...... of the Toyota Production System (TPS). But the concept and term surfaced as “lean” following a study of the Japanese car industry that tried to explain its high level of success (Liker, 2004) . Lean is deeply rooted in an industrial manufacturing environment and many of the tools that are being used...... in connection with lean also have their origins in manufacturing. The fundamental methodology when implementing lean is value stream mapping (VSM). VSM is a tool to analyze a process by mapping all activities from a specific process in sequence. The time to complete an activity and waiting times between events...

  4. A double-mutant collection targeting MAP kinase related genes in Arabidopsis for studying genetic interactions.

    Science.gov (United States)

    Su, Shih-Heng; Krysan, Patrick J

    2016-12-01

    Mitogen-activated protein kinase cascades are conserved in all eukaryotes. In Arabidopsis thaliana there are approximately 80 genes encoding MAP kinase kinase kinases (MAP3K), 10 genes encoding MAP kinase kinases (MAP2K), and 20 genes encoding MAP kinases (MAPK). Reverse genetic analysis has failed to reveal abnormal phenotypes for a majority of these genes. One strategy for uncovering gene function when single-mutant lines do not produce an informative phenotype is to perform a systematic genetic interaction screen whereby double-mutants are created from a large library of single-mutant lines. Here we describe a new collection of 275 double-mutant lines derived from a library of single-mutants targeting genes related to MAP kinase signaling. To facilitate this study, we developed a high-throughput double-mutant generating pipeline using a system for growing Arabidopsis seedlings in 96-well plates. A quantitative root growth assay was used to screen for evidence of genetic interactions in this double-mutant collection. Our screen revealed four genetic interactions, all of which caused synthetic enhancement of the root growth defects observed in a MAP kinase 4 (MPK4) single-mutant line. Seeds for this double-mutant collection are publicly available through the Arabidopsis Biological Resource Center. Scientists interested in diverse biological processes can now screen this double-mutant collection under a wide range of growth conditions in order to search for additional genetic interactions that may provide new insights into MAP kinase signaling. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  5. Nature in the metropolis: Mapping biodiversity using metropolitan landscape characterization tools

    OpenAIRE

    Tisma, A.; van der Velde, J.R.T.; Nijhuis, S.; Pouderoijen, M.T.

    2014-01-01

    Cities can be planned and designed to reduce their effect on biodiversity loss and may even be able to sustain biodiversity levels in some instances, due to ‘beta-diversity’. The heterogeneity of metropolitan regions can be expected to have a strong impact on beta-diversity. Tools such as landscape characterization can assist in the understanding of betadiversity in metropolitan regions by mapping the extent and configuration of beta-diversity conditions, in particular microhabitats and habit...

  6. Expanding baker maps: A first tool to study homoclinic biffurcations of 3-D diffeomorphisms

    OpenAIRE

    Vigil Álvarez, Enrique

    2015-01-01

    Under the title Expanding Baker Maps: A First Tool To Study Homoclinic Bifurcations Of 3-D Diffeomorphisms¿ this thesis explores an interesting part of the Dynamical Systems: the study of the dynamics emerging when a family of diffeomorphisms unfolds a homoclinic tangency in a three-dimensional manifold. Even though this problem has been deeply considered in the case of two-dimensional tangencies, short time until little or nothing was known in three-dimensional framework. In a paper...

  7. MAP-IT: A Practical Tool for Planning Complex Behavior Modification Interventions.

    Science.gov (United States)

    Hansen, Sylvia; Kanning, Martina; Lauer, Romy; Steinacker, Jürgen M; Schlicht, Wolfgang

    2017-09-01

    Health research often aims to prevent noncommunicable diseases and to improve individual and public health by discovering intervention strategies that are effective in changing behavior and/or environments that are detrimental to one's health. Ideally, findings from original research support practitioners in planning and implementing effective interventions. Unfortunately, interventions often fail to overcome the translational block between science and practice. They often ignore theoretical knowledge, overlook empirical evidence, and underrate the impact of the environment. Accordingly, sustainable changes in individual behavior and/or the environment are difficult to achieve. Developing theory-driven and evidence-based interventions in the real world is a complex task. Existing implementation frameworks and theories often do not meet the needs of health practitioners. The purpose of this article is to synthesize existing frameworks and to provide a tool, the Matrix Assisting Practitioner's Intervention Planning Tool (MAP-IT), that links research to practice and helps practitioners to design multicomponent interventions. In this article, we use physical activity of older adults as an example to explain the rationale of MAP-IT. In MAP-IT, individual as well as environmental mechanisms are listed and behavior change techniques are linked to these mechanisms and to intervention components. MAP-IT is theory-driven and evidence-based. It is time-saving and helpful for practitioners when planning complex interventions.

  8. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

    Directory of Open Access Journals (Sweden)

    Shi Weisong

    2011-06-01

    Full Text Available Abstract Background Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS. However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. Results To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80% mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http

  9. An integrated user-friendly ArcMAP tool for bivariate statistical modeling in geoscience applications

    Science.gov (United States)

    Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusof, Z.; Tehrany, M. S.

    2014-10-01

    Modeling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modeling. Bivariate statistical analysis (BSA) assists in hazard modeling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, BSM (bivariate statistical modeler), for BSA technique is proposed. Three popular BSA techniques such as frequency ratio, weights-of-evidence, and evidential belief function models are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and is created by a simple graphical user interface, which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

  10. Social dataset analysis and mapping tools for Risk Perception: resilience, people preparation and communication tools

    Science.gov (United States)

    Peters-Guarin, Graciela; Garcia, Carolina; Frigerio, Simone

    2010-05-01

    Perception has been identified as resource and part of the resilience of a community to disasters. Risk perception, if present, may determine the potential damage a household or community experience. Different levels of risk perception and preparedness can influence directly people's susceptibility and the way they might react in case of an emergency caused by natural hazards. In spite of the profuse literature about risk perception, works to spatially portray this feature are really scarce. The spatial relationship to danger or hazard is being recognised as an important factor of the risk equation; it can be used as a powerful tool either for better knowledge or for operational reasons (e.g. management of preventive information). Risk perception and people's awareness when displayed in a spatial format can be useful for several actors in the risk management arena. Local authorities and civil protection can better address educational activities to increase the preparation of particularly vulnerable groups of clusters of households within a community. It can also be useful for the emergency personal in order to optimally direct the actions in case of an emergency. In the framework of the Marie Curie Research Project, a Community Based Early Warning System (CBEWS) it's been developed in the Mountain Community Valtellina of Tirano, northern Italy. This community has been continuously exposed to different mass movements and floods, in particular, a large event in 1987 which affected a large portion of the valley and left 58 dead. The actual emergency plan for the study area is composed by a real time, highly detailed, decision support system. This emergency plan contains detailed instructions for the rapid deployment of civil protection and other emergency personal in case of emergency, for risk scenarios previously defined. Especially in case of a large event, where timely reaction is crucial for reducing casualties, it is important for those in charge of emergency

  11. Potential benefits of a spatially targeted regulation based on detailed N-reduction maps to decrease N-load from agriculture in a small groundwater dominated catchment

    DEFF Research Database (Denmark)

    Hansen, A L; Refsgaard, J C; Olesen, Jørgen Eivind

    2017-01-01

    Denmark must further decrease the N-load to coastal waters from agricultural areas to comply with the Baltic Sea Action Plan and the EU Water Framework Directive. A new spatially targeted regulation is under development that focuses on locating N-mitigation measures in areas with low natural...... reduction of nitrate (N-reduction). A key tool in this respect is N-reduction maps showing how much N is removed by natural reduction processes, i.e. the ratio between the N-load out of the catchment and the N-leaching from the root zone for each spatial unit within the catchment. For the 85 km2 groundwater...... dominated Norsminde catchment in Denmark we have analysed the potential benefits of a spatially targeted regulation and how its efficiency is affected by uncertainty in the N-reduction map. Our results suggest that there are potential benefits of implementing a spatially targeted regulation compared...

  12. Application of Advanced Functional Maps to the Radiation Treatment Plan for Biological Clinical Target Volumes

    International Nuclear Information System (INIS)

    Park, Ji Yeon; Jung, Won Gyun; Suh, Tae Suk; Lee, Jeong Woo; Ahn, Kook Jin

    2010-01-01

    Anatomical images including computerized tomography (CT) and T1-weighted magnetic resonance (T1-MR) images have been generally used to determine target volumes in radiation treatment plan (RTP). As only conventional images were referenced, tumors have tendency not to be enhanced by administrating agents depending on the tumor grade and patients. Recent advanced MR images, however, could guide physiologically and pathologically significant tumor characteristics. Furthermore, if the multi-functional images are employed, errors from using only one type of image will be complemented and distinct biological parameters can be applied as histological activity index. In this study, biological clinical target volumes (bCTVs) considered vascularity and cellularity can be determined based on multifunctional parametric maps using the in-house software for image registration and analysis. Using the developed software, rCBV and ADC maps were analyzed and bCTVs can be resolved considering vascularity and cellularity. In result, the bCTVs are exported on conventional images for biological RTP using image registration. Based on the multi-functional parametric maps of overlapped tumor regions, malignant sub-volumes can be determined. Multi-functional parametric maps would contribute to the detection of physiological and pathological tumor characteristics which are not be found in conventional images. They would reflect individual tumor biological characteristics to RTP for local tumor control.

  13. Excel Spreadsheet Tools for Analyzing Groundwater Level Records and Displaying Information in ArcMap

    Science.gov (United States)

    Tillman, Fred D.

    2009-01-01

    When beginning hydrologic investigations, a first action is often to gather existing sources of well information, compile this information into a single dataset, and visualize this information in a geographic information system (GIS) environment. This report presents tools (macros) developed using Visual Basic for Applications (VBA) for Microsoft Excel 2007 to assist in these tasks. One tool combines multiple datasets into a single worksheet and formats the resulting data for use by the other tools. A second tool produces summary information about the dataset, such as a list of unique site identification numbers, the number of water-level observations for each, and a table of the number of sites with a listed number of water-level observations. A third tool creates subsets of the original dataset based on user-specified options and produces a worksheet with water-level information for each well in the subset, including the average and standard deviation of water-level observations and maximum decline and rise in water levels between any two observations, among other information. This water-level information worksheet can be imported directly into ESRI ArcMap as an 'XY Data' file, and each of the fields of summary well information can be used for custom display. A separate set of VBA tools distributed in an additional Excel workbook creates hydrograph charts of each of the wells in the data subset produced by the aforementioned tools and produces portable document format (PDF) versions of the hydrograph charts. These PDF hydrographs can be hyperlinked to well locations in ArcMap or other GIS applications.

  14. European Antibiotic Awareness Day 2012: general practitioners encouraged to TARGET antibiotics through guidance, education and tools.

    Science.gov (United States)

    McNulty, Cliodna A M

    2012-11-01

    On 18 November 2012, the UK will once again support the annual European Antibiotic Awareness Day (EAAD). In particular, hospitals will be asked to promote the Start Smart-Then Focus guidance for hospitals launched in 2011, while the Royal College of General Practitioners will publish the TARGET Antibiotics toolkit on their web site. TARGET (Treat Antibiotics Responsibly, Guidance, Education, Tools) emphasizes the need for both primary care staff and the public to use antibiotics responsibly, and provides guidance, education and tools. The web site has been developed by a multiprofessional group and hosts national antibiotic guidance, an antibiotic app, leaflets designed to be shared by patients during consultations, a presentation for clinicians, an interactive self-assessment tool, audit tools, posters and videos for the waiting room and links to other materials. The EAAD is still very relevant and worth promoting enthusiastically through all clinical professionals in an effort to encourage responsible use of antibiotics and thereby control antibiotic resistance.

  15. Automated planning target volume generation: an evaluation pitting a computer-based tool against human experts

    International Nuclear Information System (INIS)

    Ketting, Case H.; Austin-Seymour, Mary; Kalet, Ira; Jacky, Jon; Kromhout-Schiro, Sharon; Hummel, Sharon; Unger, Jonathan; Fagan, Lawrence M.; Griffin, Tom

    1997-01-01

    Purpose: Software tools are seeing increased use in three-dimensional treatment planning. However, the development of these tools frequently omits careful evaluation before placing them in clinical use. This study demonstrates the application of a rigorous evaluation methodology using blinded peer review to an automated software tool that produces ICRU-50 planning target volumes (PTVs). Methods and Materials: Seven physicians from three different institutions involved in three-dimensional treatment planning participated in the evaluation. Four physicians drew partial PTVs on nine test cases, consisting of four nasopharynx and five lung primaries. Using the same information provided to the human experts, the computer tool generated PTVs for comparison. The remaining three physicians, designated evaluators, individually reviewed the PTVs for acceptability. To exclude bias, the evaluators were blinded to the source (human or computer) of the PTVs they reviewed. Their scorings of the PTVs were statistically examined to determine if the computer tool performed as well as the human experts. Results: The computer tool was as successful as the human experts in generating PTVs. Failures were primarily attributable to insufficient margins around the clinical target volume and to encroachment upon critical structures. In a qualitative analysis, the human and computer experts displayed similar types and distributions of errors. Conclusions: Rigorous evaluation of computer-based radiotherapy tools requires comparison to current practice and can reveal areas for improvement before the tool enters clinical practice

  16. Remote sensing is a viable tool for mapping soil salinity in agricultural lands

    Directory of Open Access Journals (Sweden)

    Elia Scudiero

    2017-04-01

    Full Text Available Soil salinity negatively impacts the productivity and profitability of western San Joaquin Valley (WSJV farmland. Many factors, including drought, climate change, reduced water allocations, and land-use changes could worsen salinity conditions there, and in other agricultural lands in the state. Mapping soil salinity at regional and state levels is essential for identifying drivers and trends in agricultural soil salinity, and for developing mitigation strategies, but traditional soil sampling for salinity does not allow for accurate large-scale mapping. We tested remote-sensing modeling to map root zone soil salinity for farmland in the WSJV. According to our map, 0.78 million acres are salt affected (i.e., ECe > 4 dS/m, which represents 45% of the mapped farmland; 30% of that acreage is strongly or extremely saline. Independent validations of the remote-sensing estimations indicated acceptable to excellent correspondences, except in areas of low salinity and high soil heterogeneity. Remote sensing is a viable tool for helping landowners make decisions about land use and also for helping water districts and state agencies develop salinity mitigation strategies.

  17. In silico tools used for compound selection during target-based drug discovery and development.

    Science.gov (United States)

    Caldwell, Gary W

    2015-01-01

    The target-based drug discovery process, including target selection, screening, hit-to-lead (H2L) and lead optimization stage gates, is the most common approach used in drug development. The full integration of in vitro and/or in vivo data with in silico tools across the entire process would be beneficial to R&D productivity by developing effective selection criteria and drug-design optimization strategies. This review focuses on understanding the impact and extent in the past 5 years of in silico tools on the various stage gates of the target-based drug discovery approach. There are a large number of in silico tools available for establishing selection criteria and drug-design optimization strategies in the target-based approach. However, the inconsistent use of in vitro and/or in vivo data integrated with predictive in silico multiparameter models throughout the process is contributing to R&D productivity issues. In particular, the lack of reliable in silico tools at the H2L stage gate is contributing to the suboptimal selection of viable lead compounds. It is suggested that further development of in silico multiparameter models and organizing biologists, medicinal and computational chemists into one team with a single accountable objective to expand the utilization of in silico tools in all phases of drug discovery would improve R&D productivity.

  18. CADYRI, a dynamic mapping tool of human risk associated with flooding in urban areas

    Science.gov (United States)

    Tanguy, M.; Chokmani, K.; Bernier, M.; Poulin, J.

    2013-12-01

    When a flood affects an urban area, the managers and services responsible for public safety need precise and real time information on the localization of the flooded areas, on the submersion heights in those areas, but also on the vulnerability of people exposed to this hazard. Such information is essential for an effective crisis management. Despite a growing interest in this topic over the last 15 years, the development of flood risk assessment tools mainly focused on quantitative modeling of the monetary damages caused by floods to residential buildings or to critical infrastructures. Little attention was paid to the vulnerability of people exposed to flooding but also to the effects of the failure or destruction of critical infrastructures and residential building on people health and security during the disaster. Moreover, these models do not integrate the dynamic features of the flood (extent, submersion heights) and the evolution of human vulnerability in the same mapping tool. Thus, an accurate and precise evaluation of human risk induced by urban flooding is hardly feasible using such models. This study presents CADYRI, a dynamic mapping tool of human risk associated with flooding in urban areas, which fills the actual needs in terms of flood risk evaluation and management. This innovative tool integrates a methodology of flood hazard mapping that simulates, for a given discharge, the associated water level, and subsequently determines the extent of the flooded area and the submersion heights at each point of the flooded area, using a DEM. The dynamics of human vulnerability is then mapped at the household level, according to the characteristics of the flood hazard. Three key components of human vulnerability have been identified and are integrated to CADYRI: 1, the intrinsic vulnerability of the population, estimated by specific socio-economic indicators; 2, the vulnerability of buildings, assessed by their structural features; 3, the vulnerability of

  19. A metacognitive tool: Theoretical and operational analysis of skills exercised in structured concept maps

    Directory of Open Access Journals (Sweden)

    Marie-Pierre Chevron

    2014-01-01

    Full Text Available Developing meaningful learning is not only difficult to achieve but also time consuming, because it requires a large number of different skills to develop and master. Many studies have shown that organizing knowledge in concept maps helps teachers and students to develop such a meaningful learning (Nesbit, J.C., Adescope, O.O., 2006. Learning with concept and knowledge maps: a meta-analysis. Rev. Educ. Res. 76:3, 413–446. Based on the work of Tyler (Tyler, R.W., 1950. Basic principles of Curriculum and Instruction. University of Chicago Press, Chicago, IL and Anderson (Anderson, L.W., Krathwohl, D.R., Airasian, P.W., Cruikshank, K.A., Mayer, R.E., Pintrich, P.R., Raths, J., Wittrock, M.C., 2001. A Taxonomy for Learning, Teaching, and Assessing: A revision of Bloom׳s Taxonomy of Educational Objectives. Longman, New York, this study proposes to characterize and to organize precisely, rigorously, and operationally in a two-dimensional matrix, the skills exercised during the elaboration of concept maps, here referred to as context-dependent and hierarchically structured concept maps (sCM. These skills correspond to those actually needed in transfer of knowledge, and the matrix could be used as an instructional tool to assist learners and teachers in this transfer. In addition it allows them to pay attention to the cognitive processes and types of knowledge involved during sCM elaboration. Making explicit the taxonomic levels of cognitive efforts implemented while organizing knowledge in a concept map could constitute a useful metacognitive tool to focus the teachers and learners׳ attention and efforts towards achieving higher-order thinking skills and meaningful learning.

  20. Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses.

    Science.gov (United States)

    Oliveira, Arthur C; Bovolenta, Luiz A; Nachtigall, Pedro G; Herkenhoff, Marcos E; Lemke, Ney; Pinhal, Danillo

    2017-01-01

    Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection). For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR-34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p) and 1,400 genes (700 validated and 700 non-validated) as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions.

  1. GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

    Science.gov (United States)

    Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano

    2014-01-01

    Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads. PMID:24842718

  2. GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

    Directory of Open Access Journals (Sweden)

    Andrea Manconi

    Full Text Available Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.

  3. Speaking Spontaneously in the Modern Foreign Languages Classroom: Tools for Supporting Successful Target Language Conversation

    Science.gov (United States)

    Christie, Colin

    2016-01-01

    This article reports on the findings of a study into the conditions which promote spontaneous learner talk in the target language in the modern foreign languages (MFL) classroom. A qualitative case study approach was adopted. French lessons, with school students aged 11-16 years old, were observed and analysed with the aim of identifying tools and…

  4. Cancer-associated fibroblasts as target and tool in cancer therapeutics and diagnostics.

    Science.gov (United States)

    De Vlieghere, Elly; Verset, Laurine; Demetter, Pieter; Bracke, Marc; De Wever, Olivier

    2015-10-01

    Cancer-associated fibroblasts (CAFs) are drivers of tumour progression and are considered as a target and a tool in cancer diagnostic and therapeutic applications. An increased abundance of CAFs or CAF signatures are recognized as a bad prognostic marker in several cancer types. Tumour-environment biomimetics strongly improve our understanding of the communication between CAFs, cancer cells and other host cells. Several experimental drugs targeting CAFs are in clinical trials for multiple tumour entities; alternatively, CAFs can be exploited as a tool to characterize the functionality of circulating tumour cells or to capture them as a tool to prevent metastasis. The continuous interaction between tissue engineers, biomaterial experts and cancer researchers creates the possibility to biomimic the tumour-environment and provides new opportunities in cancer diagnostics and management.

  5. Towards Innovative Geospatial Tools for Fit-For Land Rights Mapping

    Science.gov (United States)

    Koeva, M.; Bennett, R.; Gerke, M.; Crommelinck, S.; Stöcker, C.; Crompvoets, J.; Ho, S.; Schwering, A.; Chipofya, M.; Schultz, C.; Zein, T.; Biraro, M.; Alemie, B.; Wayumba, R.; Kundert, K.

    2017-09-01

    In large parts of sub Saharan Africa it remains an ongoing challenging to map millions of unrecognized land rights. Existing approaches for recognizing these rights have proven inappropriate in many cases. A new generation of tools needs to be developed to support faster, cheaper, easier, and more responsible land rights mapping. This is the main goal of its4land, an European Commission Horizon 2020 project that aims to develop innovative tools inspired by the continuum of land rights, fit-for-purpose land administration, and cadastral intelligence. its4land is using strategic collaboration between the EU and East Africa to deliver innovative, scalable, and transferrable ICT solutions. The innovation process incorporates a broad range of stakeholders and emergent geospatial technologies, including smart sketchmaps, UAVs, automated feature extraction, as well as geocloud services. The aim is to combine innovative technologies, capture the specific needs, market opportunities and readiness of end-users in the domain of land tenure information recording in Eastern Africa. The project consists of a four year work plan, € 3.9M funding, and eight consortium partners collaborating with stakeholders from six case study locations in Ethiopia, Kenya, and Rwanda. The major tasks include tool development, prototyping, and demonstration for local, national, regional, and international interest groups. The case locations cover different land uses such as: urban, peri-urban, rural smallholder, and (former) pastoralist. This paper describes the project's activities within the first 18 months and covers barriers discovered, lessons learned and results achieved.

  6. OPTIMASI LINI PRODUKSI DENGAN VALUE STREAM MAPPING DAN VALUE STREAM ANALYSIS TOOLS

    Directory of Open Access Journals (Sweden)

    Yosua Caesar Fernando

    2014-12-01

    Full Text Available Meminimalkan pemborosan dalam proses produksi adalah salah satu tujuan dari suatu perusahaan. Lean adalah metode yang dapat meminimalkan pemborosan dalam proses produksi. Dalam penelitian ini, metode yang digunakan untuk meminimalkan limbah di PT. Bonindo Abadi adalah Value Stream Analysis Tools (VALSAT dan Value Stream Mapping (VSM. VSM digunakan untuk melihat kondisi peta keadaan pada perusahaan. Pengurangan pemborosan dilakukan dengan menggunakan salah satu alat dari VALSAT yaitu Process Activity Mapping (PAM. Jumlah non value added (NVA yang ditemukan dalam proses produksi PT. X adalah 90,17% diikuti oleh necessary but non value added (NNVA dengan jumlah 9,79% dan value added (VA sebesar 0,04%. Usulan perbaikan yang diberikan adalah dengan mengurangi jumlah waktu aktivitas NVA atau menghilangkannya.

  7. U.S. Environmental Protection Agency Office of Enforcement and Compliance Assurance New Mapping Tool for Enforcement Cases

    Data.gov (United States)

    U.S. Environmental Protection Agency — The new mapping tool shows facilities in the United States where the EPA concluded formal environmental enforcement actions between October 1, 2008 and September 30,...

  8. The global hidden hunger indices and maps: an advocacy tool for action.

    Science.gov (United States)

    Muthayya, Sumithra; Rah, Jee Hyun; Sugimoto, Jonathan D; Roos, Franz F; Kraemer, Klaus; Black, Robert E

    2013-01-01

    The unified global efforts to mitigate the high burden of vitamin and mineral deficiency, known as hidden hunger, in populations around the world are crucial to the achievement of most of the Millennium Development Goals (MDGs). We developed indices and maps of global hidden hunger to help prioritize program assistance, and to serve as an evidence-based global advocacy tool. Two types of hidden hunger indices and maps were created based on i) national prevalence data on stunting, anemia due to iron deficiency, and low serum retinol levels among preschool-aged children in 149 countries; and ii) estimates of Disability Adjusted Life Years (DALYs) attributed to micronutrient deficiencies in 136 countries. A number of countries in sub-Saharan Africa, as well as India and Afghanistan, had an alarmingly high level of hidden hunger, with stunting, iron deficiency anemia, and vitamin A deficiency all being highly prevalent. The total DALY rates per 100,000 population, attributed to micronutrient deficiencies, were generally the highest in sub-Saharan African countries. In 36 countries, home to 90% of the world's stunted children, deficiencies of micronutrients were responsible for 1.5-12% of the total DALYs. The pattern and magnitude of iodine deficiency did not conform to that of other micronutrients. The greatest proportions of children with iodine deficiency were in the Eastern Mediterranean (46.6%), European (44.2%), and African (40.4%) regions. The current indices and maps provide crucial data to optimize the prioritization of program assistance addressing global multiple micronutrient deficiencies. Moreover, the indices and maps serve as a useful advocacy tool in the call for increased commitments to scale up effective nutrition interventions.

  9. The Global Hidden Hunger Indices and Maps: An Advocacy Tool for Action

    Science.gov (United States)

    Muthayya, Sumithra; Rah, Jee Hyun; Sugimoto, Jonathan D.; Roos, Franz F.; Kraemer, Klaus; Black, Robert E.

    2013-01-01

    The unified global efforts to mitigate the high burden of vitamin and mineral deficiency, known as hidden hunger, in populations around the world are crucial to the achievement of most of the Millennium Development Goals (MDGs). We developed indices and maps of global hidden hunger to help prioritize program assistance, and to serve as an evidence-based global advocacy tool. Two types of hidden hunger indices and maps were created based on i) national prevalence data on stunting, anemia due to iron deficiency, and low serum retinol levels among preschool-aged children in 149 countries; and ii) estimates of Disability Adjusted Life Years (DALYs) attributed to micronutrient deficiencies in 136 countries. A number of countries in sub-Saharan Africa, as well as India and Afghanistan, had an alarmingly high level of hidden hunger, with stunting, iron deficiency anemia, and vitamin A deficiency all being highly prevalent. The total DALY rates per 100,000 population, attributed to micronutrient deficiencies, were generally the highest in sub-Saharan African countries. In 36 countries, home to 90% of the world’s stunted children, deficiencies of micronutrients were responsible for 1.5-12% of the total DALYs. The pattern and magnitude of iodine deficiency did not conform to that of other micronutrients. The greatest proportions of children with iodine deficiency were in the Eastern Mediterranean (46.6%), European (44.2%), and African (40.4%) regions. The current indices and maps provide crucial data to optimize the prioritization of program assistance addressing global multiple micronutrient deficiencies. Moreover, the indices and maps serve as a useful advocacy tool in the call for increased commitments to scale up effective nutrition interventions. PMID:23776712

  10. Visualization of Near-Infrared Spectral Data of Eros Using the Small Body Mapping Tool

    Science.gov (United States)

    Klima, Rachel L.; Ernst, Carolyn

    2016-10-01

    One of the primary drivers for many missions visiting asteroids is to advance our understanding of their composition beyond what can be (and is) already measured by telescopes. Without sample return or lander missions, this task relies primarily on resolved near-infrared spectroscopic measurements. Scientific analysis using spectral data collected by point spectrometers is not as straightforward as for imaging spectrometers, where the local spatial context is immediately available. In the case of Eros and other highly non-spherical bodies, this problem becomes even more severe when trying to locate spectra that cross a mapped feature that bends over an irregularly shaped surface. Thus, it is often the case that outside of the mission teams, few from the community at large delve into these data sets, as they lack the tools necessary to incorporate the spectral information into geological analyses of the asteroids. Ultimately, we seek to make such spectral datasets, which NASA has invested significant amounts of money to obtain, more widely accessible and user-friendly. The Small Bodies Mapping Tool (SBMT) is a Java-based, interactive, three-dimensional visualization tool written and developed at APL to map and analyze features on irregularly shaped solar system bodies. The SBMT can be used to locate and then "drape" spacecraft images, spectra, and laser altimetry around the shape model of such bodies. It provides a means for rapid identification of available data in a region of interest and allows features to be mapped directly onto the shape model. The program allows the free rotation of a shape model (including any overlain data) in all directions, so that the correlation and distribution of mapped features can be easily and globally observed.We will present the results of our work on the NEAR/Near-Infrared Spectrograph (NIS) data, including improvements to the calibration made by using the geometric information provided by the SBMT and improvements to the SMBT

  11. Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

    Directory of Open Access Journals (Sweden)

    Gogarten J Peter

    2002-02-01

    Full Text Available Abstract Background Horizontal gene transfer (HGT played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes. Results We adapted the Maximum Likelihood (ML mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group. Conclusions In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny . Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately

  12. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.

    Directory of Open Access Journals (Sweden)

    Manuel Stemmer

    Full Text Available Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.

  13. An integrated user-friendly ArcMAP tool for bivariate statistical modelling in geoscience applications

    Science.gov (United States)

    Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusoff, Z. M.; Tehrany, M. S.

    2015-03-01

    Modelling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modelling. Bivariate statistical analysis (BSA) assists in hazard modelling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time-consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, bivariate statistical modeler (BSM), for BSA technique is proposed. Three popular BSA techniques, such as frequency ratio, weight-of-evidence (WoE), and evidential belief function (EBF) models, are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and created by a simple graphical user interface (GUI), which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve (AUC) is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

  14. Implementing Dementia Care Mapping as a practice development tool in dementia care services: a systematic review

    Directory of Open Access Journals (Sweden)

    Surr CA

    2018-01-01

    Full Text Available Claire A Surr, Alys W Griffiths, Rachael Kelley Centre for Dementia Research, School of Health and Community Studies, Leeds Beckett University, Leeds, UK Abstract: Dementia Care Mapping (DCM is an observational tool set within a practice development process. Following training in the method, DCM is implemented via a cyclic process of briefing staff, conducting mapping observations, data analysis and report preparation, feedback to staff and action planning. Recent controlled studies of DCM’s efficacy have found heterogeneous results, and variability in DCM implementation has been indicated as a potential contributing factor. This review aimed to examine the primary research evidence on the processes and the barriers and facilitators to implementing DCM as a practice development method within formal dementia care settings. PUBMED, PsycINFO, CINAHL, The Cochrane Library-Cochrane reviews, HMIC (Ovid, Web of Science and Social Care Online were searched using the term “Dementia Care Mapping”. Inclusion criterion was primary research studies in any formal dementia care settings where DCM was used as a practice development tool and which included discussion/critique of the implementation processes. Assessment of study quality was conducted using the Mixed Methods Appraisal Tool. Twelve papers were included in the review, representing nine research studies. The papers included discussion of various components of the DCM process, including mapper selection and preparation; mapping observations; data analysis, report writing and feedback; and action planning. However, robust evidence on requirements for successful implementation of these components was limited. Barriers and facilitators to mapping were also discussed. The review found some consensus that DCM is more likely to be successfully implemented if the right people are selected to be trained as mappers, with appropriate mapper preparation and ongoing support and with effective leadership for

  15. Using a Concept Mapping Tool with a Photograph Association Technique (CoMPAT) to Elicit Children's Ideas about Microbial Activity

    Science.gov (United States)

    Byrne, Jenny; Grace, Marcus

    2010-01-01

    Concept mapping is a technique used to provide a visual representation of an individual's ideas about a concept or set of related concepts. This paper describes a concept mapping tool using a photograph association technique (CoMPAT) that is considered to be a novel way of eliciting children's ideas. What children at 11 years of age know about…

  16. Science Teachers' Use of a Concept Map Marking Guide as a Formative Assessment Tool for the Concept of Energy

    Science.gov (United States)

    Won, Mihye; Krabbe, Heiko; Ley, Siv Ling; Treagust, David F.; Fischer, Hans E.

    2017-01-01

    In this study, we investigated the value of a concept map marking guide as an alternative formative assessment tool for science teachers to adopt for the topic of energy. Eight high school science teachers marked students' concept maps using an itemized holistic marking guide. Their marking was compared with the researchers' marking and the scores…

  17. Dynamic contrast enhanced magnetic resonance imaging for hypoxia mapping and potential for brachytherapy targeting

    Directory of Open Access Journals (Sweden)

    Anna Li

    2017-03-01

    Full Text Available Background and purpose: Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI may be used to visualize tumor hypoxia, and was in this work explored in treatment planning of hypoxia-guided brachytherapy of patients with locally advanced cervical cancer (LACC. Materials and methods: Pharmacokinetic ABrix maps were derived from DCE-MR images taken prior to chemoradiotherapy of 78 patients with LACC. A logistic regression procedure was used to segment the tumor volume fraction from the ABrix maps that showed the strongest association with patient survival, denoted biological target volume (BTV fraction. A hypoxia gene score was calculated from a biopsy-based gene signature and correlated against the BTV fraction. Brachytherapy planning based on the ABrix maps was performed, for 23 patients. A general planning aim was a minimum D90 dose of 7.5 Gy to the tumor per brachytherapy fraction. Two planning approaches were explored: (1 a conventional uniform and (2 a non-uniform approach targeting the BTV to the highest dose possible. Results: The segmented BTV fraction was significantly associated local and locoregional control (P = 0.025 and the hypoxia gene score (P = 0.002. Comparing brachytherapy approaches 1 and 2, it was possible to dose escalate the BTV with 0.4 Gy per fraction in median (D90; cohort range [0, 3.8]. Some tumors could not be dose escalated without violating the dose constraints to the organs at risk. Conclusions: Tumor regions associated with hypoxia may be targeted with brachytherapy. The presented methodology may become useful in future strategies to improve cure probability of resistant tumors. Keywords: Hypoxia, Uterine cervical cancer, Computer-assisted image analysis, Magnetic resonance imaging, Brachytherapy

  18. Risk-targeted versus current seismic design maps for the conterminous United States

    Science.gov (United States)

    Luco, Nicolas; Ellingwood, Bruce R.; Hamburger, Ronald O.; Hooper, John D.; Kimball, Jeffrey K.; Kircher, Charles A.

    2007-01-01

    The probabilistic portions of the seismic design maps in the NEHRP Provisions (FEMA, 2003/2000/1997), and in the International Building Code (ICC, 2006/2003/2000) and ASCE Standard 7-05 (ASCE, 2005a), provide ground motion values from the USGS that have a 2% probability of being exceeded in 50 years. Under the assumption that the capacity against collapse of structures designed for these "uniformhazard" ground motions is equal to, without uncertainty, the corresponding mapped value at the location of the structure, the probability of its collapse in 50 years is also uniform. This is not the case however, when it is recognized that there is, in fact, uncertainty in the structural capacity. In that case, siteto-site variability in the shape of ground motion hazard curves results in a lack of uniformity. This paper explains the basis for proposed adjustments to the uniform-hazard portions of the seismic design maps currently in the NEHRP Provisions that result in uniform estimated collapse probability. For seismic design of nuclear facilities, analogous but specialized adjustments have recently been defined in ASCE Standard 43-05 (ASCE, 2005b). In support of the 2009 update of the NEHRP Provisions currently being conducted by the Building Seismic Safety Council (BSSC), herein we provide examples of the adjusted ground motions for a selected target collapse probability (or target risk). Relative to the probabilistic MCE ground motions currently in the NEHRP Provisions, the risk-targeted ground motions for design are smaller (by as much as about 30%) in the New Madrid Seismic Zone, near Charleston, South Carolina, and in the coastal region of Oregon, with relatively little (<15%) change almost everywhere else in the conterminous U.S.

  19. TabSQL: a MySQL tool to facilitate mapping user data to public databases.

    Science.gov (United States)

    Xia, Xiao-Qin; McClelland, Michael; Wang, Yipeng

    2010-06-23

    With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.

  20. Pressure Mapping in Elderly Care: A Tool to Increase Pressure Injury Knowledge and Awareness Among Staff.

    Science.gov (United States)

    Hultin, Lisa; Olsson, Estrid; Carli, Cheryl; Gunningberg, Lena

    The purpose of this study was to evaluate the use of a pressure mapping system with real-time feedback of pressure points in elderly care, with specific focus on pressure injury (PI) knowledge/attitudes (staff), interface pressure, and PI prevention activities (residents). Descriptive, 1-group pretest/posttest study. A convenience sample of 40 assistant nurses and aides participated in the study; staff members were recruited at daytime, and 1 nighttime meeting was held at the facility. A convenience sample of 12 residents with risk for PI were recruited, 4 from each ward. Inclusion criteria were participants older than 65 years, Modified Norton Scale score 20 or less, and in need of help with turning in order to prevent PI. The study setting was a care facility for the elderly in Uppsala, Sweden. A descriptive, comparative pretest/posttest study design was used. The intervention consisted of the use of a pressure mapping system, combined with theoretical and practical teaching. Theoretical and practical information related to PI prevention and the pressure mapping system was presented to the staff. The staff (n = 40) completed the Pressure Ulcer Knowledge and Assessment Tool (PUKAT) and Attitudes towards Pressure Ulcer (APuP) before and following study intervention. Residents' beds were equipped with a pressure mapping system during 7 consecutive days. Peak pressures and preventive interventions were registered 3 times a day by trained study nurses, assistant nurses, and aides. Staff members' PUKAT scores increased significantly (P = .002), while their attitude scores, which were high pretest, remained unchanged. Peak interface pressures were significantly reduced (P = .016), and more preventive interventions (n = 0.012) were implemented when the staff repositioned residents after feedback from the pressure mapping system. A limited educational intervention, combined with the use of a pressure mapping system, was successful as it improved staff members' knowledge

  1. Color Doppler Ultrasonography-Targeted Perforator Mapping and Angiosome-Based Flap Reconstruction

    DEFF Research Database (Denmark)

    Gunnarsson, Gudjon Leifur; Tei, Troels; Thomsen, Jørn Bo

    2016-01-01

    Knowledge about perforators and angiosomes has inspired new and innovative flap designs for reconstruction of defects throughout the body. The purpose of this article is to share our experience using color Doppler ultrasonography (CDU)-targeted perforator mapping and angiosome-based flap...... reconstruction throughout the body. The CDU was used to identify the largest and best-located perforator adjacent to the defect to target the reconstruction. The cutaneous or fasciocutaneous flaps were raised, mobilized, and designed according to the reconstructive needs as rotation, advancement, or turnover...... flaps. We performed 148 reconstructions in 130 patients. Eleven facial reconstructions, 118 reconstructions in the body, 7 in the upper limbs, and 12 in the lower limbs. The propeller flap was used in 135 of 148 (91%) cases followed by the turnover design in 10 (7%) and the V to Y flap in 3 (2%) cases...

  2. Visualizing the Geography of the Diseases of China: Western Disease Maps from Analytical Tools to Tools of Empire, Sovereignty, and Public Health Propaganda, 1878-1929.

    Science.gov (United States)

    Hanson, Marta

    2017-09-01

    Argument This article analyzes for the first time the earliest western maps of diseases in China spanning fifty years from the late 1870s to the end of the 1920s. The 24 featured disease maps present a visual history of the major transformations in modern medicine from medical geography to laboratory medicine wrought on Chinese soil. These medical transformations occurred within new political formations from the Qing dynasty (1644-1911) to colonialism in East Asia (Hong Kong, Taiwan, Manchuria, Korea) and hypercolonialism within China (Tianjin, Shanghai, Amoy) as well as the new Republican Chinese nation state (1912-49). As a subgenre of persuasive graphics, physicians marshaled disease maps for various rhetorical functions within these different political contexts. Disease maps in China changed from being mostly analytical tools to functioning as tools of empire, national sovereignty, and public health propaganda legitimating new medical concepts, public health interventions, and political structures governing over human and non-human populations.

  3. Concept maps: A tool for knowledge management and synthesis in web-based conversational learning.

    Science.gov (United States)

    Joshi, Ankur; Singh, Satendra; Jaswal, Shivani; Badyal, Dinesh Kumar; Singh, Tejinder

    2016-01-01

    Web-based conversational learning provides an opportunity for shared knowledge base creation through collaboration and collective wisdom extraction. Usually, the amount of generated information in such forums is very huge, multidimensional (in alignment with the desirable preconditions for constructivist knowledge creation), and sometimes, the nature of expected new information may not be anticipated in advance. Thus, concept maps (crafted from constructed data) as "process summary" tools may be a solution to improve critical thinking and learning by making connections between the facts or knowledge shared by the participants during online discussion This exploratory paper begins with the description of this innovation tried on a web-based interacting platform (email list management software), FAIMER-Listserv, and generated qualitative evidence through peer-feedback. This process description is further supported by a theoretical construct which shows how social constructivism (inclusive of autonomy and complexity) affects the conversational learning. The paper rationalizes the use of concept map as mid-summary tool for extracting information and further sense making out of this apparent intricacy.

  4. Digital administrative maps – A tool for visualization of epidemiological data

    Directory of Open Access Journals (Sweden)

    Ewa Niewiadomska

    2013-08-01

    Full Text Available Background: The aim of the study is to present the methods for visualization of epidemiological data using digital contour maps that take into account administrative division of Poland. Materials and Methods: The possibility of epidemiological data visualization in a geographical order, limited to the administrative level of the country, voivodeships and poviats (counties, are presented. They are crucial for the process of identifying and undertaking adequate prophylactic activities directed towards decreasing the risk and improving the population's health. This paper presents tools and techniques available in Geographic Information System ArcGIS and statistical software package R. Results: The work includes our own data reflecting: 1 the values of specific mortality rates due to respiratory diseases, Poland, 2010, based on the Central Statistical Office data, using the R statistical software package; 2 the averaged registered incidence rates of sarcoidosis in 2006-2010 for the population aged 19+ in the Silesian voivodeship, using Geographic Information System ArcGIS; and 3 the number of children with diagnosed respiratory diseases in the city of Legnica in 2009, taking into account their place of residence, using layered maps in Geographic Information System ArcGIS. Conclusions: The tools presented and described in this paper make it possible to visualize the results of research, to increase attractiveness of courses for students, as well as to enhance the skills and competence of students and participants of courses. Med Pr 2013;64(4:533–539

  5. GERLUMPH DATA RELEASE 1: HIGH-RESOLUTION COSMOLOGICAL MICROLENSING MAGNIFICATION MAPS AND eResearch TOOLS

    Energy Technology Data Exchange (ETDEWEB)

    Vernardos, G.; Fluke, C. J.; Croton, D. [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria, 3122 (Australia); Bate, N. F. [Sydney Institute for Astronomy, School of Physics, A28, University of Sydney, NSW, 2006 (Australia)

    2014-03-01

    As synoptic all-sky surveys begin to discover new multiply lensed quasars, the flow of data will enable statistical cosmological microlensing studies of sufficient size to constrain quasar accretion disk and supermassive black hole properties. In preparation for this new era, we are undertaking the GPU-Enabled, High Resolution cosmological MicroLensing parameter survey (GERLUMPH). We present here the GERLUMPH Data Release 1, which consists of 12,342 high resolution cosmological microlensing magnification maps and provides the first uniform coverage of the convergence, shear, and smooth matter fraction parameter space. We use these maps to perform a comprehensive numerical investigation of the mass-sheet degeneracy, finding excellent agreement with its predictions. We study the effect of smooth matter on microlensing induced magnification fluctuations. In particular, in the minima and saddle-point regions, fluctuations are enhanced only along the critical line, while in the maxima region they are always enhanced for high smooth matter fractions (≈0.9). We describe our approach to data management, including the use of an SQL database with a Web interface for data access and online analysis, obviating the need for individuals to download large volumes of data. In combination with existing observational databases and online applications, the GERLUMPH archive represents a fundamental component of a new microlensing eResearch cloud. Our maps and tools are publicly available at http://gerlumph.swin.edu.au/.

  6. BAMS: A Tool for Supervised Burned Area Mapping Using Landsat Data

    Directory of Open Access Journals (Sweden)

    Aitor Bastarrika

    2014-12-01

    Full Text Available A new supervised burned area mapping software named BAMS (Burned Area Mapping Software is presented in this paper. The tool was built from standard ArcGISTM libraries. It computes several of the spectral indexes most commonly used in burned area detection and implements a two-phase supervised strategy to map areas burned between two Landsat multitemporal images. The only input required from the user is the visual delimitation of a few burned areas, from which burned perimeters are extracted. After the discrimination of burned patches, the user can visually assess the results, and iteratively select additional sampling burned areas to improve the extent of the burned patches. The final result of the BAMS program is a polygon vector layer containing three categories: (a burned perimeters, (b unburned areas, and (c non-observed areas. The latter refer to clouds or sensor observation errors. Outputs of the BAMS code meet the requirements of file formats and structure of standard validation protocols. This paper presents the tool’s structure and technical basis. The program has been tested in six areas located in the United States, for various ecosystems and land covers, and then compared against the National Monitoring Trends in Burn Severity (MTBS Burned Area Boundaries Dataset.

  7. Geomorphic Flood Area (GFA): a DEM-based tool for flood susceptibility mapping at large scales

    Science.gov (United States)

    Manfreda, S.; Samela, C.; Albano, R.; Sole, A.

    2017-12-01

    Flood hazard and risk mapping over large areas is a critical issue. Recently, many researchers are trying to achieve a global scale mapping encountering several difficulties, above all the lack of data and implementation costs. In data scarce environments, a preliminary and cost-effective floodplain delineation can be performed using geomorphic methods (e.g., Manfreda et al., 2014). We carried out several years of research on this topic, proposing a morphologic descriptor named Geomorphic Flood Index (GFI) (Samela et al., 2017) and developing a Digital Elevation Model (DEM)-based procedure able to identify flood susceptible areas. The procedure exhibited high accuracy in several test sites in Europe, United States and Africa (Manfreda et al., 2015; Samela et al., 2016, 2017) and has been recently implemented in a QGIS plugin named Geomorphic Flood Area (GFA) - tool. The tool allows to automatically compute the GFI, and turn it into a linear binary classifier capable of detecting flood-prone areas. To train this classifier, an inundation map derived using hydraulic models for a small portion of the basin is required (the minimum is 2% of the river basin's area). In this way, the GFA-tool allows to extend the classification of the flood-prone areas across the entire basin. We are also defining a simplified procedure for the estimation of the river depth, which may be helpful for large-scale analyses to approximatively evaluate the expected flood damages in the surrounding areas. ReferencesManfreda, S., Nardi, F., Samela, C., Grimaldi, S., Taramasso, A. C., Roth, G., & Sole, A. (2014). Investigation on the use of geomorphic approaches for the delineation of flood prone areas. J. Hydrol., 517, 863-876. Manfreda, S., Samela, C., Gioia, A., Consoli, G., Iacobellis, V., Giuzio, L., & Sole, A. (2016). Flood-prone areas assessment using linear binary classifiers based on flood maps obtained from 1D and 2D hydraulic models. Nat. Hazards, Vol. 79 (2), pp 735-754. Samela, C

  8. An interactive mapping tool for visualizing lacunarity of laser scanned point clouds

    Science.gov (United States)

    Kania, Adam; Székely, Balázs

    2016-04-01

    Lacunarity, a measure of the spatial distribution of the empty space in a certain model or real space over large spatial scales, is found to be a useful descriptive quantity in many fields using imagery, including, among others, geology, dentistry, neurology. Its application in ecology was suggested more than 20 years ago. The main problem of its application was the lack of appropriate high resolution data. Nowadays, full-waveform laser scanning, also known as FWF LiDAR, provides the tool for mapping the vegetation in unprecedented details and accuracy. Consequently, the lacunarity concept can be revitalized, in order to study the structure of the vegetation in this sense as well. Calculation of lacunarity, even if it is done in two dimensions (2D), is still has its problems: on one hand it is a number-crunching procedure, on the other hand, it produces 4D results: at each 3D point it returns a set of data that are function of scale. These data sets are difficult to visualize, to evaluate, and to compare. In order to solve this problem, an interactive mapping tool has been conceptualized that is designed to manipulate and visualize the data, lets the user set parameters for best visualization or comparison results. The system is able to load large amounts of data, visualize them as lacunarity curves, or map view as horizontal slices or in 3D point clouds coloured according to the user's choice. Lacunarity maps are presented as a series of (usually) horizontal profiles, e.g. rasters, which cells contain color-mapped values of selected lacunarity of the point cloud. As lacunarity is usually analysed in a series of successive windows sizes, the tool can show a series of rasters with sequentially animated lacunarity maps calculated for various window sizes. A very fast switching of colour schemes is possible to facilitate rapid visual feedback to better understand underlying data patterns exposed by lacunarity functions. In the comparison mode, two sites (or two areas

  9. Evidence & Gap Maps: A tool for promoting evidence informed policy and strategic research agendas.

    Science.gov (United States)

    Snilstveit, Birte; Vojtkova, Martina; Bhavsar, Ami; Stevenson, Jennifer; Gaarder, Marie

    2016-11-01

    A range of organizations are engaged in the production of evidence on the effects of health, social, and economic development programs on human welfare outcomes. However, evidence is often scattered around different databases, web sites, and the gray literature and is often presented in inaccessible formats. Lack of overview of the evidence in a specific field can be a barrier to the use of existing research and prevent efficient use of limited resources for new research. Evidence & Gap Maps (EGMs) aim to address these issues and complement existing synthesis and mapping approaches. EGMs are a new addition to the tools available to support evidence-informed policymaking. To provide an accessible resource for researchers, commissioners, and decision makers, EGMs provide thematic collections of evidence structured around a framework which schematically represents the types of interventions and outcomes of relevance to a particular sector. By mapping the existing evidence using this framework, EGMs provide a visual overview of what we know and do not know about the effects of different programs. They make existing evidence available, and by providing links to user-friendly summaries of relevant studies, EGMs can facilitate the use of existing evidence for decision making. They identify key "gaps" where little or no evidence from impact evaluations and systematic reviews is available and can be a valuable resource to inform a strategic approach to building the evidence base in a particular sector. The article will introduce readers to the concept and methods of EGMs and present a demonstration of the EGM tool using existing examples. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. TOWARDS INNOVATIVE GEOSPATIAL TOOLS FOR FIT-FOR-PURPOSE LAND RIGHTS MAPPING

    Directory of Open Access Journals (Sweden)

    M. Koeva

    2017-09-01

    Full Text Available In large parts of sub Saharan Africa it remains an ongoing challenging to map millions of unrecognized land rights. Existing approaches for recognizing these rights have proven inappropriate in many cases. A new generation of tools needs to be developed to support faster, cheaper, easier, and more responsible land rights mapping. This is the main goal of its4land, an European Commission Horizon 2020 project that aims to develop innovative tools inspired by the continuum of land rights, fit-for-purpose land administration, and cadastral intelligence. its4land is using strategic collaboration between the EU and East Africa to deliver innovative, scalable, and transferrable ICT solutions. The innovation process incorporates a broad range of stakeholders and emergent geospatial technologies, including smart sketchmaps, UAVs, automated feature extraction, as well as geocloud services. The aim is to combine innovative technologies, capture the specific needs, market opportunities and readiness of end-users in the domain of land tenure information recording in Eastern Africa. The project consists of a four year work plan, € 3.9M funding, and eight consortium partners collaborating with stakeholders from six case study locations in Ethiopia, Kenya, and Rwanda. The major tasks include tool development, prototyping, and demonstration for local, national, regional, and international interest groups. The case locations cover different land uses such as: urban, peri-urban, rural smallholder, and (former pastoralist. This paper describes the project’s activities within the first 18 months and covers barriers discovered, lessons learned and results achieved.

  11. e-Health Tools for Targeting and Improving Melanoma Screening: A Review

    International Nuclear Information System (INIS)

    Tyagi, A.; Miller, K.; Cockburn, M.

    2012-01-01

    The key to improved prognosis for melanoma is early detection and diagnosis, achieved by skin surveillance and secondary prevention (screening). However, adherence to screening guidelines is low, with population-based estimates of approximately 26% for physician-based skin cancer screening and 20-25% for skin self-examination. The recent proliferation of melanoma detection e -Health t ools, digital resources that facilitate screening in patients often outside of the clinical setting, may offer new strategies to promote adherence and expand the proportion and range of individuals performing skin self-examination. The purpose of this paper is to catalog and categorize melanoma screening e-Health tools to aid in the determination of their efficacy and potential for adoption. The availability and accessibility of such tools, their costs, target audience, and, where possible, information on their efficacy, will be discussed with potential benefits and limitations considered. While e-Health tools targeting melanoma screening are widely available, little has been done to formally evaluate their efficacy and ability to aid in overcoming screening barriers. Future research needs to formally evaluate the potential role of e-Health tools in melanoma prevention.

  12. Spin polarized solid target as a prospective tool for radioactive ion beam physics

    Science.gov (United States)

    Urrego-Blanco, J. P.; van den Brandt, B.; Bunyatova, E. I.; Galindo-Uribarri, A.; Hautle, P.; Konter, J. A.

    2005-12-01

    Spin polarized probes are used in a wide range of experiments in nuclear physics including the determination of spin structure functions and tests of fundamental symmetries. At low energies, light stable polarized beams have been used for spectroscopic purposes. We propose to extend these types of experiments to nuclei far from stability by using radioactive ion beams (RIBs) and polarized targets. Towards this goal we intend to develop a solid polarized proton and/or deuterium target in the thickness range between 20 μm and 100 μm based on a scintillating (active) polymeric foil. Such a target would be a useful tool in the determination of excitation functions in resonant reactions, in studies of one-nucleon transfer reactions using RIBs as well as in probing the matter density of atomic nuclei. If scintillating, it could also help remove the background associated with the scattering of the radioactive beam.

  13. Spin polarized solid target as a prospective tool for radioactive ion beam physics

    Energy Technology Data Exchange (ETDEWEB)

    Urrego-Blanco, J.P. [Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996 (United States); Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6371 (United States); Paul Scherrer Institute, CH-5232 Villigen PSI (Switzerland); Brandt, B. van den [Paul Scherrer Institute, CH-5232 Villigen PSI (Switzerland); Bunyatova, E.I. [Joint Institute for Nuclear Research, Dubna, Head P.O. Box 79, 101000 Moscow (Russian Federation); Galindo-Uribarri, A. [Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6371 (United States)]. E-mail: uribarri@mail.phy.ornl.gov; Hautle, P. [Paul Scherrer Institute, CH-5232 Villigen PSI (Switzerland); Konter, J.A. [Paul Scherrer Institute, CH-5232 Villigen PSI (Switzerland)

    2005-12-15

    Spin polarized probes are used in a wide range of experiments in nuclear physics including the determination of spin structure functions and tests of fundamental symmetries. At low energies, light stable polarized beams have been used for spectroscopic purposes. We propose to extend these types of experiments to nuclei far from stability by using radioactive ion beams (RIBs) and polarized targets. Towards this goal we intend to develop a solid polarized proton and/or deuterium target in the thickness range between 20 {mu}m and 100 {mu}m based on a scintillating (active) polymeric foil. Such a target would be a useful tool in the determination of excitation functions in resonant reactions, in studies of one-nucleon transfer reactions using RIBs as well as in probing the matter density of atomic nuclei. If scintillating, it could also help remove the background associated with the scattering of the radioactive beam.

  14. Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.

    Directory of Open Access Journals (Sweden)

    Anna Cichonska

    2017-08-01

    Full Text Available Due to relatively high costs and labor required for experimental profiling of the full target space of chemical compounds, various machine learning models have been proposed as cost-effective means to advance this process in terms of predicting the most potent compound-target interactions for subsequent verification. However, most of the model predictions lack direct experimental validation in the laboratory, making their practical benefits for drug discovery or repurposing applications largely unknown. Here, we therefore introduce and carefully test a systematic computational-experimental framework for the prediction and pre-clinical verification of drug-target interactions using a well-established kernel-based regression algorithm as the prediction model. To evaluate its performance, we first predicted unmeasured binding affinities in a large-scale kinase inhibitor profiling study, and then experimentally tested 100 compound-kinase pairs. The relatively high correlation of 0.77 (p < 0.0001 between the predicted and measured bioactivities supports the potential of the model for filling the experimental gaps in existing compound-target interaction maps. Further, we subjected the model to a more challenging task of predicting target interactions for such a new candidate drug compound that lacks prior binding profile information. As a specific case study, we used tivozanib, an investigational VEGF receptor inhibitor with currently unknown off-target profile. Among 7 kinases with high predicted affinity, we experimentally validated 4 new off-targets of tivozanib, namely the Src-family kinases FRK and FYN A, the non-receptor tyrosine kinase ABL1, and the serine/threonine kinase SLK. Our sub-sequent experimental validation protocol effectively avoids any possible information leakage between the training and validation data, and therefore enables rigorous model validation for practical applications. These results demonstrate that the kernel

  15. C-mii: a tool for plant miRNA and target identification

    Directory of Open Access Journals (Sweden)

    Numnark Somrak

    2012-12-01

    Full Text Available Abstract Background MicroRNAs (miRNAs have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. Results To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. Conclusions C-mii constitutes the first complete software package with graphical user interfaces enabling

  16. Development of 87Sr/86Sr maps as targeted strategy to support wine quality.

    Science.gov (United States)

    Durante, Caterina; Bertacchini, Lucia; Cocchi, Marina; Manzini, Daniela; Marchetti, Andrea; Rossi, Maria Cecilia; Sighinolfi, Simona; Tassi, Lorenzo

    2018-07-30

    This study summarizes the results obtained from a systematic and long-term project aimed at the development of tools to assess the provenance of food in the oenological sector. In particular, 87 Sr/ 86 Sr isotope ratios were measured on statistically representative set of soils, vine branches and wines sampled in the production district of Modena, worldwide known for the Lambrusco wines production. The obtained data were used to build strontium isotopic maps able to objectively support the Lambrusco PDO wines origin as well as other products of the Modena district. Finally, a strong relationship was found between the 87 Sr/ 86 Sr isotope ratios of soils and vine branches on a large scale, highlighting and confirming once more the idea that plants can also represent an optimal sampling device to support geographical traceability. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. REALIZING BUSINESS PROCESS MANAGEMENT BY HELP OF A PROCESS MAPPING DATABASE TOOL

    CERN Document Server

    Vergili, Ceren

    2016-01-01

    In a typical business sector, processes are the building blocks of the achievement. A considerable percentage of the processes are consisting of business processes. This fact is bringing the fact that business sectors are in need of a management discipline. Business Process Management (BPM) is a discipline that combines modelling, automation, execution, control, measurement, and optimization of process by considering enterprise goals, spanning systems, employees, customers, and partners. CERN’s EN – HE – HM section desires to apply the BPM discipline appropriately for improving their necessary technical, administrative and managerial actions to supply appropriate CERN industrial transport, handling and lifting equipment and to maintain it. For this reason, a Process Mapping Database Tool is created to develop a common understanding about how the section members can visualize their processes, agree on quality standards and on how to improve. It provides a management support by establishing Process Charts...

  18. The Griffiths Question Map: A Forensic Tool For Expert Witnesses' Assessments of Witnesses and Victims' Statements.

    Science.gov (United States)

    Dodier, Olivier; Denault, Vincent

    2018-01-01

    Expert witnesses are sometimes asked to assess the reliability of young witnesses and victims' statements because of their high susceptibility to memory biases. This technical note aims to highlight the relevance of the Griffiths Question Map (GQM) as a professional forensic tool to improve expert witnesses' assessments of young witnesses and victims' testimonies. To do so, this innovative question type assessment grid was used to proceed to an in-depth analysis of the interview of an alleged 13-year-old victim of a sexual assault and two rapes. Overall, the GQM stressed how the interview was mainly conducted in an inappropriate manner. The results are examined with regard to scientific knowledge on young witnesses and victims' memory. Finally, it is argued that expert witnesses in inquisitorial systems might use the GQM while encountering difficulties to fulfill the legal standards for expert evidence in adversarial systems because of the lack of studies regarding its reliability. © 2017 American Academy of Forensic Sciences.

  19. Small-molecule inhibitors of the receptor tyrosine kinases: promising tools for targeted cancer therapies.

    Science.gov (United States)

    Hojjat-Farsangi, Mohammad

    2014-08-08

    Chemotherapeutic and cytotoxic drugs are widely used in the treatment of cancer. In spite of the improvements in the life quality of patients, their effectiveness is compromised by several disadvantages. This represents a demand for developing new effective strategies with focusing on tumor cells and minimum side effects. Targeted cancer therapies and personalized medicine have been defined as a new type of emerging treatments. Small molecule inhibitors (SMIs) are among the most effective drugs for targeted cancer therapy. The growing number of approved SMIs of receptor tyrosine kinases (RTKs) i.e., tyrosine kinase inhibitors (TKIs) in the clinical oncology imply the increasing attention and application of these therapeutic tools. Most of the current approved RTK-TKIs in preclinical and clinical settings are multi-targeted inhibitors with several side effects. Only a few specific/selective RTK-TKIs have been developed for the treatment of cancer patients. Specific/selective RTK-TKIs have shown less deleterious effects compared to multi-targeted inhibitors. This review intends to highlight the importance of specific/selective TKIs for future development with less side effects and more manageable agents. This article provides an overview of: (1) the characteristics and function of RTKs and TKIs; (2) the recent advances in the improvement of specific/selective RTK-TKIs in preclinical or clinical settings; and (3) emerging RTKs for targeted cancer therapies by TKIs.

  20. The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

    Directory of Open Access Journals (Sweden)

    Primig Michael

    2008-02-01

    Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

  1. Using concept mapping as a planning tool: Child welfare citizen review panels.

    Science.gov (United States)

    Miller, J Jay; Jones, Blake

    2015-12-01

    Citizen Review Panels (CRPs) are groups of citizen volunteers authorized by U.S. federal law to examine state child welfare agencies. These groups inspect policies and practices related to child protection responsibilities and are tasked with making recommendations for systemic improvement. Despite the federal mandate for each state to develop a CRP and the potential of these groups to positively impact child welfare practices, there is a dearth in the literature related to CRPs. Consequently, planning and evaluation processes of these groups vary widely. This study reports on the use of concept mapping (CM) to outline a framework for planning and subsequently evaluating the CRP in one southeastern state. CM is a mixed-method research approach that uses multi-dimensional scaling and hierarchical cluster analyses to explore an area of study. Through these analyses, the method creates visual depictions of conceptual relationships between ideas. Data yielded a seven cluster concept map that CRP members (N=36) utilized for planning processes, and subsequently for developing an internal evaluation tool. Results from this study offer a unifying framework by which CRPs, and similar groups in other areas can utilize for planning and evaluation purposes. After a review of pertinent literature on CRPs, this article explicates CM processes utilized in this study, describes results, discusses lessons learned, and outlines apposite areas for future CRP research. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

    Science.gov (United States)

    Tennessen, Jacob A.; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

    2014-01-01

    Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes. PMID:25477420

  3. Using GIS Mapping to Target Public Health Interventions: Examining Birth Outcomes Across GIS Techniques.

    Science.gov (United States)

    MacQuillan, E L; Curtis, A B; Baker, K M; Paul, R; Back, Y O

    2017-08-01

    With advances in spatial analysis techniques, there has been a trend in recent public health research to assess the contribution of area-level factors to health disparity for a number of outcomes, including births. Although it is widely accepted that health disparity is best addressed by targeted, evidence-based and data-driven community efforts, and despite national and local focus in the U.S. to reduce infant mortality and improve maternal-child health, there is little work exploring how choice of scale and specific GIS visualization technique may alter the perception of analyses focused on health disparity in birth outcomes. Retrospective cohort study. Spatial analysis of individual-level vital records data for low birthweight and preterm births born to black women from 2007 to 2012 in one mid-sized Midwest city using different geographic information systems (GIS) visualization techniques [geocoded address records were aggregated at two levels of scale and additionally mapped using kernel density estimation (KDE)]. GIS analyses in this study support our hypothesis that choice of geographic scale (neighborhood or census tract) for aggregated birth data can alter programmatic decision-making. Results indicate that the relative merits of aggregated visualization or the use of KDE technique depend on the scale of intervention. The KDE map proved useful in targeting specific areas for interventions in cities with smaller populations and larger census tracts, where they allow for greater specificity in identifying intervention areas. When public health programmers seek to inform intervention placement in highly populated areas, however, aggregated data at the census tract level may be preferred, since it requires lower investments in terms of time and cartographic skill and, unlike neighborhood, census tracts are standardized in that they become smaller as the population density of an area increases.

  4. SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2009-07-01

    Full Text Available Abstract Background The recent availability of genomic sequences and BAC libraries for a large number of mammals provides an excellent opportunity for identifying comparatively-anchored markers that are useful for creating high-resolution radiation-hybrid (RH and BAC-based comparative maps. To use these maps for multispecies genome comparison and evolutionary inference, robust bioinformatic tools are required for the identification of chromosomal regions shared between genomes and to localize the positions of evolutionary breakpoints that are the signatures of chromosomal rearrangements. Here we report an automated tool for the identification of homologous synteny blocks (HSBs between genomes that tolerates errors common in RH comparative maps and can be used for automated whole-genome analysis of chromosome rearrangements that occur during evolution. Findings We developed an algorithm and software tool (SyntenyTracker that can be used for automated definition of HSBs using pair-wise RH or gene-based comparative maps as input. To verify correct implementation of the underlying algorithm, SyntenyTracker was used to identify HSBs in the cattle and human genomes. Results demonstrated 96% agreement with HSBs defined manually using the same set of rules. A comparison of SyntenyTracker with the AutoGRAPH synteny tool was performed using identical datasets containing 14,380 genes with 1:1 orthology in human and mouse. Discrepancies between the results using the two tools and advantages of SyntenyTracker are reported. Conclusion SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies. The utility of SyntenyTracker will become more important for comparative genomics as the number of mapped and sequenced genomes increases.

  5. CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

    Science.gov (United States)

    Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D T; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

    2014-01-01

    Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the

  6. The use and perceptions of concept mapping as a learning tool by dietetic internship students and preceptors.

    Science.gov (United States)

    Molaison, Elaine Fontenot; Taylor, Kimberly A; Erickson, Dawn; Connell, Carol Lawson

    2009-01-01

    Critical thinking and problem solving skills are currently emphasis areas in the education of allied health professionals. Use of concept maps to teach these skills have been utilized primarily in nursing and medical education, but little has been published about their use in dietetics education. Therefore the purpose of this study was to evaluate the potential efficacy of concept mapping as a learning tool for nutrition assessment among dietetic interns and its acceptability by internship preceptors. Nineteen dietetic interns and 31 preceptors participated in a quasi-experimental pre-/post-design in which the concept mapping strategy was taught as a replacement for the traditional nutrition care plan. The pre-concept map mean score was significantly lower than the post-concept mean score (28.35 vs. 117.96; p=0.001) based on the Student t-test, thus indicating improved critical thinking skills as evidenced through concept mapping. Overall students' perceptions of concept mapping as a teaching-learning method were more positive than the preceptors' perceptions. In conclusion, internship preceptors and dietetic interns perceived concept mapping as effective in assisting interns to engage in critical thinking, to problem solve, and understand relationships among medical nutrition therapy concepts. However, preceptors had more negative attitudes toward concept mapping than the dietetic interns related to time and effort to complete and evaluate the concept map.

  7. Nanodelivery Systems as New Tools for Immunostimulant or Vaccine Administration: Targeting the Fish Immune System

    Directory of Open Access Journals (Sweden)

    Jie Ji

    2015-10-01

    Full Text Available Fish disease treatments have progressed significantly over the last few years and have moved from the massive use of antibiotics to the development of vaccines mainly based on inactivated bacteria. Today, the incorporation of immunostimulants and antigens into nanomaterials provide us with new tools to enhance the performance of immunostimulation. Nanoparticles are dispersions or solid particles designed with specific physical properties (size, surface charge, or loading capacity, which allow controlled delivery and therefore improved targeting and stimulation of the immune system. The use of these nanodelivery platforms in fish is in the initial steps of development. Here we review the advances in the application of nanoparticles to fish disease prevention including: the type of biomaterial, the type of immunostimulant or vaccine loaded into the nanoparticles, and how they target the fish immune system.

  8. Locating proteins in the cell using TargetP, SignalP and related tools

    DEFF Research Database (Denmark)

    Emanuelsson, O.; Brunak, Søren; von Heijne, G.

    2007-01-01

    of methods to predict subcellular localization based on these sorting signals and other sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed...... step-by-step instructions for the coupled use of the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful...

  9. Formalization of treatment guidelines using Fuzzy Cognitive Maps and semantic web tools.

    Science.gov (United States)

    Papageorgiou, Elpiniki I; Roo, Jos De; Huszka, Csaba; Colaert, Dirk

    2012-02-01

    Therapy decision making and support in medicine deals with uncertainty and needs to take into account the patient's clinical parameters, the context of illness and the medical knowledge of the physician and guidelines to recommend a treatment therapy. This research study is focused on the formalization of medical knowledge using a cognitive process, called Fuzzy Cognitive Maps (FCMs) and semantic web approach. The FCM technique is capable of dealing with situations including uncertain descriptions using similar procedure such as human reasoning does. Thus, it was selected for the case of modeling and knowledge integration of clinical practice guidelines. The semantic web tools were established to implement the FCM approach. The knowledge base was constructed from the clinical guidelines as the form of if-then fuzzy rules. These fuzzy rules were transferred to FCM modeling technique and, through the semantic web tools, the whole formalization was accomplished. The problem of urinary tract infection (UTI) in adult community was examined for the proposed approach. Forty-seven clinical concepts and eight therapy concepts were identified for the antibiotic treatment therapy problem of UTIs. A preliminary pilot-evaluation study with 55 patient cases showed interesting findings; 91% of the antibiotic treatments proposed by the implemented approach were in fully agreement with the guidelines and physicians' opinions. The results have shown that the suggested approach formalizes medical knowledge efficiently and gives a front-end decision on antibiotics' suggestion for cystitis. Concluding, modeling medical knowledge/therapeutic guidelines using cognitive methods and web semantic tools is both reliable and useful. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Economic gains from targeting measures based on detailed nitrate reduction maps

    DEFF Research Database (Denmark)

    Jacobsen, Brian H.; Hansen, Anne Lausten

    2015-01-01

    From 1990 until 2003 Denmark has reduced N-leaching from the root zone by 50%. However, more measures are required and in recent years the focus has been on how to differentiate measures in order to ensure that measures are implemented where the effect of N-reduction per ha of the measures...... is the highest. The purpose of the NiCA project has been to estimate the nitrate reduction potential in greater detail than before using a plot size of 1-25 ha. This article builds on these findings and presents the possible economic gains to the farmer when using this information. Targeted measures......-reduction map is used on 10 farms in the Norsminde Catchment near Århus, Denmark. The findings suggest that the average farm would gain approximately 100-150 DKK per ha per year from targeted measures as opposed to not knowing where to place the measures. The analysis indicates that the economic gain is higher...

  11. US EPA Office of Research and Development Community-Focused Exposure and Risk Screening Tool (C-FERST) Air Pollutants 2011 web mapping service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This map service displays all air-related layers used in the USEPA Community/Tribal-Focused Exposure and Risk Screening Tool (C/T-FERST) mapping application...

  12. US EPA Office of Research and Development Community-Focused Exposure and Risk Screening Tool (C-FERST) Air web mapping service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This map service displays all air-related layers used in the USEPA Community/Tribal-Focused Exposure and Risk Screening Tool (C/T-FERST) mapping application...

  13. A method for mapping tissue volume model onto target volume using volumetric self-organizing deformable model

    Science.gov (United States)

    Miyauchi, Shoko; Morooka, Ken'ichi; Tsuji, Tokuo; Miyagi, Yasushi; Fukuda, Takaichi; Kurazume, Ryo

    2016-03-01

    This paper proposes a new method for mapping volume models of human tissues onto a target volume with simple shapes. The proposed method is based on our modified self-organizing deformable model (mSDM)1, 2 which finds the one-to-one mapping with no foldovers between arbitrary surface model and a target surface. By extending mSDM to apply to volume models, the proposed method, called volumetric SDM (vSDM), establishes the one-to-one correspondence between the tissue volume model and its target volume. At the same time, vSDM can preserve geometrical properties of the original model before and after mapping. This characteristic of vSDM makes it easy to find the correspondence between tissue models.

  14. Evaluation in medical education: A topical review of target parameters, data collection tools and confounding factors

    Directory of Open Access Journals (Sweden)

    Schiekirka, Sarah

    2015-09-01

    Full Text Available Background and objective: Evaluation is an integral part of education in German medical schools. According to the quality standards set by the German Society for Evaluation, evaluation tools must provide an accurate and fair appraisal of teaching quality. Thus, data collection tools must be highly reliable and valid. This review summarises the current literature on evaluation of medical education with regard to the possible dimensions of teaching quality, the psychometric properties of survey instruments and potential confounding factors.Methods: We searched Pubmed, PsycINFO and PSYNDEX for literature on evaluation in medical education and included studies published up until June 30, 2011 as well as articles identified in the “grey literature”. Results are presented as a narrative review.Results: We identified four dimensions of teaching quality: structure, process, teacher characteristics, and outcome. Student ratings are predominantly used to address the first three dimensions, and a number of reliable tools are available for this purpose. However, potential confounders of student ratings pose a threat to the validity of these instruments. Outcome is usually operationalised in terms of student performance on examinations, but methodological problems may limit the usability of these data for evaluation purposes. In addition, not all examinations at German medical schools meet current quality standards.Conclusion: The choice of tools for evaluating medical education should be guided by the dimension that is targeted by the evaluation. Likewise, evaluation results can only be interpreted within the context of the construct addressed by the data collection tool that was used as well as its specific confounding factors.

  15. Direct Push Optical Screening Tool for High Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

    Science.gov (United States)

    2016-07-01

    sites impacted by petroleum hydrocarbon fuels, creosotes , and MGP tars. The rapid, high-resolution, real-time nature of LIF technologies described...Green Optical Screening Tool (TarGOST®) are popular tools for real-time, high-resolution mapping of petroleum hydrocarbons, creosotes , and coal tar...solvent DNAPL at many sites will have more complex architectures and be present at lower saturations and in thinner layers than MGP tar, creosote , and

  16. GIS prospectivity mapping and 3D modeling validation for potential uranium deposit targets in Shangnan district, China

    Science.gov (United States)

    Xie, Jiayu; Wang, Gongwen; Sha, Yazhou; Liu, Jiajun; Wen, Botao; Nie, Ming; Zhang, Shuai

    2017-04-01

    Integrating multi-source geoscience information (such as geology, geophysics, geochemistry, and remote sensing) using GIS mapping is one of the key topics and frontiers in quantitative geosciences for mineral exploration. GIS prospective mapping and three-dimensional (3D) modeling can be used not only to extract exploration criteria and delineate metallogenetic targets but also to provide important information for the quantitative assessment of mineral resources. This paper uses the Shangnan district of Shaanxi province (China) as a case study area. GIS mapping and potential granite-hydrothermal uranium targeting were conducted in the study area combining weights of evidence (WofE) and concentration-area (C-A) fractal methods with multi-source geoscience information. 3D deposit-scale modeling using GOCAD software was performed to validate the shapes and features of the potential targets at the subsurface. The research results show that: (1) the known deposits have potential zones at depth, and the 3D geological models can delineate surface or subsurface ore-forming features, which can be used to analyze the uncertainty of the shape and feature of prospectivity mapping at the subsurface; (2) single geochemistry anomalies or remote sensing anomalies at the surface require combining the depth exploration criteria of geophysics to identify potential targets; and (3) the single or sparse exploration criteria zone with few mineralization spots at the surface has high uncertainty in terms of the exploration target.

  17. A COMPUTATIONAL TOOL TO EVALUATE THE SAMPLE SIZE IN MAP POSITIONAL ACCURACY

    Directory of Open Access Journals (Sweden)

    Marcelo Antonio Nero

    Full Text Available Abstract: In many countries, the positional accuracy control by points in Cartography or Spatial data corresponds to the comparison between sets of coordinates of well-defined points in relation to the same set of points from a more accurate source. Usually, each country determines a maximum number of points which could present error values above a pre-established threshold. In many cases, the standards define the sample size as 20 points, with no more consideration, and fix this threshold in 10% of the sample. However, the sampling dimension (n, considering the statistical risk, especially when the percentages of outliers are around 10%, can lead to a producer risk (to reject a good map and a user risk (to accept a bad map. This article analyzes this issue and allows defining the sampling dimension considering the risk of the producer and of the user. As a tool, a program developed by us allows defining the sample size according to the risk that the producer / user can or wants to assume. This analysis uses 600 control points, each of them with a known error. We performed the simulations with a sample size of 20 points (n and calculate the associated risk. Then we changed the value of (n, using smaller and larger sizes, calculating for each situation the associated risk both for the user and for the producer. The computer program developed draws the operational curves or risk curves, which considers three parameters: the number of control points; the number of iterations to create the curves; and the percentage of control points above the threshold, that can be the Brazilian standard or other parameters from different countries. Several graphs and tables are presented which were created with different parameters, leading to a better decision both for the user and for the producer, as well as to open possibilities for other simulations and researches in the future.

  18. An innovative tool for landslide susceptibility mapping in Kyrgyzstan, Central Asia

    Science.gov (United States)

    Saponaro, Annamaria; Pilz, Marco; Wieland, Marc; Bindi, Dino; Parolai, Stefano

    2013-04-01

    Kyrgyzstan is among the most exposed countries in the world to landslide susceptibility. The high seismicity of the area, the presence of high mountain ridges and topographic relieves, the geology of the local materials and the occurrence of heavy precipitations represent the main factors responsible for slope failures. In particular, the large variability of material properties and slope conditions as well as the difficulties in forecasting heavy precipitations locally and in quantifying the level of ground shaking call for harmonized procedures for reducing the negative impact of these factors. Several studies have recently been carried out aiming at preparing landslide susceptibility and hazard maps; however, some of them - qualitative-based - suffer from the application of subjective decision rules from experts in the classification of parameters that influence the occurrence of a landslide. On the other hand, statistical methods provide objectivity over qualitative ones since they allow a numerical evaluation of landslide spatial distribution with landslide potential factors. For this reason, we will make use of a bivariate technique known as Weight-Of-Evidence method to evaluate the influence of landslide predictive factors. The aim of this study is to identify areas in Kyrgyzstan being more prone to earthquake-triggered landslides. An innovative approach which exploits the new advances of GIS technology together with statistical concepts is presented. A range of conditioning factors and their potential impact on landslide activation is quantitatively assessed on the basis of landslide spatial distribution and seismic zonation. Results show areas which are more susceptible to landslides induced by earthquakes. Our approach can be used to fill the gap of subjectivity that typically affects already performed qualitative analysis. The resulting landslide susceptibility map represents a potentially supportive tool for disaster management and planning activities

  19. Concept Mapping as an Innovative Tool for the Assessment of Learning: An Experimental Experience among Business Management Degree Students

    Science.gov (United States)

    Ruiz-Palomino, Pablo; Martinez-Canas, Ricardo

    2013-01-01

    In the search to improve the quality of education at the university level, the use of concept mapping is becoming an important instructional technique for enhancing the teaching-learning process. This educational tool is based on cognitive theories by making a distinction between learning by rote (memorizing) and learning by meaning, where…

  20. A genetic linkage map of Sole (Solea solea): A tool for evolutionary and comparative analyses of exploited (flat)fishes

    NARCIS (Netherlands)

    Diopere, E.; Maes, G.E.; Komen, J.; Volckaert, F.A.M.; Groenen, M.

    2014-01-01

    Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic

  1. Environmental Justice Radar: A Tool for Community-Based Mapping to Increase Environmental Awareness and Participatory Decision Making.

    Science.gov (United States)

    Wilson, Sacoby M; Murray, Rianna T; Jiang, Chengsheng; Dalemarre, Laura; Burwell-Naney, Kristen; Fraser-Rahim, Herb

    2015-01-01

    As part of the Charleston Area Pollution Prevention Partnership (CAPs), studies have been performed to address environmental health issues using various techniques including Geographic Information Systems (GIS) mapping. Most of the mapping has been conducted by academic team members; however, there is a need for more community-based mapping to ensure the sustainability and effectiveness of community-driven efforts to eliminate environmental hazards and health disparities. The emergence of public participatory GIS (PPGIS) has been shown as a way to democratize science, build community capacity, and empower local citizens to address environmental health issues. This article describes the development of the Environmental Justice (EJ) Radar, a PPGIS tool that provides stakeholders in South Carolina with a way to raise environmental awareness and improve citizen participation in local environmental decision-making. We describe the functionality of EJ Radar and discuss feedback received from stakeholders to improve the utility of the PPGIS tool.

  2. Application of conceptual maps as didactic and pedagogical tools in the area of resources and information services

    Directory of Open Access Journals (Sweden)

    Maria Giovanna Guedes Farias

    2016-07-01

    Full Text Available Objective. Analyze the use of concept maps as didactic and pedagogical tools, from an experiment conducted in the classroom, in the disciplines Specialized Sources and Information Services of the graduation in Librarianship. Method. The methodological approach is characterized by its applied nature, exploratory and observation. Data were collected from the students by applying a questionnaire, and analysis took place with the help of content analysis techniques. Results. The most students see the conceptual maps as facilitators of knowledge construction, and view the use of these in different contexts, like the librarian activities. Conclusions. The use of concept maps as didactic and pedagogical tools can foster in students the enhancement of learning and reflection on the establishment of a route for the shared construction of new knowledge, adding previous knowledge and transforming them for use in cognitive fill gaps.

  3. On the Use of Concept Maps as an Assessment Tool in Science: What we have Learned so Far

    Directory of Open Access Journals (Sweden)

    María Araceli Ruiz Primo

    2000-05-01

    Full Text Available In this paper I describe concept maps as an assessment tool to measure one aspect of achievement, the organization of propositional (declarative knowledge in a domain. A concept map-based assessment consists of a task that elicits structured knowledge, a response format, and a scoring system. Variation in tasks, response formats, and scoring systems produce different mapping techniques that may elicit different knowledge representations, posing construct-interpretation challenges. This paper provides an overview of the research on the technical characteristics of concept maps. It briefly describes some of the studies that have been conducted to this end, and what we have learned so far about this form of assessment.

  4. Concept Maps: A Tool to Prepare for High Fidelity Simulation in Nursing

    Science.gov (United States)

    Daley, Barbara J.; Beman, Sarah Black; Morgan, Sarah; Kennedy, Linda; Sheriff, Mandy

    2017-01-01

    In this study, the use of concept mapping as a method to prepare for high fidelity simulated learning experiences was investigated. Fourth year baccalaureate nursing students were taught how to use concept maps as a way to prepare for high fidelity simulated nursing experiences. Students prepared concept maps for two simulated experiences…

  5. Transcranial magnetic stimulation and connectivity mapping: tools for studying the neural bases of brain disorders.

    Science.gov (United States)

    Hampson, M; Hoffman, R E

    2010-01-01

    There has been an increasing emphasis on characterizing pathophysiology underlying psychiatric and neurological disorders in terms of altered neural connectivity and network dynamics. Transcranial magnetic stimulation (TMS) provides a unique opportunity for investigating connectivity in the human brain. TMS allows researchers and clinicians to directly stimulate cortical regions accessible to electromagnetic coils positioned on the scalp. The induced activation can then propagate through long-range connections to other brain areas. Thus, by identifying distal regions activated during TMS, researchers can infer connectivity patterns in the healthy human brain and can examine how those patterns may be disrupted in patients with different brain disorders. Conversely, connectivity maps derived using neuroimaging methods can identify components of a dysfunctional network. Nodes in this dysfunctional network accessible as targets for TMS by virtue of their proximity to the scalp may then permit TMS-induced alterations of components of the network not directly accessible to TMS via propagated effects. Thus TMS can provide a portal for accessing and altering neural dynamics in networks that are widely distributed anatomically. Finally, when long-term modulation of network dynamics is induced by trains of repetitive TMS, changes in functional connectivity patterns can be studied in parallel with changes in patient symptoms. These correlational data can elucidate neural mechanisms underlying illness and recovery. In this review, we focus on the application of these approaches to the study of psychiatric and neurological illnesses.

  6. Transcranial magnetic stimulation and connectivity mapping: tools for studying the neural bases of brain disorders.

    Directory of Open Access Journals (Sweden)

    Michelle Hampson

    2010-08-01

    Full Text Available There has been an increasing emphasis on characterizing pathophysiology underlying psychiatric and neurological disorders in terms of altered neural connectivity and network dynamics. Transcranial magnetic stimulation (TMS provides a unique opportunity for investigating connectivity in the human brain. TMS allows researchers and clinicians to directly stimulate cortical regions accessible to electromagnetic coils positioned on the scalp. The induced activation can then propagate through long-range connections to other brain areas. Thus, by identifying distal regions activated during TMS, researchers can infer connectivity patterns in the healthy human brain and can examine how those patterns may be disrupted in patients with different brain disorders. Conversely, connectivity maps derived using neuroimaging methods can identify components of a dysfunctional network. Nodes in this dysfunctional network accessible as targets for TMS by virtue of their proximity to the scalp may then permit TMS-induced alterations of components of the network not directly accessible to TMS via propagated effects. Thus TMS can provide a portal for accessing and altering neural dynamics in networks that are widely distributed anatomically. Finally, when long-term modulation of network dynamics is induced by trains of repetitive TMS, changes in functional connectivity patterns can be studied in parallel with changes in patient symptoms. These correlational data can elucidate neural mechanisms underlying illness and recovery. In this review, we focus on the application of these approaches to the study of psychiatric and neurological illnesses.

  7. JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps.

    Science.gov (United States)

    Salvi, Eleonora; Cantele, Francesca; Zampighi, Lorenzo; Fain, Nick; Pigino, Gaia; Zampighi, Guido; Lanzavecchia, Salvatore

    2008-03-01

    We are presenting a program for interactive segmentation of tomographic maps, based on objective criteria so as to yield reproducible results. The strategy starts with the automatic segmentation of the entire volume with the watershed algorithm in 3D. The watershed regions are clustered successively by supervised classification, allowing the segmentation of known organelles, such as membranes, vesicles and microtubules. These organelles are processed with topological models and input parameters manually derived from the tomograms. After known organelles are extracted from the volume, all other watershed regions can be organized into homogeneous assemblies on the basis of their densities. To complete the process, all voxels in the volume are assigned either to the background or individual structures, which can then be extracted for visualization with any rendering technique. The user interface of the program is written in Java, and computational routines are written in C. For some operations, involving the visualization of the tomogram, we refer to existing software, either open or commercial. While the program runs, a history file is created, that allows all parameters and other data to be saved for the purposes of comparison or exchange. Initially, the program was developed for the segmentation of synapses, and organelles belonging to these structures have thus far been the principal targets modeled with JUST. Since each organelle is clustered independently from the rest of the volume, however, the program can accommodate new models of different organelles as well as tomograms of other types of preparations of tissue, such as cytoskeletal components in vitreous ice.

  8. FEDERAL USERS CONFERENCE PRODUCT LINE TOOL SET (PLTS) MAP PRODUCTION SYSTEM (MPS) ATLAS CUSTOM GRIDS [Rev 0 was draft

    Energy Technology Data Exchange (ETDEWEB)

    HAYENGA, J.L.

    2006-12-19

    Maps, and more importantly Atlases, are assisting the user community in managing a large land area with complex issues, the most complex of which is the management of nuclear waste. The techniques and experiences discussed herein were gained while developing several atlases for use at the US Department of Energy's Hanford Site. The user community requires the ability to locate not only waste sites, but other features as well. Finding a specific waste site on a map and in the field is a difficult task at a site the size of Hanford. To find a specific waste site, the user begins by locating the item or object in an index, then locating the feature on the corresponding map within an atlas. Locating features requires a method for indexing them. The location index and how to place it on a map or atlas is the central theme presented in this article. The user requirements for atlases forced the design team to develop new and innovative solutions for requirements that Product Line Tool Set (PLTS) Map Production System (MPS)-Atlas was not designed to handle. The layout of the most complex atlases includes custom reference grids, multiple data frames, multiple map series, and up to 250 maps. All of these functional requirements are at the extreme edge of the capabilities of PLTS MPS-Atlas. This document outlines the setup of an atlas using PLTS MPS-Atlas to meet these requirements.

  9. FEDERAL USERS CONFERENCE PRODUCT LINE TOOL SET (PLTS) MAP PRODUCTION SYSTEM (MPS) ATLAS CUSTOM GRIDS [Rev 0 was draft

    International Nuclear Information System (INIS)

    HAYENGA, J.L.

    2006-01-01

    Maps, and more importantly Atlases, are assisting the user community in managing a large land area with complex issues, the most complex of which is the management of nuclear waste. The techniques and experiences discussed herein were gained while developing several atlases for use at the US Department of Energy's Hanford Site. The user community requires the ability to locate not only waste sites, but other features as well. Finding a specific waste site on a map and in the field is a difficult task at a site the size of Hanford. To find a specific waste site, the user begins by locating the item or object in an index, then locating the feature on the corresponding map within an atlas. Locating features requires a method for indexing them. The location index and how to place it on a map or atlas is the central theme presented in this article. The user requirements for atlases forced the design team to develop new and innovative solutions for requirements that Product Line Tool Set (PLTS) Map Production System (MPS)-Atlas was not designed to handle. The layout of the most complex atlases includes custom reference grids, multiple data frames, multiple map series, and up to 250 maps. All of these functional requirements are at the extreme edge of the capabilities of PLTS MPS-Atlas. This document outlines the setup of an atlas using PLTS MPS-Atlas to meet these requirements

  10. Airborne radiometric data - A tool for reconnaissance geological mapping using a GIS

    International Nuclear Information System (INIS)

    Graham, D.F.; Bonham-Carter, G.F.

    1993-01-01

    A clustering technique is applied to radioelement data, and the resulting cluster map is compared with a digitized geological map within a GIS software package. The cross tabulation clearly identifies those geological units that have a distinctive radioelement response. By reclassifying the map overlay and imposing a color coding scheme that enhances bedrock geology classes, the relationship between the bedrock geology and radioelement response is enhanced. The degree of correlation between the two cartographic images is site dependent, rather than global. Areas where the two maps differ indicate zones of possible interest for field verification of published field maps for the purposes of mineral exploration. 13 refs

  11. Agrobacterium tumefaciens-mediated transformation: an efficient tool for targeted gene disruption in Talaromyces marneffei.

    Science.gov (United States)

    Xiao, Xing; Feng, Jiao; Li, Yu; Chen, Zhiwen; Shi, Minglan; Xi, Liyan; Mylonakis, Eleftherios; Zhang, Junmin

    2017-09-25

    Talaromyces marneffei causes life-threatening infections in immunocompromised hosts. An efficient tool for genetic manipulation of T. marneffei will allow for increased understanding of this thermally dimorphic fungus. Agrobacterium tumefaciens-mediated transformation (ATMT) was optimized for targeted gene disruption in T. marneffei using the plasmid pDHt/acuD::pyrG. Molecular analyses of transformants were performed by PCR, Southern blot and semi-quantitative RT-PCR. A. tumefaciens strain EHA105 was more efficient at transformation than strain AGL-1 in ATMT via solid co-cultivation. An A. tumefaciens:T. marneffei ratio of 1000:1 in an ATMT liquid co-cultivation led to a relatively high transformation efficiency of 90 transformants per 10 6 yeast cells. Using ATMT-mediated knockout mutagenesis, we successfully deleted the acuD gene in T. marneffei. PCR and Southern blot analysis confirmed that acuD was disrupted and that the foreign pyrG gene was integrated into T. marneffei. Semi-quantitative RT-PCR analysis further confirmed that pyrG was expressed normally. These results suggest that ATMT can be a potential platform for targeted gene disruption in T. marneffei and that liquid co-cultivation may provide new opportunities to develop clinical treatments.

  12. Monocyte-Targeting Supramolecular Micellar Assemblies: A Molecular Diagnostic Tool for Atherosclerosis

    Science.gov (United States)

    Chung, E. J.; Nord, K.; Sugimoto, M. J.; Wonder, E.; Tirrell, M.; Mlinar, L. B.; Alenghat, F. J.; Fang, Y.

    2014-01-01

    Atherosclerosis is a multifactorial inflammatory disease that can progress silently for decades and result in myocardial infarction, stroke, and death. Diagnostic imaging technologies have made great strides to define the degree of atherosclerotic plaque burden through the severity of arterial stenosis. However, current technologies cannot differentiate more lethal “vulnerable plaques,” and are not sensitive enough for preventive medicine. Imaging early molecular markers and quantifying the extent of disease progression continues to be a major challenge in the field. To this end, monocyte-targeting, peptide amphiphile micelles (PAMs) are engineered through the incorporation of the chemokine receptor CCR2-binding motif of monocyte chemoattractant protein-1 (MCP-1) and MCP-1 PAMs are evaluated preclinically as diagnostic tools for atherosclerosis. Monocyte-targeting is desirable as the influx of monocytes is a marker of early lesions, accumulation of monocytes is linked to atherosclerosis progression, and rupture-prone plaques have higher numbers of monocytes. MCP-1 PAMs bind to monocytes in vitro, and MCP-1 PAMs detect and discriminate between early- and late-stage atherosclerotic aortas. Moreover, MCP-1 PAMs are found to be eliminated via renal clearance and the mononuclear phagocyte system (MPS) without adverse side effects. Thus, MCP-1 PAMs are a promising new class of diagnostic agents capable of monitoring the progression of atherosclerosis. PMID:25156590

  13. A powerful transgenic tool for fate mapping and functional analysis of newly generated neurons

    Directory of Open Access Journals (Sweden)

    Vogt Weisenhorn Daniela M

    2010-12-01

    Full Text Available Abstract Background Lack of appropriate tools and techniques to study fate and functional integration of newly generated neurons has so far hindered understanding of neurogenesis' relevance under physiological and pathological conditions. Current analyses are either dependent on mitotic labeling, for example BrdU-incorporation or retroviral infection, or on the detection of transient immature neuronal markers. Here, we report a transgenic mouse model (DCX-CreERT2 for time-resolved fate analysis of newly generated neurons. This model is based on the expression of a tamoxifen-inducible Cre recombinase under the control of a doublecortin (DCX promoter, which is specific for immature neuronal cells in the CNS. Results In the DCX-CreERT2 transgenic mice, expression of CreERT2 was restricted to DCX+ cells. In the CNS of transgenic embryos and adult DCX-CreERT2 mice, tamoxifen administration caused the transient translocation of CreERT2 to the nucleus, allowing for the recombination of loxP-flanked sequences. In our system, tamoxifen administration at E14.5 resulted in reporter gene activation throughout the developing CNS of transgenic embryos. In the adult CNS, neurogenic regions were the primary sites of tamoxifen-induced reporter gene activation. In addition, reporter expression could also be detected outside of neurogenic regions in cells physiologically expressing DCX (e.g. piriform cortex, corpus callosum, hypothalamus. Four weeks after recombination, the vast majority of reporter-expressing cells were found to co-express NeuN, revealing the neuronal fate of DCX+ cells upon maturation. Conclusions This first validation demonstrates that our new DCX-CreERT2 transgenic mouse model constitutes a powerful tool to investigate neurogenesis, migration and their long-term fate of neuronal precursors. Moreover, it allows for a targeted activation or deletion of specific genes in neuronal precursors and will thereby contribute to unravel the molecular

  14. Using the Targeted Solutions Tool® to Improve Emergency Department Handoffs in a Community Hospital.

    Science.gov (United States)

    Benjamin, Mignon F; Hargrave, Sarah; Nether, Klaus

    2016-03-01

    There is little evidence for solutions to improve the handoff process between units, particularly from the emergency department (ED) to the inpatient unit. A systematic approach was used to improve the handoff communication process between the ED and the four private physician groups serving Juneau, Alaska, that admit and deliver care to patients of a 73-bed, Level 4 trauma center community hospital. Data were collected in using the Joint Commission Center for Transforming Healthcare's Targeted Solutions Tool (®)(TST(®)) to determine the rate of defective handoff communications and the factors that contributed to those defective handoff communications. Targeted solutions were then implemented to specifically address the identified contributing factors. A random sample of 107 handoff opportunities was collected during the baseline phase (November 4, 2011- January 12, 2012) to measure performance and identify the contributing factors that led to defective handoffs. The baseline handoff communications defective rate was 29.9% (32 defective handoffs/107 handoff opportunities). The top four contributing factors, together accounting for 69.8% of all the causes of defective handoffs, were inaccurate/incomplete information, method ineffective, no standardized procedures for an effective handoff, and the person initiating the handoff, known as the "sender," lacks knowledge about the patient. After implementation of targeted solutions to the identified contributing factors, the handoff communications defective rate for the "improve" phase (April 1, 2012-July 29, 2012) was reduced from baseline by 58.2% to 12.5% (13 defective handoffs/104 handoff opportunities), p = 0.002; 2-proportions test. The number of adverse events related to hand-off communications declined as the handoff communications defective rate improved. Use of the TST was associated with improvement in the ED handoff communication process.

  15. Gene silencing by RNA interference in Sarcoptes scabiei: a molecular tool to identify novel therapeutic targets.

    Science.gov (United States)

    Fernando, Deepani D; Marr, Edward J; Zakrzewski, Martha; Reynolds, Simone L; Burgess, Stewart T G; Fischer, Katja

    2017-06-10

    Scabies is one of the most common and widespread parasitic skin infections globally, affecting a large range of mammals including humans, yet the molecular biology of Sarcoptes scabiei is astonishingly understudied. Research has been hampered primarily due to the difficulty of sampling or culturing these obligatory parasitic mites. A further and major impediment to identify and functionally analyse potential therapeutic targets from the recently emerging molecular databases is the lack of appropriate molecular tools. We performed standard BLAST based searches of the existing S. scabiei genome databases using sequences of genes described to be involved in RNA interference in Drosophila and the mite model organism Tetranychus urticae. Experimenting with the S. scabiei mu-class glutathione S-transferase (SsGST-mu1) as a candidate gene we explored the feasibility of gene knockdown in S. scabiei by double-stranded RNA-interference (dsRNAi). We provide here an analysis of the existing S. scabiei draft genomes, confirming the presence of a double stranded RNA (dsRNA) - mediated silencing machinery. We report for the first time experimental gene silencing by RNA interference (RNAi) in S. scabiei. Non-invasive immersion of S. scabiei in dsRNA encoding an S. scabiei glutathione S-transferase mu-class 1 enzyme (SsGST-mu1) resulted in a 35% reduction in the transcription of the target gene compared to controls. A series of experiments identified the optimal conditions allowing systemic experimental RNAi without detrimental side effects on mite viability. This technique can now be used to address the key questions on the fundamental aspects of mite biology and pathogenesis, and to assess the potential therapeutic benefits of silencing S. scabiei target genes.

  16. Learning how to use a tool: Mutually exclusive tool-function mappings are selectively acquired from linguistic in-group models.

    Science.gov (United States)

    Pető, Réka; Elekes, Fruzsina; Oláh, Katalin; Király, Ildikó

    2018-07-01

    The current study investigated whether 4-year-olds used language as a cue to social group membership to infer whether the tool-use behavior of a model needed to be encoded as indicative of the tool's function. We built on children's tendency to treat functions as mutually exclusive, that is, their propensity to refrain from using the same tool for more than one function. We hypothesized that children would form mutually exclusive tool-function mappings only if the source of the function information was a linguistic in-group person (native) as opposed to an out-group (foreign) person. In Experiment 1, participants (N = 39) were presented with four tool-function pairs by a model who had previously spoken either in their native language or in a foreign language. During the test phase, children encountered new purposes for which they could either use the demonstrated tools' color variant or use another equally suitable, as yet unseen, alternative tool. In line with our predictions, children preferred to use the alternative tool for the new function only in the native language condition (native: 63.3%; foreign: 42.7%). Experiment 2 replicated the initial finding using another foreign language and demonstrated that the lack of mutually exclusive tool choice in the foreign condition did not originate from children's failure to encode the demonstration. These findings suggest that children restrict learning artifact functions from linguistic in-group models. The mutual exclusivity principle in the domain of function learning is used more flexibly than previously proposed. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Retrieval interval mapping, a tool to optimize the spectral retrieval range in differential optical absorption spectroscopy

    Science.gov (United States)

    Vogel, L.; Sihler, H.; Lampel, J.; Wagner, T.; Platt, U.

    2012-06-01

    Remote sensing via differential optical absorption spectroscopy (DOAS) has become a standard technique to identify and quantify trace gases in the atmosphere. The technique is applied in a variety of configurations, commonly classified into active and passive instruments using artificial and natural light sources, respectively. Platforms range from ground based to satellite instruments and trace-gases are studied in all kinds of different environments. Due to the wide range of measurement conditions, atmospheric compositions and instruments used, a specific challenge of a DOAS retrieval is to optimize the parameters for each specific case and particular trace gas of interest. This becomes especially important when measuring close to the detection limit. A well chosen evaluation wavelength range is crucial to the DOAS technique. It should encompass strong absorption bands of the trace gas of interest in order to maximize the sensitivity of the retrieval, while at the same time minimizing absorption structures of other trace gases and thus potential interferences. Also, instrumental limitations and wavelength depending sources of errors (e.g. insufficient corrections for the Ring effect and cross correlations between trace gas cross sections) need to be taken into account. Most often, not all of these requirements can be fulfilled simultaneously and a compromise needs to be found depending on the conditions at hand. Although for many trace gases the overall dependence of common DOAS retrieval on the evaluation wavelength interval is known, a systematic approach to find the optimal retrieval wavelength range and qualitative assessment is missing. Here we present a novel tool to determine the optimal evaluation wavelength range. It is based on mapping retrieved values in the retrieval wavelength space and thus visualize the consequence of different choices of retrieval spectral ranges, e.g. caused by slightly erroneous absorption cross sections, cross correlations and

  18. Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity.

    Science.gov (United States)

    Lee, Ciaran M; Davis, Timothy H; Bao, Gang

    2018-04-01

    What is the topic of this review? In this review, we analyse the performance of recently described tools for CRISPR/Cas9 guide RNA design, in particular, design tools that predict CRISPR/Cas9 activity. What advances does it highlight? Recently, many tools designed to predict CRISPR/Cas9 activity have been reported. However, the majority of these tools lack experimental validation. Our analyses indicate that these tools have poor predictive power. Our preliminary results suggest that target site accessibility should be considered in order to develop better guide RNA design tools with improved predictive power. The recent adaptation of the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system for targeted genome engineering has led to its widespread application in many fields worldwide. In order to gain a better understanding of the design rules of CRISPR/Cas9 systems, several groups have carried out large library-based screens leading to some insight into sequence preferences among highly active target sites. To facilitate CRISPR/Cas9 design, these studies have spawned a plethora of guide RNA (gRNA) design tools with algorithms based solely on direct or indirect sequence features. Here, we demonstrate that the predictive power of these tools is poor, suggesting that sequence features alone cannot accurately inform the cutting efficiency of a particular CRISPR/Cas9 gRNA design. Furthermore, we demonstrate that DNA target site accessibility influences the activity of CRISPR/Cas9. With further optimization, we hypothesize that it will be possible to increase the predictive power of gRNA design tools by including both sequence and target site accessibility metrics. © 2017 The Authors. Experimental Physiology © 2017 The Physiological Society.

  19. COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

    Directory of Open Access Journals (Sweden)

    Thomas J Cradick

    2014-01-01

    Full Text Available Precise genome editing using engineered nucleases can significantly facilitate biological studies and disease treatment. In particular, clustered regularly interspaced short palindromic repeats (CRISPR with CRISPR-associated (Cas proteins are a potentially powerful tool for modifying a genome by targeted cleavage of DNA sequences complementary to designed guide strand RNAs. Although CRISPR/Cas systems can have on-target cleavage rates close to the transfection rates, they may also have relatively high off-target cleavage at similar genomic sites that contain one or more base pair mismatches, and insertions or deletions relative to the guide strand. We have developed a bioinformatics-based tool, COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu. Based on the user-supplied guide strand and input parameters, COSMID identifies potential off-target sites with the specified number of mismatched bases and insertions or deletions when compared with the guide strand. For each site, amplification primers optimal for the chosen application are also given as output. This ranked-list of potential off-target sites assists the choice and evaluation of intended target sites, thus helping the design of CRISPR/Cas systems with minimal off-target effects, as well as the identification and quantification of CRISPR/Cas induced off-target cleavage in cells.

  20. Midline signalling systems direct the formation of a neural map by dendritic targeting in the Drosophila motor system.

    Directory of Open Access Journals (Sweden)

    Alex Mauss

    2009-09-01

    Full Text Available A fundamental strategy for organising connections in the nervous system is the formation of neural maps. Map formation has been most intensively studied in sensory systems where the central arrangement of axon terminals reflects the distribution of sensory neuron cell bodies in the periphery or the sensory modality. This straightforward link between anatomy and function has facilitated tremendous progress in identifying cellular and molecular mechanisms that underpin map development. Much less is known about the way in which networks that underlie locomotion are organised. We recently showed that in the Drosophila embryo, dendrites of motorneurons form a neural map, being arranged topographically in the antero-posterior axis to represent the distribution of their target muscles in the periphery. However, the way in which a dendritic myotopic map forms has not been resolved and whether postsynaptic dendrites are involved in establishing sets of connections has been relatively little explored. In this study, we show that motorneurons also form a myotopic map in a second neuropile axis, with respect to the ventral midline, and they achieve this by targeting their dendrites to distinct medio-lateral territories. We demonstrate that this map is "hard-wired"; that is, it forms in the absence of excitatory synaptic inputs or when presynaptic terminals have been displaced. We show that the midline signalling systems Slit/Robo and Netrin/Frazzled are the main molecular mechanisms that underlie dendritic targeting with respect to the midline. Robo and Frazzled are required cell-autonomously in motorneurons and the balance of their opposite actions determines the dendritic target territory. A quantitative analysis shows that dendritic morphology emerges as guidance cue receptors determine the distribution of the available dendrites, whose total length and branching frequency are specified by other cell intrinsic programmes. Our results suggest that the

  1. Usability evaluation of cloud-based mapping tools for the display of very large datasets

    Science.gov (United States)

    Stotz, Nicole Marie

    The elasticity and on-demand nature of cloud services have made it easier to create web maps. Users only need access to a web browser and the Internet to utilize cloud based web maps, eliminating the need for specialized software. To encourage a wide variety of users, a map must be well designed; usability is a very important concept in designing a web map. Fusion Tables, a new product from Google, is one example of newer cloud-based distributed GIS services. It allows for easy spatial data manipulation and visualization, within the Google Maps framework. ESRI has also introduced a cloud based version of their software, called ArcGIS Online, built on Amazon's EC2 cloud. Utilizing a user-centered design framework, two prototype maps were created with data from the San Diego East County Economic Development Council. One map was built on Fusion Tables, and another on ESRI's ArcGIS Online. A usability analysis was conducted and used to compare both map prototypes in term so of design and functionality. Load tests were also ran, and performance metrics gathered on both map prototypes. The usability analysis was taken by 25 geography students, and consisted of time based tasks and questions on map design and functionality. Survey participants completed the time based tasks for the Fusion Tables map prototype quicker than those of the ArcGIS Online map prototype. While response was generally positive towards the design and functionality of both prototypes, overall the Fusion Tables map prototype was preferred. For the load tests, the data set was broken into 22 groups for a total of 44 tests. While the Fusion Tables map prototype performed more efficiently than the ArcGIS Online prototype, differences are almost unnoticeable. A SWOT analysis was conducted for each prototype. The results from this research point to the Fusion Tables map prototype. A redesign of this prototype would incorporate design suggestions from the usability survey, while some functionality would

  2. Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus

    Directory of Open Access Journals (Sweden)

    Matthew C. Hale

    2017-11-01

    Full Text Available Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from nonmodel organisms. This manuscript details the application of restriction site-associated DNA sequencing (RADseq to generate a marker-dense genetic map for Brook Trout (Salvelinus fontinalis. The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic Salmon for 38 linkage groups, with Rainbow Trout for 37 linkage groups, Arctic Char for 36 linkage groups, and with a previously published Brook Trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of 8 metacentric and 34 acrocentric chromosomes in Brook Trout. Six metacentric chromosomes seem to be conserved with Arctic Char suggesting there have been at least two species-specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome was mapped to Brook Trout BC35, which is homologous with Atlantic Salmon Ssa09qa, Rainbow Trout Omy25, and Arctic Char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.

  3. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

    Science.gov (United States)

    DiMaio, F; Chiu, W

    2016-01-01

    Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

  4. Concept Mapping as a Tool to Develop and Measure Students' Understanding in Science

    Science.gov (United States)

    Tan, Sema; Erdimez, Omer; Zimmerman, Robert

    2017-01-01

    Concept maps measured a student's understanding of the complexity of concepts, and interrelationships. Novak and Gowin (1984) claimed that the continuous use of concept maps increased the complexity and interconnectedness of students' understanding of relationships between concepts in a particular science domain. This study has two purposes; the…

  5. Science overlay maps: a new tool for research policy and library management

    NARCIS (Netherlands)

    Rafols, I.; Porter, A.L.; Leydesdorff, L.

    2010-01-01

    We present a novel approach to visually locate bodies of research within the sciences, both at each moment of time and dynamically. This article describes how this approach fits with other efforts to locally and globally map scientific outputs. We then show how these science overlay maps help

  6. The Effects of a Concept Map-Based Support Tool on Simulation-Based Inquiry Learning

    Science.gov (United States)

    Hagemans, Mieke G.; van der Meij, Hans; de Jong, Ton

    2013-01-01

    Students often need support to optimize their learning in inquiry learning environments. In 2 studies, we investigated the effects of adding concept-map-based support to a simulation-based inquiry environment on kinematics. The concept map displayed the main domain concepts and their relations, while dynamic color coding of the concepts displayed…

  7. Use of Concept Maps as an Assessment Tool in Mechanical Engineering Education

    Science.gov (United States)

    Tembe, B. L.; Kamble, S. K.

    2013-01-01

    The purpose of this study to investigate, how third year mechanical engineering students are able to use their knowledge of concept maps in their study of the topic of "Introduction to the Internal Combustion Engines (IICE)". 41 students participated in this study. Firstly, the students were taught about concept maps and then asked to…

  8. Concept Mapping as a Learning Tool for the Employment Relations Degree

    Science.gov (United States)

    Martinez-Canas, Ricardo; Ruiz-Palomino, Pablo

    2011-01-01

    Concept mapping is a technique to represent relationships between concepts that can help students to improve their meaningful learning. Using the cognitive theories proposed by Ausubel (1968), concept maps can help instructors and students to enhance their logical thinking and study skills by revealing connections among concepts that can simplify…

  9. Vulnerability mapping as a tool to manage the environmental impacts of oil and gas extraction.

    Science.gov (United States)

    Esterhuyse, Surina; Sokolic, Frank; Redelinghuys, Nola; Avenant, Marinda; Kijko, Andrzej; Glazewski, Jan; Plit, Lisa; Kemp, Marthie; Smit, Ansie; Vos, A Tascha; von Maltitz, Michael J

    2017-11-01

    Various biophysical and socio-economic impacts may be associated with unconventional oil and gas (UOG) extraction. A vulnerability map may assist governments during environmental assessments, spatial planning and the regulation of UOG extraction, as well as decision-making around UOG extraction in fragile areas. A regional interactive vulnerability map was developed for UOG extraction in South Africa. This map covers groundwater, surface water, vegetation, socio-economics and seismicity as mapping themes, based on impacts that may emanate from UOG extraction. The mapping themes were developed using a normative approach, where expert input during the identification and classification of vulnerability indicators may increase the acceptability of the resultant map. This article describes the development of the interactive vulnerability map for South Africa, where UOG extraction is not yet allowed and where regulations are still being developed to manage this activity. The importance and policy implications of using vulnerability maps for managing UOG extraction impacts in countries where UOG extraction is planned are highlighted in this article.

  10. Modified Ishikawa Diagram as a Tool for Knowledge-Mapping of Agronomic Practices

    Directory of Open Access Journals (Sweden)

    Petr Kedaj

    2015-12-01

    Full Text Available This article describes a novel method of graphical representation of agronomic practices in crop production. The influence of initial factors, the need to follow a chronology of individual operations and the possibility of using this information for creating a knowledge base are all considered in the method designed. Consequently, alternate methods of knowledge mapping are described: Mind maps, conceptual maps, cognitive maps as well as Ishikawa diagram, which is the main inspiration for our method. These established methods of knowledge mapping have been confronted with the method proposed by our research team using a qualitative survey. Results of this study suggest a high potential of use of our method in agronomy. At the end of this article, we propose additional steps for possible improvements in usability of the method described.

  11. An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Kühne Titus

    2010-07-01

    Full Text Available Abstract Background In magnetic resonance (MR imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. Results After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. Conclusions MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.

  12. Cognitive ergonomics: the use of mind mapping tool in maintaining productive sector of a Brazilian paper company.

    Science.gov (United States)

    Mattos, Diego; Mateus, José Roberto; Merino, Eugenio

    2012-01-01

    The use of mind maps as a method of building knowledge, planning, organizing activities and ideas can be seen in the literature related to ergonomics. The results of such use are relevant and its use in academic area found. However, regarding to its use in industrial environments, studies can't not be found. With this scenario, and based on the perception of the ergonomist about the importance of using methods such as mind maps in support of human cognition, it seems pertinent to its use in industry sectors whose cognitive demand requires. Given these assumptions, this study aimed to apply the method of Mind Maps in Productive Maintenance sector of a Brazilian paper. The Productive Maintenance sector in the Paper Industry has an important contribution to operational performance. With practical Predictive Maintenance, Preventive Maintenance and Corrective Maintenance, the industry advocates to make the machines to produce paper is not to stop producing when they are programmed to do so. Among the practices cited, the Preventive Maintenance is one that leads to pre-determined intervals in order to reduce the possibility of placing the equipment in a condition below the required level of acceptance. Therefore, this article aims to propose using the tool "mental maps" in order to collaborate in planning and implementation of preventive maintenance activities in the sector of mechanical maintenance of a pulp and paper industry in southern Brazil. The study investigated the maintenance sector through its employees, who went through training about the tool and then use it and ergonomists company.

  13. Small-molecule auxin inhibitors that target YUCCA are powerful tools for studying auxin function.

    Science.gov (United States)

    Kakei, Yusuke; Yamazaki, Chiaki; Suzuki, Masashi; Nakamura, Ayako; Sato, Akiko; Ishida, Yosuke; Kikuchi, Rie; Higashi, Shouichi; Kokudo, Yumiko; Ishii, Takahiro; Soeno, Kazuo; Shimada, Yukihisa

    2015-11-01

    Auxin is essential for plant growth and development, this makes it difficult to study the biological function of auxin using auxin-deficient mutants. Chemical genetics have the potential to overcome this difficulty by temporally reducing the auxin function using inhibitors. Recently, the indole-3-pyruvate (IPyA) pathway was suggested to be a major biosynthesis pathway in Arabidopsis thaliana L. for indole-3-acetic acid (IAA), the most common member of the auxin family. In this pathway, YUCCA, a flavin-containing monooxygenase (YUC), catalyzes the last step of conversion from IPyA to IAA. In this study, we screened effective inhibitors, 4-biphenylboronic acid (BBo) and 4-phenoxyphenylboronic acid (PPBo), which target YUC. These compounds inhibited the activity of recombinant YUC in vitro, reduced endogenous IAA content, and inhibited primary root elongation and lateral root formation in wild-type Arabidopsis seedlings. Co-treatment with IAA reduced the inhibitory effects. Kinetic studies of BBo and PPBo showed that they are competitive inhibitors of the substrate IPyA. Inhibition constants (Ki ) of BBo and PPBo were 67 and 56 nm, respectively. In addition, PPBo did not interfere with the auxin response of auxin-marker genes when it was co-treated with IAA, suggesting that PPBo is not an inhibitor of auxin sensing or signaling. We propose that these compounds are a class of auxin biosynthesis inhibitors that target YUC. These small molecules are powerful tools for the chemical genetic analysis of auxin function. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  14. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis.

    Science.gov (United States)

    Hur, Junguk; Schuyler, Adam D; States, David J; Feldman, Eva L

    2009-03-15

    SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multiple sources. Ambiguous acronyms are resolved by a scoring scheme based on the co-occurrence of acronyms and corresponding description terms, which incorporates optional user-defined filters. Functional enrichment analyses are used to identify highly relevant targets (genes and proteins), GO (Gene Ontology) terms, MeSH (Medical Subject Headings) terms, pathways and protein-protein interaction networks by comparing identified targets from one search result with those from other searches or to the full HGNC [HUGO (Human Genome Organization) Gene Nomenclature Committee] gene set. The performance of gene/protein name identification was evaluated using the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) version 2 (Year 2006) Gene Normalization Task as a gold standard. SciMiner achieved 87.1% recall, 71.3% precision and 75.8% F-measure. SciMiner's literature mining performance coupled with functional enrichment analyses provides an efficient platform for retrieval and summary of rich biological information from corpora of users' interests. http://jdrf.neurology.med.umich.edu/SciMiner/. A server version of the SciMiner is also available for download and enables users to utilize their institution's journal subscriptions. Supplementary data are available at Bioinformatics online.

  15. GeneRecon Users' Manual — A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, T

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...... of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position....

  16. Geographic profiling as a novel spatial tool for targeting infectious disease control

    Directory of Open Access Journals (Sweden)

    Fuller Douglas O

    2011-05-01

    Full Text Available Abstract Background Geographic profiling is a statistical tool originally developed in criminology to prioritise large lists of suspects in cases of serial crime. Here, we use two data sets - one historical and one modern - to show how it can be used to locate the sources of infectious disease. Results First, we re-analyse data from a classic epidemiological study, the 1854 London cholera outbreak. Using 321 disease sites as input, we evaluate the locations of 13 neighbourhood water pumps. The Broad Street pump - the outbreak's source- ranks first, situated in the top 0.2% of the geoprofile. We extend our study with an analysis of reported malaria cases in Cairo, Egypt, using 139 disease case locations to rank 59 mosquitogenic local water sources, seven of which tested positive for the vector Anopheles sergentii. Geographic profiling ranks six of these seven sites in positions 1-6, all in the top 2% of the geoprofile. In both analyses the method outperformed other measures of spatial central tendency. Conclusions We suggest that geographic profiling could form a useful component of integrated control strategies relating to a wide variety of infectious diseases, since evidence-based targeting of interventions is more efficient, environmentally friendly and cost-effective than untargeted intervention.

  17. A genetic linkage map of sole (Solea solea: a tool for evolutionary and comparative analyses of exploited (flatfishes.

    Directory of Open Access Journals (Sweden)

    Eveline Diopere

    Full Text Available Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L. is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes, Nile tilapia (Oreochromis niloticus, three-spined stickleback (Gasterosteus aculeatus and green spotted pufferfish (Tetraodon nigroviridis. This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus, another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.

  18. The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data.

    Science.gov (United States)

    Awale, Mahendra; Reymond, Jean-Louis

    2017-01-01

    Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictions in each case rely on similarities computed from only one or two fps. Considering that structural similarity and therefore the predicted targets strongly depend on the method used for comparison, it would be highly desirable to predict targets using a broader set of fps simultaneously. Herein, we present the polypharmacology browser (PPB), a web-based platform which predicts possible targets for small molecules by searching for nearest neighbors using ten different fps describing composition, substructures, molecular shape and pharmacophores. PPB searches through 4613 groups of at least 10 same target annotated bioactive molecules from ChEMBL and returns a list of predicted targets ranked by consensus voting scheme and p value. A validation study across 670 drugs with up to 20 targets showed that combining the predictions from all 10 fps gives the best results, with on average 50% of the known targets of a drug being correctly predicted with a hit rate of 25%. Furthermore, when profiling a new inhibitor of the calcium channel TRPV6 against 24 targets taken from a safety screen panel, we observed inhibition in 5 out of 5 targets predicted by PPB and in 7 out of 18 targets not predicted by PPB. The rate of correct (5/12) and incorrect (0/12) predictions for this compound by PPB was comparable to that of other web-based prediction tools. PPB offers a versatile platform for target prediction based on multi-fingerprint comparisons, and is freely accessible at www.gdb.unibe.ch as a valuable support for drug discovery.Graphical abstract.

  19. Community-based oral health promotion practices targeted at children and adolescents in Finland--developing an assessment tool.

    Science.gov (United States)

    Blomqvist, Pia; Ojala, Ellinoora; Kettunen, Tarja; Poskiparta, Marita; Kasila, Kirsti

    2014-06-01

    To develop an assessment tool for evaluating oral health promotion practices and to evaluate community-based oral health promotion practices targeted at children and adolescents with this tool. A theoretical framework about health promotion planning, implementation and evaluation was made on the basis of a literature review. Then, information about Finnish community-based oral health promotion practices (n=12) targeted at children and adolescents was collected using semi-structured interviews. Also, related documents, for example action plans and reports, were collected when available. Next, an assessment tool based on the theoretical framework was developed, and the recorded and transcribed interview data and other documents were evaluated with this tool. The assessment tool proved to be practical: it pointed out the strengths and weaknesses of the practices. The tool revealed strengths in the implementation and deficiencies in the planning and evaluation of oral health promotion practices. One-quarter of the 12 practices assessed could be considered 'good practices'. There is a need to improve the planning and evaluation of oral health promotion practices. The assessment tool developed in this study might be useful for practitioners both in the field of oral health promotion and general health promotion. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Visualizing complex processes using a cognitive-mapping tool to support the learning of clinical reasoning.

    Science.gov (United States)

    Wu, Bian; Wang, Minhong; Grotzer, Tina A; Liu, Jun; Johnson, Janice M

    2016-08-22

    Practical experience with clinical cases has played an important role in supporting the learning of clinical reasoning. However, learning through practical experience involves complex processes difficult to be captured by students. This study aimed to examine the effects of a computer-based cognitive-mapping approach that helps students to externalize the reasoning process and the knowledge underlying the reasoning process when they work with clinical cases. A comparison between the cognitive-mapping approach and the verbal-text approach was made by analyzing their effects on learning outcomes. Fifty-two third-year or higher students from two medical schools participated in the study. Students in the experimental group used the computer-base cognitive-mapping approach, while the control group used the verbal-text approach, to make sense of their thinking and actions when they worked with four simulated cases over 4 weeks. For each case, students in both groups reported their reasoning process (involving data capture, hypotheses formulation, and reasoning with justifications) and the underlying knowledge (involving identified concepts and the relationships between the concepts) using the given approach. The learning products (cognitive maps or verbal text) revealed that students in the cognitive-mapping group outperformed those in the verbal-text group in the reasoning process, but not in making sense of the knowledge underlying the reasoning process. No significant differences were found in a knowledge posttest between the two groups. The computer-based cognitive-mapping approach has shown a promising advantage over the verbal-text approach in improving students' reasoning performance. Further studies are needed to examine the effects of the cognitive-mapping approach in improving the construction of subject-matter knowledge on the basis of practical experience.

  1. New tools for targeted disruption of cholinergic synaptic transmission in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Monica Mejia

    Full Text Available Nicotinic acetylcholine receptors (nAChRs are pentameric ligand-gated ion channels. The α7 subtype of nAChRs is involved in neurological pathologies such as Parkinson's disease, Alzheimer's disease, addiction, epilepsy and autism spectrum disorders. The Drosophila melanogaster α7 (Dα7 has the closest sequence homology to the vertebrate α7 subunit and it can form homopentameric receptors just as the vertebrate counterpart. The Dα7 subunits are essential for the function of the Giant Fiber circuit, which mediates the escape response of the fly. To further characterize the receptor function, we generated different missense mutations in the Dα7 nAChR's ligand binding domain. We characterized the effects of targeted expression of two UAS-constructs carrying a single mutation, D197A and Y195T, as well as a UAS-construct carrying a triple D77T, L117Q, I196P mutation in a Dα7 null mutant and in a wild type background. Expression of the triple mutation was able to restore the function of the circuit in Dα7 null mutants and had no disruptive effects when expressed in wild type. In contrast, both single mutations severely disrupted the synaptic transmission of Dα7-dependent but not glutamatergic or gap junction dependent synapses in wild type background, and did not or only partially rescued the synaptic defects of the null mutant. These observations are consistent with the formation of hybrid receptors, consisting of D197A or Y195T subunits and wild type Dα7 subunits, in which the binding of acetylcholine or acetylcholine-induced conformational changes of the Dα7 receptor are altered and causes inhibition of cholinergic responses. Thus targeted expression of D197A or Y195T can be used to selectively disrupt synaptic transmission of Dα7-dependent synapses in neuronal circuits. Hence, these constructs can be used as tools to study learning and memory or addiction associated behaviors by allowing the manipulation of neuronal processing in the

  2. SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels

    Directory of Open Access Journals (Sweden)

    Franke Andre

    2010-12-01

    Full Text Available Abstract Background Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III of 3.96 million single nucleotide polymorphisms (SNPs in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL analysis. Results SNPexp is implemented as a server-side script, and publicly available on this website: http://tinyurl.com/snpexp. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results. Conclusions SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets.

  3. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

    Science.gov (United States)

    Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

    2017-07-03

    Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

  4. Geomorphological map as a tool for visualisation of geodiversity - example from Cave Park Grabovaca (Croatia)

    Science.gov (United States)

    Buzjak, Nenad; Bocic, Neven; Pahernik, Mladen

    2014-05-01

    Cave Park Grabovaca is located near Perusic in Lika region (central Croatia). It was established in 2006 at the area of 5.95 km2 (protection category: significant landscape). The main task is management and protection of Samograd, Medina and Amidzina caves that were declared as geomorphological monuments, and 6 other caves located close to each other. Owing to the central geographic location in Croatian Dinaric karst area, good traffic connections between central Europe and tourist centres of the Adriatic coast, preserved nature and easy accessible karst features typical for the Dinaric Karst, it has good potential to develop as an research, educational and tourist centre. In 2013. Cave Park management and the Department of Geography (University of Zagreb, Faculty of Science) established a core team that started to develop the project of Geoeducational centre (GEC) with following goals: exploration-evaluation-presentation-education. According to the accepted strategy, the first step in the project process is to enlarge the area and change the protection category. During the consultation process team members take into account protection, environmental, local economy, tourism and local population issues and proposed that protected area should be increased to 52,2 km2. This enlargement provides more efficient protection, greater geodiversity and biodiversity by occupying geotope, biotope, and landscape units typical for the whole Lika karst region. The next step was inventorying, evaluation, analysis and visualisation of geological, geomorphological and speleological phenomena. This 2 year task was made in cooperation between Croatian Geomorphological Society, Department of Geography, Speleological Society Karlovac and Caving Club Samobor. The inventory was made using field-work mapping and geotagged photographs, cave mapping and DEM analysis. It resulted in GIS oriented geodatabase consisting of geomorphological forms, processes and cave inventory. From those data

  5. Immunoscintigraphy as Potential Tool in the Clinical Evaluation of HER2/neu Targeted Therapy

    NARCIS (Netherlands)

    Dijkers, Eli C. F.; de Vries, Elisabeth G. E.; Kosterink, Jos G. W.; Brouwers, Adrienne H.; Hooge, Marjolijn N. Lub-de

    2008-01-01

    Many new targeted anticancer drugs have been developed. In order for these drugs to be effective, the tumor target has to be present during treatment. Currently there are only a few biomarkers available to help the physician select the appropriate targeted drug for the patient and often tumor tissue

  6. Accelerating Genome Editing in CHO Cells Using CRISPR Cas9 and CRISPy, a Web-Based Target Finding Tool

    DEFF Research Database (Denmark)

    Ronda, Carlotta; Pedersen, Lasse Ebdrup; Hansen, Henning Gram

    2014-01-01

    of the CRISPR Cas9 technology in CHO cells by generating site-specific gene disruptions in COSMC and FUT8, both of which encode proteins involved in glycosylation. The tested single guide RNAs (sgRNAs) created an indel frequency up to 47.3% in COSMC, while an indel frequency up to 99.7% in FUT8 was achieved...... mutations at the target sites, with a strong preference for single base indels. Finally, we have developed a user-friendly bioinformatics tool, named “CRISPy” for rapid identification of sgRNA target sequences in the CHO-K1 genome. The CRISPy tool identified 1,970,449 CRISPR targets divided into 27...

  7. Navigating knowledge to action: a conceptual map for facilitating translation of population health risk planning tools into practice.

    Science.gov (United States)

    Peirson, Leslea; Rosella, Laura

    2015-01-01

    A population health risk tool was created that estimates future diabetes risk and provides outputs that can inform practical and meaningful diabetes prevention strategies and support local decision making and planning. A project was designed to inform and understand knowledge translation and application of this novel tool in multiple health-related settings. Lacking published studies in this area, the authors conceived a conceptual map to guide the project that integrates and adapts elements from several planned action theories. This paper describes the rationale and basis for constructing the Population Health Planning Knowledge-to-Action Model and elaborates on the 2 connected structures of the framework: the Tool Creation Path and the Action Cycle. Although created for an express purpose, this model has the potential to inform application of other tools. This work demonstrates how a research team can adapt and integrate existing frameworks to better align with novel real-world knowledge translation issues. Furthermore, the integration of a population risk tool to support health decision making highlights the interaction between continuing education and knowledge translation. © 2015 The Alliance for Continuing Education in the Health Professions, the Society for Academic Continuing Medical Education, and the Council on Continuing Medical Education, Association for Hospital Medical Education.

  8. Science You Can Use Bulletin: Seeing red: New tools for mapping and understanding fire severity

    Science.gov (United States)

    Sue Miller; Robert Keane; Penny Morgan; Pamela Sikkink; Eva Karau; Greg Dillon

    2013-01-01

    Large, severe fires are ecologically and socially important because they have lasting effects on vegetation and soils, can potentially threaten people and property, and can be costly to manage. The goals of the Fire Severity Mapping Project (FIRESEV), which covers lands in the continental western United States, are to understand where and why fires burn severely, and...

  9. USING IMAGE PROCESSING METHODS WITH RASTER EDITING TOOLS FOR MAPPING EELGRASS DISTRIBUTIONS IN PACIFIC NORHWEST ESTUARIES

    Science.gov (United States)

    False-color near-infrared (CIR) aerial photography of seven Oregon estuaries was acquired at extreme low tides and digitally orthorectified with a ground pixel resolution of 25 cm to provide data for intertidal vegetation mapping. Exposed, semi-exposed and some submerged eelgras...

  10. A Hybrid Genetic-Algorithm Space-Mapping Tool for the Optimization of Antennas

    DEFF Research Database (Denmark)

    Pantoja, Mario Fernández; Meincke, Peter; Bretones, Amelia Rubio

    2007-01-01

    A hybrid global-local optimization technique for the design of antennas is presented. It consists of the subsequent application of a genetic algorithm (GA) that employs coarse models in the simulations and a space mapping (SM) that refines the solution found in the previous stage. The technique...

  11. New CSIR tool produces detailed maps of SA’s economic geography

    CSIR Research Space (South Africa)

    Mass media

    2007-10-01

    Full Text Available A new digital mapping and geographic analysis platform (GAP) is enabling researchers and decision-makers to estimate the spatial distribution of economic activity in South Africa in greater detail than ever before. The result of an 18 month...

  12. Concept Map as an Assessment Tool in Secondary School Mathematics: An Analysis of Teachers' Perspectives

    Science.gov (United States)

    Mutodi, Paul; Chigonga, Benard

    2016-01-01

    This paper reports on teachers' views on concept mapping: its applicability; reliability; advantages and; difficulties. A close-ended questionnaire was administered to 50 purposefully selected secondary school mathematics teachers from Sekhukhune District, Limpopo, South Africa. The findings indicate that mathematics teachers generally perceive…

  13. Concept Mapping Strategy: An Effective Tool for Improving Students' Academic Achievement in Biology

    Science.gov (United States)

    Sakiyo, John; Waziri, Kawu

    2015-01-01

    The study investigated the use of concept mapping teaching method on secondary school students' academic achievement in biology. Two hypotheses tested at 0.05 level of significance guided the study. The design of the study was quasi-experimental design with 122 Senior Secondary students selected purposively from two senior secondary schools in…

  14. HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.

    Science.gov (United States)

    Anil, Anandashankar; Spalinskas, Rapolas; Åkerborg, Örjan; Sahlén, Pelin; Berger, Bonnie

    2018-02-15

    Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gene features. Statistical significance of contact frequencies is evaluated using an empirically derived background distribution. Targeted chromosome conformation capture applications are invaluable for locating target genes of disease-associated variants found by genome-wide association studies. Hence, we believe our software suite will prove to be useful for a wider user base within clinical and functional applications. https://github.com/sahlenlab/HiCapTools. pelinak@kth.se. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies.

    Science.gov (United States)

    Valdivia-Granda, Willy; Larson, Francis

    2009-01-01

    Viruses, viroids and prions are the smallest infectious biological entities that depend on their host for replication. The number of pathogenic viruses is considerably large and their impact in human global health is well documented. Currently, the International Committee on the Taxonomy of Viruses (ICTV) has classified approximately 4379 virus species while the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) database has mapped 617 705 proteins to eight large taxonomic groups. Despite these efforts, an automated approach for mapping the ICTV master list and its officially accepted virus naming to the NCBI-VGR's taxonomical classification is not available. Due to metagenomic sequencing, it is likely that the discovery and naming of new viral species will increase by at least ten fold. Unfortunately, existing viral databases are not adequately prepared to scale, maintain and annotate automatically ultra-high throughput sequences and place this information into specific taxonomic categories. ORION-VIRCAT is a scalable and interoperable object-relational database designed to serve as a resource for the integration and verification of taxonomical classifications generated by the ICTV and NCBI-VGR. The current release (v1.0) of ORION-VIRCAT is implemented in PostgreSQL and it has been extended to ORACLE, MySQL and SyBase. ORION-VIRCAT automatically mapped and joined 617 705 entries from the NCBI-VGR to the viral naming of the ICTV. This detailed analysis revealed that 399 095 entries from the NCBI-VGR can be mapped to the ICTV classification and that one Order, 10 families, 35 genera and 503 species listed in the ICTV disagree with the the NCBI-VGR classification schema. Nevertheless, we were eable to correct several discrepancies mapping 234 000 additional entries.Database URL:http://www.orionbiosciences.com/research/orion-vircat.html.

  16. EPA Region 1 - Map Layers for Valley ID Tool (Hosted Feature Service)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Valley Service Feature Layer hosts spatial data for EPA Region 1's Valley Identification Tool. These layers contain attribute information added by EPA R1 GIS...

  17. GIS Story Maps : A Tool to Empower and Engage Stakeholders in Planning Sustainable Places

    Science.gov (United States)

    2016-10-01

    Public engagement continues to be transformed by the explosion of new digital technologies/tools, software platforms, social media networks, mobile devices, and mobile apps. Recent changes in geospatial technology offer new opportunities for use in p...

  18. Tracking changes of river morphology in Ayeyarwady River in Myanmar using earth observations and surface water mapping tool

    Science.gov (United States)

    Piman, T.; Schellekens, J.; Haag, A.; Donchyts, G.; Apirumanekul, C.; Hlaing, K. T.

    2017-12-01

    River morphology changes is one of the key issues in Ayeyarwady River in Myanmar which cause impacts on navigation, riverine habitats, agriculture lands, communities and livelihoods near the bank of the river. This study is aimed to track the changes in river morphology in the middle reach of Ayeyarwady River over last 30 years from 1984-2014 to improve understanding of riverbank dynamic, erosion and deposition procress. Earth observations including LandSat-7, LandSat-8, Digital Elevation Model from SRTM Plus and, ASTER-2 GoogleMap and Open Street Map were obtained for the study. GIS and remote sensing tools were used to analyze changes in river morphology while surface water mapping tool was applied to determine how the dynamic behaviour of the surface river and effect of river morphology changes. The tool consists of two components: (1) a Google Earth Engine (GEE) javascript or python application that performs image analysis and (2) a user-friendly site/app using Google's appspot.com that exposes the application to the users. The results of this study shown that the fluvial morphology in the middle reach of Ayeyarwady River is continuously changing under the influence of high water flows in particularly from extreme flood events and land use change from mining and deforestation. It was observed that some meandering sections of the riverbank were straightened, which results in the movement of sediment downstream and created new sections of meandering riverbank. Several large islands have formed due to the stabilization by vegetation and is enforced by sedimentation while many small bars were formed and migrated dynamically due to changes in water levels and flow velocity in the wet and dry seasons. The main channel was changed to secondary channel in some sections of the river. This results a constant shift of the navigation route. We also found that some villages were facing riverbank erosion which can force villagers to relocate. The study results demonstrated

  19. Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification.

    Science.gov (United States)

    van Rooden, Eva J; Florea, Bogdan I; Deng, Hui; Baggelaar, Marc P; van Esbroeck, Annelot C M; Zhou, Juan; Overkleeft, Herman S; van der Stelt, Mario

    2018-04-01

    Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA 10-2474, thereby providing a potential explanation for the adverse side effects observed with this compound. ABPP allows mapping of protein interaction landscapes of inhibitors in cells, tissues and animal models. Whereas our previous protocol described quantification of proteasome activity using stable-isotope labeling, this protocol describes the procedures for identifying the in vivo selectivity profile of covalent inhibitors with label-free quantitative proteomics. The optimization of our protocol for label-free quantification methods results in high proteome coverage and allows the comparison of multiple biological samples. We demonstrate our protocol by assessing the protein interaction landscape of the diacylglycerol lipase inhibitor DH376 in mouse brain, liver, kidney and testes. The stages of the protocol include tissue lysis, probe incubation, target enrichment, sample preparation, liquid chromatography-mass spectrometry (LC-MS) measurement, data processing and analysis. This approach can be used to study target engagement in a native proteome and to identify potential off targets for the inhibitor under investigation. The entire protocol takes at least 4 d, depending on the number of samples.

  20. Developing Process Maps as a Tool for a Surgical Infection Prevention Quality Improvement Initiative in Resource-Constrained Settings.

    Science.gov (United States)

    Forrester, Jared A; Koritsanszky, Luca A; Amenu, Demisew; Haynes, Alex B; Berry, William R; Alemu, Seifu; Jiru, Fekadu; Weiser, Thomas G

    2018-03-21

    Surgical infections cause substantial morbidity and mortality in low-and middle-income countries (LMICs). To improve adherence to critical perioperative infection prevention standards, we developed Clean Cut, a checklist-based quality improvement program to improve compliance with best practices. We hypothesized that process mapping infection prevention activities can help clinicians identify strategies for improving surgical safety. We introduced Clean Cut at a tertiary hospital in Ethiopia. Infection prevention standards included skin antisepsis, ensuring a sterile field, instrument decontamination/sterilization, prophylactic antibiotic administration, routine swab/gauze counting, and use of a surgical safety checklist. Processes were mapped by a visiting surgical fellow and local operating theater staff to facilitate the development of contextually-relevant solutions; processes were re-assessed for improvements. Process mapping helped identify barriers to using alcohol-based hand solution due to skin irritation, inconsistent administration of prophylactic antibiotics due to variable delivery outside of the operating theater, inefficiencies in assuring sterility of surgical instruments through lack of confirmatory measures, and occurrences of retained surgical items through inappropriate guidelines, staffing, and training in proper routine gauze counting. Compliance with most processes improved significantly following organizational changes to align tasks with specific process goals. Enumerating the steps involved in surgical infection prevention using a process mapping technique helped identify opportunities for improving adherence and plotting contextually relevant solutions, resulting in superior compliance with antiseptic standards. Simplifying these process maps into an adaptable tool could be a powerful strategy for improving safe surgery delivery in LMICs. Copyright © 2018. Published by Elsevier Inc.

  1. Technical Targets - A Tool to Support Strategic Planning in the Subsurface Contaminants Focus Area

    International Nuclear Information System (INIS)

    Looney, B.B.

    2002-01-01

    The Subsurface Contaminants Focus Area (SCFA) is supported by a lead laboratory consisting of technical representatives from DOE laboratories across the country. This broadly representative scientific group has developed and implemented a process to define Technical Targets to assist the SCFA in strategic planning and in managing their environmental research and development portfolio. At an initial meeting in Golden Colorado, an initial set of Technical Targets was identified using a rapid consensus based technical triage process. Thirteen Technical Targets were identified and described. Vital scientific and technical objectives were generated for each target. The targets generally fall into one of the following five strategic investment categories: Enhancing Environmental Stewardship, Eliminating Contaminant Sources, Isolating Contaminants, Controlling Contaminant Plumes, Enabling DOEs CleanUp Efforts. The resulting targets and the detail they comprise on what is, and what is not, needed to meet Environmental Management needs provide a comprehensive technically-based framework to assist in prioritizing future work and in managing the SCFA program

  2. Mapping the course of the EU "Power Target Model"... on its own terms

    OpenAIRE

    GLACHANT, Jean-Michel

    2016-01-01

    The European Union took more than 20 years to start defining a common market design for its internal electricity market: a European Power Target Model. And, a further 10 years to fully implement it. Meanwhile, the reference generation set of that model has shifted from CCGT burning gas to RES units transforming intermittent natural resources. Could the existing EU target model continue to work well for the short- term operation and long-term investment? If not, can the existing EU institution...

  3. TiPs: a database of therapeutic targets in pathogens and associated tools.

    KAUST Repository

    Lepore, Rosalba

    2013-05-21

    MOTIVATION: The need for new drugs and new targets is particularly compelling in an era that is witnessing an alarming increase of drug resistance in human pathogens. The identification of new targets of known drugs is a promising approach, which has proven successful in several cases. Here, we describe a database that includes information on 5153 putative drug-target pairs for 150 human pathogens derived from available drug-target crystallographic complexes. AVAILABILITY AND IMPLEMENTATION: The TiPs database is freely available at http://biocomputing.it/tips. CONTACT: anna.tramontano@uniroma1.it or allegra.via@uniroma1.it.

  4. Groundwater vulnerability and risk mapping using GIS, modeling and a fuzzy logic tool.

    Science.gov (United States)

    Nobre, R C M; Rotunno Filho, O C; Mansur, W J; Nobre, M M M; Cosenza, C A N

    2007-12-07

    A groundwater vulnerability and risk mapping assessment, based on a source-pathway-receptor approach, is presented for an urban coastal aquifer in northeastern Brazil. A modified version of the DRASTIC methodology was used to map the intrinsic and specific groundwater vulnerability of a 292 km(2) study area. A fuzzy hierarchy methodology was adopted to evaluate the potential contaminant source index, including diffuse and point sources. Numerical modeling was performed for delineation of well capture zones, using MODFLOW and MODPATH. The integration of these elements provided the mechanism to assess groundwater pollution risks and identify areas that must be prioritized in terms of groundwater monitoring and restriction on use. A groundwater quality index based on nitrate and chloride concentrations was calculated, which had a positive correlation with the specific vulnerability index.

  5. Large scale mapping of groundwater resources using a highly integrated set of tools

    DEFF Research Database (Denmark)

    Søndergaard, Verner; Auken, Esben; Christiansen, Anders Vest

    platforms (e.g. SkyTEM) have made large-scale mapping attractive and affordable in the planning and administration of groundwater resources. The handling and optimized use of huge amounts of geophysical data covering large areas has also required a comprehensive database, where data can easily be stored......The aim of this abstract is to give a short description of the essential ideas of the Danish national strategy for large scale mapping of the groundwater resources.Emphasis will be put on a description of the advantages obtained by combining acquirement of spatially dense geophysical data covering...... large areas with information from an optimum number of new investigation boreholes, existing boreholes, logs and water samples to get an integrated and detailed description of the groundwater resources and their vulnerability.Development of more time efficient and airborne geophysical data acquisition...

  6. Mapping of inhibitors and activity data to the human kinome and exploring promiscuity from a ligand and target perspective.

    Science.gov (United States)

    Hu, Ye; Kunimoto, Ryo; Bajorath, Jürgen

    2017-06-01

    An up-to-date collection of publicly available kinase inhibitors and activity data was mapped to the human kinome to comprehensively analyze current small molecule-kinase interactions. Compound distributions across the kinome were explored, structural relationships between inhibitors determined, and the tendency to form activity cliffs assessed. Furthermore, promiscuity was analyzed at the level of inhibitors and kinases, and a number of kinase targets with distinct preferences for single- or multitarget inhibitors were identified. Taken together, the results of current analysis provide a detailed view of kinase-inhibitor interaction characteristics across the human kinome. © 2016 John Wiley & Sons A/S.

  7. Development of a GIS-based, real-time Internet mapping tool for rabies surveillance

    Directory of Open Access Journals (Sweden)

    Manangan Jamie

    2006-11-01

    Full Text Available Abstract Background Oral rabies vaccination programs have been implemented to control the spread of wildlife rabies in the United States. However, current surveillance systems are inadequate for the efficient management and evaluation of these large scale vaccine baiting programs. With this in mind, a GIS-based rabies surveillance database and Internet mapping application was created. This surveillance system, RabID, provides a new resource for the rapid mapping and dissemination of data on animal rabies cases in relation to unaffected, enzootic, and baited areas where current interventions are underway. Results RabID is a centralized database for diagnostic and demographic information collected by local, state, and federal agencies involved in rabies surveillance. The geo-referenced database remits data to an Internet-accessible mapping application that displays rabies surveillance data in relation to environmental and geographic features. Conclusion RabID provides a pioneering example of the power of geographically based Internet-accessible, infectious disease surveillance. This surveillance system was developed from existing technology and is readily adaptable to other infectious diseases and may be particularly useful for zoonoses. The development and application of public health informatics technology may enhance the effectiveness of public health interventions and allow better evaluation of public health interventions.

  8. Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

    Science.gov (United States)

    Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Minor, Wladek

    2018-01-01

    Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼90% are an interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric. The possible consequences of basing research on suboptimal models make it imperative to inspect the agreement of a model with its experimental evidence. Molstack, a web-based interactive publishing platform for structural data, allows users to present density maps and structural models by displaying a collection of maps and models, including different interpretation of one's own data, re-refinements, and corrections of existing structures. Molstack organizes the sharing and dissemination of these structural models along with their experimental evidence as an interactive session. Molstack was designed with three groups of users in mind; researchers can present the evidence of their interpretation, reviewers and readers can independently judge the experimental evidence of the authors' conclusions, and other researchers can present or even publish their new hypotheses in the context of prior results. The server is available at http://molstack.bioreproducibility.org. © 2017 The Protein Society.

  9. Panoramic Images Mapping Tools Integrated Within the ESRI ArcGIS Software

    International Nuclear Information System (INIS)

    Guo, Jiao; Zhong, Ruofei; Zeng, Fanyang

    2014-01-01

    There is a general study on panoramic images which are presented along with appearance of the Google street map. Despite 360 degree viewing of street, we can realize more applications over panoramic images. This paper developed a toolkits plugged in ArcGIS, which can view panoramic photographs at street level directly from ArcMap and measure and capture all visible elements as frontages, trees and bridges. We use a series of panoramic images adjoined with absolute coordinate through GPS and IMU. There are two methods in this paper to measure object from these panoramic images: one is to intersect object position through a stereogram; the other one is multichip matching involved more than three images which all cover the object. While someone wants to measure objects from these panoramic images, each two panoramic images which both contain the object can be chosen to display on ArcMap. Then we calculate correlation coefficient of the two chosen panoramic images so as to calculate the coordinate of object. Our study test different patterns of panoramic pairs and compare the results of measurement to the real value of objects so as to offer the best choosing suggestion. The article has mainly elaborated the principles of calculating correlation coefficient and multichip matching

  10. Unsupervised self-organized mapping: a versatile empirical tool for object selection, classification and redshift estimation in large surveys

    Science.gov (United States)

    Geach, James E.

    2012-01-01

    We present an application of unsupervised machine learning - the self-organized map (SOM) - as a tool for visualizing, exploring and mining the catalogues of large astronomical surveys. Self-organization culminates in a low-resolution representation of the 'topology' of a parameter volume, and this can be exploited in various ways pertinent to astronomy. Using data from the Cosmological Evolution Survey (COSMOS), we demonstrate two key astronomical applications of the SOM: (i) object classification and selection, using galaxies with active galactic nuclei as an example, and (ii) photometric redshift estimation, illustrating how SOMs can be used as totally empirical predictive tools. With a training set of ˜3800 galaxies with zspec≤ 1, we achieve photometric redshift accuracies competitive with other (mainly template fitting) techniques that use a similar number of photometric bands [σ(Δz) = 0.03 with a ˜2 per cent outlier rate when using u* band to 8 ?m photometry]. We also test the SOM as a photo-z tool using the PHoto-z Accuracy Testing (PHAT) synthetic catalogue of Hildebrandt et al., which compares several different photo-z codes using a common input/training set. We find that the SOM can deliver accuracies that are competitive with many of the established template fitting and empirical methods. This technique is not without clear limitations, which are discussed, but we suggest it could be a powerful tool in the era of extremely large -'petabyte'- data bases where efficient data mining is a paramount concern.

  11. Applying the self-organization feature map (SOM) algorithm to AE-based tool wear monitoring in micro-cutting

    Science.gov (United States)

    Yen, Chia-Liang; Lu, Ming-Chyuan; Chen, Jau-Liang

    2013-01-01

    This study applies a self-organization feature map (SOM) neural network to acoustic emission (AE) signal-based tool wear monitoring for a micro-milling process. An experiment was set up to collect the signal during cutting for the system development and performance analysis. The AE signal generated on the workpiece was first transformed to the frequency domain by Fast Fourier transformation (FFT), followed by feature extraction processing using the SOM algorithm. The performance verification in this study adopts a learning vector quantification (LVQ) network to evaluate the effects of the SOM algorithm on the classification performance for tool wear monitoring. To investigate the improvement achieved by the SOM algorithms, this study also investigates cases applying only the LVQ classifier and based on the class mean scatter feature selection (CMSFS) criterion and LVQ. Results show that accurate classification of the tool wear can be obtained by properly selecting features closely related to the tool wear based on the CMSFS and frequency resolution of spectral features. However, the SOM algorithms provide a more reliable methodology of reducing the effect on the system performance contributed by noise or variations in the cutting system.

  12. EpiTools, A software suite for presurgical brain mapping in epilepsy: Intracerebral EEG.

    Science.gov (United States)

    Medina Villalon, S; Paz, R; Roehri, N; Lagarde, S; Pizzo, F; Colombet, B; Bartolomei, F; Carron, R; Bénar, C-G

    2018-03-29

    In pharmacoresistant epilepsy, exploration with depth electrodes can be needed to precisely define the epileptogenic zone. Accurate location of these electrodes is thus essential for the interpretation of Stereotaxic EEG (SEEG) signals. As SEEG analysis increasingly relies on signal processing, it is crucial to make a link between these results and patient's anatomy. Our aims were thus to develop a suite of software tools, called "EpiTools", able to i) precisely and automatically localize the position of each SEEG contact and ii) display the results of signal analysis in each patient's anatomy. The first tool, GARDEL (GUI for Automatic Registration and Depth Electrode Localization), is able to automatically localize SEEG contacts and to label each contact according to a pre-specified nomenclature (for instance that of FreeSurfer or MarsAtlas). The second tool, 3Dviewer, enables to visualize in the 3D anatomy of the patient the origin of signal processing results such as rate of biomarkers, connectivity graphs or Epileptogenicity Index. GARDEL was validated in 30 patients by clinicians and proved to be highly reliable to determine within the patient's individual anatomy the actual location of contacts. GARDEL is a fully automatic electrode localization tool needing limited user interaction (only for electrode naming or contact correction). The 3Dviewer is able to read signal processing results and to display them in link with patient's anatomy. EpiTools can help speeding up the interpretation of SEEG data and improving its precision. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Nature in the metropolis : Mapping biodiversity using metropolitan landscape characterization tools

    NARCIS (Netherlands)

    Tisma, A.; van der Velde, J.R.T.; Nijhuis, S.; Pouderoijen, M.T.

    2014-01-01

    Cities can be planned and designed to reduce their effect on biodiversity loss and may even be able to sustain biodiversity levels in some instances, due to ‘beta-diversity’. The heterogeneity of metropolitan regions can be expected to have a strong impact on beta-diversity. Tools such as landscape

  14. SURFmap: A Network Monitoring Tool Based on the Google Maps API

    NARCIS (Netherlands)

    Hofstede, R.J.; Hofstede, R. J.; Fioreze, Tiago

    2009-01-01

    Network monitoring allows network managers to get a better insight in the network traffic transiting in a managed network. In order to make the tasks of a network manager easier, many network monitoring tools are made available for a wide range of purposes (e.g., traffic accounting, performance

  15. SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

    Directory of Open Access Journals (Sweden)

    Mecit Sari

    Full Text Available Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases.Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD. SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis.SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms.

  16. INFOMAR - Ireland's National Seabed Mapping Programme: A Tool For Marine Spatial Planning

    Science.gov (United States)

    Furey, T. M.

    2016-02-01

    INFOMAR is Ireland's national seabed mapping programme and is a key action in the national integrated marine plan, Harnessing Our Ocean Wealth. It comprises a multi-platform approach to delivering marine integrated mapping in 2 phases, over a projected 20 year timeline (2006-2026). The programme has three work strands; Data Acquisition, Data Exchange and Integration, and Value Added Exploitation. The Data Acquisition strand includes collection of hydrographic, oceanographic, geological, habitat and heritage datasets that will underpin future sustainable development and management of Ireland's marine resource. INFOMAR outputs are delivered through the Data Exchange and Integration strand. Uses of these outputs are wide ranging and multipurpose, from management plans for fisheries, aquaculture and coastal protection works, to environmental impact assessments, ocean renewable development and integrated coastal zone management. In order to address the evolution and diversification of maritime user requirements, the programme has realigned and developed outputs and new products, in part, through an innovative research funding initiative. Development is also fostered through the Value Added Exploitation strand. INFOMAR outputs and products serve to underpin delivery of Ireland's statutory obligations and enhance compliance with EU and national legislation. This is achieved through co-operation with the agencies responsible for supporting Ireland's international obligations and for the implementation of marine spatial planning. A strategic national seabed mapping programme such as INFOMAR, provides a critical baseline dataset which underpins development of the marine economy, and improves our understanding of the response of marine systems to pressures, and the effect of cumulative impacts. This paper will focus on the evolution and scope of INFOMAR, and look at examples of outputs being harnessed to serve approaches to the management of activities having an impact on the

  17. Data Mining and Knowledge Discovery in Gaia survey: GUASOM, an analysis tool based on Self Organizing Maps

    Science.gov (United States)

    Manteiga, Minia; Dafonte, Jose Carlos; Ulla, Ana; Alvarez, Marco Antonio; Garabato, Daniel; Fustes, Diego

    2015-08-01

    Gaia, the astrometric cornerstone mission of the European Space Agency (ESA) was successfully launched in December 2013. In June 2014 Gaia started its scientific operations phase scanning the sky with the different instruments on board. Gaia was designed to measure positions, parallaxes and motions to the microarcsec level, thus providing the first highly accurate 6-D map of about a thousand million objects of the Milky Way. A vast community of astronomers are looking forward to the delivery of the promise of the first non-biased survey of the entire sky down to magnitude 20.We present GUASOM a data mining tool designed for knowledge discovery in large astronomical spectrophotometric archives, that was developed in the framework of Gaia DPAC (Data Processing and Analysis Consocium). Our tool is based on a type of unsupervised learning Artificial Neural Networks named Self-organizing maps (SOMs).SOMs are used to organize the information in clusters of objects, as homogeneously as possible according to their spectral energy distributions, and to project them onto a 2D grid where the data structure can be visualized. Each cluster has a representative, called prototype which is a virtual pattern that better represents or resembles the set of input patterns belonging to such a cluster. Prototypes make easier the task of determining the physical nature of the objects populating each cluster. Our algorithm has been tested on SDSS observations and theoretical spectral libraries covering a wide sample of astronomical objects.Self-organizing maps permit the grouping and visualization of big amount of data for which there is no a priori knowledge..GUASOM provides a useful toolbox for data visualization and crossmatching. To this effect, we have used SIMBAD catalog to perform astrometric crossmatching with a sample of SDSS classification outliers, seeking for identifications.

  18. A program development tool for KEK VME-MAP control system

    International Nuclear Information System (INIS)

    Nakagawa, H.; Katoh, T.; Kadokura, E.; Akiyama, A.; Nigorikawa, K.; Ishii, K.

    1992-01-01

    The control system for KEK 12 GeV Proton Synchrotron has been replaced with a distributed VME-bus based microcomputer system and a MAP local area network. In order to simplify programming for network application tasks, a set of a preprocessor for a PASCAL compiler and a network communication server has been developed. Application programs for accelerator control system have blocks with similar codes; sending, waiting for, receiving, analyzing messages, etc. The preprocessor called 'OBJP' incorporates such common codes into the source code written by an application programmer. In case of a simple program, the size of the source code is reduced by one tenth of a full coding. (author)

  19. A Programmable Video Platform and Its Application Mapping Framework Using the Target Application's SystemC Models

    Directory of Open Access Journals (Sweden)

    Kim Daewoong

    2011-01-01

    Full Text Available Abstract HD video applications can be represented with multiple tasks consisting of tightly coupled multiple threads. Each task requires massive computation, and their communication can be categorized as asynchronous distributed small data and large streaming data transfers. In this paper, we propose a high performance programmable video platform that consists of four processing element (PE clusters. Each PE cluster runs a task in the video application with RISC cores, a hardware operating system kernel (HOSK, and task-specific accelerators. PE clusters are connected with two separate point-to-point networks: one for asynchronous distributed controls and the other for heavy streaming data transfers among the tasks. Furthermore, we developed an application mapping framework, with which parallel executable codes can be obtained from a manually developed SystemC model of the target application without knowing the detailed architecture of the video platform. To show the effectivity of the platform and its mapping framework, we also present mapping results for an H.264/AVC 720p decoder/encoder and a VC-1 720p decoder with 30 fps, assuming that the platform operates at 200 MHz.

  20. 3D Surface Mapping of Capsule Fill-Tube Assemblies used in Laser-Driven Fusion Targets

    International Nuclear Information System (INIS)

    Buice, E.S.; Alger, E.T.; Antipa, N.A.; Bhandarkar, S.D.; Biesiada, T.A.; Conder, A.D.; Dzenitis, E.G.; Flegel, M.S.; Hamza, A.V.; Heinbockel, C.L.; Horner, J.; Johnson, M.A.; Kegelmeyer, L.M.; Meyer, J.S.; Montesanti, R.C.; Reynolds, J.L.; Taylor, J.S.; Wegner, P.J.

    2011-01-01

    This paper presents the development of a 3D surface mapping system used to measure the surface of a fusion target Capsule Fill-Tube Assembly (CFTA). The CFTA consists of a hollow Ge-doped plastic sphere, called a capsule, ranging in outer diameter between 2.2 mm and 2.6 mm and an attached 150 (micro)m diameter glass-core fill-tube that tapers down to a 10(micro) diameter at the capsule. The mapping system is an enabling technology to facilitate a quality assurance program and to archive 3D surface information of each capsule used in fusion ignition experiments that are currently being performed at the National Ignition Facility (NIF). The 3D Surface Mapping System is designed to locate and quantify surface features with a height of 50 nm and 300 nm in width or larger. Additionally, the system will be calibrated such that the 3D measured surface can be related to the capsule surface angular coordinate system to within 0.25 degree (1σ), which corresponds to approximately 5 (micro)m linear error on the capsule surface.

  1. 3D Surface Mapping of Capsule Fill-Tube Assemblies used in Laser-Driven Fusion Targets

    Energy Technology Data Exchange (ETDEWEB)

    Buice, E S; Alger, E T; Antipa, N A; Bhandarkar, S D; Biesiada, T A; Conder, A D; Dzenitis, E G; Flegel, M S; Hamza, A V; Heinbockel, C L; Horner, J; Johnson, M A; Kegelmeyer, L M; Meyer, J S; Montesanti, R C; Reynolds, J L; Taylor, J S; Wegner, P J

    2011-02-18

    This paper presents the development of a 3D surface mapping system used to measure the surface of a fusion target Capsule Fill-Tube Assembly (CFTA). The CFTA consists of a hollow Ge-doped plastic sphere, called a capsule, ranging in outer diameter between 2.2 mm and 2.6 mm and an attached 150 {micro}m diameter glass-core fill-tube that tapers down to a 10{micro} diameter at the capsule. The mapping system is an enabling technology to facilitate a quality assurance program and to archive 3D surface information of each capsule used in fusion ignition experiments that are currently being performed at the National Ignition Facility (NIF). The 3D Surface Mapping System is designed to locate and quantify surface features with a height of 50 nm and 300 nm in width or larger. Additionally, the system will be calibrated such that the 3D measured surface can be related to the capsule surface angular coordinate system to within 0.25 degree (1{sigma}), which corresponds to approximately 5 {micro}m linear error on the capsule surface.

  2. Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan.

    Directory of Open Access Journals (Sweden)

    Maleeha Maria

    Full Text Available Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD.We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA, retinitis pigmentosa (RP, congenital stationary night blindness (CSNB, or cone dystrophy (CD. We employed genome-wide single nucleotide polymorphism (SNP array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families.Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1.Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.

  3. The Global Livestock Impact Mapping System (GLIMS as a tool for animal health applications

    Directory of Open Access Journals (Sweden)

    Gianluca Franceschini

    2009-12-01

    Full Text Available Recent concerns expressed by various national and international organisations about global livestock sector development and its consequences on the environment and on human and animal health suggest the need to reinforce efforts to monitor and collect more accurate and detailed statistics on livestock. Modern technologies for the organisation, analysis, dissemination and presentation of data and results enhance the contribution that these statistics can make towards the planning of efficient and sustainable animal production and health interventions. To this end, the Food and Agriculture Organization Animal Production and Health Division (FAO-AGA has developed the Global Livestock Impact Mapping System (GLIMS. GLIMS provides a repository for sub-national data pertaining to the livestock sector and produces and distributes, through various channels and formats, a number of global public products, namely: the Gridded Livestock of the World (GLW, mapping the spatial distribution of the main livestock species, the Global Livestock Production and Health Atlas (GLiPHA, disseminating sub-national geo-referenced statistics, and the AGA Livestock Sector Briefs, which are concise national reports on the livestock sector. These products have a variety of applications. The authors focus attention on applications in the field of animal health, both to increase knowledge of the occurrence of livestock diseases and to assess their impact.

  4. The World Stress Map - A Freely Accessible Tool For Geohazard Assessment

    International Nuclear Information System (INIS)

    Mueller, Birgit; Heidbach, Oliver; Tingay, Mark

    2006-01-01

    The World Stress Map (WSM) database contains over 16,000 indicators on contemporary crustal tectonic stress and provides an essential parameter for geohazard assessment. This paper focuses on the importance of database accessibility for geohazard assessment and presents the basic concepts and availability of the WSM. The WSM can be applied to several key aspects of geohazard assessment, in particular the mapping of stress patterns and places of stress concentration for improved delineation of zones of seismic hazard. Furthermore, contemporary tectonic stresses can be used in combination with numerical modeling to identify faults or sections of fault systems with high failure potential and can help to predict the likely type of fault reactivation. This approach is especially valuable for assessing the likelihood of strong and rare seismic events for which probabilistic hazard assessment will fail and physically based methodologies are required. Herein, we use the Caspian-Caucasian region as an example to apply WSM data for geohazard assessment. The Caspian-Caucasian area is characterized by the occurrence of a number of stress related geohazards on different spatial scales, in particular crustal earthquakes, seismically triggered landslides and mud volcanism

  5. Use of GIS Mapping as a Public Health Tool-From Cholera to Cancer.

    Science.gov (United States)

    Musa, George J; Chiang, Po-Huang; Sylk, Tyler; Bavley, Rachel; Keating, William; Lakew, Bereketab; Tsou, Hui-Chen; Hoven, Christina W

    2013-01-01

    The field of medical geographic information systems (Medical GIS) has become extremely useful in understanding the bigger picture of public health. The discipline holds a substantial capacity to understand not only differences, but also similarities in population health all over the world. The main goal of marrying the disciplines of medical geography, public health and informatics is to understand how countless health issues impact populations, and the trends by which these populations are affected. From the 1990s to today, this practical approach has become a valued and progressive system in analyzing medical and epidemiological phenomena ranging from cholera to cancer. The instruments supporting this field include geographic information systems (GIS), disease surveillance, big data, and analytical approaches like the Geographical Analysis Machine (GAM), Dynamic Continuous Area Space Time Analysis (DYCAST), cellular automata, agent-based modeling, spatial statistics and self-organizing maps. The positive effects on disease mapping have proven to be tremendous as these instruments continue to have a great impact on the mission to improve worldwide health care. While traditional uses of GIS in public health are static and lacking real-time components, implementing a space-time animation in these instruments will be monumental as technology and data continue to grow.

  6. Target Costing as a Strategic Tool to Commercialize the Product and Service Innovation

    DEFF Research Database (Denmark)

    Jiang, Liping; Hansen, Carsten Ørts

    . What can be done? The implementation of target costing will increase the odds of commercial success of an innovation. It aims at fulfilling the economic potential of an innovation by focusing on the market and customers during the design and price setting stages. This price will, on one hand, impose...... the cost-reduction target in the organization. On the other hand, it can be a driving force for improving the cost-effective design and internal operations....

  7. Implementation of structure-mapping inference by event-file binding and action planning: a model of tool-improvisation analogies.

    Science.gov (United States)

    Fields, Chris

    2011-03-01

    Structure-mapping inferences are generally regarded as dependent upon relational concepts that are understood and expressible in language by subjects capable of analogical reasoning. However, tool-improvisation inferences are executed by members of a variety of non-human primate and other species. Tool improvisation requires correctly inferring the motion and force-transfer affordances of an object; hence tool improvisation requires structure mapping driven by relational properties. Observational and experimental evidence can be interpreted to indicate that structure-mapping analogies in tool improvisation are implemented by multi-step manipulation of event files by binding and action-planning mechanisms that act in a language-independent manner. A functional model of language-independent event-file manipulations that implement structure mapping in the tool-improvisation domain is developed. This model provides a mechanism by which motion and force representations commonly employed in tool-improvisation structure mappings may be sufficiently reinforced to be available to inwardly directed attention and hence conceptualization. Predictions and potential experimental tests of this model are outlined.

  8. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

    Science.gov (United States)

    Clark, Alex M; Sarker, Malabika; Ekins, Sean

    2014-01-01

    We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

  9. Development of a personalized dosimetric tool for radiation protection in case of internal contamination and targeted radiotherapy in nuclear medicine

    International Nuclear Information System (INIS)

    Chiavassa, S.

    2005-12-01

    Current internal dosimetric estimations are based on the M.I.R.D. formalism and used standard mathematical models. These standard models are often far from a given patient morphology and do not allow to perform patient-specific dosimetry. The aim of this study was to develop a personalized dosimetric tool, which takes into account real patient morphology, composition and densities. This tool, called O.E.D.I.P.E., a French acronym of Tool for the Evaluation of Personalized Internal Dose, is a user-friendly graphical interface. O.E.D.I.P.E. allows to create voxel-based patient-specific geometries and associates them with the M.C.N.P.X. Monte Carlo code. Radionuclide distribution and absorbed dose calculation can be performed at the organ and voxel scale. O.E.D.I.P.E. can be used in nuclear medicine for targeted radiotherapy and in radiation protection in case of internal contamination. (author)

  10. Atomic Force Microscopy as a Tool to Assess the Specificity of Targeted Nanoparticles in Biological Models of High Complexity.

    Science.gov (United States)

    Gomes, Carla P; Lopes, Cátia D F; Leitner, Michael; Ebner, Andreas; Hinterdorfer, Peter; Pêgo, Ana P

    2017-11-01

    The ability to design nanoparticle delivery systems capable of selectively target their payloads to specific cell populations is still a major caveat in nanomedicine. One of the main hurdles is the fact that each nanoparticle formulation needs to be precisely tuned to match the specificities of the target cell and route of administration. In this work, molecular recognition force spectroscopy (MRFS) is presented as a tool to evaluate the specificity of neuron-targeted trimethyl chitosan nanoparticles to neuronal cell populations in biological samples of different complexity. The use of atomic force microscopy tips functionalized with targeted or non-targeted nanoparticles made it possible to assess the specific interaction of each formulation with determined cell surface receptors in a precise fashion. More importantly, the combination of MRFS with fluorescent microscopy allowed to probe the nanoparticles vectoring capacity in models of high complexity, such as primary mixed cultures, as well as specific subcellular regions in histological tissues. Overall, this work contributes for the establishment of MRFS as a powerful alternative technique to animal testing in vector design and opens new avenues for the development of advanced targeted nanomedicines. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. REMA: A computer-based mapping tool for analysis of restriction sites in multiple DNA sequences.

    Science.gov (United States)

    Szubert, Jan; Reiff, Caroline; Thorburn, Andrew; Singh, Brajesh K

    2007-05-01

    REMA is an interactive web-based program which predicts endonuclease cut sites in DNA sequences. It analyses multiple sequences simultaneously and predicts the number and size of fragments as well as provides restriction maps. The users can select single or paired combinations of all commercially available enzymes. Additionally, REMA permits prediction of multiple sequence terminal fragment sizes and suggests suitable restriction enzymes for maximally discriminatory results. REMA is an easy to use, web based program which will have a wide application in molecular biology research. REMA is written in Perl and is freely available for non-commercial use. Detailed information on installation can be obtained from Jan Szubert (jan.szubert@gmail.com) and the web based application is accessible on the internet at the URL http://www.macaulay.ac.uk/rema b.singh@macaulay.ac.uk.

  12. Mapping a nucleolar targeting sequence of an RNA binding nucleolar protein, Nop25

    International Nuclear Information System (INIS)

    Fujiwara, Takashi; Suzuki, Shunji; Kanno, Motoko; Sugiyama, Hironobu; Takahashi, Hisaaki; Tanaka, Junya

    2006-01-01

    Nop25 is a putative RNA binding nucleolar protein associated with rRNA transcription. The present study was undertaken to determine the mechanism of Nop25 localization in the nucleolus. Deletion experiments of Nop25 amino acid sequence showed Nop25 to contain a nuclear targeting sequence in the N-terminal and a nucleolar targeting sequence in the C-terminal. By expressing derivative peptides from the C-terminal as GFP-fusion proteins in the cells, a lysine and arginine residue-enriched peptide (KRKHPRRAQDSTKKPPSATRTSKTQRRRR) allowed a GFP-fusion protein to be transported and fully retained in the nucleolus. When the peptide was fused with cMyc epitope and expressed in the cells, a cMyc epitope was then detected in the nucleolus. Nop25 did not localize in the nucleolus by deletion of the peptide from Nop25. Furthermore, deletion of a subdomain (KRKHPRRAQ) in the peptide or amino acid substitution of lysine and arginine residues in the subdomain resulted in the loss of Nop25 nucleolar localization. These results suggest that the lysine and arginine residue-enriched peptide is the most prominent nucleolar targeting sequence of Nop25 and that the long stretch of basic residues might play an important role in the nucleolar localization of Nop25. Although Nop25 contained putative SUMOylation, phosphorylation and glycosylation sites, the amino acid substitution in these sites had no effect on the nucleolar localization, thus suggesting that these post-translational modifications did not contribute to the localization of Nop25 in the nucleolus. The treatment of the cells, which expressed a GFP-fusion protein with a nucleolar targeting sequence of Nop25, with RNase A resulted in a complete dislocation of the protein from the nucleolus. These data suggested that the nucleolar targeting sequence might therefore play an important role in the binding of Nop25 to RNA molecules and that the RNA binding of Nop25 might be essential for the nucleolar localization of Nop25

  13. EPA Region 1 - Map Layers for Valley ID Tool (Hosted Feature Service)

    Science.gov (United States)

    The Valley Service Feature Layer hosts spatial data for EPA Region 1's Valley Identification Tool. These layers contain attribute information added by EPA R1 GIS Center to help identify populated valleys:- Fac_2011NEI: Pollution sources selected from the National Emissions Inventory (EPA, 2011).- NE_Towns_PopValleys: New England Town polygons (courtesy USGS), with Population in Valleys and Population Density in Valleys calculated by EPA R1 GIS, from 2010 US Census blocks. - VT_E911: Vermont residences (courtesy VT Center for Geographic Information E-911).

  14. IASMHYN: A web tool for mapping Soil Water Budget and agro-hydrological assessment trough the integration of monitoring and remote sensing data

    Science.gov (United States)

    Bagli, Stefano; Pistocchi, Alberto; Mazzoli, Paolo; Borga, Marco; Bertoldi, Giacomo; Brenner, Johannes; Luzzi, Valerio

    2016-04-01

    Climate change, increasing pressure on farmland to satisfy the growing demand, and need to ensure environmental quality for agriculture in order to be competitive require an increasing capacity of water management. In this context, web-based for forecasting and monitoring the hydrological conditions of topsoil can be an effective means to save water, maximize crop protection and reduce soil loss and the leaching of pollutants. Such tools need to be targeted to the users and be accessible in a simple way in order to allow adequate take up in the practice. IASMHYN "Improved management of Agricultural Systems by Monitoring and Hydrological evaluation" is a web mapping service designed to provide and update on a daily basis the main water budget variables for farmland management. A beta version of the tool is available at www.gecosistema.com/iasmhyn . IASMHYN is an instrument for "second level monitoring" that takes into account accurate hydro-meteorological information's from ground stations and remote sensing sources, and turns them into practically usable decision variables for precision farming, making use of geostatistical analysis and hydrological models The main routines embedded in IASMYHN exclusively use open source libraries (R packages and Python), to perform following operations: (1) Automatic acquisition of observed data, both from ground stations and remote sensing, concerning precipitation (RADAR) and temperature (MODIS-LST) available from various sources; (2) Interpolation of acquisitions through regression kriging in order to spatially map the meteorological data; (3) Run of hydrological models to obtain spatial information of hydrological soil variables of immediate interest in agriculture. The real time results that are produced are available trough a web interface and provide the user with spatial maps and time series of the following variables, supporting decision on irrigation, soil protection from erosion, pollution risk of groundwater and

  15. Viruses as a tool in nanotechnology and target for conjugated polymers

    NARCIS (Netherlands)

    Gruszka, Agnieszka

    2016-01-01

    Viruses are unique and diverse biological entities that continuously remain in the focus of medicine and science. Today they are not only being recognized for their clinical implications, but also as an inspiration and a powerful tool in multidisciplinary materials science. In this work, we address

  16. An interactive economic GIS tool for Europe using map objects for Java

    Science.gov (United States)

    Srinivasan, Vaishnavi

    Europe is one of the world's seven continents, which has approximately 50 countries and all are rich in culture, traditions, economy, biodiversity, among other things. This thesis focuses on creating a GIS application about Europe which will give an overview of Europe in various aspects. It covers 50 countries including financial centers, currency used, population, GDP growth, private banks, central banks, stock exchange, coat of arms and flags for each country, using the HotLink Tool. A reference link is also provided for detailed understanding of the above mentioned aspects. The other part of the thesis mainly focuses on the economics of the European Union as well as each country independently, which gives a thorough knowledge about the current investment climate in Europe. A part of this idea is to ensure transparency after the financial crisis in 2008. Further the capital markets of the European Union and other European countries are brought to light to provide a clear picture of their present financial situation. The application can help in improving policy and decision making, foreign investments, business environment for various development organizations. So this GIS application will be an effective tool for customers to understand the risks in investments by learning about the economic conditions of Europe.

  17. OPEN SOURCE WEB TOOL FOR TRACKING IN A LOWCOST MOBILE MAPPING SYSTEM

    Directory of Open Access Journals (Sweden)

    F. Fissore

    2017-11-01

    Full Text Available During the last decade several Mobile Mapping Systems (MMSs, i.e. systems able to acquire efficiently three dimensional data using moving sensors (Guarnieri et al., 2008, Schwarz and El-Sheimy, 2004, have been developed. Research and commercial products have been implemented on terrestrial, aerial and marine platforms, and even on human-carried equipment, e.g. backpack (Lo et al., 2015, Nex and Remondino, 2014, Ellum and El-Sheimy, 2002, Leica Pegasus backpack, 2016, Masiero et al., 2017, Fissore et al., 2018. Such systems are composed of an integrated array of time-synchronised navigation sensors and imaging sensors mounted on a mobile platform (Puente et al., 2013, Tao and Li, 2007. Usually the MMS implies integration of different types of sensors, such as GNSS, IMU, video camera and/or laser scanners that allow accurate and quick mapping (Li, 1997, Petrie, 2010, Tao, 2000. The typical requirement of high-accuracy 3D georeferenced reconstruction often makes such systems quite expensive. Indeed, at time of writing most of the terrestrial MMSs on the market have a cost usually greater than 50000, which might be expensive for certain applications (Ellum and El-Sheimy, 2002, Piras et al., 2008. In order to allow best performance sensors have to be properly calibrated (Dong et al., 2007, Ellum and El-Sheimy, 2002. Sensors in MMSs are usually integrated and managed through a dedicated software, which is developed ad hoc for the devices mounted on the mobile platform and hence tailored for the specific used sensors. Despite the fact that commercial solutions are complete, very specific and particularly related to the typology of survey, their price is a factor that restricts the number of users and the possible interested sectors. This paper describes a (relatively low cost terrestrial Mobile Mapping System developed at the University of Padua (TESAF, Department of Land Environment Agriculture and Forestry by the research team in CIRGEO, in order to

  18. Open Source Web Tool for Tracking in a Lowcost Mobile Mapping System

    Science.gov (United States)

    Fissore, F.; Pirotti, F.; Vettore, A.

    2017-11-01

    During the last decade several Mobile Mapping Systems (MMSs), i.e. systems able to acquire efficiently three dimensional data using moving sensors (Guarnieri et al., 2008, Schwarz and El-Sheimy, 2004), have been developed. Research and commercial products have been implemented on terrestrial, aerial and marine platforms, and even on human-carried equipment, e.g. backpack (Lo et al., 2015, Nex and Remondino, 2014, Ellum and El-Sheimy, 2002, Leica Pegasus backpack, 2016, Masiero et al., 2017, Fissore et al., 2018). Such systems are composed of an integrated array of time-synchronised navigation sensors and imaging sensors mounted on a mobile platform (Puente et al., 2013, Tao and Li, 2007). Usually the MMS implies integration of different types of sensors, such as GNSS, IMU, video camera and/or laser scanners that allow accurate and quick mapping (Li, 1997, Petrie, 2010, Tao, 2000). The typical requirement of high-accuracy 3D georeferenced reconstruction often makes such systems quite expensive. Indeed, at time of writing most of the terrestrial MMSs on the market have a cost usually greater than 50000, which might be expensive for certain applications (Ellum and El-Sheimy, 2002, Piras et al., 2008). In order to allow best performance sensors have to be properly calibrated (Dong et al., 2007, Ellum and El-Sheimy, 2002). Sensors in MMSs are usually integrated and managed through a dedicated software, which is developed ad hoc for the devices mounted on the mobile platform and hence tailored for the specific used sensors. Despite the fact that commercial solutions are complete, very specific and particularly related to the typology of survey, their price is a factor that restricts the number of users and the possible interested sectors. This paper describes a (relatively low cost) terrestrial Mobile Mapping System developed at the University of Padua (TESAF, Department of Land Environment Agriculture and Forestry) by the research team in CIRGEO, in order to test an

  19. Specific tools for targeting and expression in Müller glial cells

    NARCIS (Netherlands)

    Pellissier, Lucie P; Hoek, Robert M; Vos, Rogier M; Aartsen, Wendy M; Klimczak, Ryan R; Hoyng, Stefan A; Flannery, John G; Wijnholds, J.

    2014-01-01

    Despite their physiological roles, Müller glial cells are involved directly or indirectly in retinal disease pathogenesis and are an interesting target for therapeutic approaches for retinal diseases and regeneration such as CRB1 inherited retinal dystrophies. In this study, we characterized the

  20. Peptide Phage Display as a Tool for Drug Discovery: Targeting Membrane Receptors

    Directory of Open Access Journals (Sweden)

    Tomaz Bratkovic

    2011-01-01

    Full Text Available Ligands selected from phage-displayed random peptide libraries tend to be directed to biologically relevant sites on the surface of the target protein. Consequently, peptides derived from library screenings often modulate the target protein’s activity in vitro and in vivo and can be used as lead compounds in drug design and as alternatives to antibodies for target validation in both genomics and drug discovery. This review discusses the use of phage display to identify membrane receptor modulators with agonistic or antagonistic activities. Because isolating or producing recombinant membrane proteins for use as target molecules in library screening is often impossible, innovative selection strategies such as panning against whole cells or tissues, recombinant receptor ectodomains, or neutralizing antibodies to endogenous binding partners were devised. Prominent examples from a two-decade history of peptide phage display will be presented, focusing on the design of affinity selection experiments, methods for improving the initial hits, and applications of the identified peptides.

  1. Development of a dynamic network monitoring tool – Interactive map based on LLDP and SNMP

    CERN Document Server

    Haen, Christophe; Mesnard, E

    2010-01-01

    The European Organization for Nuclear Research (French: Organisation Européenne pour la Recherche Nucléaire), known as CERN is the world’s largest particle physics laboratory, established in 1954 near Geneva. CERN’s main function is to provide the particle accelerators and other infrastructure needed for high-energy physics research. The LHCb (standing for “Large Hadron Collider beauty”) experiment is one of six particle physics detector experiments built on the Large Hadron Collider, the world’s largest and highest-energy particle accelerator. This experiment produces a large amount of data which needs to be treated. This task is processed by some 2000 computing servers and 400 control servers. The LHCb Online team is responsible of the data, from their creation in the detector, till the storage. The purpose of my internship was to develop a software from scratch able to dynamically discover the network, draw a map of it, gather information of the network equipments, and implement basic monitorin...

  2. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    Science.gov (United States)

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Mapping Urban Heat Demand with the Use of GIS-Based Tools

    Directory of Open Access Journals (Sweden)

    Artur Wyrwa

    2017-05-01

    Full Text Available This article presents a bottom-up approach for calculation of the useful heat demand for space heating and hot water preparation using geo-referenced datasets for buildings at the city level. This geographic information system (GIS based approach was applied in the case study for the city of Krakow, where on the one hand the district heat network is well developed, while on the other hand there are still substantial number of buildings burning solid fuels in individual boilers and stoves, causing air pollution. The calculated heat demand was aggregated in the grid with 100 m × 100 m spatial resolution to deliver the heat map depicting the current situation for 21 buildings types. The results show that the residential buildings, in particular one- and multi-family buildings, have the highest share in overall demand for heat. By combining the results with location of the district heat (DH network, the potential areas in its close vicinity that have sufficient heat demand density for developing the net were pointed out. Future evolution in heat demand for space heating in one-family houses was evaluated with the use of deterministic method employing building stock model. The study lays a foundation for planning the development of the heating system at the city level.

  4. Use of geological mapping tools to improve the hydraulic performance of SuDS.

    Science.gov (United States)

    Bockhorn, Britta; Klint, Knud Erik Strøyberg; Jensen, Marina Bergen; Møller, Ingelise

    2015-01-01

    Most cities in Denmark are situated on low permeable clay rich deposits. These sediments are of glacial origin and range among the most heterogeneous, with hydraulic conductivities spanning several orders of magnitude. This heterogeneity has obvious consequences for the sizing of sustainable urban drainage systems (SuDS). We have tested methods to reveal geological heterogeneity at field scale to identify the most suitable sites for the placement of infiltration elements and to minimize their required size. We assessed the geological heterogeneity of a clay till plain in Eastern Jutland, Denmark measuring the shallow subsurface resistivity with a geoelectrical multi-electrode system. To confirm the resistivity data we conducted a spear auger mapping. The exposed sediments ranged from clay tills over sandy clay tills to sandy tills and correspond well to the geoelectrical data. To verify the value of geological information for placement of infiltration elements we carried out a number of infiltration tests on geologically different areas across the field, and we observed infiltration rates two times higher in the sandy till area than in the clay till area, thus demonstrating that the hydraulic performance of SuDS can be increased considerably and oversizing avoided if field geological heterogeneity is revealed before placing SuDS.

  5. Visible-near infrared spectroscopy as a tool to improve mapping of soil properties

    Science.gov (United States)

    Evgrafova, Alevtina; Kühnel, Anna; Bogner, Christina; Haase, Ina; Shibistova, Olga; Guggenberger, Georg; Tananaev, Nikita; Sauheitl, Leopold; Spielvogel, Sandra

    2017-04-01

    Spectroscopic measurements, which are non-destructive, precise and rapid, can be used to predict soil properties and help estimate the spatial variability of soil properties at the pedon scale. These estimations are required for quantifying soil properties with higher precision, identifying the changes in soil properties and ecosystem response to climate change as well as increasing the estimation accuracy of soil-related models. Our objectives were to (i) predict soil properties for nested samples (n = 296) using the laboratory-based visible-near infrared (vis-NIR) spectra of air-dried (ICP-OES, Agilent Technologies, USA). We predicted the above-mentioned soil properties for all nested samples using partial least squares regression, which was performed using R program. We can conclude that vis-NIR spectroscopy can be used effectively in order to describe, estimate and further map the spatial patterns of soil properties using geostatistical methods. This research could also help to improve the global soil spectral library taking into account that only few previous applications of vis-NIR spectroscopy were conducted on permafrost-affected soils of Northern Siberia. Keywords: Visible-near infrared spectroscopy, vis-NIR, permafrost-affected soils, Siberia, partial least squares regression.

  6. OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.

    Science.gov (United States)

    Croce, Olivier; Chevenet, François; Christen, Richard

    2008-07-01

    The efficiency of molecular methods involving DNA/DNA hybridizations depends on the accurate prediction of the melting temperature (T(m)) of the duplex. Many softwares are available for T(m) calculations, but difficulties arise when one wishes to check if a given oligomer (PCR primer or probe) hybridizes well or not on more than a single sequence. Moreover, the presence of mismatches within the duplex is not sufficient to estimate specificity as it does not always significantly decrease the T(m). OHM (OligoHeatMap) is an online tool able to provide estimates of T(m) for a set of oligomers and a set of aligned sequences, not only as text files of complete results but also in a graphical way: T(m) values are translated into colors and displayed as a heat map image, either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree. OHM is freely available at http://bioinfo.unice.fr/ohm/, with links to the full source code and online help.

  7. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions

    DEFF Research Database (Denmark)

    Bracken, Adrian P; Dietrich, Nikolaj; Pasini, Diego

    2006-01-01

    The Polycomb group (PcG) proteins form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer. Here, we identify their target genes using genome-wide location analysis in human embryonic fibroblasts. We find...... that Polycomb-Repressive Complex 1 (PRC1), PRC2, and tri-methylated histone H3K27 co-occupy >1000 silenced genes with a strong functional bias for embryonic development and cell fate decisions. We functionally identify 40 genes derepressed in human embryonic fibroblasts depleted of the PRC2 components (EZH2...... that PcGs are part of a preprogrammed memory system established during embryogenesis marking certain key genes for repressive signals during subsequent developmental and differentiation processes....

  8. Mapping of HNF4alpha target genes in intestinal epithelial cells

    DEFF Research Database (Denmark)

    Boyd, Mette; Bressendorff, Simon; Moller, Jette

    2009-01-01

    not previously been described as being regulated by HNF4alpha. The 1,541 genes contributed significantly to gene ontology (GO) pathways categorized by lipid and amino acid transport and metabolism. An analysis of the homeodomain transcription factor Cdx-2 (CDX2), the disaccharidase trehalase (TREH......ABSTRACT: BACKGROUND: The role of HNF4alpha has been extensively studied in hepatocytes and pancreatic beta-cells, and HNF4alpha is also regarded as key regulator of intestinal epithelial cell differentiation as well. The aim of the present work is to identify novel HNF4alpha target genes...... in the human intestinal epithelial cells in order to elucidate the role of HNF4alpha in the intestinal differentiation progress. METHODS: We have performed a ChIP-chip analysis of the human intestinal cell line Caco-2 in order to make a genome-wide identification of HNF4alpha binding to promoter regions...

  9. Development and application of two semi-automated tools for targeted medical product surveillance in a distributed data network.

    Science.gov (United States)

    Connolly, John G; Wang, Shirley V; Fuller, Candace C; Toh, Sengwee; Panozzo, Catherine A; Cocoros, Noelle; Zhou, Meijia; Gagne, Joshua J; Maro, Judith C

    2017-12-01

    An important component of the Food and Drug Administration's Sentinel Initiative is the active post-market risk identification and analysis (ARIA) system, which utilizes semi-automated, parameterized computer programs to implement propensity-score adjusted and self-controlled risk interval designs to conduct targeted surveillance of medical products in the Sentinel Distributed Database. In this manuscript, we review literature relevant to the development of these programs and describe their application within the Sentinel Initiative. These quality-checked and publicly available tools have been successfully used to conduct rapid, replicable, and targeted safety analyses of several medical products. In addition to speed and reproducibility, use of semi-automated tools allows investigators to focus on decisions regarding key methodological parameters. We also identified challenges associated with the use of these methods in distributed and prospective datasets like the Sentinel Distributed Database, namely uncertainty regarding the optimal approach to estimating propensity scores in dynamic data among data partners of heterogeneous size. Future research should focus on the methodological challenges raised by these applications as well as developing new modular programs for targeted surveillance of medical products.

  10. A high-speed spatial (linear) scanning pyrometer: A tool for diagnostics, temperature mapping, and property determinations at high temperatures

    Science.gov (United States)

    Cezairliyan, A.; Chang, R. F.; Foley, G. M.

    1990-01-01

    Development of a fast spatial scanning pyrometer for temperature measurements above 1500 K is described. The salient features of the pyrometer are: (1) it measures spectral radiance temperature (at 0.65 micron) at 1024 points along a straight line (25 mm long) on the target; (2) it has no moving parts and uses a self-scanning linear array of silicon photodiodes as the detector; (3) its output is recorded digitally every 1 microsec with a full-scale resolution of about 1 part in 4000, permitting performance of a complete cycle of measurements (1024 points) in about 1 ms. Operational characteristics of the pyrometer are given. Examples of measurements of the temperature along rapidly heated (resistive self-heating) specimens (rod, tube, strip) are presented. Potential use of the pyrometer in the experiments, both ground-based and in microgravity, requiring temperature mapping and property distribution of the specimen at high temperatures is discussed.

  11. Squidpops: A Simple Tool to Crowdsource a Global Map of Marine Predation Intensity.

    Directory of Open Access Journals (Sweden)

    J Emmett Duffy

    Full Text Available We present a simple, standardized assay, the squidpop, for measuring the relative feeding intensity of generalist predators in aquatic systems. The assay consists of a 1.3-cm diameter disk of dried squid mantle tethered to a rod, which is either inserted in the sediment in soft-bottom habitats or secured to existing structure. Each replicate squidpop is scored as present or absent after 1 and 24 hours, and the data for analysis are proportions of replicate units consumed at each time. Tests in several habitats of the temperate southeastern USA (Virginia and North Carolina and tropical Central America (Belize confirmed the assay's utility for measuring variation in predation intensity among habitats, among seasons, and along environmental gradients. In Belize, predation intensity varied strongly among habitats, with reef > seagrass = mangrove > unvegetated bare sand. Quantitative visual surveys confirmed that assayed feeding intensity increased with abundance and species richness of fishes across sites, with fish abundance and richness explaining up to 45% and 70% of the variation in bait loss respectively. In the southeastern USA, predation intensity varied seasonally, being highest during summer and declining in late autumn. Deployments in marsh habitats generally revealed a decline in mean predation intensity from fully marine to tidal freshwater sites. The simplicity, economy, and standardization of the squidpop assay should facilitate engagement of scientists and citizens alike, with the goal of constructing high-resolution maps of how top-down control varies through space and time in aquatic ecosystems, and addressing a broad array of long-standing hypotheses in macro- and community ecology.

  12. Nanosensors as Reservoir Engineering Tools to Map Insitu Temperature Distributions in Geothermal Reservoirs

    Energy Technology Data Exchange (ETDEWEB)

    Morgan Ames

    2011-06-15

    The feasibility of using nanosensors to measure temperature distribution and predict thermal breakthrough in geothermal reservoirs is addressed in this report. Four candidate sensors were identified: melting tin-bismuth alloy nanoparticles, silica nanoparticles with covalently-attached dye, hollow silica nanoparticles with encapsulated dye and impermeable melting shells, and dye-polymer composite time-temperature indicators. Four main challenges associated with the successful implementation of temperature nanosensors were identified: nanoparticle mobility in porous and fractured media, the collection and detection of nanoparticles at the production well, engineering temperature sensing mechanisms that are both detectable and irreversible, and inferring the spatial geolocation of temperature measurements in order to map temperature distribution. Initial experiments were carried out to investigate each of these challenges. It was demonstrated in a slim-tube injection experiment that it is possible to transport silica nanoparticles over large distances through porous media. The feasibility of magnetic collection of nanoparticles from produced fluid was evaluated experimentally, and it was estimated that 3% of the injected nanoparticles were recovered in a prototype magnetic collection device. An analysis technique was tailored to nanosensors with a dye-release mechanism to estimate temperature measurement geolocation by analyzing the return curve of the released dye. This technique was used in a hypothetical example problem, and good estimates of geolocation were achieved. Tin-bismuth alloy nanoparticles were synthesized using a sonochemical method, and a bench heating experiment was performed using these nanoparticles. Particle growth due to melting was observed, indicating that tin-bismuth nanoparticles have potential as temperature nanosensors

  13. RNAi as a tool for target discovery in early pharmaceutical research.

    Science.gov (United States)

    Adams, R; Steckel, M; Nicke, B; Pohlenz, H D

    2016-01-01

    The pharmaceutical industry is currently faced with increasing pressure due to patent expirations for block busters, healthcare reforms with strained budgets and growing demands for approval by administrative organizations like the FDA and the EMA. High attrition rates especially in the later expensive stages of the drug development process ask for thoroughly validated drug targets at the beginning of such projects. The great potential of RNA interference strategies toward reaching this goal is outlined in this article.

  14. ADP-ribosyltransferases: plastic tools for inactivating protein and small molecular weight targets

    OpenAIRE

    Koch-Nolte, Friedrich; Reche, Pedro A; Haag, Friedrich; Bazan, Fernando

    2001-01-01

    ADP-ribosyltransferases (ADPRTs) form an interesting class of enzymes with well-established roles as potent bacterial toxins and metabolic regulators. ADPRTs catalyze the transfer of the ADP-ribose moiety from NAD(+) onto specific substrates including proteins. ADP-ribosylation usually inactivates the function of the target. ADPRTs have become adapted to function in extra- and intracellular settings. Regulation of ADPRT activity can be mediated by ligand binding to associated regulatory domai...

  15. Accumulation of specific sterol precursors targets a MAP kinase cascade mediating cell–cell recognition and fusion

    Science.gov (United States)

    Weichert, Martin; Lichius, Alexander; Priegnitz, Bert-Ewald; Brandt, Ulrike; Gottschalk, Johannes; Nawrath, Thorben; Groenhagen, Ulrike; Read, Nick D.; Schulz, Stefan; Fleißner, André

    2016-01-01

    Sterols are vital components of eukaryotic cell membranes. Defects in sterol biosynthesis, which result in the accumulation of precursor molecules, are commonly associated with cellular disorders and disease. However, the effects of these sterol precursors on the metabolism, signaling, and behavior of cells are only poorly understood. In this study, we show that the accumulation of only ergosterol precursors with a conjugated double bond in their aliphatic side chain specifically disrupts cell–cell communication and fusion in the fungus Neurospora crassa. Genetically identical germinating spores of this fungus undergo cell–cell fusion, thereby forming a highly interconnected supracellular network during colony initiation. Before fusion, the cells use an unusual signaling mechanism that involves the coordinated and alternating switching between signal sending and receiving states of the two fusion partners. Accumulation of only ergosterol precursors with a conjugated double bond in their aliphatic side chain disrupts this coordinated cell–cell communication and suppresses cell fusion. These specific sterol precursors target a single ERK-like mitogen-activated protein (MAP) kinase (MAK-1)-signaling cascade, whereas a second MAP kinase pathway (MAK-2), which is also involved in cell fusion, is unaffected. These observations indicate that a minor specific change in sterol structure can exert a strong detrimental effect on a key signaling pathway of the cell, resulting in the absence of cell fusion. PMID:27708165

  16. Tumor-homing peptides as tools for targeted delivery of payloads to the placenta

    Science.gov (United States)

    King, Anna; Ndifon, Cornelia; Lui, Sylvia; Widdows, Kate; Kotamraju, Venkata R.; Agemy, Lilach; Teesalu, Tambet; Glazier, Jocelyn D.; Cellesi, Francesco; Tirelli, Nicola; Aplin, John D.; Ruoslahti, Erkki; Harris, Lynda K.

    2016-01-01

    The availability of therapeutics to treat pregnancy complications is severely lacking mainly because of the risk of causing harm to the fetus. As enhancement of placental growth and function can alleviate maternal symptoms and improve fetal growth in animal models, we have developed a method for targeted delivery of payloads to the placenta. We show that the tumor-homing peptide sequences CGKRK and iRGD bind selectively to the placental surface of humans and mice and do not interfere with normal development. Peptide-coated nanoparticles intravenously injected into pregnant mice accumulated within the mouse placenta, whereas control nanoparticles exhibited reduced binding and/or fetal transfer. We used targeted liposomes to efficiently deliver cargoes of carboxyfluorescein and insulin-like growth factor 2 to the mouse placenta; the latter significantly increased mean placental weight when administered to healthy animals and significantly improved fetal weight distribution in a well-characterized model of fetal growth restriction. These data provide proof of principle for targeted delivery of drugs to the placenta and provide a novel platform for the development of placenta-specific therapeutics. PMID:27386551

  17. Targeted proteomics as a tool for porcine acute phase proteins measurements

    DEFF Research Database (Denmark)

    Marco-Ramell, Anna; Bassols, Anna; Bislev, Stine Lønnerup

    2013-01-01

    ) and there is recent evidence that they can be also considered as welfare markers (Giannetto et al., 2011). During an acute stress situation, the levels of some interleukins (IL-1β, IL-6 and TNF-α) are increased (Elenkov and Chrousos, 2002) and consequently the concentration of the APPs varies dramatically. In pigs...... the most important APPs include haptoglobin (Hp), C-reactive protein (CRP), the inter-α-inhibitor-heavy chain 4 (ITIH4, also called Pig major acute phase protein, or Pig-MAP), serum amyloid A (SAA) and apolipoprotein A-I (Apo A-I), but also other proteins are well known to mark the acute phase response......, as albumin, transferrin (Heegaard et al., 2011) and fetuin A (Brown et al., 1992)....

  18. Archaeological Map of the Czech Republic. Current state and future visions of virtual research tools in the Czech Republic

    Directory of Open Access Journals (Sweden)

    Martin Kuna

    2017-03-01

    Full Text Available The Archaeological Map of the Czech Republic (AMCR project will soon be finished and one chapter of building digital infrastructures in the Czech Republic will be closed. It is a natural occasion to evaluate national state-of-the-art in dealing with Digital Culture Heritage, particularly archaeological data. It is a also good time to summarise our knowledge about using digital tools and to outline prospects of development for the coming years. What are the key points? The AMCR represents both an administrative system of field archaeology management and a kind of 'sites and monuments records' for the territory of the CR. Its fundamental underlying principles are interoperability, standardisation, data re-use, crowdsourcing and networking. However, a reasonable question should also concern the theoretical background to the process of digitisation of the archaeological world. Infrastructures should every time stay on the level of service for the community of researchers and every digital tool has to fulfil real needs in the fields of both archaeological theory and practice. On the other hand, the application of this virtual research environment is inseparable from archaeological legislation and institutional management.

  19. Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography.

    Science.gov (United States)

    Oghbaey, Saeed; Sarracini, Antoine; Ginn, Helen M; Pare-Labrosse, Olivier; Kuo, Anling; Marx, Alexander; Epp, Sascha W; Sherrell, Darren A; Eger, Bryan T; Zhong, Yinpeng; Loch, Rolf; Mariani, Valerio; Alonso-Mori, Roberto; Nelson, Silke; Lemke, Henrik T; Owen, Robin L; Pearson, Arwen R; Stuart, David I; Ernst, Oliver P; Mueller-Werkmeister, Henrike M; Miller, R J Dwayne

    2016-08-01

    The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.

  20. Utilizing Retinotopic Mapping for a Multi-Target SSVEP BCI With a Single Flicker Frequency.

    Science.gov (United States)

    Maye, Alexander; Zhang, Dan; Engel, Andreas K

    2017-07-01

    In brain-computer interfaces (BCIs) that use the steady-state visual evoked response (SSVEP), the user selects a control command by directing attention overtly or covertly to one out of several flicker stimuli. The different control channels are encoded in the frequency, phase, or time domain of the flicker signals. Here, we present a new type of SSVEP BCI, which uses only a single flicker stimulus and yet affords controlling multiple channels. The approach rests on the observation that the relative position between the stimulus and the foci of overt attention result in distinct topographies of the SSVEP response on the scalp. By classifying these topographies, the computer can determine at which position the user is gazing. Offline data analysis in a study on 12 healthy volunteers revealed that 9 targets can be recognized with about 95±3% accuracy, corresponding to an information transfer rate (ITR) of 40.8 ± 3.3 b/min on average. We explored how the classification accuracy is affected by the number of control channels, the trial length, and the number of EEG channels. Our findings suggest that the EEG data from five channels over parieto-occipital brain areas are sufficient for reliably classifying the topographies and that there is a large potential to improve the ITR by optimizing the trial length. The robust performance and the simple stimulation setup suggest that this approach is a prime candidate for applications on desktop and tablet computers.

  1. What is needed to implement a computer-assisted health risk assessment tool? An exploratory concept mapping study

    Directory of Open Access Journals (Sweden)

    Ahmad Farah

    2012-12-01

    Full Text Available Abstract Background Emerging eHealth tools could facilitate the delivery of comprehensive care in time-constrained clinical settings. One such tool is interactive computer-assisted health-risk assessments (HRA, which may improve provider-patient communication at the point of care, particularly for psychosocial health concerns, which remain under-detected in clinical encounters. The research team explored the perspectives of healthcare providers representing a variety of disciplines (physicians, nurses, social workers, allied staff regarding the factors required for implementation of an interactive HRA on psychosocial health. Methods The research team employed a semi-qualitative participatory method known as Concept Mapping, which involved three distinct phases. First, in face-to-face and online brainstorming sessions, participants responded to an open-ended central question: “What factors should be in place within your clinical setting to support an effective computer-assisted screening tool for psychosocial risks?” The brainstormed items were consolidated by the research team. Then, in face-to-face and online sorting sessions, participants grouped the items thematically as ‘it made sense to them’. Participants also rated each item on a 5-point scale for its ‘importance’ and ‘action feasibility’ over the ensuing six month period. The sorted and rated data was analyzed using multidimensional scaling and hierarchical cluster analyses which produced visual maps. In the third and final phase, the face-to-face Interpretation sessions, the concept maps were discussed and illuminated by participants collectively. Results Overall, 54 providers participated (emergency care 48%; primary care 52%. Participants brainstormed 196 items thought to be necessary for the implementation of an interactive HRA emphasizing psychosocial health. These were consolidated by the research team into 85 items. After sorting and rating, cluster analysis

  2. What is needed to implement a computer-assisted health risk assessment tool? An exploratory concept mapping study.

    Science.gov (United States)

    Ahmad, Farah; Norman, Cameron; O'Campo, Patricia

    2012-12-19

    Emerging eHealth tools could facilitate the delivery of comprehensive care in time-constrained clinical settings. One such tool is interactive computer-assisted health-risk assessments (HRA), which may improve provider-patient communication at the point of care, particularly for psychosocial health concerns, which remain under-detected in clinical encounters. The research team explored the perspectives of healthcare providers representing a variety of disciplines (physicians, nurses, social workers, allied staff) regarding the factors required for implementation of an interactive HRA on psychosocial health. The research team employed a semi-qualitative participatory method known as Concept Mapping, which involved three distinct phases. First, in face-to-face and online brainstorming sessions, participants responded to an open-ended central question: "What factors should be in place within your clinical setting to support an effective computer-assisted screening tool for psychosocial risks?" The brainstormed items were consolidated by the research team. Then, in face-to-face and online sorting sessions, participants grouped the items thematically as 'it made sense to them'. Participants also rated each item on a 5-point scale for its 'importance' and 'action feasibility' over the ensuing six month period. The sorted and rated data was analyzed using multidimensional scaling and hierarchical cluster analyses which produced visual maps. In the third and final phase, the face-to-face Interpretation sessions, the concept maps were discussed and illuminated by participants collectively. Overall, 54 providers participated (emergency care 48%; primary care 52%). Participants brainstormed 196 items thought to be necessary for the implementation of an interactive HRA emphasizing psychosocial health. These were consolidated by the research team into 85 items. After sorting and rating, cluster analysis revealed a concept map with a seven-cluster solution: 1) the HRA

  3. Computationally efficient particle release map determination for direct tumor-targeting in a representative hepatic artery system.

    Science.gov (United States)

    Childress, E M; Kleinstreuer, C

    2014-01-01

    Implementation of a novel direct tumor-targeting technique requires a computer modeling stage to generate particle release maps (PRMs) which allow for optimal catheter positioning and selection of best injection intervals for drug-particles. This simulation task for a patient-specific PRM may require excessive computational resources and a relatively long turn-around time for a fully transient analysis. Hence, steady-state conditions were sought which generates PRMs equivalent to the pulsatile arterial flow environment. Fluid-particle transport in a representative hepatic artery system was simulated under fully transient and steady-state flow conditions and their corresponding PRMs were analyzed and compared. Comparisons of the transient PRMs from ten equal intervals of the cardiac pulse revealed that the diastolic phase produced relatively constant PRMs due to its semisteady flow conditions. Furthermore, steady-state PRMs, which best matched the transient particle release maps, were found for each interval and over the entire cardiac pulse. From these comparisons, the flow rate and outlet pressure differences proved to be important parameters for estimating the PRMs. The computational times of the fully transient and steady simulations differed greatly, i.e., about 10 days versus 0.5 to 1 h, respectively. The time-averaged scenario may provide the best steady conditions for estimating the transient particle release maps. However, given the considerable changes in the PRMs due to the accelerating and decelerating phases of the cardiac cycle, it may be better to model several steady scenarios, which encompass the wide range of flows and pressures experienced by the arterial system in order to observe how the PRMs may change throughout the pulse. While adding more computation time, this method is still significantly faster than running the full transient case. Finally, while the best steady PRMs provide a qualitative guide for best catheter placement, the final

  4. Targeting the new generation woman: voice-over as a tool in gender repositioning traditionally male dominant product

    OpenAIRE

    Staunton, Ciara

    1995-01-01

    This exploratory research study examines the power of the voice-over as a tool in gender re-positioning of a traditionally male dominant product and the response of the female market to such re-positioning. The increasing consumption by females of masculine products has led marketers to question how they can target such products at the female market, without losing the existing male customers. A potentially appropriate method of doing so is through subtle gender re-positioning by altering the...

  5. Asset Mapping at Halifax Public Libraries: A Tool for Beginning to Discover the Library’s Role with the Immigrant Community in Halifax

    Directory of Open Access Journals (Sweden)

    Kenneth William Williment

    2012-04-01

    Full Text Available As library systems across Canada begin to grapple with the implications community-led service planning has on program and service development, new tools are being developed to assist library staff. Asset mapping is one community entry tool which allows library staff to access community members (or organizational representatives and gather in-depth information impacting services and program identification, development, and implementation – either across a library system or within a branch catchment. By using this tool, through face-to-face conversations with service providers, library staff find out about existing community assets (such as programs and services different organizations offer and begin to develop relationships with community members receiving services. Asset mapping provides libraries with information to identify priority services that complement existing community resources. The information collected extends beyond a directory and is used to develop and deliver services relevant to the needs of community. This paper, based on a presentation given at the 2011 Canadian Library Association conference, discusses asset mapping as a first step to actively engaging community. As a first step in the engagement process, it specifically focuses on the process of asset mapping organizations that provide services to immigrants. Asset mapping is a powerful tool which can be implemented by librarians with any group of interest in order to understand community identified information needs, determine existing community strengths and assets, and to help understand the library's role in developing service and program responses to these needs.

  6. CRISPR/Cas9 Technology as an Emerging Tool for Targeting Amyotrophic Lateral Sclerosis (ALS).

    Science.gov (United States)

    Kruminis-Kaszkiel, Ewa; Juranek, Judyta; Maksymowicz, Wojciech; Wojtkiewicz, Joanna

    2018-03-19

    The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) is a genome editing tool that has recently caught enormous attention due to its novelty, feasibility, and affordability. This system naturally functions as a defense mechanism in bacteria and has been repurposed as an RNA-guided DNA editing tool. Unlike zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), CRISPR/Cas9 takes advantage of an RNA-guided DNA endonuclease enzyme, Cas9, which is able to generate double-strand breaks (DSBs) at specific genomic locations. It triggers cellular endogenous DNA repair pathways, contributing to the generation of desired modifications in the genome. The ability of the system to precisely disrupt DNA sequences has opened up new avenues in our understanding of amyotrophic lateral sclerosis (ALS) pathogenesis and the development of new therapeutic approaches. In this review, we discuss the current knowledge of the principles and limitations of the CRISPR/Cas9 system, as well as strategies to improve these limitations. Furthermore, we summarize novel approaches of engaging the CRISPR/Cas9 system in establishing an adequate model of neurodegenerative disease and in the treatment of SOD1-linked forms of ALS. We also highlight possible applications of this system in the therapy of ALS, both the inherited type as well as ALS of sporadic origin.

  7. CRISPR/Cas9 Technology as an Emerging Tool for Targeting Amyotrophic Lateral Sclerosis (ALS

    Directory of Open Access Journals (Sweden)

    Ewa Kruminis-Kaszkiel

    2018-03-01

    Full Text Available The clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated protein-9 nuclease (Cas9 is a genome editing tool that has recently caught enormous attention due to its novelty, feasibility, and affordability. This system naturally functions as a defense mechanism in bacteria and has been repurposed as an RNA-guided DNA editing tool. Unlike zinc-finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs, CRISPR/Cas9 takes advantage of an RNA-guided DNA endonuclease enzyme, Cas9, which is able to generate double-strand breaks (DSBs at specific genomic locations. It triggers cellular endogenous DNA repair pathways, contributing to the generation of desired modifications in the genome. The ability of the system to precisely disrupt DNA sequences has opened up new avenues in our understanding of amyotrophic lateral sclerosis (ALS pathogenesis and the development of new therapeutic approaches. In this review, we discuss the current knowledge of the principles and limitations of the CRISPR/Cas9 system, as well as strategies to improve these limitations. Furthermore, we summarize novel approaches of engaging the CRISPR/Cas9 system in establishing an adequate model of neurodegenerative disease and in the treatment of SOD1-linked forms of ALS. We also highlight possible applications of this system in the therapy of ALS, both the inherited type as well as ALS of sporadic origin.

  8. Is TNF-a-targeted short hairpin RNA (shRNA) a novel potential therapeutic tool in psoriasis treatment?

    DEFF Research Database (Denmark)

    Stenderup, Karin; Jakobsen, Maria; Rosada, Cecilia

    2008-01-01

      TNF-α is a well known target in psoriasis treatment and biological treatments targeting TNF-a are already clinically used against psoriasis and psoriasis arthritis. Attention is however given to a novel therapeutic tool: RNA interference that controls gene silencing. This study investigates...... the efficiency of targeting TNF-a with specific short hairpin RNA (shRNA) and explores its potential in treating psoriasis. ShRNAs targeting human TNF-α mRNA were generated. Their efficiency in down-regulating TNF-a protein expression was evaluated using a Renilla luciferase screening-assay and a transient co...... TNF-a shRNA was used to transduce HEK293 cells and verify vector-derived TNF-a knockdown in vitro. In vivo, psoriasis skin was exposed to lentiviral TNF-a shRNAs by a single intra-dermal injection. Psoriasis skin for the in vivo study was obtained from psoriatic plaque skin biopsies that were...

  9. Mapping calcium phosphate activated gene networks as a strategy for targeted osteoinduction of human progenitors.

    Science.gov (United States)

    Eyckmans, Jeroen; Roberts, Scott J; Bolander, Johanna; Schrooten, Jan; Chen, Christopher S; Luyten, Frank P

    2013-06-01

    Although calcium phosphate-containing biomaterials are promising scaffolds for bone regenerative strategies, the osteoinductive capacity of such materials is poorly understood. In this study, we investigated whether endogenous mechanisms of in vivo calcium phosphate-driven, ectopic bone formation could be identified and used to induce enhanced differentiation in vitro of the same progenitor population. To accomplish this, human periosteum derived cells (hPDCs) were seeded on hydroxyapatite/collagen scaffolds (calcium phosphate rich matrix or CPRM), or on decalcified scaffolds (calcium phosphate depleted matrix or CPDM), followed by subcutaneous implantation in nude mice to trigger ectopic bone formation. In this system, osteoblast differentiation occurred in CPRM scaffolds, but not in CPDM scaffolds. Gene expression was assessed by human full-genome microarray at 20 h after seeding, and 2, 8 and 18 days after implantation. In both matrices, implantation of the cell constructs triggered a similar gene expression cascade, however, gene expression dynamics progressed faster in CPRM scaffolds than in CPDM scaffolds. The difference in gene expression dynamics was associated with differential activation of hub genes and molecular signaling pathways related to calcium signaling (CREB), inflammation (TNFα, NFkB, and IL6) and bone development (TGFβ, β-catenin, BMP, EGF, and ERK signaling). Starting from this set of pathways, a growth factor cocktail was developed that robustly enhanced osteogenesis in vitro and in vivo. Taken together, our data demonstrate that through the identification and subsequent stimulation of genes, proteins and signaling pathways associated with calcium phosphate mediated osteoinduction, a focused approach to develop targeted differentiation protocols in adult progenitor cells can be achieved. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Target Detection Method for Water Mapping Using Landsat 8 OLI/TIRS Imagery

    Directory of Open Access Journals (Sweden)

    Luyan Ji

    2015-02-01

    Full Text Available Extracting surface water distribution with satellite imagery has been an important subject in remote sensing. Spectral indices of water only use information from a limited number of bands, thus they may have poor performance from pixels contaminated by ice/snow, clouds, etc. The detection algorithms using information from all spectral bands, such as constrained energy minimization (CEM, could avoid this problem to some extent. However, these are mostly designed for hyperspectral imagery, and may fail when applied to multispectral data. It has been proved that adding linearly irrelevant data to original data could improve the performance of CEM. In this study, two kinds of linearly irrelevant data are added for water extraction: the spectral indices and the spectral similarity metric data. CEM is designed for targets with low-probability distribution in an image, but water bodies do not always satisfy this condition. We thereby impose a sensible coefficient for each pixel to form the weighted autocorrelation matrix. In this study, the weight is based on the orthogonal subspace projection, so this new method is named Orthogonal subspace projection Weighted CEM (OWCEM. The newly launched Landsat 8 images over two lakes, the Hala Lake in China with ice/snow distributed in the north, and the Huron Lake in North America, a lake with a very large surface area, are selected to test the accuracy and robustness of our algorithm. The Kappa coefficient and the receiver operating characteristic (ROC curve are calculated as an accuracy evaluation standard. For both lakes, our method can greatly suppress the background (including ice/snow and clouds and extract the complete water surface with a high accuracy (Kappa coefficient > 0.96.

  11. Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

    Science.gov (United States)

    Peat, Julian R; Dean, Wendy; Clark, Stephen J; Krueger, Felix; Smallwood, Sébastien A; Ficz, Gabriella; Kim, Jong Kyoung; Marioni, John C; Hore, Timothy A; Reik, Wolf

    2014-12-24

    Fertilization triggers global erasure of paternal 5-methylcytosine as part of epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by TET3, but our understanding of its targets and the wider context of demethylation is limited to a small fraction of the genome. We employed an optimized bisulfite strategy to generate genome-wide methylation profiles of control and TET3-deficient zygotes, using SNPs to access paternal alleles. This revealed that in addition to pervasive removal from intergenic sequences and most retrotransposons, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation and at gene bodies is also linked to increased transcriptional noise in early development. Our data map the primary contribution of oxidative demethylation to a subset of gene bodies and intergenic sequences and implicate redundant pathways at many loci. Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation

    Directory of Open Access Journals (Sweden)

    Julian R. Peat

    2014-12-01

    Full Text Available Fertilization triggers global erasure of paternal 5-methylcytosine as part of epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by TET3, but our understanding of its targets and the wider context of demethylation is limited to a small fraction of the genome. We employed an optimized bisulfite strategy to generate genome-wide methylation profiles of control and TET3-deficient zygotes, using SNPs to access paternal alleles. This revealed that in addition to pervasive removal from intergenic sequences and most retrotransposons, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation and at gene bodies is also linked to increased transcriptional noise in early development. Our data map the primary contribution of oxidative demethylation to a subset of gene bodies and intergenic sequences and implicate redundant pathways at many loci. Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup.

  13. Hitting a Moving Target: A Strategic Tool for Analyzing Terrorist Threats.

    Science.gov (United States)

    Coleman, Ken; Ishisoko, Noriko; Trounce, Milana; Bernard, Kenneth

    The subject of terrorism risk can be confusing for both the general public and for those responsible for protecting us from attack. Relatively minor terrorist threats are often conflated with much more serious ones, in part because it is hard to quantify either intent or technical ability to carry out an attack. Plotting threats on a "potential mass casualties" versus "ease of obtainment or production" matrix creates some order out of a seemingly endless array of worldwide threats, and it highlights those threats that are in need of more urgent attention. The specific threats on this 2x2 matrix can fall into one or multiple quadrants, which can be qualitatively described as "most dangerous," "dangerous but difficult," "worrisome," and "persistent terror." By placing threats into these quadrants and illustrating movement within and between them, the matrix can help (1) visualize and parse a diverse set of threats, (2) view how threats have changed over time and judge the efficacy of current countermeasures, and (3) evaluate the merit of future actions and investments. Having a dynamic matrix that can visually map the comparative risk of terrorist threat events in toto and that can help us monitor the effectiveness of present and future resource investments can add intellectual rigor to some of the most difficult and daunting decisions pertaining to our nation's safety and security.

  14. Comparison of new generation low-complexity flood inundation mapping tools with a hydrodynamic model

    Science.gov (United States)

    Afshari, Shahab; Tavakoly, Ahmad A.; Rajib, Mohammad Adnan; Zheng, Xing; Follum, Michael L.; Omranian, Ehsan; Fekete, Balázs M.

    2018-01-01

    The objective of this study is to compare two new generation low-complexity tools, AutoRoute and Height Above the Nearest Drainage (HAND), with a two-dimensional hydrodynamic model (Hydrologic Engineering Center-River Analysis System, HEC-RAS 2D). The assessment was conducted on two hydrologically different and geographically distant test-cases in the United States, including the 16,900 km2 Cedar River (CR) watershed in Iowa and a 62 km2 domain along the Black Warrior River (BWR) in Alabama. For BWR, twelve different configurations were set up for each of the models, including four different terrain setups (e.g. with and without channel bathymetry and a levee), and three flooding conditions representing moderate to extreme hazards at 10-, 100-, and 500-year return periods. For the CR watershed, models were compared with a simplistic terrain setup (without bathymetry and any form of hydraulic controls) and one flooding condition (100-year return period). Input streamflow forcing data representing these hypothetical events were constructed by applying a new fusion approach on National Water Model outputs. Simulated inundation extent and depth from AutoRoute, HAND, and HEC-RAS 2D were compared with one another and with the corresponding FEMA reference estimates. Irrespective of the configurations, the low-complexity models were able to produce inundation extents similar to HEC-RAS 2D, with AutoRoute showing slightly higher accuracy than the HAND model. Among four terrain setups, the one including both levee and channel bathymetry showed lowest fitness score on the spatial agreement of inundation extent, due to the weak physical representation of low-complexity models compared to a hydrodynamic model. For inundation depth, the low-complexity models showed an overestimating tendency, especially in the deeper segments of the channel. Based on such reasonably good prediction skills, low-complexity flood models can be considered as a suitable alternative for fast

  15. Kidney disease models: tools to identify mechanisms and potential therapeutic targets

    Science.gov (United States)

    Bao, Yin-Wu; Yuan, Yuan; Chen, Jiang-Hua; Lin, Wei-Qiang

    2018-01-01

    Acute kidney injury (AKI) and chronic kidney disease (CKD) are worldwide public health problems affecting millions of people and have rapidly increased in prevalence in recent years. Due to the multiple causes of renal failure, many animal models have been developed to advance our understanding of human nephropathy. Among these experimental models, rodents have been extensively used to enable mechanistic understanding of kidney disease induction and progression, as well as to identify potential targets for therapy. In this review, we discuss AKI models induced by surgical operation and drugs or toxins, as well as a variety of CKD models (mainly genetically modified mouse models). Results from recent and ongoing clinical trials and conceptual advances derived from animal models are also explored. PMID:29515089

  16. ADP-ribosyltransferases: plastic tools for inactivating protein and small molecular weight targets.

    Science.gov (United States)

    Koch-Nolte, F; Reche, P; Haag, F; Bazan, F

    2001-12-28

    ADP-ribosyltransferases (ADPRTs) form an interesting class of enzymes with well-established roles as potent bacterial toxins and metabolic regulators. ADPRTs catalyze the transfer of the ADP-ribose moiety from NAD(+) onto specific substrates including proteins. ADP-ribosylation usually inactivates the function of the target. ADPRTs have become adapted to function in extra- and intracellular settings. Regulation of ADPRT activity can be mediated by ligand binding to associated regulatory domains, proteolytic cleavage, disulphide bond reduction, and association with other proteins. Crystallisation has revealed a conserved core set of elements that define an unusual minimal scaffold of the catalytic domain with remarkably plastic sequence requirements--only a single glutamic acid residue critical to catalytic activity is invariant. These inherent properties of ADPRTs suggest that the ADPRT catalytic fold is an attractive, malleable subject for protein design.

  17. Passive sampling - a tool for targeted screening of emerging pollutants in rivers

    Science.gov (United States)

    Kodes, Vit; Grabic, Roman

    2016-04-01

    A screening of more than 300 pollutants such as pharmaceuticals (analgesics, psycholeptics, antidepressants, antibiotics, beta blockers), PCPs (UV blockers, musk's, repellents), illicit drugs, pesticides, perfluorinated compounds and their metabolites at 22 monitoring sites throughout the Czech Republic was conducted in 2013. POCIS samplers were used in this study. Two types of passive samplers (pesticide and pharmaceutical POCIS) were deployed for 14 days in May and in October, 88 samples were collected in total. In total 265 and 310 target compounds were analyzed in pharmaceutical and pesticide samplers respectively. The chemicals of interest were extracted from the passive samplers according to standardized procedures. LC -MS/MS and LC-MS/HRMS methods were applied for analyses of extracts. 150 of 310 (48%) and 127 of 265 (48%) analyzed substances had been found in pesticide and pharmaceutical samplers respectively. 27 substances (pharmaceuticals, PCPs, pesticides, caffeine, nicotine metabolite cotinine) occurred at all sampled sites, additional 39 substances (pharmaceuticals, PCPs, pesticides) occurred at more than 17 (75%) sites. One of perfluorinated compounds (PFOA) occurred at 68% of sites, whilst one of illicit drugs (Methamphetamine) was found at 61% of sites. The highest number of contaminants found in one POCIS at a single monitoring site was 111. The concentrations varied from nanograms to thousands of nanograms per sampler. Emerging contaminants occurring in highest concentrations (> 1000 ng/sampler) were BP-4 and PBSA (UV blockers), caffeine, DEET (insect repellent), imidacloprid (insecticide), telmisartan (hypertension drug) and tramadol (analgesic). Monitoring in the Czech Republic has demonstrated that many target compounds enter river waters and a number of these compounds reach high concentrations.

  18. Fast electron and X-ray scattering as a tool to study target's structure

    International Nuclear Information System (INIS)

    Amusia, M.Ya.

    2007-01-01

    We concentrate on several relatively new aspects of the study of fast electron and X-ray scattering by atoms and atom-like objects, namely endohedral atoms and fullerenes. However, main attention is given to fast charge particle scattering. We show that the corresponding cross-sections, being expressed via so-called generalized oscillator strengths (GOS), give information on the electronic structure of the target and on the role of electron correlations in it. We consider what sort of information became available when analyzing the dependence of GOS upon their multipolarity, transferred momentum q and energy ω. To obtain theoretical results, we employ both the one-electron Hartree-Fock approximation and account for the multi-electron correlation in the target, using the random phase approximation with exchange. We demonstrate the role of non-dipole corrections in the small-angle fast-electron inelastic scattering. There dipole contribution dominates while non-dipole corrections can be considerably and controllably enhanced as compared to the case of low and medium energy photoionization. We show also that analyses of GOS for discrete level excitations permit to clarify their multipolarity. The results of calculations of Compton excitation and ionization cross-sections are presented. Attention is given to cooperative effects in inelastic fast electron-atom scattering that results in directed motion of the secondary electrons, a phenomenon that is similar to 'drag currents' in photoionization. We demonstrate how one should derive GOS for endohedral atoms, e.g. A-C 60 and what is the additional information that can be obtained from corresponding GOS. Most of discussions are illustrated by the results of concrete calculations

  19. Using the Lives Saved Tool to aid country planning in meeting mortality targets: a case study from Mali

    Directory of Open Access Journals (Sweden)

    Youssouf Keita

    2017-11-01

    Full Text Available Abstract Background Mali is one of four countries implementing a National Evaluation Platform (NEP to build local capacity to answer evaluation questions for maternal, newborn, child health and nutrition (MNCH&N. In 2014-15, NEP-Mali addressed questions about the potential impact of Mali’s MNCH&N plans and strategies, and identified priority interventions to achieve targeted mortality reductions. Methods The NEP-Mali team modeled the potential impact of three intervention packages in the Lives Saved Tool (LiST from 2014 to 2023. One projection included the interventions and targets from Mali’s ten-year health strategy (PDDSS for 2014-2023, and two others modeled intervention packages that included scale up of antenatal, intrapartum, and curative interventions, as well as reductions in stunting and wasting. We modeled the change in maternal, newborn and under-five mortality rates under these three projections, as well as the number of lives saved, overall and by intervention. Results If Mali were to achieve the MNCH&N coverage targets from its health strategy, under-5 mortality would be reduced from 121 per 1000 live births to 93 per 1000, far from the target of 69 deaths per 1000. Projections 1 and 2 produced estimated mortality reductions from 121 deaths per 1000 to 70 and 68 deaths per 1000, respectively. With respect to neonatal mortality, the mortality rate would be reduced from 39 to 32 deaths per 1000 live births under the current health strategy, and to 25 per 1000 under projections 1 and 2. Conclusions This study revealed that achieving the coverage targets for the MNCH&N interventions in the 2014-23 PDDSS would likely not allow Mali to achieve its mortality targets. The NEP-Mali team was able to identify two packages of MNCH&N interventions (and targets that achieved under-5 and neonatal mortality rates at, or very near, the PDDSS targets. The Malian Ministry of Health and Public Hygiene is using these results to revise its plans

  20. Asset Mapping at Halifax Public Libraries: A Tool for Beginning to Discover the Library’s Role with the Immigrant Community in Halifax

    OpenAIRE

    Kenneth William Williment; Tracey Jones-Grant

    2012-01-01

    As library systems across Canada begin to grapple with the implications community-led service planning has on program and service development, new tools are being developed to assist library staff. Asset mapping is one community entry tool which allows library staff to access community members (or organizational representatives) and gather in-depth information impacting services and program identification, development, and implementation – either across a library system or within a branch ca...

  1. In-situ ground gamma spectrometry — an effective tool for geological mapping (the Male Karpaty Mts., Slovakia)

    Science.gov (United States)

    Mojzeš, Andrej; Porubčanová, Barbara

    2016-06-01

    This contribution presents the results of profile in-situ gamma spectrometry measurements that sought to determine the content of natural radionuclides 40K, 238U and 232Th in a near surface horizon of rocks, their weathering cover and soils in the area of the Malé Karpaty Mts. It is widely established that the exploration of radioactivity of bedrocks and cover rocks can be a very effective and useful tool for both geological mapping, for identifying deposits of mineral resources, and even addressing the issues of structural and tectonic geology. This assertion is equally confirmed by the ground gamma spectrometry measurements carried out as part of this case study on larger scales, seeking more detailed geological structure solutions. The results obtained provide a welcome addition to an already existing database, which monitors the content of naturally occurring radionuclides individually for every rock lithotype of the Western Carpathians, by elaborating on the data collected by previous research and by updating this database for any future needs. The presented results confirmed the low to medium radioactivity levels of rocks and soils in the studied area. The highest values were detected in granitoids and metamorfic phyllitic rocks of the Malé Karpaty Mts. core; the lowest values were detected in carbonates, arenaceous sediments and, above all, amphibolite bodies. In this way, the presented results of the interpreted profile (P5) confirm the model of local geological structure as represented on the most up-to-date edition of the geological map of the Male Karpaty Mts. (Polak et al. 2011).

  2. Mapping Patterns of Ipsilateral Supraclavicular Nodal Metastases in Breast Cancer: Rethinking the Clinical Target Volume for High-risk Patients

    Energy Technology Data Exchange (ETDEWEB)

    Jing, Hao [Department of Radiation Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Wang, Shu-Lian, E-mail: wsl20040118@yahoo.com [Department of Radiation Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Li, Jing; Xue, Mei; Xiong, Zu-Kun [Department of Radiology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Jin, Jing; Wang, Wei-Hu; Song, Yong-Wen; Liu, Yue-Ping; Ren, Hua; Fang, Hui; Yu, Zi-Hao; Liu, Xin-Fan [Department of Radiation Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Li, Ye-Xiong, E-mail: yexiong12@163.com [Department of Radiation Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China)

    2015-10-01

    Purpose: To map the location of metastatic supraclavicular (SCV) lymph nodes (LNMs) in breast cancer patients with SCV node involvement and determine whether and where the radiation therapy clinical target volume (CTV) of this region could be modified in high-risk subsets. Methods and Materials: Fifty-five patients with metastatic SCV LNMs were eligible for geographic mapping and atlas coverage analysis. All LNMs and their epicenters were registered proportionally by referencing the surrounding landmarks onto simulation computed tomography images of a standard patient. CTVs based on selected SCV atlases, including the one by the Radiation Therapy Oncology Group (RTOG) were contoured. A modified SCV CTV was tried and shown to have better involved-node coverage and thus theoretically improved prophylaxis in this setting. Results: A total of 50 (91%) and 45 (81.8%) patients had LNMs in the medial and lateral SCV subregions, respectively. Also, 36 patients (65.5%) had LNMs located at the junction of the jugular-subclavian veins. All nodes were covered in only 25.5% to 41.8% of patients by different atlases. The RTOG atlas covered all nodes in 25.5% of patients. Stratified by the nodes in all the patients as a whole, 49.2% to 81.3% were covered, and the RTOG atlas covered 62.6%. The lateral and posterior borders were the most overlooked locations. Modification by extending the borders to natural anatomic barriers allowed the new CTV to cover all the nodes in 81.8% of patients and encompass 96.1% of all the nodes. Conclusions: According to the distribution of SCV LNMs, the extent of existing atlases might not be adequate for potential metastatic sites in certain groups of patients. The extension of the lateral and posterior CTV borders in high-risk or recurrent patients might be a reasonable approach for increasing coverage. However, additional data in more homogeneous populations with localized disease are needed before routine application.

  3. Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing.

    Science.gov (United States)

    Mathias, Patrick C; Turner, Emily H; Scroggins, Sheena M; Salipante, Stephen J; Hoffman, Noah G; Pritchard, Colin C; Shirts, Brian H

    2016-03-01

    To apply techniques for ancestry and sex computation from next-generation sequencing (NGS) data as an approach to confirm sample identity and detect sample processing errors. We combined a principal component analysis method with k-nearest neighbors classification to compute the ancestry of patients undergoing NGS testing. By combining this calculation with X chromosome copy number data, we determined the sex and ancestry of patients for comparison with self-report. We also modeled the sensitivity of this technique in detecting sample processing errors. We applied this technique to 859 patient samples with reliable self-report data. Our k-nearest neighbors ancestry screen had an accuracy of 98.7% for patients reporting a single ancestry. Visual inspection of principal component plots was consistent with self-report in 99.6% of single-ancestry and mixed-ancestry patients. Our model demonstrates that approximately two-thirds of potential sample swaps could be detected in our patient population using this technique. Patient ancestry can be estimated from NGS data incidentally sequenced in targeted panels, enabling an inexpensive quality control method when coupled with patient self-report. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Electrotransfer parameters as a tool for controlled and targeted gene expression in skin

    Directory of Open Access Journals (Sweden)

    Spela Kos

    2016-01-01

    Full Text Available Skin is an attractive target for gene electrotransfer. It consists of different cell types that can be transfected, leading to various responses to gene electrotransfer. We demonstrate that these responses could be controlled by selecting the appropriate electrotransfer parameters. Specifically, the application of low or high electric pulses, applied by multi-electrode array, provided the possibility to control the depth of the transfection in the skin, the duration and the level of gene expression, as well as the local or systemic distribution of the transgene. The influence of electric pulse type was first studied using a plasmid encoding a reporter gene (DsRed. Then, plasmids encoding therapeutic genes (IL-12, shRNA against endoglin, shRNA against melanoma cell adhesion molecule were used, and their effects on wound healing and cutaneous B16F10 melanoma tumors were investigated. The high-voltage pulses resulted in gene expression that was restricted to superficial skin layers and induced a local response. In contrast, the low-voltage electric pulses promoted transfection into the deeper skin layers, resulting in prolonged gene expression and higher transgene production, possibly with systemic distribution. Therefore, in the translation into the clinics, it will be of the utmost importance to adjust the electrotransfer parameters for different therapeutic approaches and specific mode of action of the therapeutic gene.

  5. The Evaluation of Argument Mapping as a Learning Tool: Comparing the Effects of Map Reading versus Text Reading on Comprehension and Recall of Arguments

    Science.gov (United States)

    Dwyer, Christopher P.; Hogan, Michael J.; Stewart, Ian

    2010-01-01

    The current study compared the effects on comprehension and memory of learning via text versus learning via argument map. Argument mapping is a method of diagrammatic representation of arguments designed to simplify the reading of an argument structure and allow for easy assimilation of core propositions and relations. In the current study, 400…

  6. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-05-06

    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  7. New machine learning tools for predictive vegetation mapping after climate change: Bagging and Random Forest perform better than Regression Tree Analysis

    Science.gov (United States)

    L.R. Iverson; A.M. Prasad; A. Liaw

    2004-01-01

    More and better machine learning tools are becoming available for landscape ecologists to aid in understanding species-environment relationships and to map probable species occurrence now and potentially into the future. To thal end, we evaluated three statistical models: Regression Tree Analybib (RTA), Bagging Trees (BT) and Random Forest (RF) for their utility in...

  8. Development and Evaluation of a Web Map Mind Tool Environment with the Theory of Spatial Thinking and Project-Based Learning Strategy

    Science.gov (United States)

    Hou, Huei-Tse; Yu, Tsai-Fang; Wu, Yi-Xuan; Sung, Yao-Ting; Chang, Kuo-En

    2016-01-01

    The theory of spatial thinking is relevant to the learning and teaching of many academic domains. One promising method to facilitate learners' higher-order thinking is to utilize a web map mind tool to assist learners in applying spatial thinking to cooperative problem solving. In this study, an environment is designed based on the theory of…

  9. Flash Flood Hazard Mapping Using Satellite Images and GIS Tools: A case study of Najran City, Kingdom of Saudi Arabia (KSA

    Directory of Open Access Journals (Sweden)

    Ismail Elkhrachy

    2015-12-01

    Full Text Available Flash flood in the cities led to high levels of water in the streets and roads, causing many problems such as bridge collapse, building damage and traffic problems. It is impossible to avoid risks of floods or prevent their occurrence, however it is plausible to work on the reduction of their effects and to reduce the losses which they may cause. Flash flood mapping to identify sites in high risk flood zones is one of the powerful tools for this purpose. Mapping flash flood will be beneficial to urban and infrastructure planners, risk managers and disaster response or emergency services during extreme and intense rainfall events. The objective of this paper is to generate flash flood map for Najran city, Saudi Arabia, using satellite images and GIS tools. To do so, we use SPOT and SRTM DEMs data for which accuracy assessment is achieved by using check points, obtained by GPS observations. Analytical Hierarchical Process (AHP is used to determine relative impact weight of flood causative factors to get a composite flood hazard index (FHI. The causative factors in this study are runoff, soil type, surface slope, surface roughness, drainage density, distance to main channel and land use. All used data are finally integrated in an ArcMap to prepare a final flood hazard map for study area. The areas in high risk flood zones are obtained by overlaying the flood hazard index map with the zone boundaries layer. The affected population number and land area are determined and compared.

  10. Energy Zones Study: A Comprehensive Web-Based Mapping Tool to Identify and Analyze Clean Energy Zones in the Eastern Interconnection

    Energy Technology Data Exchange (ETDEWEB)

    Koritarov, V.; Kuiper, J.; Hlava, K.; Orr, A.; Rollins, K.; Brunner, D.; Green, H.; Makar, J.; Ayers, A.; Holm, M.; Simunich, K.; Wang, J.; Augustine, C.; Heimiller, D.; Hurlbut, D. J.; Milbrandt, A.; Schneider, T. R.; et al.

    2013-09-01

    This report describes the work conducted in support of the Eastern Interconnection States’ Planning Council (EISPC) Energy Zones Study and the development of the Energy Zones Mapping Tool performed by a team of experts from three National Laboratories. The multi-laboratory effort was led by Argonne National Laboratory (Argonne), in collaboration with the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL). In June 2009, the U.S. Department of Energy (DOE) and the National Energy Technology Laboratory published Funding Opportunity Announcement FOA-0000068, which invited applications for interconnection-level analysis and planning. In December 2009, the Eastern Interconnection Planning Collaborative (EIPC) and the EISPC were selected as two award recipients for the Eastern Interconnection. Subsequently, in 2010, DOE issued Research Call RC-BM-2010 to DOE’s Federal Laboratories to provide research support and assistance to FOA-0000068 awardees on a variety of key subjects. Argonne was selected as the lead laboratory to provide support to EISPC in developing a methodology and a mapping tool for identifying potential clean energy zones in the Eastern Interconnection. In developing the EISPC Energy Zones Mapping Tool (EZ Mapping Tool), Argonne, NREL, and ORNL closely collaborated with the EISPC Energy Zones Work Group which coordinated the work on the Energy Zones Study. The main product of the Energy Zones Study is the EZ Mapping Tool, which is a web-based decision support system that allows users to locate areas with high suitability for clean power generation in the U.S. portion of the Eastern Interconnection. The mapping tool includes 9 clean (low- or no-carbon) energy resource categories and 29 types of clean energy technologies. The EZ Mapping Tool contains an extensive geographic information system database and allows the user to apply a flexible modeling approach for the identification and analysis of potential energy zones

  11. Sensory cortical re-mapping following upper-limb amputation and subsequent targeted reinnervation: A case report

    Directory of Open Access Journals (Sweden)

    Jun Yao

    2015-01-01

    Full Text Available This case study demonstrates the change of sensory cortical representations of the residual parts of the arm in an individual who underwent a trans-humeral amputation and subsequent targeted reinnervation (TR. As a relatively new surgical technique, TR restores a direct neural connection from amputated sensorimotor nerves to specific target muscles. This method has been successfully applied to upper-limb and lower-limb amputees, and has shown effectiveness in regaining control signals via the newly re-innervated muscles. Correspondingly, recent study results have shown that motor representations for the missing limb move closer to their original locations following TR. Besides regaining motor control signals, TR also restores the sensation in the re-innervated skin areas. We therefore hypothesize that TR causes analogous cortical sensory remapping that may return closer to their original locations. In order to test this hypothesis, cortical activity in response to sensory-level electrical stimulation in different parts of the arm was studied longitudinally in one amputated individual before and up to 2 years after TR. Our results showed that 1 before TR, the cortical response to sensory electrical stimulation in the residual limb showed a diffuse bilateral pattern without a clear focus in either the time or spatial domain; and 2 2 years after TR, the sensory map of the reinnervated median nerve reorganized, showing predominant activity over the contralateral S1 hand area as well as moderate activity over the ipsilateral S1. Therefore, this work provides new evidence for long-term sensory cortical plasticity in the human brain after TR.

  12. Sensory cortical re-mapping following upper-limb amputation and subsequent targeted reinnervation: A case report.

    Science.gov (United States)

    Yao, Jun; Chen, Albert; Kuiken, Todd; Carmona, Carolina; Dewald, Julius

    2015-01-01

    This case study demonstrates the change of sensory cortical representations of the residual parts of the arm in an individual who underwent a trans-humeral amputation and subsequent targeted reinnervation (TR). As a relatively new surgical technique, TR restores a direct neural connection from amputated sensorimotor nerves to specific target muscles. This method has been successfully applied to upper-limb and lower-limb amputees, and has shown effectiveness in regaining control signals via the newly re-innervated muscles. Correspondingly, recent study results have shown that motor representations for the missing limb move closer to their original locations following TR. Besides regaining motor control signals, TR also restores the sensation in the re-innervated skin areas. We therefore hypothesize that TR causes analogous cortical sensory remapping that may return closer to their original locations. In order to test this hypothesis, cortical activity in response to sensory-level electrical stimulation in different parts of the arm was studied longitudinally in one amputated individual before and up to 2 years after TR. Our results showed that 1) before TR, the cortical response to sensory electrical stimulation in the residual limb showed a diffuse bilateral pattern without a clear focus in either the time or spatial domain; and 2) 2 years after TR, the sensory map of the reinnervated median nerve reorganized, showing predominant activity over the contralateral S1 hand area as well as moderate activity over the ipsilateral S1. Therefore, this work provides new evidence for long-term sensory cortical plasticity in the human brain after TR.

  13. Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): Data and Tools for Dynamic Management and Decision Support

    Science.gov (United States)

    Humphries, G. R. W.; Naveen, R.; Schwaller, M.; Che-Castaldo, C.; McDowall, P.; Schrimpf, M.; Schrimpf, Michael; Lynch, H. J.

    2017-01-01

    The Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) is a web-based, open access, decision-support tool designed to assist scientists, non-governmental organizations and policy-makers working to meet the management objectives as set forth by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) and other components of the Antarctic Treaty System (ATS) (that is, Consultative Meetings and the ATS Committee on Environmental Protection). MAPPPD was designed specifically to complement existing efforts such as the CCAMLR Ecosystem Monitoring Program (CEMP) and the ATS site guidelines for visitors. The database underlying MAPPPD includes all publicly available (published and unpublished) count data on emperor, gentoo, Adelie) and chinstrap penguins in Antarctica. Penguin population models are used to assimilate available data into estimates of abundance for each site and year.Results are easily aggregated across multiple sites to obtain abundance estimates over any user-defined area of interest. A front end web interface located at www.penguinmap.com provides free and ready access to the most recent count and modelled data, and can act as a facilitator for data transfer between scientists and Antarctic stakeholders to help inform management decisions for the continent.

  14. A fully automatic tool to perform accurate flood mapping by merging remote sensing imagery and ancillary data

    Science.gov (United States)

    D'Addabbo, Annarita; Refice, Alberto; Lovergine, Francesco; Pasquariello, Guido

    2016-04-01

    Flooding is one of the most frequent and expansive natural hazard. High-resolution flood mapping is an essential step in the monitoring and prevention of inundation hazard, both to gain insight into the processes involved in the generation of flooding events, and from the practical point of view of the precise assessment of inundated areas. Remote sensing data are recognized to be useful in this respect, thanks to the high resolution and regular revisit schedules of state-of-the-art satellites, moreover offering a synoptic overview of the extent of flooding. In particular, Synthetic Aperture Radar (SAR) data present several favorable characteristics for flood mapping, such as their relative insensitivity to the meteorological conditions during acquisitions, as well as the possibility of acquiring independently of solar illumination, thanks to the active nature of the radar sensors [1]. However, flood scenarios are typical examples of complex situations in which different factors have to be considered to provide accurate and robust interpretation of the situation on the ground: the presence of many land cover types, each one with a particular signature in presence of flood, requires modelling the behavior of different objects in the scene in order to associate them to flood or no flood conditions [2]. Generally, the fusion of multi-temporal, multi-sensor, multi-resolution and/or multi-platform Earth observation image data, together with other ancillary information, seems to have a key role in the pursuit of a consistent interpretation of complex scenes. In the case of flooding, distance from the river, terrain elevation, hydrologic information or some combination thereof can add useful information to remote sensing data. Suitable methods, able to manage and merge different kind of data, are so particularly needed. In this work, a fully automatic tool, based on Bayesian Networks (BNs) [3] and able to perform data fusion, is presented. It supplies flood maps

  15. Combat Stories Map: A Historical Repository and After Action Tool for Capturing, Storing, and Analyzing Georeferenced Individual Combat Narratives

    Science.gov (United States)

    2016-06-01

    visibility to that level. Other basemaps used by the Combat Stories Map , such as “ Open Street Map ” and “World Imagery,” do provide details to the...organizing their combat experiences.41 The Combat Stories Map allows users to zoom in to street level to identify specific locations where their combat... Map zoom in and out at preset scales depending on what one can clearly discern at that scale. Hence, one can clearly distinguish streets at the

  16. The energy ratio mapping algorithm: a tool to improve the energy-based detection of odontocete echolocation clicks.

    Science.gov (United States)

    Klinck, Holger; Mellinger, David K

    2011-04-01

    The energy ratio mapping algorithm (ERMA) was developed to improve the performance of energy-based detection of odontocete echolocation clicks, especially for application in environments with limited computational power and energy such as acoustic gliders. ERMA systematically evaluates many frequency bands for energy ratio-based detection of echolocation clicks produced by a target species in the presence of the species mix in a given geographic area. To evaluate the performance of ERMA, a Teager-Kaiser energy operator was applied to the series of energy ratios as derived by ERMA. A noise-adaptive threshold was then applied to the Teager-Kaiser function to identify clicks in data sets. The method was tested for detecting clicks of Blainville's beaked whales while rejecting echolocation clicks of Risso's dolphins and pilot whales. Results showed that the ERMA-based detector correctly identified 81.6% of the beaked whale clicks in an extended evaluation data set. Average false-positive detection rate was 6.3% (3.4% for Risso's dolphins and 2.9% for pilot whales).

  17. Economic gains from targeted measures related to non-point pollution in agriculture based on detailed nitrate reduction maps.

    Science.gov (United States)

    Jacobsen, Brian H; Hansen, Anne Lausten

    2016-06-15

    From 1990 to 2003, Denmark reduced N-leaching from the root zone by 50%. However, more measures are required, and in recent years, the focus has been on how to differentiate measures in order to ensure that they are implemented where the effect on N-loss reductions per ha is the greatest. The purpose of the NiCA project has been to estimate the natural nitrate reduction in the groundwater more precisely than before using a plot size down to 1ha. This article builds on these findings and presents the possible economic gains for the farmer when using this information to reach a given N-loss level. Targeted measures are especially relevant where the subsurface N-reduction varies significantly within the same farm and national analyses have shown that a cost reduction of around 20-25% using targeted measures is likely. The analyses show an increasing potential with increasing variation in N-reduction in the catchment. In this analysis, the knowledge of spatial variation in N-reduction potential is used to place measures like catch crops or set-a-side at locations with the greatest effect on 10 case farms in the Norsminde Catchment, Denmark. The findings suggest that the gains are from 0 to 32€/ha and the average farm would gain approximately 14-21€/ha/year from the targeted measures approach. The analysis indicates that the economic gain is greater than the costs of providing the detailed maps of 5-10€/ha/year. When N-loss reduction requirements are increased, the economic gains are greater. When combined with new measures like mini-wetlands and early sowing the economic advantage is increased further. The paper also shows that not all farms can use the detailed information on N-reduction and there is not a clear link between spatial variation in N-reduction at the farm level and possible economic gains for all these 10 farms. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Translocator Protein (18 kDa: A Promising Therapeutic Target and Diagnostic Tool for Cardiovascular Diseases

    Directory of Open Access Journals (Sweden)

    Xiaolong Qi

    2012-01-01

    Full Text Available The translocator protein (18 kDa (TSPO is a five transmembrane domain protein in mitochondria, abundantly expressed in a variety of organs and tissues. TSPO contributes to a wide range of biological processes, including cholesterol transportation, mitochondrial membrane potential and respiratory chain regulation, apoptosis, and oxidative stress. Recent studies have demonstrated that TSPO might also be involved in the physiological regulation of cardiac chronotropy and inotropy. Accordingly, TSPO ligands play significant roles in protecting the cardiovascular systems under pathological conditions through cardiac electrical activity retention, intracellular calcium maintenance, mitochondrial energy provision, mitochondrial membrane potential equilibrium, and reactive oxygen species inhibition. This paper focuses on the physiological and pathological characteristics of TSPO in the cardiovascular systems and also summarizes the properties of TSPO ligands. TSPO represents a potential therapeutic target and diagnostic tool for cardiovascular diseases including arrhythmia, myocardial infarction, cardiac hypertrophy, atherosclerosis, myocarditis, and large vessel vasculitis.

  19. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

    Science.gov (United States)

    Zhang, Yuan; Sun, Yanni; Cole, James R

    2014-08-01

    Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.

  20. A scalable and accurate targeted gene assembly tool (SAT-Assembler for next-generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Yuan Zhang

    2014-08-01

    Full Text Available Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.

  1. A Robust Profitability Assessment Tool for Targeting Agricultural Investments in Developing Countries: Modeling Spatial Heterogeneity and Uncertainty

    Science.gov (United States)

    Quinn, J. D.; Zeng, Z.; Shoemaker, C. A.; Woodard, J.

    2014-12-01

    In sub-Saharan Africa, where the majority of the population earns their living from agriculture, government expenditures in many countries are being re-directed to the sector to increase productivity and decrease poverty. However, many of these investments are seeing low returns because they are poorly targeted. A geographic tool that accounts for spatial heterogeneity and temporal variability in the factors of production would allow governments and donors to optimize their investments by directing them to farmers for whom they are most profitable. One application for which this is particularly relevant is fertilizer recommendations. It is well-known that soil fertility in much of sub-Saharan Africa is declining due to insufficient nutrient inputs to replenish those lost through harvest. Since fertilizer application rates in sub-Saharan Africa are several times smaller than in other developing countries, it is often assumed that African farmers are under-applying fertilizer. However, this assumption ignores the risk farmers face in choosing whether or how much fertilizer to apply. Simply calculating the benefit/cost ratio of applying a given level of fertilizer in a particular year over a large, aggregated region (as is often done) overlooks the variability in yield response seen at different sites within the region, and at the same site from year to year. Using Ethiopia as an example, we are developing a 1 km resolution fertilizer distribution tool that provides pre-season fertilizer recommendations throughout the agricultural regions of the country, conditional on seasonal climate forecasts. By accounting for spatial heterogeneity in soil, climate, market and travel conditions, as well as uncertainty in climate and output prices at the time a farmer must purchase fertilizer, this stochastic optimization tool gives better recommendations to governments, fertilizer companies, and aid organizations looking to optimize the welfare benefits achieved by their

  2. Convergence of human brain mapping tools: neuronavigated TMS parameters and fMRI activity in the hand motor area.

    Science.gov (United States)

    Sarfeld, Anna-Sophia; Diekhoff, Svenja; Wang, Ling E; Liuzzi, Gianpiero; Uludağ, Kamil; Eickhoff, Simon B; Fink, Gereon R; Grefkes, Christian

    2012-05-01

    Functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) are well-established tools for investigating the human motor system in-vivo. We here studied the relationship between movement-related fMRI signal changes in the primary motor cortex (M1) and electrophysiological properties of the hand motor area assessed with neuronavigated TMS in 17 healthy subjects. The voxel showing the highest task-related BOLD response in the left hand motor area during right hand movements was identified for each individual subject. This fMRI peak voxel in M1 served as spatial target for coil positioning during neuronavigated TMS. We performed correlation analyses between TMS parameters, BOLD signal estimates and effective connectivity parameters of M1 assessed with dynamic causal modeling (DCM). The results showed a negative correlation between the movement-related BOLD signal in left M1 and resting as well as active motor threshold (MT) obtained for left M1. The DCM analysis revealed that higher excitability of left M1 was associated with a stronger coupling between left supplementary motor area (SMA) and M1. Furthermore, BOLD activity in left M1 correlated with ipsilateral silent period (ISP), i.e. the stronger the task-related BOLD response in left M1, the higher interhemispheric inhibition effects targeting right M1. DCM analyses revealed a positive correlation between the coupling of left SMA with left M1 and the duration of ISP. The data show that TMS parameters assessed for the hand area of M1 do not only reflect the intrinsic properties at the stimulation site but also interactions with remote areas in the human motor system. Copyright © 2011 Wiley-Liss, Inc.

  3. Combat stories map: a historical repository and after action tool for capturing, storing, and analyzing georeferenced individual combat narratives

    OpenAIRE

    Hayes, Jonathan L.

    2016-01-01

    Approved for public release; distribution is unlimited Despite the proliferation of technology and near-global Internet accessibility, a web-based program incorporating interactive maps to record personal combat experiences does not exist. The Combat Stories Map addresses this deficiency. The Combat Stories Map is a web-based Geographic Information System specifically designed to collect and store U.S. service members' georeferenced combat stories. The stories are immediately available for...

  4. CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis.

    Science.gov (United States)

    McCaffrey, Jennifer; Sibert, Justin; Zhang, Bin; Zhang, Yonggang; Hu, Wenhui; Riethman, Harold; Xiao, Ming

    2016-01-29

    We have developed a new, sequence-specific DNA labeling strategy that will dramatically improve DNA mapping in complex and structurally variant genomic regions, as well as facilitate high-throughput automated whole-genome mapping. The method uses the Cas9 D10A protein, which contains a nuclease disabling mutation in one of the two nuclease domains of Cas9, to create a guide RNA-directed DNA nick in the context of an in vitro-assembled CRISPR-CAS9-DNA complex. Fluorescent nucleotides are then incorporated adjacent to the nicking site with a DNA polymerase to label the guide RNA-determined target sequences. This labeling strategy is very powerful in targeting repetitive sequences as well as in barcoding genomic regions and structural variants not amenable to current labeling methods that rely on uneven distributions of restriction site motifs in the DNA. Importantly, it renders the labeled double-stranded DNA available in long intact stretches for high-throughput analysis in nanochannel arrays as well as for lower throughput targeted analysis of labeled DNA regions using alternative methods for stretching and imaging the labeled long DNA molecules. Thus, this method will dramatically improve both automated high-throughput genome-wide mapping as well as targeted analyses of complex regions containing repetitive and structurally variant DNA. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. The South Florida Ecosystem Portfolio Model - A Map-Based Multicriteria Ecological, Economic, and Community Land-Use Planning Tool

    Science.gov (United States)

    Labiosa, William B.; Bernknopf, Richard; Hearn, Paul; Hogan, Dianna; Strong, David; Pearlstine, Leonard; Mathie, Amy M.; Wein, Anne M.; Gillen, Kevin; Wachter, Susan

    2009-01-01

    The South Florida Ecosystem Portfolio Model (EPM) prototype is a regional land-use planning Web tool that integrates ecological, economic, and social information and values of relevance to decision-makers and stakeholders. The EPM uses a multicriteria evaluation framework that builds on geographic information system-based (GIS) analysis and spatially-explicit models that characterize important ecological, economic, and societal endpoints and consequences that are sensitive to regional land-use/land-cover (LULC) change. The EPM uses both economics (monetized) and multiattribute utility (nonmonetized) approaches to valuing these endpoints and consequences. This hybrid approach represents a methodological middle ground between rigorous economic and ecological/ environmental scientific approaches. The EPM sacrifices some degree of economic- and ecological-forecasting precision to gain methodological transparency, spatial explicitness, and transferability, while maintaining credibility. After all, even small steps in the direction of including ecosystem services evaluation are an improvement over current land-use planning practice (Boyd and Wainger, 2003). There are many participants involved in land-use decision-making in South Florida, including local, regional, State, and Federal agencies, developers, environmental groups, agricultural groups, and other stakeholders (South Florida Regional Planning Council, 2003, 2004). The EPM's multicriteria evaluation framework is designed to cut across the objectives and knowledge bases of all of these participants. This approach places fundamental importance on social equity and stakeholder participation in land-use decision-making, but makes no attempt to determine normative socially 'optimal' land-use plans. The EPM is thus a map-based set of evaluation tools for planners and stakeholders to use in their deliberations of what is 'best', considering a balancing of disparate interests within a regional perspective. Although

  6. 4D Geomodeling: a Tool for Targeting New Potential Mineralization - Example of the Kupferschiefer in the Lubin Region, Poland

    Science.gov (United States)

    Mejia-Herrera, Pablo; Royer, Jean-Jacques; Fraboulet, Jean-Gabriel; Zielinska, Agata

    2013-04-01

    Understanding the history of sedimentary basins is of paramount importance for reconstituting oil and gas migration, but also in mineral exploration for identifying brine pathways. Advanced modeling technology such as 3&4D geomodeling can be fruitfully used to explore with new eyes old matured mining field. The Polish Kupferschiefers, a sediment-hosted polymetallic (Cu, Ag, Au, PGE) deposit, is one of the most important sources for copper and silver in the world. Within the framework of the ProMine European project, the Lubin region (south west of Poland), was selected for modeling in 3&4D the geological formations in order to better understand the distribution of the Cu-Ag mineralization, and possibly to define new potential targets. A regional scale 4D reconstitution of the North European basin was undertaken to better understand the burial, deformation and natural hydro-fracturing history of the Lubin Kupferschiefer. It comprises the creation of a 3D model of the present geological formation including more than 200 wells coming from the mining exploitation of the Kupferschiefer, cross sections from seismic exploration and geological maps. This 3D model has been then restored and decompacted using the Kine3D-2 Gocad plug-in. The PetroMode 1D was then used to reconstitute the temperatures, pressures, fluid overpressure, and oil and gas maturation during the burying history of the Southern-Western Poland basin. Conditions for hydraulic fracturing were identified within the base of the Zechstein shales, during an inversion phase at the Late Cretaceous-Early Paleocene time. This up-lifting yields the conditions for hydrothermal recirculation of mineralizing brines explaining the location of Cu (Cu-Fe) sulfides ores in the area. The low permeable Zechstein series (including evaporite, clays and marls) seem to have played an important role as an impermeable cover confining the hydrothermal fluids in the pre-Triassic series. The 4D restoring-decompacting modeling allows

  7. A visualization and data-sharing tool for ecosystem service maps : Lessons learnt, challenges and the way forward

    NARCIS (Netherlands)

    Drakou, E. G.; Crossman, N.D.; Willemen, L.; Burkhard, B.; Palomo, I.; Maes, J.; Peedell, S.

    2015-01-01

    A plurality in methods, models, terminologies is used to assess, quantify, map and communicate ecosystem services (ES). The Thematic Working Groups on Mapping (TWG4) and Modeling ES (TWG5) of the Ecosystem Service Partnership (ESP), recent literature and expert workshops, have highlighted the need

  8. Optical Whole-Genome Restriction Mapping as a Tool for Rapidly Distinguishing and Identifying Bacterial Contaminants in Clinical Samples

    Science.gov (United States)

    2015-08-01

    Assay development, Bacterial detection, Genome identification , Technical evaluation, Whole genome mapping 16. SECURITY CLASSIFICATION OF: 17...detection, Genome identification , Technical evaluation, Whole genome mapping IntrOductIOn One of the primary goals of public health agencies is the early...multiple bacteria could be uniquely identified within mixtures. In the first set of experiments, three unique organisms ( Bacillus subtilis subsp. globigii

  9. Concept Maps as Instructional Tools for Improving Learning of Phase Transitions in Object-Oriented Analysis and Design

    Science.gov (United States)

    Shin, Shin-Shing

    2016-01-01

    Students attending object-oriented analysis and design (OOAD) courses typically encounter difficulties transitioning from requirements analysis to logical design and then to physical design. Concept maps have been widely used in studies of user learning. The study reported here, based on the relationship of concept maps to learning theory and…

  10. Stream sediments analysis for geochemical mapping of Romagna Apennines (Northern Italy): monitoring and management tool of environmental resources at various scales

    OpenAIRE

    Lancianese, Valerio

    2014-01-01

    Geochemical mapping is a valuable tool for the control of territory that can be used not only in the identification of mineral resources and geological, agricultural and forestry studies but also in the monitoring of natural resources by giving solutions to environmental and economic problems. Stream sediments are widely used in the sampling campaigns carried out by the world's governments and research groups for their characteristics of broad representativeness of rocks and soils, for ease o...

  11. Energy Zones Study: A Comprehensive Web-Based Mapping Tool to Identify and Analyze Clean Energy Zones in the Eastern Interconnection

    Energy Technology Data Exchange (ETDEWEB)

    Koritarov, Vladimir [Argonne National Lab. (ANL), Argonne, IL (United States); Kuiper, James [Argonne National Lab. (ANL), Argonne, IL (United States); Hlava, Kevin [Argonne National Lab. (ANL), Argonne, IL (United States); Orr, Andrew [Argonne National Lab. (ANL), Argonne, IL (United States); Rollins, Katherine [Argonne National Lab. (ANL), Argonne, IL (United States); Brunner, Donna [Argonne National Lab. (ANL), Argonne, IL (United States); Green, Jr., Herman [Argonne National Lab. (ANL), Argonne, IL (United States); Makar, Jeffrey [Argonne National Lab. (ANL), Argonne, IL (United States); Ayers, Andrew [Argonne National Lab. (ANL), Argonne, IL (United States); Holm, Michael [Argonne National Lab. (ANL), Argonne, IL (United States); Simunich, Kathy [Argonne National Lab. (ANL), Argonne, IL (United States); Wang, Jianhui [Argonne National Lab. (ANL), Argonne, IL (United States); McLamore, Michael [Argonne National Lab. (ANL), Argonne, IL (United States); Shamsuddin, Shabbir [Argonne National Lab. (ANL), Argonne, IL (United States); Kavicky, James [Argonne National Lab. (ANL), Argonne, IL (United States); Portante, Edgar [Argonne National Lab. (ANL), Argonne, IL (United States); Conzelmann, Guenter [Argonne National Lab. (ANL), Argonne, IL (United States); Molburg, John [Argonne National Lab. (ANL), Argonne, IL (United States); Clark, Corrie [Argonne National Lab. (ANL), Argonne, IL (United States); Snyder, Seth [Argonne National Lab. (ANL), Argonne, IL (United States); Darling, Seth [Argonne National Lab. (ANL), Argonne, IL (United States); Braun, Joseph [Argonne National Lab. (ANL), Argonne, IL (United States); Botterud, Audun [Argonne National Lab. (ANL), Argonne, IL (United States); Gasper, John [Argonne National Lab. (ANL), Argonne, IL (United States); Richmond, Pamela [Argonne National Lab. (ANL), Argonne, IL (United States); Beardsley, Brett [Argonne National Lab. (ANL), Argonne, IL (United States); Schlueter, Scott [Argonne National Lab. (ANL), Argonne, IL (United States); Augustine, Chad [National Renewable Energy Lab. (NREL), Golden, CO (United States); Heimiller, Donna [National Renewable Energy Lab. (NREL), Golden, CO (United States); Hurlbut, David J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Milbrandt, Anelia [National Renewable Energy Lab. (NREL), Golden, CO (United States); Schneider, Thomas R. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Hadley, Stanton W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Gracia, Jose R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mays, Gary T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Belles, Randy [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Omitaomu, Olufemi A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fernandez, Steven [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hadjerioua, Boualem [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stewart, Kevin M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kodysh, Jeffrey [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Smith, Travis [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-11-01

    This report describes the work conducted in support of the Eastern Interconnection States’ Planning Council (EISPC) Energy Zones Study and the development of the Energy Zones Mapping Tool performed by a team of experts from three National Laboratories. The multi-laboratory effort was led by Argonne National Laboratory (Argonne), in collaboration with the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL).

  12. Targeting fungal genes by diced siRNAs: a rapid tool to decipher gene function in Aspergillus nidulans.

    Science.gov (United States)

    Kalleda, Natarajaswamy; Naorem, Aruna; Manchikatla, Rajam V

    2013-01-01

    Gene silencing triggered by chemically synthesized small interfering RNAs (siRNAs) has become a powerful tool for deciphering gene function in many eukaryotes. However, prediction and validation of a single siRNA duplex specific to a target gene is often ineffective. RNA interference (RNAi) with synthetic siRNA suffers from lower silencing efficacy, off-target effects and is cost-intensive, especially for functional genomic studies. With the explosion of fungal genomic information, there is an increasing need to analyze gene function in a rapid manner. Therefore, studies were performed in order to investigate the efficacy of gene silencing induced by RNase III-diced-siRNAs (d-siRNA) in model filamentous fungus, Aspergillus nidulans. Stable expression of heterologous reporter gene in A. nidulans eases the examination of a new RNAi-induction route. Hence, we have optimized Agrobacterium tumefaciens-mediated transformation (AMT) of A. nidulans for stable expression of sGFP gene. This study demonstrates that the reporter GFP gene stably introduced into A. nidulans can be effectively silenced by treatment of GFP-d-siRNAs. We have shown the down-regulation of two endogenous genes, AnrasA and AnrasB of A. nidulans by d-siRNAs. We have also elucidated the function of an uncharacterized Ras homolog, rasB gene, which was found to be involved in hyphal growth and development. Further, silencing potency of d-siRNA was higher as compared to synthetic siRNA duplex, targeting AnrasA. Silencing was shown to be sequence-specific, since expression profiles of other closely related Ras family genes in d-siRNA treated AnrasA and AnrasB silenced lines exhibited no change in gene expression. We have developed and applied a fast, specific and efficient gene silencing approach for elucidating gene function in A. nidulans using d-siRNAs. We have also optimized an efficient AMT in A. nidulans, which is useful for stable integration of transgenes.

  13. Agrobacterium tumefaciens-mediated transformation: An efficient tool for insertional mutagenesis and targeted gene disruption in Harpophora oryzae.

    Science.gov (United States)

    Liu, Ning; Chen, Guo-Qing; Ning, Guo-Ao; Shi, Huan-Bin; Zhang, Chu-Long; Lu, Jian-Ping; Mao, Li-Juan; Feng, Xiao-Xiao; Liu, Xiao-Hong; Su, Zhen-Zhu; Lin, Fu-Cheng

    2016-01-01

    The endophytic filamentous fungus Harpophora oryzae is a beneficial endosymbiont isolated from the wild rice. H. oryzae could not only effectively improve growth rate and biomass yield of rice crops, but also induce systemic resistance against the rice blast fungus, Magnaporthe oryzae. In this study, Agrobacterium tumefaciens-mediated transformation (ATMT) was employed and optimized to modify the H. oryzae genes by either random DNA fragment integration or targeted gene replacement. Our results showed that co-cultivation of H. oryzae conidia with A. tumefaciens in the presence of acetosyringone for 48 h at 22 °C could lead to a relatively highest frequency of transformation, and 200 μM acetosyringone (AS) pre-cultivation of A. tumefaciens is also suggested. ATMT-mediated knockout mutagenesis was accomplished with the gene-deletion cassettes using a yeast homologous recombination method with a yeast-Escherichia-Agrobacterium shuttle vector pKOHo. Using the ATMT-mediated knockout mutagenesis, we successfully deleted three genes of H. oryzae (HoATG5, HoATG7, and HoATG8), and then got the null mutants ΔHoatg5, ΔHoatg7, and ΔHoatg8. These results suggest that ATMT is an efficient tool for gene modification including randomly insertional mutagenesis and gene deletion mutagenesis in H. oryzae. Copyright © 2015 Elsevier GmbH. All rights reserved.

  14. Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon

    DEFF Research Database (Denmark)

    Mailund, T; Schauser, Leif

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...... of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position....

  15. The map: An essential tool in the teaching-learning process of the Marxism-Leninism and History curriculum

    Directory of Open Access Journals (Sweden)

    Montero, Martiza Isabel

    2012-05-01

    Full Text Available This paper evaluates the use of maps in teaching Geography by a sample of professor at “José Marti” College of Education. A systematic use of maps constitutes one of the major problems in the teaching-learning process in the Marxism-Leninism and History Curriculum. Likewise, it has been identify as a shortcoming in graduates and in-service trainees. It would be recommendable to highlight the value and importance of maps in teaching, consequently a number of suggestions are given to lead, reflection and discussion by the teacher’s.

  16. The map: An essential tool in the teaching-learning process of the Marxism-Leninism and History curriculum

    OpenAIRE

    Montero, Martiza Isabel; Martínez, Nilda Herminia; Alfonso, Luis Francisco

    2012-01-01

    This paper evaluates the use of maps in teaching Geography by a sample of professor at “José Marti” College of Education. A systematic use of maps constitutes one of the major problems in the teaching-learning process in the Marxism-Leninism and History Curriculum. Likewise, it has been identify as a shortcoming in graduates and in-service trainees. It would be recommendable to highlight the value and importance of maps in teaching, consequently a number of suggestions are given to lead, refl...

  17. The Shoreline Management Tool, an ArcMap Tool for Analyzing Water Depth, Inundated Area, Volume, and Selected Habitats, with an Example for the Lower Wood River Valley, Oregon

    Science.gov (United States)

    Snyder, D. T.; Haluska, T. L.; Respini-Irwin, D.

    2012-12-01

    The Shoreline Management Tool is a GIS-based program developed to assist water- and land-resource managers in assessing the benefits and impacts of changes in surface-water stage on water depth, inundated area, and water volume. In addition, the tool can be used to identify aquatic or terrestrial habitat areas where conditions may be suitable for specific plants or animals as defined by user-specified criteria, including water depth, land-surface slope, and land-surface aspect or to delineate areas for use in determining a variety of hydrologic budget components such as surface-water storage, precipitation, runoff, or evapotranspiration. The Shoreline Management Tool consists of two parts, a graphical user interface for use with ArcMap GIS software to interact with the user to define scenarios and map results, and a spreadsheet in Microsoft Excel® developed to display tables and graphs of the results. The graphical user interface allows the user to define a scenario consisting of an inundation level (stage), land areas (parcels), and habitats (areas meeting user-specified conditions) based on water depth, slope, and aspect criteria. The tool uses data consisting of land-surface elevation, tables of stage/volume and stage/area, and delineated parcel boundaries to produce maps (data layers) of inundated areas and areas that meet the habitat criteria. The tool can be run in a Single-Time Scenario mode or in a Time-Series Scenario mode which uses an input file of dates and associated stages. The spreadsheet portion of the tool uses a macro to process the results from the graphical user interface to create tables and graphs of inundated water volume, inundated area, dry area, and mean water depth for each land parcel based on the user-specified stage. The macro also creates tables and graphs of the area, perimeter, and number of polygons comprising the user-specified habitat areas within each parcel. The Shoreline Management Tool is designed to be highly transferable

  18. Automated pattern recognition to support geological mapping and exploration target generation: a case study from southern Namibia

    CSIR Research Space (South Africa)

    Eberle, D

    2015-06-01

    Full Text Available 31573236; +264 81 7781480 fax: +49 341 235 1939 Email: d.eberle@rohstoffe.org Keywords: Cluster analysis; discriminant analysis; lineament detection; mapping; southern Namibia, Namaqua Metamorphic Belt. Manuscript submitted for publication... gamma-ray data were integrated with selected Landsat band data using unsupervised fuzzy partitioning clustering. The outcome of this unsupervised clustering is a classified (zonal) map which in terms of spatial resolution is superior to any geological...

  19. Visually directed vs. software-based targeted biopsy compared to transperineal template mapping biopsy in the detection of clinically significant prostate cancer.

    Science.gov (United States)

    Valerio, Massimo; McCartan, Neil; Freeman, Alex; Punwani, Shonit; Emberton, Mark; Ahmed, Hashim U

    2015-10-01

    Targeted biopsy based on cognitive or software magnetic resonance imaging (MRI) to transrectal ultrasound registration seems to increase the detection rate of clinically significant prostate cancer as compared with standard biopsy. However, these strategies have not been directly compared against an accurate test yet. The aim of this study was to obtain pilot data on the diagnostic ability of visually directed targeted biopsy vs. software-based targeted biopsy, considering transperineal template mapping (TPM) biopsy as the reference test. Prospective paired cohort study included 50 consecutive men undergoing TPM with one or more visible targets detected on preoperative multiparametric MRI. Targets were contoured on the Biojet software. Patients initially underwent software-based targeted biopsies, then visually directed targeted biopsies, and finally systematic TPM. The detection rate of clinically significant disease (Gleason score ≥3+4 and/or maximum cancer core length ≥4mm) of one strategy against another was compared by 3×3 contingency tables. Secondary analyses were performed using a less stringent threshold of significance (Gleason score ≥4+3 and/or maximum cancer core length ≥6mm). Median age was 68 (interquartile range: 63-73); median prostate-specific antigen level was 7.9ng/mL (6.4-10.2). A total of 79 targets were detected with a mean of 1.6 targets per patient. Of these, 27 (34%), 28 (35%), and 24 (31%) were scored 3, 4, and 5, respectively. At a patient level, the detection rate was 32 (64%), 34 (68%), and 38 (76%) for visually directed targeted, software-based biopsy, and TPM, respectively. Combining the 2 targeted strategies would have led to detection rate of 39 (78%). At a patient level and at a target level, software-based targeted biopsy found more clinically significant diseases than did visually directed targeted biopsy, although this was not statistically significant (22% vs. 14%, P = 0.48; 51.9% vs. 44.3%, P = 0.24). Secondary

  20. Relative performances of artificial neural network and regression mapping tools in evaluation of spinal loads and muscle forces during static lifting.

    Science.gov (United States)

    Arjmand, N; Ekrami, O; Shirazi-Adl, A; Plamondon, A; Parnianpour, M

    2013-05-31

    Two artificial neural networks (ANNs) are constructed, trained, and tested to map inputs of a complex trunk finite element (FE) model to its outputs for spinal loads and muscle forces. Five input variables (thorax flexion angle, load magnitude, its anterior and lateral positions, load handling technique, i.e., one- or two-handed static lifting) and four model outputs (L4-L5 and L5-S1 disc compression and anterior-posterior shear forces) for spinal loads and 76 model outputs (forces in individual trunk muscles) are considered. Moreover, full quadratic regression equations mapping input-outputs of the model developed here for muscle forces and previously for spine loads are used to compare the relative accuracy of these two mapping tools (ANN and regression equations). Results indicate that the ANNs are more accurate in mapping input-output relationships of the FE model (RMSE= 20.7 N for spinal loads and RMSE= 4.7 N for muscle forces) as compared to regression equations (RMSE= 120.4 N for spinal loads and RMSE=43.2 N for muscle forces). Quadratic regression equations map up to second order variations of outputs with inputs while ANNs capture higher order variations too. Despite satisfactory achievement in estimating overall muscle forces by the ANN, some inadequacies are noted including assigning force to antagonistic muscles with no activity in the optimization algorithm of the FE model or predicting slightly different forces in bilateral pair muscles in symmetric lifting activities. Using these user-friendly tools spine loads and trunk muscle forces during symmetric and asymmetric static lifts can be easily estimated. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Spatiotemporal hazard mapping of a flood event "migration" in a transboundary river basin as an operational tool in flood risk management

    Science.gov (United States)

    Perrou, Theodora; Papastergios, Asterios; Parcharidis, Issaak; Chini, Marco

    2017-10-01

    Flood disaster is one of the heaviest disasters in the world. It is necessary to monitor and evaluate the flood disaster in order to mitigate the consequences. As floods do not recognize borders, transboundary flood risk management is imperative in shared river basins. Disaster management is highly dependent on early information and requires data from the whole river basin. Based on the hypothesis that the flood events over the same area with same magnitude have almost identical evolution, it is crucial to develop a repository database of historical flood events. This tool, in the case of extended transboundary river basins, could constitute an operational warning system for the downstream area. The utility of SAR images for flood mapping, was demonstrated by previous studies but the SAR systems in orbit were not characterized by high operational capacity. Copernicus system will fill this gap in operational service for risk management, especially during emergency phase. The operational capabilities have been significantly improved by newly available satellite constellation, such as the Sentinel-1A AB mission, which is able to provide systematic acquisitions with a very high temporal resolution in a wide swath coverage. The present study deals with the monitoring of a transboundary flood event in Evros basin. The objective of the study is to create the "migration story" of the flooded areas on the basis of the evolution in time for the event occurred from October 2014 till May 2015. Flood hazard maps will be created, using SAR-based semi-automatic algorithms and then through the synthesis of the related maps in a GIS-system, a spatiotemporal thematic map of the event will be produced. The thematic map combined with TanDEM-X DEM, 12m/pixel spatial resolution, will define the non- affected areas which is a very useful information for the emergency planning and emergency response phases. The Sentinels meet the main requirements to be an effective and suitable

  2. A Mapping of Tools for Informing Water Sensitive Urban Design Planning Decisions—Questions, Aspects and Context Sensitivity

    Directory of Open Access Journals (Sweden)

    Sara Maria Lerer

    2015-03-01

    Full Text Available Water Sensitive Urban Design (WSUD poses new challenges for decision makers compared with traditional stormwater management, e.g., because WSUD offers a larger selection of measures and because many measures are multifunctional. These challenges have motivated the development of many decision support tools. This review shows that the tools differ in terms of the types of questions they can assist in answering. We identified three main groups: “How Much”-tools, “Where”-tools and “Which”-tools. The “How Much”-tools can further be grouped into tools quantifying hydraulic impacts, hydrologic impacts, water quality impacts, non-flow-related impacts and economic impacts. Additionally, the tools differ in terms of how many aspects of water they address, from those focused only on bio-physical aspects to those attempting to find the best WSUD based on multiple criteria. Finally, we suggest that variability among the tools can partly be explained by variability in local context including conditions such as type of existing stormwater systems, groundwater conditions and legislative frameworks.

  3. Digital surveying and mapping of forest road network for development of a GIS tool for the effective protection and management of natural ecosystems

    Science.gov (United States)

    Drosos, Vasileios C.; Liampas, Sarantis-Aggelos G.; Doukas, Aristotelis-Kosmas G.

    2014-08-01

    In our time, the Geographic Information Systems (GIS) have become important tools, not only in the geosciences and environmental sciences, as well as virtually for all researches that require monitoring, planning or land management. The purpose of this paper was to develop a planning tool and decision making tool using AutoCAD Map software, ArcGIS and Google Earth with emphasis on the investigation of the suitability of forest roads' mapping and the range of its implementation in Greece in prefecture level. Integrating spatial information into a database makes data available throughout the organization; improving quality, productivity, and data management. Also working in such an environment, you can: Access and edit information, integrate and analyze data and communicate effectively. To select desirable information such as forest road network in a very early stage in the planning of silviculture operations, for example before the planning of the harvest is carried out. The software programs that were used were AutoCAD Map for the export in shape files for the GPS data, and ArcGIS in shape files (ArcGlobe), while Google Earth with KML files (Keyhole Markup Language) in order to better visualize and evaluate existing conditions, design in a real-world context and exchange information with government agencies, utilities, and contractors in both CAD and GIS data formats. The automation of the updating procedure and transfer of any files between agencies-departments is one of the main tasks of the integrated GIS-tool among the others should be addressed.

  4. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  5. Targeted Metagenomics as a Tool to Tap Into Marine Natural Product Diversity for the Discovery and Production of Drug Candidates

    Directory of Open Access Journals (Sweden)

    Marla eTrindade

    2015-08-01

    Full Text Available Microbial natural products exhibit immense structural diversity and complexity and have captured the attention of researchers for several decades. They have been explored for a wide spectrum of applications, most noteworthy being their prominent role in medicine, and their versatility expands to application as drugs for many diseases. Accessing unexplored environments harboring unique microorganisms is expected to yield novel bioactive metabolites with distinguishing functionalities, which can be supplied to the starved pharmaceutical market. For this purpose the oceans have turned out to be an attractive and productive field. Owing to the enormous biodiversity of marine microorganisms, as well as the growing evidence that many metabolites previously isolated from marine invertebrates and algae are actually produced by their associated bacteria, the interest in marine microorganisms has intensified. Since the majority of the microorganisms are uncultured, metagenomic tools are required to exploit the untapped biochemistry. However, after years of employing metagenomics for marine drug discovery, new drugs are vastly under-represented. While a plethora of natural product biosynthetic genes and clusters are reported, only a minor number of potential therapeutic compounds have resulted through functional metagenomic screening. This review explores specific obstacles that have led to the low success rate. In addition to the typical problems encountered with traditional functional metagenomic-based screens for novel biocatalysts, there are enormous limitations which are particular to drug-like metabolites. We also present how targeted and function-guided strategies, employing modern and multi-disciplinary approaches have yielded some of the most exciting discoveries attributed to uncultured marine bacteria. These discoveries set the stage for progressing the production of drug candidates from uncultured bacteria for pre-clinical and clinical

  6. The Shoreline Management Tool - an ArcMap tool for analyzing water depth, inundated area, volume, and selected habitats, with an example for the lower Wood River Valley, Oregon

    Science.gov (United States)

    Snyder, Daniel T.; Haluska, Tana L.; Respini-Irwin, Darius

    2013-01-01

    The Shoreline Management Tool is a geographic information system (GIS) based program developed to assist water- and land-resource managers in assessing the benefits and effects of changes in surface-water stage on water depth, inundated area, and water volume. Additionally, the Shoreline Management Tool can be used to identify aquatic or terrestrial habitat areas where conditions may be suitable for specific plants or animals as defined by user-specified criteria including water depth, land-surface slope, and land-surface aspect. The tool can also be used to delineate areas for use in determining a variety of hydrologic budget components such as surface-water storage, precipitation, runoff, or evapotranspiration. The Shoreline Management Tool consists of two parts, a graphical user interface for use with Esri™ ArcMap™ GIS software to interact with the user to define scenarios and map results, and a spreadsheet in Microsoft® Excel® developed to display tables and graphs of the results. The graphical user interface allows the user to define a scenario consisting of an inundation level (stage), land areas (parcels), and habitats (areas meeting user-specified conditions) based on water depth, slope, and aspect criteria. The tool uses data consisting of land-surface elevation, tables of stage/volume and stage/area, and delineated parcel boundaries to produce maps (data layers) of inundated areas and areas that meet the habitat criteria. The tool can be run in a Single-Time Scenario mode or in a Time-Series Scenario mode, which uses an input file of dates and associated stages. The spreadsheet part of the tool uses a macro to process the results from the graphical user interface to create tables and graphs of inundated water volume, inundated area, dry area, and mean water depth for each land parcel based on the user-specified stage. The macro also creates tables and graphs of the area, perimeter, and number of polygons comprising the user-specified habitat areas

  7. Multitemperature mapping of dust structures throughout the Galactic Plane using the PPMAP tool with Herschel Hi-GAL data

    Science.gov (United States)

    Marsh, K. A.; Whitworth, A. P.; Lomax, O.; Ragan, S. E.; Becciani, U.; Cambrésy, L.; Di Giorgio, A.; Eden, D.; Elia, D.; Kacsuk, P.; Molinari, S.; Palmeirim, P.; Pezzuto, S.; Schneider, N.; Sciacca, E.; Vitello, F.

    2017-11-01

    We describe new Hi-GAL based maps of the entire Galactic Plane, obtained using continuum data in the wavelength range 70-500 μm. These maps are derived with the PPMAP procedure, and therefore represent a significant improvement over those obtained with standard analysis techniques. Specifically they have greatly improved resolution (12 arcsec) and, in addition to more accurate integrated column densities and mean dust temperatures, they give temperature-differential column densities, I.e., separate column density maps in twelve distinct dust temperature intervals, along with the corresponding uncertainty maps. The complete set of maps is available online. We briefly describe PPMAP and present some illustrative examples of the results. These include (a) multi-temperature maps of the Galactic H II region W5-E, (b) the temperature decomposition of molecular cloud column-density probability distribution functions, and (c) the global variation of mean dust temperature as a function of Galactocentric distance. Amongst our findings are: (I) a strong localised temperature gradient in W5-E in a direction orthogonal to that towards the ionising star, suggesting an alternative heating source and providing possible guidance for models of the formation of the bubble complex, and (II) the overall radial profile of dust temperature in the Galaxy shows a monotonic decrease, broadly consistent both with models of the interstellar radiation field and with previous estimates at lower resolution. However, we also find a central temperature plateau within ˜6 kpc of the Galactic centre, outside of which is a pronounced steepening of the radial profile. This behaviour may reflect the greater proportion of molecular (as opposed to atomic) gas in the central region of the Galaxy.

  8. Using an audit tool (MAPS Global to assess the characteristics of the physical environment related to walking for transport in youth: reliability of Belgian data

    Directory of Open Access Journals (Sweden)

    Griet Vanwolleghem

    2016-11-01

    Full Text Available Abstract Background The aim was to examine inter-rater and alternate-form reliability of the Microscale Audit of Pedestrian Streetscapes (MAPS Global tool to assess the physical environment along likely walking routes in Belgium. Methods For 65 children participating in the BEPAS-children study, routes between their individual homes and the nearest pre-defined destination were defined. Using MAPS Global, physical environmental characteristics of the routes were audited by 4 trained auditors (2 on-site, 2 online using Google Street View. Inter-rater reliability was studied for on-site and online ratings separately. Alternate-form reliability was examined by comparing on-site with online ratings. Results Inter-rater reliability for on-site ratings was acceptable for 68% of items (kappa range 0.03–1.00 and for online ratings for 60% of items (kappa range −0.03 to 1.00. Acceptable alternate-form reliability was reported for 60% of items (kappa range −0.01 to 1.00/r range 0.31–1.00. Conclusions MAPS Global can be used to assess the physical environment of potential walking routes. For areas where Google Street View imagery is widely covered and often updated, MAPS Global can be completed online.

  9. The microtubule-associated protein 1A (MAP1A) is an early molecular target of soluble Aβ-peptide

    DEFF Research Database (Denmark)

    Clemmensen, C; Aznar, S; Knudsen, G M

    2012-01-01

    ) protein, proposing that microtubule perturbations might be central for the Aβ-induced neuronal dysfunctions as PSD-95 plays a key role in synaptic plasticity. In conclusion, this study suggests that disruption of MAP1A could be a very early manifestation of Aβ-mediated synaptic dysfunction...

  10. Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes

    DEFF Research Database (Denmark)

    Mahajan, Anubha; Wessel, Jennifer; Willems, Sara M

    2018-01-01

    are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence...

  11. Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan

    NARCIS (Netherlands)

    Maria, M.; Ajmal, M.; Azam, M.; Waheed, N.K.; Siddiqui, S.N.; Mustafa, B.; Ayub, H.; Ali, L.; Ahmad, S.; Micheal, S.; Hussain, A.; Shah, S.T.; Ali, S.H.; Ahmed, W.; Khan, Y.M.; Hollander, A.I. den; Haer-Wigman, L.; Collin, R.W.J.; Khan, M.I.; Qamar, R.; Cremers, F.P.M.

    2015-01-01

    BACKGROUND: Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective

  12. Mediated learning experience and concept maps: a pedagogical tool for achieving meaningful learning in medical physiology students.

    Science.gov (United States)

    González, Hilda Leonor; Palencia, Alberto Pardo; Umaña, Luis Alfredo; Galindo, Leonor; Villafrade M, Luz Adriana

    2008-12-01

    Even though comprehension of human physiology is crucial in the clinical setting, students frequently learn part of this subject using rote memory and then are unable to transfer knowledge to other contexts or to solve clinical problems. This study evaluated the impact of articulating the concept map strategy with the mediated learning experience on meaningful learning during the cardiovascular module of a medical physiology course at Universidad Autónoma de Bucaramanga. This research was based on the ideas of David Ausubel (meaningful learning), Joseph Novak (concept maps), and Reuven Feuerstein (mediated learning experience). Students were randomly allocated to either an intervention group (mediated learning experience articulated with concept mapping) or a control group (traditional methodology). The intervention group constructed concept maps related to cardiovascular physiology and used them to solve problems related to this subject. The control group attended traditional discussion sessions and problem-solving sessions. All students were evaluated with two types of exams: problem-solving and multiple-choice exams. The intervention group performed significantly better on the problem-solving exams, but the difference was not significant in the multiple-choice exam. It was concluded that intervention promoted meaningful learning that allowed the students to transfer this knowledge to solve problems. The implemented strategy had a greater impact on the students who came into the study with the lowest cognitive competence, possibly because they were empowered by the intervention.

  13. Mapping Prehistoric, Historic, and Channel Sediment Distribution, South Fork Noyo River: A Tool For Understanding Sources, Storage, and Transport

    Science.gov (United States)

    Rich D. Koehler; Keith I. Kelson; Graham Matthews; K.H. Kang; Andrew D. Barron

    2007-01-01

    The South Fork Noyo River (SFNR) watershed in coastal northern California contains large volumes of historic sediment that were delivered to channels in response to past logging operations. This sediment presently is stored beneath historic terraces and in present-day channels. We conducted geomorphic mapping on the SFNR valley floor to assess the volume and location...

  14. A Tool that Can be Effective in the Self-Regulated Learning of Pre-Service Teachers: The Mind Map

    Science.gov (United States)

    Tanriseven, Isil

    2014-01-01

    The aim of this study is to analyse the effect of task planning with mind maps on the self-regulation strategies and motivational beliefs of pre-service teachers. A quasi-experimental design, with a pre-test and post-test control group, was applied in the research. The research group comprised of 60 pre-service teachers taking "Teaching…

  15. Utilization of geoinformation tools for the development of forest fire hazard mapping system: example of Pekan fire, Malaysia

    Science.gov (United States)

    Mahmud, Ahmad Rodzi; Setiawan, Iwan; Mansor, Shattri; Shariff, Abdul Rashid Mohamed; Pradhan, Biswajeet; Nuruddin, Ahmed

    2009-12-01

    A study in modeling fire hazard assessment will be essential in establishing an effective forest fire management system especially in controlling and preventing peat fire. In this paper, we have used geographic information system (GIS), in combination with other geoinformation technologies such as remote sensing and computer modeling, for all aspects of wild land fire management. Identifying areas that have a high probability of burning is an important component of fire management planning. The development of spatially explicit GIS models has greatly facilitated this process by allowing managers to map and analyze variables contributing to fire occurrence across large, unique geographic units. Using the model and its associated software engine, the fire hazard map was produced. Extensive avenue programming scripts were written to provide additional capabilities in the development of these interfaces to meet the full complement of operational software considering various users requirements. The system developed not only possesses user friendly step by step operations to deliver the fire vulnerability mapping but also allows authorized users to edit, add or modify parameters whenever necessary. Results from the model can support fire hazard mapping in the forest and enhance alert system function by simulating and visualizing forest fire and helps for contingency planning.

  16. Shifting from Fear to Self-Confidence: Body Mapping as a Transformative Tool in Music Teacher Education

    Science.gov (United States)

    Griffin, Shelley M.

    2015-01-01

    Fear and lack of self-confidence toward music teaching are frequently experienced by many Bachelor of Education teacher candidates when they imagine themselves as future elementary general music teachers. Integrating visual art body mapping in elementary music methods fosters a unique opportunity to identify and interrogate musical experience.…

  17. Value stream mapping as a tool for systematic employee based improvement of the psychosocial work environment in hospitals

    DEFF Research Database (Denmark)

    Hasle, Peter; Starheim, Liv; Jensen, Per Langaa

    2016-01-01

    Problems in communication and coordination in hospitals often hamper operations and constitute important stress factor for the staff. A specific methodology (P-lean) based on value stream mapping (VSM) has been developed and tested in practice. Key processes with a potential for psychosocial strain...

  18. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  19. Sensory cortical re-mapping following upper-limb amputation and subsequent targeted reinnervation: A case report

    OpenAIRE

    Jun Yao; Albert Chen; Todd Kuiken; Carolina Carmona; Julius Dewald

    2015-01-01

    This case study demonstrates the change of sensory cortical representations of the residual parts of the arm in an individual who underwent a trans-humeral amputation and subsequent targeted reinnervation (TR). As a relatively new surgical technique, TR restores a direct neural connection from amputated sensorimotor nerves to specific target muscles. This method has been successfully applied to upper-limb and lower-limb amputees, and has shown effectiveness in regaining control signals via th...

  20. Epitope mapping of inhibitory antibodies targeting the C2 domain of coagulation factor VIII by hydrogen-deuterium exchange mass spectrometry

    Science.gov (United States)

    Sevy, Alexander M.; Healey, John F.; Deng, Wei; Spiegel, P. Clint; Meeks, Shannon L.; Li, Renhao

    2014-01-01

    Summary Background The development of anti-factor VIII (fVIII) antibodies (inhibitors) is a significant complication in the management of patients with hemophilia A, leading to significant increases in morbidity and treatment cost. Using a panel of anti-fVIII monoclonal antibodies (MAbs) to different epitopes on fVIII, we recently have shown that epitope specificity, inhibitor kinetics, and time to maximum inhibition are more important than inhibitor titer in predicting response to fVIII and the combination of fVIII and recombinant factor VIIa. In particular, a subset of high-titer inhibitors responded to high dose fVIII, which would not be predicted based on their inhibitor titer alone. Thus the ability to quickly map the epitope spectrum of patient plasma using a clinically feasible assay may fundamentally change how clinicians approach the treatment of high-titer inhibitor patients. Objectives To map the epitopes of anti-fVIII MAbs, of which 3 are classical inhibitors and one non-classical, using hydrogen-deuterium exchange coupled with liquid chromatography-mass spectrometry (HDX-MS). Methods Binding epitopes of 4 MAbs targeting fVIII C2 domain were mapped using HDX-MS. Results The epitopes determined by HDX-MS are consistent with those obtained earlier through structural characterization and antibody competition assays. In addition classical and non-classical inhibitor epitopes could be distinguished using a limited subset of C2-derived peptic fragments. Conclusion Our results demonstrate the effectiveness and robustness of the HDX-MS method for epitope mapping and suggest a potential role of rapid mapping of fVIII inhibitor epitopes in facilitating individualized treatment of inhibitor patients. PMID:24152306

  1. Epitope mapping of inhibitory antibodies targeting the C2 domain of coagulation factor VIII by hydrogen-deuterium exchange mass spectrometry.

    Science.gov (United States)

    Sevy, A M; Healey, J F; Deng, W; Spiegel, P C; Meeks, S L; Li, R

    2013-12-01

    The development of anti-factor VIII antibodies (inhibitors) is a significant complication in the management of patients with hemophilia A, leading to significant increases in morbidity and treatment cost. Using a panel of mAbs against different epitopes on FVIII, we have recently shown that epitope specificity, inhibitor kinetics and time to maximum inhibition are more important than inhibitor titer in predicting responses to FVIII and the combination of FVIII and recombinant FVIIa. In particular, a subset of high-titer inhibitors responded to high-dose FVIII, which would not be predicted on the basis of their inhibitor titer alone. Thus, the ability to quickly map the epitope spectrum of patient plasma with a clinically feasible assay may fundamentally change how clinicians approach the treatment of high-titer inhibitor patients. To map the epitopes of anti-FVIII mAbs, three of which are classic inhibitors and one of which is a non-classic inhibitor, by the use of hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS). The binding epitopes of four mAbs targeting the FVIII C2 domain were mapped with HDX-MS. The epitopes determined with HDX-MS are consistent with those obtained earlier through structural characterization and antibody competition assays. In addition, classic and non-classic inhibitor epitopes could be distinguished by the use of a limited subset of C2 domain-derived peptic fragments. Our results demonstrate the effectiveness and robustness of the HDX-MS method for epitope mapping, and suggest a potential role of rapid mapping of FVIII inhibitor epitopes in facilitating individualized treatment of inhibitor patients. © 2013 International Society on Thrombosis and Haemostasis.

  2. X-Ray Map Analyser: A new ArcGIS® based tool for the quantitative statistical data handling of X-ray maps (Geo- and material-science applications)

    Science.gov (United States)

    Ortolano, Gaetano; Zappalà, Luigi; Mazzoleni, Paolo

    2014-11-01

    A new semi-automated image processing procedure based on multivariate statistical analysis of X-ray maps of petrological and material science interest has been developed to generate high contrast pseudo-coloured images highlighting the element distribution between and within detected mineral phases. This new tool package, developed in Python and integrated with ArcGis®, generates in only a few minutes several graphical outputs useful for classifying chemically homogeneous zones as well as extracting quantitative information through the statistical data handling of X-ray maps. The code, largely based on the use of functions implemented in ArcGis® 9.3 equipped with Spatial Analyst and Data Management licences, has been suitably integrated with original cyclic functions that hugely reduce the time taken to complete lengthy procedures. In particular these tools, after the acquisition of any kind of multispectral images allow fast and powerful data processing for efficient illustration and documentation of key compositional and microtextural relationships in rocks and materials.

  3. Developing a Data Discovery Tool for Interdisciplinary Science: Leveraging a Web-based Mapping Application and Geosemantic Searching

    Science.gov (United States)

    Albeke, S. E.; Perkins, D. G.; Ewers, S. L.; Ewers, B. E.; Holbrook, W. S.; Miller, S. N.

    2015-12-01

    The sharing of data and results is paramount for advancing scientific research. The Wyoming Center for Environmental Hydrology and Geophysics (WyCEHG) is a multidisciplinary group that is driving scientific breakthroughs to help manage water resources in the Western United States. WyCEHG is mandated by the National Science Foundation (NSF) to share their data. However, the infrastructure from which to share such diverse, complex and massive amounts of data did not exist within the University of Wyoming. We developed an innovative framework to meet the data organization, sharing, and discovery requirements of WyCEHG by integrating both open and closed source software, embedded metadata tags, semantic web technologies, and a web-mapping application. The infrastructure uses a Relational Database Management System as the foundation, providing a versatile platform to store, organize, and query myriad datasets, taking advantage of both structured and unstructured formats. Detailed metadata are fundamental to the utility of datasets. We tag data with Uniform Resource Identifiers (URI's) to specify concepts with formal descriptions (i.e. semantic ontologies), thus allowing users the ability to search metadata based on the intended context rather than conventional keyword searches. Additionally, WyCEHG data are geographically referenced. Using the ArcGIS API for Javascript, we developed a web mapping application leveraging database-linked spatial data services, providing a means to visualize and spatially query available data in an intuitive map environment. Using server-side scripting (PHP), the mapping application, in conjunction with semantic search modules, dynamically communicates with the database and file system, providing access to available datasets. Our approach provides a flexible, comprehensive infrastructure from which to store and serve WyCEHG's highly diverse research-based data. This framework has not only allowed WyCEHG to meet its data stewardship

  4. Developing a tool for mapping adult mental health care provision in Europe: the REMAST research protocol and its contribution to better integrated care

    Directory of Open Access Journals (Sweden)

    Luis Salvador-Carulla

    2015-12-01

    Full Text Available Introduction: Mental health care is a critical area to better understand integrated care and to pilot the different components of the integrated care model. However, there is an urgent need for better tools to compare and understand the context of integrated mental health care in Europe.Method: The REMAST tool (REFINEMENT MApping Services Tool combines a series of standardised health service research instruments and geographical information systems (GIS to develop local atlases of mental health care from the perspective of horizontal and vertical integrated care. It contains five main sections: (a Population Data; (b the Verona Socio-economic Status (SES Index; (c the Mental Health System Checklist; (d the Mental Health Services Inventory using the DESDE-LTC instrument; and (e Geographical Data.Expected results: The REMAST tool facilitates context analysis in mental health by providing the comparative rates of mental health service provision according to the availability of main types of care; care placement capacity; workforce capacity; and geographical accessibility to services in the local areas in eight study areas in Austria, England, Finland, France, Italy, Norway, Romania and Spain.Discussion: The outcomes of this project will facilitate cooperative work and knowledge transfer on mental health care to the different agencies involved in mental health planning and provision. This project would improve the information to users and society on the available resources for mental health care and system thinking at the local level by the different stakeholders. The techniques used in this project and the knowledge generated could eventually be transferred to the mapping of other fields of integrated care.

  5. Developing a tool for mapping adult mental health care provision in Europe: the REMAST research protocol and its contribution to better integrated care

    Directory of Open Access Journals (Sweden)

    Luis Salvador-Carulla

    2015-12-01

    Full Text Available Introduction: Mental health care is a critical area to better understand integrated care and to pilot the different components of the integrated care model. However, there is an urgent need for better tools to compare and understand the context of integrated mental health care in Europe. Method: The REMAST tool (REFINEMENT MApping Services Tool combines a series of standardised health service research instruments and geographical information systems (GIS to develop local atlases of mental health care from the perspective of horizontal and vertical integrated care. It contains five main sections: (a Population Data; (b the Verona Socio-economic Status (SES Index; (c the Mental Health System Checklist; (d the Mental Health Services Inventory using the DESDE-LTC instrument; and (e Geographical Data. Expected results: The REMAST tool facilitates context analysis in mental health by providing the comparative rates of mental health service provision according to the availability of main types of care; care placement capacity; workforce capacity; and geographical accessibility to services in the local areas in eight study areas in Austria, England, Finland, France, Italy, Norway, Romania and Spain. Discussion: The outcomes of this project will facilitate cooperative work and knowledge transfer on mental health care to the different agencies involved in mental health planning and provision. This project would improve the information to users and society on the available resources for mental health care and system thinking at the local level by the different stakeholders. The techniques used in this project and the knowledge generated could eventually be transferred to the mapping of other fields of integrated care.

  6. Developing a tool for mapping adult mental health care provision in Europe: the REMAST research protocol and its contribution to better integrated care.

    Science.gov (United States)

    Salvador-Carulla, Luis; Amaddeo, Francesco; Gutiérrez-Colosía, Mencia R; Salazzari, Damiano; Gonzalez-Caballero, Juan Luis; Montagni, Ilaria; Tedeschi, Federico; Cetrano, Gaia; Chevreul, Karine; Kalseth, Jorid; Hagmair, Gisela; Straßmayr, Christa; Park, A-La; Sfetcu, Raluca; Wahlbeck, Kristian; Garcia-Alonso, Carlos

    2015-01-01

    Mental health care is a critical area to better understand integrated care and to pilot the different components of the integrated care model. However, there is an urgent need for better tools to compare and understand the context of integrated mental health care in Europe. The REMAST tool (REFINEMENT MApping Services Tool) combines a series of standardised health service research instruments and geographical information systems (GIS) to develop local atlases of mental health care from the perspective of horizontal and vertical integrated care. It contains five main sections: (a) Population Data; (b) the Verona Socio-economic Status (SES) Index; (c) the Mental Health System Checklist; (d) the Mental Health Services Inventory using the DESDE-LTC instrument; and (e) Geographical Data. The REMAST tool facilitates context analysis in mental health by providing the comparative rates of mental health service provision according to the availability of main types of care; care placement capacity; workforce capacity; and geographical accessibility to services in the local areas in eight study areas in Austria, England, Finland, France, Italy, Norway, Romania and Spain. The outcomes of this project will facilitate cooperative work and knowledge transfer on mental health care to the different agencies involved in mental health planning and provision. This project would improve the information to users and society on the available resources for mental health care and system thinking at the local level by the different stakeholders. The techniques used in this project and the knowledge generated could eventually be transferred to the mapping of other fields of integrated care.

  7. Development of an expert analysis tool based on an interactive subsidence hazard map for urban land use in the city of Celaya, Mexico

    Science.gov (United States)

    Alloy, A.; Gonzalez Dominguez, F.; Nila Fonseca, A. L.; Ruangsirikulchai, A.; Gentle, J. N., Jr.; Cabral, E.; Pierce, S. A.

    2016-12-01

    Land Subsidence as a result of groundwater extraction in central Mexico's larger urban centers initiated in the 80's as a result of population and economic growth. The city of Celaya has undergone subsidence for a few decades and a consequence is the development of an active normal fault system that affects its urban infrastructure and residential areas. To facilitate its analysis and a land use decision-making process we created an online interactive map enabling users to easily obtain information associated with land subsidence. Geological and socioeconomic data of the city was collected, including fault location, population data, and other important infrastructure and structural data has been obtained from fieldwork as part of a study abroad interchange undergraduate course. The subsidence and associated faulting hazard map was created using an InSAR derived subsidence velocity map and population data from INEGI to identify hazard zones using a subsidence gradient spatial analysis approach based on a subsidence gradient and population risk matrix. This interactive map provides a simple perspective of different vulnerable urban elements. As an accessible visualization tool, it will enhance communication between scientific and socio-economic disciplines. Our project also lays the groundwork for a future expert analysis system with an open source and easily accessible Python coded, SQLite database driven website which archives fault and subsidence data along with visual damage documentation to civil structures. This database takes field notes and provides an entry form for uniform datasets, which are used to generate a JSON. Such a database is useful because it allows geoscientists to have a centralized repository and access to their observations over time. Because of the widespread presence of the subsidence phenomena throughout cities in central Mexico, the spatial analysis has been automated using the open source software R. Raster, rgeos, shapefiles, and rgdal

  8. Saturated genic SNP mapping identified functional candidates and selection tools for the Pinus monticola Cr2 locus controlling resistance to white pine blister rust.

    Science.gov (United States)

    Liu, Jun-Jun; Sniezko, Richard A; Zamany, Arezoo; Williams, Holly; Wang, Ning; Kegley, Angelia; Savin, Douglas P; Chen, Hao; Sturrock, Rona N

    2017-09-01

    Molecular breeding incorporates efficient tools to increase rust resistance in five-needle pines. Susceptibility of native five-needle pines to white pine blister rust (WPBR), caused by the non-native invasive fungus Cronartium ribicola (J.C. Fisch.), has significantly reduced wild populations of these conifers in North America. Major resistance (R) genes against specific avirulent pathotypes have been found in several five-needle pine species. In this study, we screened genic SNP markers by comparative transcriptome and genetic association analyses and constructed saturated linkage maps for the western white pine (Pinus monticola) R locus (Cr2). Phenotypic segregation was measured by a hypersensitive reaction (HR)-like response on the needles and disease symptoms of cankered stems post inoculation by the C. ribicola avcr2 race. SNP genotypes were determined by HRM- and TaqMan-based SNP genotyping. Saturated maps of the Cr2-linkage group (LG) were constructed in three seed families using a total of 34 SNP markers within 21 unique genes. Cr2 was consistently flanked by contig_2142 (encoding a ruvb-like protein) and contig_3772 (encoding a delta-fatty acid desaturase) across the three seed families. Cr2 was anchored to the Pinus consensus LG-1, which differs from LGs where other R loci of Pinus species were mapped. GO annotation identified a set of NBS-LRR and other resistance-related genes as R candidates in the Cr2 region. Association of one nonsynonymous SNP locus of an NBS-LRR gene with Cr2-mediated phenotypes provides a valuable tool for marker-assisted selection (MAS), which will shorten the breeding cycle of resistance screening and aid in the restoration of WPBR-disturbed forest ecosystems. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  9. Mapas conceituais: estratégia de ensino/aprendizagem e ferramenta avaliativa Conceptual maps: teaching and learning strategies and an evaluative tool

    Directory of Open Access Journals (Sweden)

    Nadia Aparecida de Souza

    2010-12-01

    Full Text Available O presente ensaio tem por objetivo apresentar uma reflexão sobre as potencia lidades do mapa conceitual como estratégia de ensino/aprendizagem e ferramenta ava liativa. Revisitar o referencial teórico relativo à temática possibilitou contemplar a utili dade do mapa conceitual sob diferentes perspectivas: daquele que ensina e daquele que aprende. Valer-se dos mapas conceituais como estratégias de ensino/aprendizagem, também e concomitantemente como ferramenta avaliativa, é criar possibilidades para a organiza ção do conhecimento pela promoção de experiências educativas que provoquem não somen te reflexão, busca de compreensão e processamento profundo da informação, mas tam bém o desenvolvimento da autorregulação, da metacognição e do aprender a aprenderThis essay has the purpose of reflecting upon the potential benefits of con ceptual map as teaching and learning strategies and an evaluative tool. To revisit the the oretical framework of this theme made it possible to analyze the utility of conceptual map under different perspectives: the teachers´ and the students´. It became clear that the use of conceptual map as teaching and learning strategies, as well as an evaluative tool, leads to knowledge organization by means of promotion of learning experiences which not only generate reflection, comprehension and deep processing of information, but also contributes to the development of metacognition, self-regulation and learning to learn processes

  10. Digital bedrock mapping at the Geological Survey of Norway: BGS SIGMA tool and in-house database structure

    Science.gov (United States)

    Gasser, Deta; Viola, Giulio; Bingen, Bernard

    2016-04-01

    Since 2010, the Geological Survey of Norway has been implementing and continuously developing a digital workflow for geological bedrock mapping in Norway, from fieldwork to final product. Our workflow is based on the ESRI ArcGIS platform, and we use rugged Windows computers in the field. Three different hardware solutions have been tested over the past 5 years (2010-2015). (1) Panasonic Toughbook CE-19 (2.3 kg), (2) Panasonic Toughbook CF H2 Field (1.6 kg) and (3) Motion MC F5t tablet (1.5 kg). For collection of point observations in the field we mainly use the SIGMA Mobile application in ESRI ArcGIS developed by the British Geological Survey, which allows the mappers to store georeferenced comments, structural measurements, sample information, photographs, sketches, log information etc. in a Microsoft Access database. The application is freely downloadable from the BGS websites. For line- and polygon work we use our in-house database, which is currently under revision. Our line database consists of three feature classes: (1) bedrock boundaries, (2) bedrock lineaments, and (3) bedrock lines, with each feature class having up to 24 different attribute fields. Our polygon database consists of one feature class with 38 attribute fields enabling to store various information concerning lithology, stratigraphic order, age, metamorphic grade and tectonic subdivision. The polygon and line databases are coupled via topology in ESRI ArcGIS, which allows us to edit them simultaneously. This approach has been applied in two large-scale 1:50 000 bedrock mapping projects, one in the Kongsberg domain of the Sveconorwegian orogen, and the other in the greater Trondheim area (Orkanger) in the Caledonian belt. The mapping projects combined collection of high-resolution geophysical data, digital acquisition of field data, and collection of geochronological, geochemical and petrological data. During the Kongsberg project, some 25000 field observation points were collected by eight

  11. Value stream mapping as a tool for systematic employee based improvement of the psychosocial work environment in hospitals

    DEFF Research Database (Denmark)

    Hasle, Peter; Starheim, Liv; Jensen, Per Langaa

    2016-01-01

    Problems in communication and coordination in hospitals often hamper operations and constitute important stress factor for the staff. A specific methodology (P-lean) based on value stream mapping (VSM) has been developed and tested in practice. Key processes with a potential for psychosocial strain...... are selected and analysed in employee groups. VSM is followed up by collection of data and development of solutions. Results from the practical test show that VSM and process data provide new insights to the employees which help to improve the psychosocial work environment. However, working across departmental...

  12. Training Institutions as places of reproduction of official and scientific knowledge on ecological transition. An analysis with mapping controversies tools

    International Nuclear Information System (INIS)

    Bargues, Emilie; Landivar, Diego

    2016-01-01

    Through an exploratory approach mobilizing a 'mapping controversies methodology', this article analyses the role of training institutions in producing, distributing and criticizing knowledge related to ecological transition. The current work deals with the case of biomass production and activity, a central sector in French ecological transition. The analysis of semantic and unstructured data crawled from 3900 web sites highlights the major issues of controversy, the actors of the controversy, the points of agreement/disagreement among actors, and the particular position of training organizations in the knowledge structure. We find that these organizations are strongly correlated to official and scientific knowledge and less related to critical and marginal knowledge

  13. A comparison of Agrobacterium-mediated transformation and protoplast-mediated transformation with CRISPR-Cas9 and bipartite gene targeting substrates, as effective gene targeting tools for Aspergillus carbonarius.

    Science.gov (United States)

    Weyda, István; Yang, Lei; Vang, Jesper; Ahring, Birgitte K; Lübeck, Mette; Lübeck, Peter S

    2017-04-01

    In recent years, versatile genetic tools have been developed and applied to a number of filamentous fungi of industrial importance. However, the existing techniques have limitations when it comes to achieve the desired genetic modifications, especially for efficient gene targeting. In this study, we used Aspergillus carbonarius as a host strain due to its potential as a cell factory, and compared three gene targeting techniques by disrupting the ayg1 gene involved in the biosynthesis of conidial pigment in A. carbonarius. The absence of the ayg1 gene leads to phenotypic change in conidia color, which facilitated the analysis on the gene targeting frequency. The examined transformation techniques included Agrobacterium-mediated transformation (AMT) and protoplast-mediated transformation (PMT). Furthermore, the PMT for the disruption of the ayg1 gene was carried out with bipartite gene targeting fragments and the recently adapted CRISPR-Cas9 system. All three techniques were successful in generating Δayg1 mutants, but showed different efficiencies. The most efficient method for gene targeting was AMT, but further it was shown to be dependent on the choice of Agrobacterium strain. However, there are different advantages and disadvantages of all three gene targeting methods which are discussed, in order to facilitate future approaches for fungal strain improvements. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Google Maps API za izradu interaktivne karte sa ciljem utvrđivanja lokacije : Google Maps API as a development tool for implementing a dynamic map for the purpose of locating points of interest

    Directory of Open Access Journals (Sweden)

    Amir Hajdar

    2014-12-01

    Full Text Available Google Maps API je programibilno korisničko okruženje razvijeno od strane Google-a kako bi se omogućio razvoj softverskih rješenja koji zahtijevaju funkcionalnosti manipulacije kartama. Koristeći internet tehnologije, današnje karte se razvijaju kako bi bile interaktivne (dinamičke, a ne samo statičke kako je to bilo do sada. U radu je opisana ideja zasnovana na Google Maps API, te su postavljeni okviri o tome šta je sve potrebno da se karta implementira. Kao i sve ostale tehnologije, i ova tehnologija ima svoje nedostatke koji su opisani u radu. Implementiranjem testnih rezultata zaključeno je da proizvođači nisu standardizovali uređaje za zapis položajnih podataka u snimak po EXIF standardu. Dakle, važno je znati o kojem se proizvođaču i uređaju radi, te sa testnim snimkom tog uređaja testirati softver, a prije svega PHP instalaciju, kako bi ustanovili da li je moguće preuzeti podatke o lokaciji iz snimka. Također je kreirana internet stranica na kojoj korisnik može testirati snimke koji imaju položajne podatke. : Google Maps API is an application programming interface developed by Google in order to aid software developers to easier develop mapping software. Using internet technologies, todays maps are created to be dynamic, and not static as they used to be. This paper defines the concept of using Google Maps API, and explains the steps needed to start developing a mapping software. Like any other technologies, this technology also has weakneses which are described in the paper. Through testing, it was concluded that manufacturers are not yet fully complied with EXIF standard. So, it is absolutely necessary to test the device and PHP installation before we can be sure that the data from the photo can be read. Web page has been created. At this web page user is able to test his/her own photographs with location embedded data and the link is given in the paper.

  15. Planetary Geologic Mapping Handbook - 2009

    Science.gov (United States)

    Tanaka, K. L.; Skinner, J. A.; Hare, T. M.

    2009-01-01

    Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces (e.g., Varnes, 1974). Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962 (Hackman, 1962). Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete

  16. Evaluating Crop Area Mapping from MODIS Time-Series as an Assessment Tool for Zimbabwe's "Fast Track Land Reform Programme".

    Science.gov (United States)

    Hentze, Konrad; Thonfeld, Frank; Menz, Gunter

    2016-01-01

    Moderate Resolution Imaging Spectroradiometer (MODIS) data forms the basis for numerous land use and land cover (LULC) mapping and analysis frameworks at regional scale. Compared to other satellite sensors, the spatial, temporal and spectral specifications of MODIS are considered as highly suitable for LULC classifications which support many different aspects of social, environmental and developmental research. The LULC mapping of this study was carried out in the context of the development of an evaluation approach for Zimbabwe's land reform program. Within the discourse about the success of this program, a lack of spatially explicit methods to produce objective data, such as on the extent of agricultural area, is apparent. We therefore assessed the suitability of moderate spatial and high temporal resolution imagery and phenological parameters to retrieve regional figures about the extent of cropland area in former freehold tenure in a series of 13 years from 2001-2013. Time-series data was processed with TIMESAT and was stratified according to agro-ecological potential zoning of Zimbabwe. Random Forest (RF) classifications were used to produce annual binary crop/non crop maps which were evaluated with high spatial resolution data from other satellite sensors. We assessed the cropland products in former freehold tenure in terms of classification accuracy, inter-annual comparability and heterogeneity. Although general LULC patterns were depicted in classification results and an overall accuracy of over 80% was achieved, user accuracies for rainfed agriculture were limited to below 65%. We conclude that phenological analysis has to be treated with caution when rainfed agriculture and grassland in semi-humid tropical regions have to be separated based on MODIS spectral data and phenological parameters. Because classification results significantly underestimate redistributed commercial farmland in Zimbabwe, we argue that the method cannot be used to produce spatial

  17. The Effects of a MAP2K5 MicroRNA Target Site SNP on Risk for Anxiety and Depressive Disorders

    Science.gov (United States)

    Jensen, Kevin P.; Kranzler, Henry R.; Stein, Murray B.; Gelernter, Joel

    2014-01-01

    Functional variants that contribute to genomewide association study (GWAS) signals are difficult to identify. MicroRNAs could contribute to some of these gene-trait relationships. We compiled a set of GWAS trait gene SNPs that were predicted to affect microRNA regulation of mRNA. Trait associations were tested in a sample of 6725 European-American (EA) and African-American (AA) subjects that were interviewed using the polydiagnostic SSADDA to diagnose major psychiatric disorders. A predicted miR-330-3p target site SNP (rs41305272) in mitogen-activated protein kinase kinase 5 (MAP2K5) mRNA was in LD (d’=1.0, r2=0.02) with a reported GWAS-identified variant for restless legs syndrome (RLS), a disorder frequently comorbid with anxiety and depression, possibly because of a shared pathophysiology. We examined the SNP’s association with mood and anxiety-related disorders. Rs41305272 was associated with agoraphobia (Ag) in EAs (odds ratio[OR]=1.95, p=0.007; 195 cases) and AAs (OR=3.2, p=0.03; 148 cases) and major depressive disorder (MDD) in AAs (OR=2.64, p=0.01; 427 cases), but not EAs (465 cases). Rs41305272*T carrier frequency was correlated with the number of anxiety and depressive disorders diagnosed per subject. RLS was not evaluated in our subjects. Predicted miR-330-3p target genes were enriched in pathways relevant to psychiatric disorders. These findings suggest that microRNA target site information may be useful in the analysis of GWAS signals for complex traits. MiR-330-3p and MAP2K5 are potentially important contributors to mood and anxiety-related traits. With support from additional studies, these findings could add to the large number of risk genes identified through association to medical disorders that have primary psychiatric effects. PMID:24436253

  18. Visualizing the Crowd Web-based Participatory Practices as Innovative Tools in drawing and mapping Milano Città Metropolitana

    Directory of Open Access Journals (Sweden)

    Daniele Villa

    2014-05-01

    Full Text Available Many new questions arise with regard to Web3.0- based technologies, which are more and more frequently used by non-experts to generate and share geographic information, new collective urban visions and place-based knowledge. This paper discusses the role of participatory planning and mapping practices in the context of Milan metropolitan region. In particular taking into account the collaborative use of new technologies (such as the use of microblogging and geo-social networks within the processes of social sharing of the great urban transformations. Specific attention is given to the problems of perception and definition of shared landscape quality. In this context, the role of expert knowledge in the analysis and definition of the social perception of the urban landscape is now changing rapidly and radically.

  19. Development, application and evaluation of a computational tool for management high voltage break disconnector based on self-organizing maps and image processing

    International Nuclear Information System (INIS)

    Freitas Colaco, Daniel; Alexandria, Auzuir R. de; Cortez, Paulo Cesar; Frota, Joao Batista B.; Nunes de Lima, Jose Nunes de; Albuquerque, Victor Hugo C. de

    2010-01-01

    This work has the objective of developing, analysing and applying a new tool for management the status of break disconnectors in high voltage substations from digital images. This tool uses a non-supervised kind of artificial neural network using the Kohonen learning algorithm, known as a self-organizing maps. In order to develop the proposed tool, C/C++ programming language, provided with easily used interfaces, is used. In order to obtain the results, three environments are considered: one for laboratory simulation and two pilot projects installed in the Fortaleza II/CHESF substation. These pilots are used for 230 kV EV-2000 type and 500 kV semi-pantographic type break disconnector management tests. The results prove the developed system's efficiency, because it is able to detect 100% of open and closed identification situations. However, the neural network utilised for management break disconnectors has become suitable for installation in high voltage substations in order to support the maintenance team in safely handling these disconnectors.

  20. Development, application and evaluation of a computational tool for management high voltage break disconnector based on self-organizing maps and image processing

    Energy Technology Data Exchange (ETDEWEB)

    Freitas Colaco, Daniel, E-mail: colaco@deti.ufc.b [Universidade Federal do Ceara (UFC), Centro de Tecnologia (CT), Departamento de Engenharia de Teleinformatica - DETI, Campus do PICI S/N, Bloco 723, 60455-970 Fortaleza, Ceara (Brazil); Alexandria, Auzuir R. de, E-mail: auzuir@ifce.edu.b [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara (IFCE), Area da industria, Nucleo de Simulacao Computacional-N5IMCO, Campus Fortaleza, Av. Treze de Maio, 2081, 60040-531 Fortaleza, Ceara (Brazil); Cortez, Paulo Cesar, E-mail: cortez@deti.ufc.b [Universidade Federal do Ceara (UFC), Centro de Tecnologia (CT), Departamento de Engenharia de Teleinformatica - DETI, Campus do PICI S/N, Bloco 723, 60455-970 Fortaleza, Ceara (Brazil); Frota, Joao Batista B., E-mail: jb@ifce.edu.b [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara (IFCE), Area da industria, Nucleo de Simulacao Computacional-N5IMCO, Campus Fortaleza, Av. Treze de Maio, 2081, 60040-531 Fortaleza, Ceara (Brazil); Nunes de Lima, Jose Nunes de, E-mail: josenl@chesf.gov.b [Companhia Hidro Eletrica do Sao Francisco (CHESF), Rua Delmiro Gouveia, 333, 50761-901 Recife, Pernambuco (Brazil); Albuquerque, Victor Hugo C. de, E-mail: victor.albuquerque@fe.up.p [Universidade de Fortaleza (UNIFOR), Centro de Ciencias Tecnologicas (CCT), Nucleo de Pesquisas Tecnologicas - NPT, Av. Washington Soares, 1321, Sala NPT/CCT, CEP 60.811-905, Edson Queiroz (Brazil); Universidade Federal da Paraiba (UFPB), Departamento de Engenharia Mecanica (DEM), Cidade Universitaria, S/N, 58059-900 Joao Pessoa, Paraiba (Brazil)

    2010-11-15

    This work has the objective of developing, analysing and applying a new tool for management the status of break disconnectors in high voltage substations from digital images. This tool uses a non-supervised kind of artificial neural network using the Kohonen learning algorithm, known as a self-organizing maps. In order to develop the proposed tool, C/C++ programming language, provided with easily used interfaces, is used. In order to obtain the results, three environments are considered: one for laboratory simulation and two pilot projects installed in the Fortaleza II/CHESF substation. These pilots are used for 230 kV EV-2000 type and 500 kV semi-pantographic type break disconnector management tests. The results prove the developed system's efficiency, because it is able to detect 100% of open and closed identification situations. However, the neural network utilised for management break disconnectors has become suitable for installation in high voltage substations in order to support the maintenance team in safely handling these disconnectors.

  1. An open-water electrical geophysical tool for mapping sub-seafloor heavy placer minerals in 3D and migrating hydrocarbon plumes in 4D

    Science.gov (United States)

    Wynn, Jefferey C.; Urquhart, Scott; Williamson, Mike; Fleming, John B.

    2011-01-01

    A towed-streamer technology has been developed for mapping placer heavy minerals and dispersed hydrocarbon plumes in the open ocean. The approach uses induced polarization (IP), an electrical measurement that encompasses several different surface-reactive capacitive and electrochemical phenomena, and thus is ideally suited for mapping dispersed or disseminated targets. The application is operated at sea by towing active electrical geophysical streamers behind a ship; a wide area can be covered in three dimensions by folding tow-paths over each other in lawn-mower fashion. This technology has already been proven in laboratory and ocean settings to detect IP-reactive titanium- and rare-earth (REE) minerals such as ilmenite and monazite. By extension, minerals that weather and accumulate/concentrate by a similar mechanism, including gold, platinum, and diamonds, may be rapidly detected and mapped indirectly- even when dispersed and covered with thick, inert sediment. IP is also highly reactive to metal structures such as pipelines and cables. Currently, the only means for mapping an oil-spill plume is to park a large ship in the ocean and drop a sampling string over the side, requiring hours of time per sampling point. The samples must then be chemically analyzed, adding additional time and expense. We believe that an extension of the marine IP technology could also apply to rapidly mapping both seafloor- blanket and disseminated hydrocarbon plumes in the open ocean, as hydrocarbon droplets in conductive seawater are topologically equivalent to a metal-plates-and-dielectric capacitor. Because the effective capacitance would be frequency-dependent on droplet size, the approach we advocate holds the potential to not only map, but also to characterize the evolution and degradation of such a plume over time. In areas where offshore oil field development has been practiced for extended periods, making IP measurements from a towed streamer may be useful for locating buried

  2. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

    Science.gov (United States)

    Aubrey, Wayne; Riley, Michael C; Young, Michael; King, Ross D; Oliver, Stephen G; Clare, Amanda

    2015-01-01

    Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.

  3. Mapping Mutations on Phylogenies

    DEFF Research Database (Denmark)

    Nielsen, Rasmus

    2005-01-01

    This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety...... uncertainty in the mapping. Recently developed probabilistic methods can incorporate statistical uncertainty in the character mappings. In these methods, focus is on a probability distribution of mutational mappings instead of a single estimate of the mutational mapping....

  4. Peroxisomal Targeting as a Sensitive Tool to Detect Protein-Small RNA Interactions through in Vivo Piggybacking

    Directory of Open Access Journals (Sweden)

    Marco Incarbone

    2018-02-01

    Full Text Available Peroxisomes are organelles that play key roles in eukaryotic metabolism. Their protein complement is entirely imported from the cytoplasm thanks to a unique pathway that is able to translocate folded proteins and protein complexes across the peroxisomal membrane. The import of molecules bound to a protein targeted to peroxisomes is an active process known as ‘piggybacking’ and we have recently shown that P15, a virus-encoded protein possessing a peroxisomal targeting sequence, is able to piggyback siRNAs into peroxisomes. Here, we extend this observation by analyzing the small RNA repertoire found in peroxisomes of P15-expressing plants. A direct comparison with the P15-associated small RNA retrieved during immunoprecipitation (IP experiments, revealed that in vivo piggybacking coupled to peroxisome isolation could be a more sensitive means to determine the various small RNA species bound by a given protein. This increased sensitivity of peroxisome isolation as opposed to IP experiments was also striking when we analyzed the small RNA population bound by the Tomato bushy stunt virus-encoded P19, one of the best characterized viral suppressors of RNA silencing (VSR, artificially targeted to peroxisomes. These results support that peroxisomal targeting should be considered as a novel/alternative experimental approach to assess in vivo interactions that allows detection of labile binding events. The advantages and limitations of this approach are discussed.

  5. MRI anatomical mapping and direct stereotactic targeting in the subthalamic region: functional and anatomical correspondence in Parkinson's disease

    International Nuclear Information System (INIS)

    Lemaire, Jean-Jacques; Coste, Jerome; Ouchchane, Lemlih; Hemm, Simone; Derost, Philippe; Ulla, Miguel; Durif, Franck; Siadoux, Severine; Gabrillargues, Jean; Chazal, Jean

    2007-01-01

    Object Relationships between clinical effects, anatomy, and electrophysiology are not fully understood in DBS of the subthalamic region in Parkinson's disease. We proposed an anatomic study based on direct image-guided stereotactic surgery with a multiple source data analysis. Materials and Methods A manual anatomic mapping was realized on coronal 1.5-Tesla MRI of 15 patients. Biological data were collected under local anesthesia: the spontaneous neuron activities and the clinical efficiency and the appearance of adverse effects. They were related to relevant current values (mA), the benefit threshold (bt, minimal current leading an clear efficiency), the adverse effect threshold (at, minimal current leading an adverse effect) and the stimulation margin (sm = at - bt); they were matched with anatomy. Results We found consistent relationships between anatomy and biological data. The optimal stimulation parameters (low bt + high sm) were noted in the dorsolateral STN. The highest spontaneous neuron activity was found in the ventromedial STN. Dorsolateral (sensorimotor) STN seems the main DBS effector. The highest spontaneous neuron activity seems related to the anterior (rostral) ventromedial (limbic) STN. Conclusion 1.5 Tesla images provide sufficiently detailed subthalamic anatomy for image-guided stereotactic surgery and may aid in understanding DBS mechanisms. (orig.)

  6. THE USE OF NOISE MAPS AND PLANNING TOOLS IN THE MANAGEMENT OF AN ACOUSTIC CLIMATE IN AN URBAN AREA

    Directory of Open Access Journals (Sweden)

    Tomasz Zubala

    2016-09-01

    Full Text Available Nowadays, noise is considered as one of the most significant factors polluting the environment. It is classified in the first place among the indicators of the comfort of home, leisure and work. Therefore, more and more attention is paid to the need to study the sources and effects of noise on the environment and to develop effective methods of protection against nuisance and harmful sounds. Analysis of environmental factors is an especially important part of the process of spatial planning. The article covers characteristics of spatial and temporal differentiation of acoustic phenomena occurring within selected district of Lublin – the largest Polish city east of the Vistula River. Field measurements and analytical operations, which enable mapping noise, and consequently measuring the exposure of residents to the impact of abnormal sound levels, were made. There was also an attempt to evaluate the spatial development and its relationship with prevailing acoustic conditions. The collected results allowed developing recommendations for planning the city centre area acting as a standard. The need to design buffer zones to reduce the sound level near roads or locating residential areas away from sources of noise was underlined. The study should prove helpful in forecasting changes in the acoustic conditions and spatial planning and deciding on protection measures in urban areas.

  7. Animal movement network analysis as a tool to map farms serving as contamination source in cattle cysticercosis

    Directory of Open Access Journals (Sweden)

    Samuel C. Aragão

    Full Text Available ABSTRACT: Bovine cysticercosis is a problem distributed worldwide that result in economic losses mainly due to the condemnation of infected carcasses. One of the difficulties in applying control measures is the identification of the source of infection, especially because cattle are typically acquired from multiple farms. Here, we tested the utility of an animal movement network constructed with data from a farm that acquires cattle from several other different farms to map the major contributors of cysticercosis propagation. Additionally, based on the results of the network analysis, we deployed a sanitary management and drug treatment scheme to decrease cysticercosis’ occurrence in the farm. Six farms that had commercial trades were identified by the animal movement network and characterized as the main contributors to the occurrence of cysticercosis in the studied farm. The identification of farms with a putative risk of Taenia saginata infection using the animal movement network along with the proper sanitary management and drug treatment resulted in a gradual decrease in cysticercosis prevalence, from 25% in 2010 to 3.7% in 2011 and 1.8% in 2012. These results suggest that the animal movement network can contribute towards controlling bovine cysticercosis, thus minimizing economic losses and preventing human taeniasis.

  8. Transit shapes and self-organizing maps as a tool for ranking planetary candidates: application to Kepler and K2

    Science.gov (United States)

    Armstrong, D. J.; Pollacco, D.; Santerne, A.

    2017-03-01

    A crucial step in planet hunting surveys is to select the best candidates for follow-up observations, given limited telescope resources. This is often performed by human 'eyeballing', a time consuming and statistically awkward process. Here, we present a new, fast machine learning technique to separate true planet signals from astrophysical false positives. We use self-organizing maps (SOMs) to study the transit shapes of Kepler and K2 known and candidate planets. We find that SOMs are capable of distinguishing known planets from known false positives with a success rate of 87.0 per cent, using the transit shape alone. Furthermore, they do not require any candidate to be dispositioned prior to use, meaning that they can be used early in a mission's lifetime. A method for classifying candidates using a SOM is developed, and applied to previously unclassified members of the Kepler Objects of Interest (KOI) list as well as candidates from the K2 mission. The method is extremely fast, taking minutes to run the entire KOI list on a typical laptop. We make PYTHON code for performing classifications publicly available, using either new SOMs or those created in this work. The SOM technique represents a novel method for ranking planetary candidate lists, and can be used both alone or as part of a larger autovetting code.

  9. Self-organizing maps as a chemometric tool for aromatic pattern recognition of soluble coffee - doi: 10.4025/actascitechnol.v34i1.10892

    Directory of Open Access Journals (Sweden)

    Evandro Bona

    2011-11-01

    Full Text Available The electronic nose (EN is an instrument very used for food flavor analysis. However, it is also necessary to integrate the equipment with a multivariable pattern recognition system, and to this end the principal component analysis (PCA is the first choice. Alternatively, self-organizing maps (SOM had been also suggested, since they are a nonlinear and reliable technique. In this study SOM were used to distinguish soluble coffee according to EN data. The proposed methodology had identified all of the seven coffees evaluated; in addition, the groups and relationships detected were similar to those obtained through PCA. Also, the analysis of network weights allowed gathering the e-nose sensors into 4 groups according to the behavior regarding the samples. Results confirm SOM as an efficient tool to EN data pos-processing, and have showed the methodology as a promising choice for the development of new products and quality control of soluble coffee.

  10. Targeted selection of brownfields from portfolios for sustainable regeneration: User experiences from five cases testing the Timbre Brownfield Prioritization Tool.

    Science.gov (United States)

    Bartke, Stephan; Martinát, Stanislav; Klusáček, Petr; Pizzol, Lisa; Alexandrescu, Filip; Frantál, Bohumil; Critto, Andrea; Zabeo, Alex

    2016-12-15

    Prioritizing brownfields for redevelopment in real estate portfolios can contribute to more sustainable regeneration and land management. Owners of large real estate and brownfield portfolios are challenged to allocate their limited resources to the development of the most critical or promising sites, in terms of time and cost efficiency. Authorities worried about the negative impacts of brownfields - in particular in the case of potential contamination - on the environment and society also need to prioritize their resources to those brownfields that most urgently deserve attention and intervention. Yet, numerous factors have to be considered for prioritizing actions, in particular when adhering to sustainability principles. Several multiple-criteria decision analysis (MCDA) approaches and tools have been suggested in order to support these actors in managing their brownfield portfolios. Based on lessons learned from the literature on success factors, sustainability assessment and MCDA approaches, researchers from a recent EU project have developed the web-based Timbre Brownfield Prioritization Tool (TBPT). It facilitates assessment and prioritization of a portfolio of sites on the basis of the probability of successful and sustainable regeneration or according to individually specified objectives. This paper introduces the challenges of brownfield portfolio management in general and reports about the application of the TBPT in five cases: practical test-uses by two large institutional land owners from Germany, a local and a regional administrative body from the Czech Republic, and an expert from a national environmental authority from Romania. Based on literature requirements for sustainability assessment tools and on the end-users' feedbacks from the practical tests, we discuss the TBPT's strengths and weaknesses in order to inform and give recommendations for future development of prioritization tools. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools.

    Science.gov (United States)

    Sreenivasulu, Nese; Usadel, Björn; Winter, Andreas; Radchuk, Volodymyr; Scholz, Uwe; Stein, Nils; Weschke, Winfriede; Strickert, Marc; Close, Timothy J; Stitt, Mark; Graner, Andreas; Wobus, Ulrich

    2008-04-01

    Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley (Hordeum vulgare) grain maturation, desiccation, and germination in two tissue fractions (starchy endosperm/aleurone and embryo/scutellum) using the Affymetrix Barley1 GeneChip. To aid data evaluation, Arabidopsis thaliana MapMan and PageMan tools were adapted to barley. The analyses allow a number of conclusions: (1) Cluster analysis revealed a smooth transition in transcription programs between late seed maturation and germination within embryo tissues, but not in the endosperm/aleurone. (2) More than 12,000 transcripts are stored in the embryo of dry barley grains, many of which are presumably activated during germination. (3) Transcriptional activation of storage reserve mobilization events occurs at an early stage of germination, well before radicle protrusion. (4) Key genes of gibberellin (GA) biosynthesis are already active during grain maturation at a time when abscisic acid peaks suggesting the formation of an endogenous store of GA in the aleurone. This GA probably acts later during germination in addition to newly synthesized GA. (5) Beside the well-known role of GA in gene activation during germination spatiotemporal expression data and cis-element searches in homologous rice promoters confirm an equally important gene-activating role of abscisic acid during this developmental period. The respective regulatory webs are linked to auxin and ethylene controlled networks. In summary, new bioinformatics PageMan and MapMan tools developed in barley have been successfully used to investigate in detail the transcriptome relationships between seed maturation and germination in an important crop plant.

  12. Airport environmental noise mapping and land use management as an environmental protection action policy tool. The case of the Larnaka International Airport (Cyprus).

    Science.gov (United States)

    Vogiatzis, Konstantinos

    2012-05-01

    The evidence from epidemiological studies on the association between exposure to traffic and aircraft noise and hypertension and ischemic heart disease has increased during the recent years. Both road traffic and aircraft noise increase the risk of high blood pressure. Environmental noise mapping, as per the 2002/49/EC Directive, is an obligation of all European Union (EU) member states. In the framework of the present article a complete Strategic Noise Mapping research and Action Noise Plans assessment and evaluation are presented and aim to access land use management as an effective tool for protection from aircraft noise. The case of the Larnaka International Airport in Cyprus, a typical Mediterranean airport, (considered as a "large airport" according to the above EU Directive and the recent Cyprus Legislation Law No. 224(Ι)/2004), is presented. In this paper a review of both assessment and action implementation procedures focusing on the dominant--in the area--aircraft traffic noise is presented, with emphasis to (a) a full calculation of Strategic Noise Map (SNM) scenarios of actual and future airport operation using the ECAC.CEAC Doc 29 methodology for both EU common indicators L(den) and L(night) in scales of 5 dB, (b) a full evaluation of results with emphasis to the Larnaka greater area land uses and the exposure of inhabitants in residences in various levels of environmental noise, and (c) a full evaluation of Noise Action Plans (NAP) introducing especially a new land use management scheme for the future Larnaka Town Land Use Plan. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Using ESRI Online Mapping Tools to Support STEM Learning through Analysis of the Impact of Land Use/Land Cover Change on Water Quality

    Science.gov (United States)

    Powley, C.; Alian, S.; Mayer, A.

    2017-12-01

    In the 2004 National Water Quality Report to the Congress, the US EPA states that about 44% of the streams, 64% of lakes and 30% of estuaries that were assessed were not suitable for basic use like fishing and swimming. Pollutants from nonpoint sources are most likely the cause. The needs of landowners to use their land for other uses is enormous and most are likely willing to forgo the potential damage to achieve monetary gains. These are difficult decisions as there are many positive gains in commercialized development, although this comes with a cost. So it is imperative for all entities to work together in developing an awareness that benefits all stakeholders. We used this water quality management context to prepare lessons for high school students to map water quality problem areas in Rifle River and the West Branch in Ogemaw County, Michigan based on field samples and by using ESRI online data entry and mapping tools. The students also used Long Term Hydrologic Impact Analysis (L-THIA) to evaluate the impacts of different land use/cover types, developing an understanding of the implication of land management on surface water quality.

  14. Rational design of urea-based glutamate carboxypeptidase II (GCPII) inhibitors as versatile tools for specific drug targeting and delivery

    Czech Academy of Sciences Publication Activity Database

    Tykvart, Jan; Schimer, Jiří; Bařinková, Jitka; Pachl, Petr; Poštová Slavětínská, Lenka; Majer, Pavel; Konvalinka, Jan; Šácha, Pavel

    2014-01-01

    Roč. 22, č. 15 (2014), s. 4099-4108 ISSN 0968-0896 R&D Projects: GA ČR GBP208/12/G016 Grant - others:OPPK(CZ) CZ.2.16/3.1.00/24016 Institutional support: RVO:61388963 Keywords : GCPII * PSMA * structure-aided drug design * specific drug targeting Subject RIV: CE - Biochemistry Impact factor: 2.793, year: 2014

  15. siRNA as a tool to improve the treatment of brain diseases: Mechanism, targets and delivery.

    Science.gov (United States)

    Gomes, Maria João; Martins, Susana; Sarmento, Bruno

    2015-05-01

    As the population ages, brain pathologies such as neurodegenerative diseases and brain cancer increase their incidence, being the need to find successful treatments of upmost importance. Drug delivery to the central nervous system (CNS) is required in order to reach diseases causes and treat them. However, biological barriers, mainly blood-brain barrier (BBB), are the key obstacles that prevent the effectiveness of possible treatments due to their ability to strongly limit the perfusion of compounds into the brain. Over the past decades, new approaches towards overcoming BBB and its efflux transporters had been proposed. One of these approaches here reviewed is through small interfering RNA (siRNA), which is capable to specifically target one gene and silence it in a post-transcriptional way. There are different possible functional proteins at the BBB, as the ones responsible for transport or just for its tightness, which could be a siRNA target. As important as the effective silence is the way to delivery siRNA to its anatomical site of action. This is where nanotechnology-based systems may help, by protecting siRNA circulation and providing cell/tissue-targeting and intracellular siRNA delivery. After an initial overview on incidence of brain diseases and basic features of the CNS, BBB and its efflux pumps, this review focuses on recent strategies to reach brain based on siRNA, and how to specifically target these approaches in order to treat brain diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Effects of deformable registration algorithms on the creation of statistical maps for preoperative targeting in deep brain stimulation procedures

    Science.gov (United States)

    Liu, Yuan; D'Haese, Pierre-Francois; Dawant, Benoit M.

    2014-03-01

    Deep brain stimulation, which is used to treat various neurological disorders, involves implanting a permanent electrode into precise targets deep in the brain. Accurate pre-operative localization of the targets on pre-operative MRI sequence is challenging as these are typically located in homogenous regions with poor contrast. Population-based statistical atlases can assist with this process. Such atlases are created by acquiring the location of efficacious regions from numerous subjects and projecting them onto a common reference image volume using some normalization method. In previous work, we presented results concluding that non-rigid registration provided the best result for such normalization. However, this process could be biased by the choice of the reference image and/or registration approach. In this paper, we have qualitatively and quantitatively compared the performance of six recognized deformable registration methods at normalizing such data in poor contrasted regions onto three different reference volumes using a unique set of data from 100 patients. We study various metrics designed to measure the centroid, spread, and shape of the normalized data. This study leads to a total of 1800 deformable registrations and results show that statistical atlases constructed using different deformable registration methods share comparable centroids and spreads with marginal differences in their shape. Among the six methods being studied, Diffeomorphic Demons produces the largest spreads and centroids that are the furthest apart from the others in general. Among the three atlases, one atlas consistently outperforms the other two with smaller spreads for each algorithm. However, none of the differences in the spreads were found to be statistically significant, across different algorithms or across different atlases.

  17. Comparing the performance of cluster random sampling and integrated threshold mapping for targeting trachoma control, using computer simulation.

    Directory of Open Access Journals (Sweden)

    Jennifer L Smith

    Full Text Available Implementation of trachoma control strategies requires reliable district-level estimates of trachomatous inflammation-follicular (TF, generally collected using the recommended gold-standard cluster randomized surveys (CRS. Integrated Threshold Mapping (ITM has been proposed as an integrated and cost-effective means of rapidly surveying trachoma in order to classify districts according to treatment thresholds. ITM differs from CRS in a number of important ways, including the use of a school-based sampling platform for children aged 1-9 and a different age distribution of participants. This study uses computerised sampling simulations to compare the performance of these survey designs and evaluate the impact of varying key parameters.Realistic pseudo gold standard data for 100 districts were generated that maintained the relative risk of disease between important sub-groups and incorporated empirical estimates of disease clustering at the household, village and district level. To simulate the different sampling approaches, 20 clusters were selected from each district, with individuals sampled according to the protocol for ITM and CRS. Results showed that ITM generally under-estimated the true prevalence of TF over a range of epidemiological settings and introduced more district misclassification according to treatment thresholds than did CRS. However, the extent of underestimation and resulting misclassification was found to be dependent on three main factors: (i the district prevalence of TF; (ii the relative risk of TF between enrolled and non-enrolled children within clusters; and (iii the enrollment rate in schools.Although in some contexts the two methodologies may be equivalent, ITM can introduce a bias-dependent shift as prevalence of TF increases, resulting in a greater risk of misclassification around treatment thresholds. In addition to strengthening the evidence base around choice of trachoma survey methodologies, this study illustrates

  18. Development of a workplace intervention for sick-listed employees with stress-related mental disorders: Intervention Mapping as a useful tool.

    Science.gov (United States)

    van Oostrom, Sandra H; Anema, Johannes R; Terluin, Berend; Venema, Anita; de Vet, Henrica C W; van Mechelen, Willem

    2007-08-15

    To date, mental health problems and mental workload have been increasingly related to long-term sick leave and disability. However, there is, as yet, no structured protocol available for the identification and application of an intervention for stress-related mental health problems at the workplace. This paper describes the structured development, implementation and planning for the evaluation of a return-to-work intervention for sick-listed employees with stress-related mental disorders (SMDs). The intervention is based on an existing successful return-to-work intervention for sick-listed employees with low back pain. The principles of Intervention Mapping were applied to combine theory and evidence in the development, implementation and planning for the evaluation of a participatory workplace intervention, aimed at an early return-to-work for sick-listed employees with SMDs. All stakeholders were involved in focus group interviews: i.e. employees recently sick-listed with SMDs, supervisors and occupational health professionals. The development of the participatory workplace intervention according to the Intervention Mapping principles resulted in a structured return-to-work intervention, specifically tailored to the needs of sick-listed employees with SMDs. Return-to-work was proposed as a behavioural change, and the Attitude - Social influence - self-Efficacy model was identified as a theoretical framework. Stakeholder involvement in focus group interviews served to enhance the implementation. The cost-effectiveness of the intervention will be evaluated in a randomised controlled trial. Intervention Mapping was found to be a promising method to develop interventions tailored to a specific target group in the field of occupational health.

  19. Development of a workplace intervention for sick-listed employees with stress-related mental disorders: Intervention Mapping as a useful tool

    Directory of Open Access Journals (Sweden)

    Anema Johannes R

    2007-08-01

    Full Text Available Abstract Background To date, mental health problems and mental workload have been increasingly related to long-term sick leave and disability. However, there is, as yet, no structured protocol available for the identification and application of an intervention for stress-related mental health problems at the workplace. This paper describes the structured development, implementation and planning for the evaluation of a return-to-work intervention for sick-listed employees with stress-related mental disorders (SMDs. The intervention is based on an existing successful return-to-work intervention for sick-listed employees with low back pain. Methods The principles of Intervention Mapping were applied to combine theory and evidence in the development, implementation and planning for the evaluation of a participatory workplace intervention, aimed at an early return-to-work for sick-listed employees with SMDs. All stakeholders were involved in focus group interviews: i.e. employees recently sick-listed with SMDs, supervisors and occupational health professionals. Results The development of the participatory workplace intervention according to the Intervention Mapping principles resulted in a structured return-to-work intervention, specifically tailored to the needs of sick-listed employees with SMDs. Return-to-work was proposed as a behavioural change, and the Attitude – Social influence – self-Efficacy model was identified as a theoretical framework. Stakeholder involvement in focus group interviews served to enhance the implementation. The cost-effectiveness of the intervention will be evaluated in a randomised controlled trial. Conclusion Intervention Mapping was found to be a promising method to develop interventions tailored to a specific target group in the field of occupational health. Trial registration ISRCTN92307123

  20. CoC GIS Tools (GIS Tool)

    Data.gov (United States)

    Department of Housing and Urban Development — This tool provides a no-cost downloadable software tool that allows users to interact with professional quality GIS maps. Users access pre-compiled projects through...

  1. Assessing Flood Risks and Planning for Resiliency in New Jersey: A Case Study on the Use of Online Flood Mapping and Resilience Planning Tools

    Science.gov (United States)

    Auermuller, L. M.; Gatto, J.; Huch, C.

    2015-12-01

    The highly developed nature of New Jersey's coastline, barrier island and lagoon communities make them particularly vulnerable to storm surge, sea level rise and flooding. The impacts of Hurricane Sandy have enlightened coastal communities to these realities. Recognizing these vulnerabilities, the Jacques Cousteau National Research Reserve (JC NERR), Rutgers Center for Remote Sensing and Spatial Analysis (CRSSA), Rutgers Bloustein School and the Barnegat Bay Partnership (BBP) have developed web-based tools to assist NJ's coastal communities in visualizing and planning for future local impacts. NJFloodMapper and NJAdapt are two complementary interactive mapping websites that visualize different current and future flood hazards. These hazard layers can be combined with additional data including critical facilities, evacuation routes, socioeconomic and environmental data. Getting to Resilience is an online self-assessment tool developed to assist communities reduce vulnerability and increase preparedness by linking planning, mitigation, and adaptation. Through this interactive process communities will learn how their preparedness can yield valuable points through voluntary programs like FEMA's Community Rating System and Sustainable Jersey. The assessment process can also increase the community's understanding of where future vulnerabilities should be addressed through hazard mitigation planning. Since Superstorm Sandy, more than thirty communities in New Jersey have been provided technical assistance in assessing their risks and vulnerabilities to coastal hazards, and have begun to understand how to better plan and prepare for short and long-term changes along their shorelines.

  2. A basic tool for post-seismic rebuilding: the new 1:5.000 scale geological map of Amatrice town

    Science.gov (United States)

    Mancini, Marco; Vignaroli, Gianluca; Ardizzone, Francesca; Bucci, Francesco; Cardinali, Mauro; Cavinato, Gian Paolo; Cosentino, Giuseppe; Di Salvo, Cristina; Fiorucci, Federica; Gaudiosi, Iolanda; Giallini, Silvia; Peronace, Edoardo; Polpetta, Federica; Putignano, Maria Luisa; Reichenbach, Paola; Santangelo, Michele; Scionti, Veronica; Simionato, Maurizio; Sirianni, Pietro; Stigliano, Francesco

    2017-04-01

    A geological survey has been carried out in the area of Amatrice, the most damaged town after the 24 August 2016 event, to provide a basic reference for geophysical and geotechnical data useful for seismic response analyses and microzonation studies. The morphologies and the stratigraphic-structural setting of the investigated area are detailed on a 1:5000 scale geological map and cross sections, which derive from the integration of field-based observations and photo-geological interpretation. The Amatrice basin is filled by the one km-thick Laga Formation, composed of Messinian syn-orogenic marine sandstones and siltstones (Marini et al., 2015) and covered with disconformity by Quaternary conglomerates and sands, referred to alluvial fans, fluvial terraces and landslides. Presently, the Amatrice basin is a structurally-controlled depression bounded eastward by the Gorzano Mt ridge, and westward by the Sibillini Mts thrust front (Koopman, 1983). Our observations focus on (i) relationships between geometry and extent of cover deposits, (ii) bedding of the substratum, and (iii) areal arrangement and distribution of the main fault systems. Amatrice is located on a N-S trending mesa bounded by steep escarpments. The siliciclastic substratum was folded by syn-orogenic movements, broadly forming a NW-SE-trending synform, and is dissected by two main fault systems of the Plio-Quaternary post-orogenic tectonics. The first system consists of N-S striking high angle normal fault segments, each one having continuous length of up to 2 km; the second consists of E-W-striking normal-to-strike slip fault systems dissecting the first one. N-S-striking faults are morphologically expressed by fault plane scarps and triangular facets, and control the areal distribution of the Quaternary fluvial deposits. These are up to 50 m thick below Amatrice and thin to few metres along the north west direction. East of Amatrice, the stratigraphic setting is dominated by SW-prograding alluvial

  3. Using GeoMapApp as an Analytical Tool for the Journey From Data Visualization to Synthesis

    Science.gov (United States)

    Ryan, W. B.; Coplan, J. O.; Melkonian, A. K.; Carbotte, S. M.

    2008-12-01

    The potential to explore and understand our world has forever changed since the appearance of the NASA World Wind and Google Earth virtual globes. Now, in the duration of a single breath, we can zoom from the planetary scale of an orbiting spacecraft down to a roadside outcrop and expose layers of information with different and rich contents. But how do we digest all this information into new knowledge that explains the processes that have shaped the land and oceans into their present configurations and behaviors? In our opinion we need to transition beyond visualization to interactive inquiry of multiple datasets across a span of expertise - from the classroom to the research laboratory. Although the virtual globe enables an unprecedented means as revolutionary as the textural search engine to discover information, presently most data on the WEB are not adequately described with metadata to make the subsequent steps of analysis productive. We have begun to address this limitation by linking GeoMapApp to databases in the earth and ocean sciences where content has been vetted for thoroughness, accuracy and global coverage. With structure in the content, the virtual globe can then manipulate these databases in what if? exercises, compare the various attributes of a dataset with each other via graphs and symbols, and correlate results across different scientific domains. We will show examples of such data integration using the results of four decades of ocean floor drilling, the focal mechanisms from thousands of earthquakes, and the chemistry of the volcanic bedrock along the crest of the mid-ocean ridge. A synthesis of ocean drilling shows the dependency of the sediment and faunal content on bedrock age, subsidence history and plate motions relative to the past equator and deserts. A synthesis of earthquake rupture shows focal mechanism dependency on segmentation of the plate boundaries. Patterns in the chemistry of erupted lava are intricately related to the fine

  4. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.

    Science.gov (United States)

    Wang, Qiong; Quensen, John F; Fish, Jordan A; Lee, Tae Kwon; Sun, Yanni; Tiedje, James M; Cole, James R

    2013-09-17

    Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase (nifH). We obtained 1.1 million nifH 454 amplicon sequences from 222 soil samples collected from 4 National Ecological Observatory Network (NEON) sites in Alaska, Hawaii, Utah, and Florida. To accurately detect and correct frameshifts caused by indel sequencing errors, we developed FrameBot, a tool for frameshift correction and nearest-neighbor classification, and compared its accuracy to that of two other rapid frameshift correction tools. We found FrameBot was, in general, more accurate as long as a reference protein sequence with 80% or greater identity to a query was available, as was the case for virtually all nifH reads for the 4 NEON sites. Frameshifts were present in 12.7% of the reads. Those nifH sequences related to the Proteobacteria phylum were most abundant, followed by those for Cyanobacteria in the Alaska and Utah sites. Predominant genera with nifH sequences similar to reads included Azospirillum, Bradyrhizobium, and Rhizobium, the latter two without obvious plant hosts at the sites. Surprisingly, 80% of the sequences had greater than 95% amino acid identity to known nifH gene sequences. These samples were grouped by site and correlated with soil environmental factors, especially drainage, light intensity, mean annual temperature, and mean annual precipitation. FrameBot was tested successfully on three ecofunctional genes but should be applicable to any. High-throughput phylogenetic analysis of microbial communities using rRNA-targeted sequencing is now commonplace; however, such data often allow little inference with respect to either the presence or the diversity of genes involved in most important ecological processes. To study the gene pool for these processes, it is more

  5. Co-development of diagnostic vectors to support targeted therapies and theranostics: Essential tools in Personalized Cancer Therapy.

    Directory of Open Access Journals (Sweden)

    Nicholas C Nicolaides

    2014-06-01

    Full Text Available Novel technologies are being developed to improve patient therapy through the identification of targets and surrogate molecular signatures that can help direct appropriate treatment regimens for efficacy and drug safety. This is particularly the case in oncology whereby patient tumor and biofluids are routinely isolated and analyzed for genetic, immunohistochemical and/or soluble markers to determine if a predictive biomarker signature exists as a means for selecting optimal treatment. Improvements in diagnostics that can prescreen predictive response biomarker profiles will continue to optimize the ability to enhance patient therapy via molecularly defined disease-specific treatment. A goal for drug developers is to identify and implement new strategies that can rapidly enable the development of beneficial disease-specific therapies for broad, patient-specific targeting without the need of tedious predictive biomarker discovery and validation efforts, currently a bottleneck for development timelines. Here we discuss the use of co-developing diagnostic-targeting vectors to identify patients whose malignant tissue can specifically uptake a drug linked vector prior to treatment. Using this system, a patient can be predetermined in real time as to whether or not their tumor(s can uptake a drug-linked diagnostic vector, thus inferring the uptake of a similar vector linked to an anti-cancer agent. If tumor-specific uptake is observed, then the patient may be suitable for drug-linked vector therapy and have a higher likelihood of clinical benefit while patients with no tumor uptake should consider other therapeutic options. This approach offers complementary opportunities to rapidly develop broad tumor-specific agents for use in personalized medicine.

  6. S-layer fusion protein as a tool functionalizing emulsomes and CurcuEmulsomes for antibody binding and targeting.

    Science.gov (United States)

    Ucisik, Mehmet H; Küpcü, Seta; Breitwieser, Andreas; Gelbmann, Nicola; Schuster, Bernhard; Sleytr, Uwe B

    2015-04-01

    Selective targeting of tumor cells by nanoparticle-based drug delivery systems is highly desirable because it maximizes the drug concentration at the desired target while simultaneously protecting the surrounding healthy tissues. Here, we show a design for smart nanocarriers based on a biomimetic approach that utilizes the building principle of virus envelope structures. Emulsomes and CurcuEmulsomes comprising a tripalmitin solid core surrounded by phospholipid layers are modified by S-layer proteins that self-assemble into a two-dimensional array to form a surface layer. One significant advantage of this nanoformulation is that it increases the solubility of the lipophilic anti-cancer agent curcumin in the CurcuEmulsomes by a factor of 2700. In order to make the emulsomes specific for IgG, the S-layer protein is fused with two protein G domains. This S-layer fusion protein preserves its recrystallization characteristics, forming an ordered surface layer (square lattice with 13 nm unit-by-unit distance). The GG domains are presented in a predicted orientation and exhibit a selective binding affinity for IgG. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design.

    Science.gov (United States)

    AhYoung, Andrew P; Koehl, Antoine; Cascio, Duilio; Egea, Pascal F

    2015-09-01

    Caseinolytic chaperones and proteases (Clp) belong to the AAA+ protein superfamily and are part of the protein quality control machinery in cells. The eukaryotic parasite Plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of Clp proteins including two distinct ClpB ATPases. ClpB1 and ClpB2 are involved in different aspects of parasitic proteostasis. ClpB1 is present in the apicoplast, a parasite-specific and plastid-like organelle hosting various metabolic pathways necessary for parasite growth. ClpB2 localizes to the parasitophorous vacuole membrane where it drives protein export as core subunit of a parasite-derived protein secretion complex, the Plasmodium Translocon of Exported proteins (PTEX); this process is central to parasite virulence and survival in the human host. The functional associations of these two chaperones with parasite-specific metabolism and protein secretion make them prime drug targets. ClpB proteins function as unfoldases and disaggregases and share a common architecture consisting of four domains-a variable N-terminal domain that binds different protein substrates, followed by two highly conserved catalytic ATPase domains, and a C-terminal domain. Here, we report and compare the first crystal structures of the N terminal domains of ClpB1 and ClpB2 from Plasmodium and analyze their molecular surfaces. Solution scattering analysis of the N domain of ClpB2 shows that the average solution conformation is similar to the crystalline structure. These structures represent the first step towards the characterization of these two malarial chaperones and the reconstitution of the entire PTEX to aid structure-based design of novel anti-malarial drugs. © 2015 The Protein Society.

  8. Mapping calcium phosphate activated gene networks as a strategy for targeted osteoinduction of human progenitors in vitro and in vivo

    Science.gov (United States)

    Eyckmans, J.; Roberts, S.J.; Bolander, J.; Schrooten, J.; Chen, C.S.; Luyten, F.P.

    2014-01-01

    Although calcium phosphate-containing biomaterials are promising scaffolds for bone regenerative strategies, the osteoinductive capacity of such materials is poorly understood. In this study, we investigated whether endogenous mechanisms of in vivo calcium phosphate-driven, ectopic bone formation could be identified and used to induce enhanced differentiation in vitro of the same progenitor population. To accomplish this, human periosteum derived cells (hPDCs) were seeded on hydroxyapatite/collagen scaffolds (calcium phosphate rich matrix or CPRM), or on decalcified scaffolds (calcium phosphate depleted matrix or CPDM), followed by subcutaneous implantation in nude mice to trigger ectopic bone formation. In this system, osteoblast differentiation occurred in CPRM scaffolds, but not in CPDM scaffolds. Gene expression was assessed by human full-genome microarray at 20 hours after seeding, and 2, 8 and 18 days after implantation. In both matrices, implantation of the cell constructs triggered a similar gene expression cascade, however, gene expression dynamics progressed faster in CPRM scaffolds than in CPDM scaffolds. The difference in gene expression dynamics was associated with differential activation of hub genes and molecular signaling pathways related to calcium signaling (CREB), inflammation (TNFα, NFkB, and IL6) and bone development (TGFβ, β-catenin, BMP, EGF, and ERK signaling). Starting from this set of pathways, a growth factor cocktail was developed that robustly enhanced osteogenesis in vitro and in vivo. Taken together, our data demonstrate that through the identification and subsequent stimulation of genes, proteins and signaling pathways associated with calcium phosphate mediated osteoinduction, a focused approach to develop targeted differentiation protocols in adult progenitor cells can be achieved. PMID:23537666

  9. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

    DEFF Research Database (Denmark)

    Yu, Jun; Feng, Qiang; Wong, Sunny Hei

    2017-01-01

    OBJECTIVE: To evaluate the potential for diagnosing colorectal cancer (CRC) from faecal metagenomes. DESIGN: We performed metagenome-wide association studies on faecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark....... We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls. RESULTS: Besides confirming...... known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with CRC, we found significant associations with several species, including Parvimonas micra and Solobacterium moorei. We identified 20 microbial gene markers that differentiated CRC and control microbiomes, and validated 4...

  10. Body condition score as a selection tool for targeted selective treatment-based nematode control strategies in Merino ewes.

    Science.gov (United States)

    Cornelius, M P; Jacobson, C; Besier, R B

    2014-12-15

    Sheep nematode control utilising refugia-based strategies have been shown to delay anthelmintic resistance, but the optimal indices to select individuals to be left untreated under extensive sheep grazing conditions are not clear. This experiment tested the hypothesis that high body condition can indicate ability of mature sheep to better cope with worms and therefore remain untreated in a targeted treatment programme. Adult Merino ewes from flocks on two private farms located in south-west Western Australia (Farm A, n = 271, and Farm B, n = 258) were measured for body condition score (BCS), body weight and worm egg counts (WEC) on four occasions between May and December (pre-lambing, lamb marking, lamb weaning and post-weaning). Half of the ewes in each flock received anthelmintic treatments to suppress WEC over the experimental period and half remained untreated (unless critical limits were reached). Response to treatment was analysed in terms of BCS change and percentage live weight change. No effect of high or low initial WEC groups was shown for BCS response, and liveweight responses were inconsistent. A relatively greater BCS response to treatment was observed in ewes in low BCS pre-lambing compared to better-conditioned ewes on one farm where nutrition was sub-optimal and worm burdens were high. Sheep in low body condition pre-lambing were more than three times more likely to fall into a critically low BCS (<2.0) if left untreated. Recommendations can be made to treat ewes in lower BCS and leave a proportion of the higher body condition sheep untreated in a targeted selective treatment programme, to provide a population of non-resistant worms to delay the development of resistance. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

    Science.gov (United States)

    Manocheewa, Siriphan; Mittler, John E; Samudrala, Ram; Mullins, James I

    2015-11-04

    Rapid evolution and high sequence diversity enable Human Immunodeficiency Virus (HIV) populations to acquire mutations to escape antiretroviral drugs and host immune responses, and thus are major obstacles for the control of the pandemic. One strategy to overcome this problem is to focus drugs and vaccines on regions of the viral genome in which mutations are likely to cripple function through destabilization of viral proteins. Studies relying on sequence conservation alone have had only limited success in determining critically important regions. We tested the ability of two structure-based computational models to assign sites in the HIV-1 capsid protein (CA) that would be refractory to mutational change. The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%. Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity. Based on the predicted stability, we identified 45 CA sites prone to destabilizing mutations. More than half of these sites are targets of one or more known CA inhibitors. The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals. Lastly, a joint scoring metric that takes into account both sequence conservation and protein structure stability performed better at identifying deleterious mutations than sequence conservation or structure stability information alone. The computational sequence-structure stability approach proposed here might therefore be useful for identifying immutable sites in a protein for experimental validation as potential targets for drug and vaccine development.

  12. Fast electron and X-ray scattering as a tool to study target's structure

    Energy Technology Data Exchange (ETDEWEB)

    Amusia, M.Ya. [Racah Institute of Physics, Hebrew University, Jerusalem 91904 (Israel); A.F. Ioffe Physical-Technical Institute, St. Petersburg 194021 (Russian Federation)], E-mail: amusia@vms.huji.ac.il

    2007-06-15

    We concentrate on several relatively new aspects of the study of fast electron and X-ray scattering by atoms and atom-like objects, namely endohedral atoms and fullerenes. However, main attention is given to fast charge particle scattering. We show that the corresponding cross-sections, being expressed via so-called generalized oscillator strengths (GOS), give information on the electronic structure of the target and on the role of electron correlations in it. We consider what sort of information became available when analyzing the dependence of GOS upon their multipolarity, transferred momentum q and energy {omega}. To obtain theoretical results, we employ both the one-electron Hartree-Fock approximation and account for the multi-electron correlation in the target, using the random phase approximation with exchange. We demonstrate the role of non-dipole corrections in the small-angle fast-electron inelastic scattering. There dipole contribution dominates while non-dipole corrections can be considerably and controllably enhanced as compared to the case of low and medium energy photoionization. We show also that analyses of GOS for discrete level excitations permit to clarify their multipolarity. The results of calculations of Compton excitation and ionization cross-sections are presented. Attention is given to cooperative effects in inelastic fast electron-atom scattering that results in directed motion of the secondary electrons, a phenomenon that is similar to 'drag currents' in photoionization. We demonstrate how one should derive GOS for endohedral atoms, e.g. A-C{sub 60} and what is the additional information that can be obtained from corresponding GOS. Most of discussions are illustrated by the results of concrete calculations.

  13. Mapping with Drupal

    CERN Document Server

    Palazzolo, Alan

    2011-01-01

    Build beautiful interactive maps on your Drupal website, and tell engaging visual stories with your data. This concise guide shows you how to create custom geographical maps from top to bottom, using Drupal 7 tools and out-of-the-box modules. You'll learn how mapping works in Drupal, with examples on how to use intuitive interfaces to map local events, businesses, groups, and other custom data. Although building maps with Drupal can be tricky, this book helps you navigate the system's complexities for creating sophisticated maps that match your site design. Get the knowledge and tools you ne

  14. RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2018-01-01

    Full Text Available Background With the continuous discovery of microRNA’s (miRNA association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS analysis. Methods The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs. Results By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow. Conclusions With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS. More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865.

  15. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    Directory of Open Access Journals (Sweden)

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  16. Morphology of TiAlN Thin Film onto HSS as Cutting Tools by Using Mosaic-Styled Target RF Sputtering Method

    Directory of Open Access Journals (Sweden)

    Sigit Tri Wicaksono

    2016-05-01

    Full Text Available High Speed Steel (HSS has been widely used in manufacturing industry as cutting tools. Several methods have been used to improve the cutting performance of HSS in dry cutting. One of them was by growing a thin layer of hard coating on the contact surface of the cutting tool material. In this research, Titanium Aluminum Nitride (TiAlN layer were deposited on AISI M41 HSS substrate by using Radio Frequency (RF sputtering method with mosaic styled of target materials. The aluminum surface area ratios on the Titanium target are 10, 20, 30, and 40 % respectively. The deposition time are 15, 30, and 45 minutes respectively. The formation of TiAlN and AlN crystalline compounds were observed by X-Ray Diffraction method. The morphology of thin film layer with a thickness range from 1.4 to 5.2 µm was observed by using a Scanning Electron Microscopy. It was known that the deposition time affect to the thickness and also the roughness of the layer. The topography images by Atomic Force Microscopy showed that the deposition time of 45 minutes produce the finest layer with the surface roughness of 10.8 nm.

  17. CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems.

    Directory of Open Access Journals (Sweden)

    Md Khaledur Rahman

    Full Text Available The CRISPR/Cas9-sgRNA system has recently become a popular tool for genome editing and a very hot topic in the field of medical research. In this system, Cas9 protein is directed to a desired location for gene engineering and cleaves target DNA sequence which is complementary to a 20-nucleotide guide sequence found within the sgRNA. A lot of experimental efforts, ranging from in vivo selection to in silico modeling, have been made for efficient designing of sgRNAs in CRISPR/Cas9 system. In this article, we present a novel tool, called CRISPRpred, for efficient in silico prediction of sgRNAs on-target activity which is based on the applications of Support Vector Machine (SVM model. To conduct experiments, we have used a benchmark dataset of 17 genes and 5310 guide sequences where there are only 20% true values. CRISPRpred achieves Area Under Receiver Operating Characteristics Curve (AUROC-Curve, Area Under Precision Recall Curve (AUPR-Curve and maximum Matthews Correlation Coefficient (MCC as 0.85, 0.56 and 0.48, respectively. Our tool shows approximately 5% improvement in AUPR-Curve and after analyzing all evaluation metrics, we find that CRISPRpred is better than the current state-of-the-art. CRISPRpred is enough flexible to extract relevant features and use them in a learning algorithm. The source code of our entire software with relevant dataset can be found in the following link: https://github.com/khaled-buet/CRISPRpred.

  18. Funnel plots and choropleth maps in cancer risk communication: a comparison of tools for disseminating population-based incidence data to stakeholders.

    Science.gov (United States)

    Mazzucco, Walter; Cusimano, Rosanna; Zarcone, Maurizio; Mazzola, Sergio; Vitale, Francesco

    2017-03-30

    Population-based cancer registries provide epidemiological cancer information, but the indicators are often too complex to be interpreted by local authorities and communities, due to numeracy and literacy limitations. The aim of this paper is to compare the commonly used visual formats to funnel plots to enable local public health authorities and communities to access valid and understandable cancer incidence data obtained at the municipal level. A funnel plot representation of standardised incidence ratio (SIR) was generated for the 82 municipalities of the Palermo Province with the 2003-2011 data from the Palermo Province Cancer Registry (Sicily, Italy). The properties of the funnel plot and choropleth map methodologies were compared within the context of disseminating epidemiological data to stakeholders. The SIRs of all the municipalities remained within the control limits, except for Palermo city area (SIR=1.12), which was sited outside the upper control limit line of 99.8%. The Palermo Province SIRs funnel plot representation was congruent with the choropleth map generated from the same data, but the former resulted more informative as shown by the comparisons of the weaknesses and strengths of the 2 visual formats. Funnel plot should be used as a complementary valuable tool to communicate epidemiological data of cancer registries to communities and local authorities, visually conveying an efficient and simple way to interpret cancer incidence data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  19. Three-dimensional visualisation of the large bowel: a potential tool for assessing targeted drug delivery and colonic pathology

    International Nuclear Information System (INIS)

    Perkins, A.C.; Mann, C.; Wilson, C.G.

    1995-01-01

    A study has been undertaken to assess the feasibility of three-dimensional imaging of the dispersion of a non-absorbable tracer released into the colon of normal subjects. Six healthy volunteers were selected who were participating in a scintigraphic study designed to assess the spreading of 1 MBq indium-111 Amberlite resin delivered from a delayed capsule system targeted to release in the ascending colon. In each case subjects were imaged using a rotating gamma camera over a data collection period of approximately 20 min. Three-dimensional volume rendered images demonstrated good visualisation of the dispersion of the tracer throughout the ascending, transverse and descending colon and provided good anatomical visualisation of the shape of the colon, not previously apparent from the planar views. The present study demonstrates for the first time, the successful three-dimensional imaging of a radiolabelled tracer dispersed throughout the colon and opens up the prospects for more detailed study of quantification of the volume and distribution of tracers contained within the colon. (orig.). With 1 fig

  20. Combining `OMIC tools and other targeted molecular methods to evaluate iron limitation of diatoms in the Northeast Pacific Ocean.

    Science.gov (United States)

    Chappell, D.; Wallace, J.; Jenkins, B. D.; Powell, K.

    2016-02-01

    Diatoms are an abundant and widespread group of phytoplankton capable of exerting a profound influence on global carbon cycling. It is widely accepted that iron (Fe) controls diatom production in many ocean systems and the Fe stress response has been a focus of research for some time. Assessing the Fe status of natural diatom populations has proven challenging, as diatom species in the same genus may be difficult to distinguish using microscopy and the physiological and molecular responses to Fe stress can vary widely within a genus. A targeted high-throughput sequencing method to characterize the diatom community in field samples has been developed. Additionally, comparative transcriptomics of laboratory experiments with ecologically relevant species have been used to elucidate genes whose expression is tightly coupled to specific limitation scenarios. These two methods have been combined with data mining of the growing database of diatom transcriptomes to develop species-specific markers of physiological status in field populations. Data will be presented on the development and use of these methods to analyze samples collected on field expeditions to the Northeast Pacific Ocean sampling across gradients of Fe.

  1. Towards a common effort in mapping marine geohazard features in the Mediterranean Sea. An unavoidable tool for the "blue growth" and marine spatial planning.

    Science.gov (United States)

    Chiocci, F. L.; Gorini, C.; Ercilla, G.; Sakellariou, D.; Casalbore, D.; Ridente, D.

    2017-12-01

    46,000 km of densely settled coastlines characterise the Mediterranean Sea. The region connects three continents, where the population doubled in the last 20 years, and among which, trade, maritime transports and migratory fluxes have been increasing. Moreover, the Mediterranean is by far the world's largest tourist destination, attracting almost a third of international tourists and generating more than a quarter of tourism-related revenues worldwide. The Mediterranean area lays in a plate boundary zone highly active in terms of seismicity, volcanism and submarine geological processes that over recent time have repeatedly demonstrated to be able to generate catastrophic events.. As an example 98 tsunamis where recorded in the Mediterranean on historical times (on average one every century). This census do not encompasses small events, such as minor tsunamis generated by submarine landslides that can produce serious damage in the near field. In Stromboli volcanic island (Southern Tyrrhenian Sea) for instance, the frequency of such events accounts for 5 events over the last century Mapping the seafloor for geohazard assessment becomes, therefore, especially important for the sustainable development of the marine and coastal areas both economically and socially. The increasing amount of high resolution seafloor mapping data allows defining geohazard features such as volcanic vents, active faults, submarine landslide, canyon head migrating bedforms fluid expulsion structure with a detail able to highlight even locally dangerous situations. If the marine geoscience community will be able to build common standards to interpret and cartographically represent the marine geohazard features private industries and public agencies will benefit of an unvaluable tool which will help in better exploit the marine resource and/or preserve the marine and coastal environment. This contribution will present spectacular examples of marine geohazards from the Mediterranean Seas; the

  2. Using a map-based assesment tool for the development of cost-effective WFD river basin action programmes in a changing climate

    DEFF Research Database (Denmark)

    Kaspersen, Bjarke Stoltze; Vammen Jacobsen, Torsten; Brian Butts, Michael

    2016-01-01

    For the 2nd and 3rd river basin management cycles (2015–2027) of the Water Framework Directive (WFD), EU Member States are required to fully integrate climate change into the process of river basin management planning (RBMP). Complying with the main WFD objective of achieving ‘good ecological......, there is still a need for further reductions. In addition, the impacts of climate change are projected to lead to a situation where nutrient loads will have to be reduced still further in comparison to current climate conditions. There is an urgent need to address this challenge in WFD action programmes in order...... Basin in the north east of Denmark. The tool facilitates assessments of the application of agri-environmental measures that are targeted towards low retention agricultural areas, where limited or no surface and subsurface N reduction takes place. Effects of climate change on nitrate leaching were...

  3. Roles of Mitogen-Activating Protein Kinase Kinase Kinase Kinase-3 (MAP4K3) in Preterm Skeletal Muscle Satellite Cell Myogenesis and Mammalian Target of Rapamycin Complex 1 (mTORC1) Activation Regulation.

    Science.gov (United States)

    Guo, Chu-Yi; Yu, Mu-Xue; Dai, Jie-Min; Pan, Si-Nian; Lu, Zhen-Tong; Qiu, Xiao-Shan; Zhuang, Si-Qi

    2017-07-21

    BACKGROUND Preterm skeletal muscle genesis is a paradigm for myogenesis. The role of mitogen-activating protein kinase kinase kinase kinase-3 (MAP4K3) in preterm skeletal muscle satellite cells myogenesis or its relationship to mammalian target of rapamycin complex 1 (mTORC1) activity have not been previously elaborated. MATERIAL AND METHODS Small interfering RNA (siRNA) interference technology was used to inhibit MAP4K3 expression. Leucine stimulation experiments were performed following MAP4K3-siRNA interference. The differentiation of primary preterm skeletal muscle satellite cells was observed after siRNA-MAP4K3 interference. Western blot analysis was used to determine the expression of MAP4K3, MyHC, MyoD, myogenin, p-mTOR, and p-S6K1. The immunofluorescence fusion index of MyHC and myogenin were detected. MAP4K3 effects on preterm rat satellite cells differentiation and its relationship to mTORC1 activity are reported. RESULTS MAP4K3 siRNA knockdown inhibited myotube formation and both MyoD and myogenin expression in primary preterm rat skeletal muscle satellite cells, but MAP4K3 siRNA had no effect on the activity of mTORC1. In primary preterm rat skeletal muscle satellite cells, MAP4K3 knockdown resulted in significantly weaker, but not entirely blunted, leucine-induced mTORC1 signaling. CONCLUSIONS MAP4K3 positively regulates preterm skeletal muscle satellite cell myogenesis, but may not regulate mTORC1 activity. MAP4K3 may play a role in mTORC1 full activation in response to leucine.

  4. Health risk estimates for groundwater and soil contamination in the Slovak Republic: a convenient tool for identification and mapping of risk areas.

    Science.gov (United States)

    Fajčíková, K; Cvečková, V; Stewart, A; Rapant, S

    2014-10-01

    We undertook a quantitative estimation of health risks to residents living in the Slovak Republic and exposed to contaminated groundwater (ingestion by adult population) and/or soils (ingestion by adult and child population). Potential risk areas were mapped to give a visual presentation at basic administrative units of the country (municipalities, districts, regions) for easy discussion with policy and decision-makers. The health risk estimates were calculated by US EPA methods, applying threshold values for chronic risk and non-threshold values for cancer risk. The potential health risk was evaluated for As, Ba, Cd, Cu, F, Hg, Mn, NO3 (-), Pb, Sb, Se and Zn for groundwater and As, B, Ba, Be, Cd, Cu, F, Hg, Mn, Mo, Ni, Pb, Sb, Se and Zn for soils. An increased health risk was identified mainly in historical mining areas highly contaminated by geogenic-anthropogenic sources (ore deposit occurrence, mining, metallurgy). Arsenic and antimony were the most significant elements in relation to health risks from groundwater and soil contamination in the Slovak Republic contributing a significant part of total chronic risk levels. Health risk estimation for soil contamination has highlighted the significance of exposure through soil ingestion in children. Increased cancer risks from groundwater and soil contamination by arsenic were noted in several municipalities and districts throughout the country in areas with significantly high arsenic levels in the environment. This approach to health risk estimations and visualization represents a fast, clear and convenient tool for delineation of risk areas at national and local levels.

  5. Realizing modeling and mapping tools to study the upsurge of noise pollution as a result of open-cast mining and transportation activities.

    Science.gov (United States)

    Lokhande, Satish K; Jain, Mohindra C; Dhawale, Satyajeet A; Gautam, Rakesh; Bodhe, Ghanshyam L

    2018-01-01

    In open-cast mines, noise pollution has become a serious concern due to the extreme use of heavy earth moving machinery (HEMM). This study is focused to measure and assess the effects of the existing noise levels of major operational mines in the Keonjhar, Sundergadh, and Mayurbhanj districts of Odisha, India. The transportation noise levels were also considered in this study, which was predicted using the modified Federal Highway Administration (FHWA) model. It was observed that noise induced by HEMM such as rock breakers, jackhammers, dumpers, and excavators, blasting noise in the mining terrain, as well as associated transportation noise became a major source of annoyance to the habitants living in proximity to the mines. The noise produced by mechanized mining operations was observed between 74.3 and 115.2 dB(A), and its impact on residential areas was observed between 49.4 and 58.9 dB(A). In addition, the noise contour maps of sound level dispersion were demonstrated with the utilization of advanced noise prediction software tools for better understanding. Finally, the predicted values at residential zone and traffic noise are correlated with observed values, and the coefficient of determination, R 2 , was calculated to be 0.6891 and 0.5967, respectively.

  6. Physio-biochemical parameters: a potential tool for target-selective treatment of haemonchosis in the small ruminants.

    Science.gov (United States)

    Das, Bhupamani; Kumar, Niranjan; Jadav, Mehul M; Solanki, Jayesh B; Rao, T K S

    2017-12-01

    This study aims to evaluate the conjunctiva colour-based FAMACHA score (FS) coupled with a body condition score (BCS), haemogram and stressor hormone level estimation, in identifying post-mortem (PM)/coproscopically proven individuals wanting therapy for economically important gastrointestinal (GI) helminths, Haemonchus contortus, in the small ruminants. The incidence of haemonchosis was significantly (p  0.05). The infected animals of FS 2, 3 and 4 measured 8.2 ± 0.0, 7.5 ± 0.23 and 6.7 ± 0.34 g/dl Hb (r = -0.452, p = 0.01) in goats/9.3 ± 0.8, 8.6 ± 0.5 and 7.6 ± 0.3 g/dl Hb (r = -0.511, p = 0.05) in sheep with 21.2, 19.8 ± 1.8 and 17.8 ± 0.2% PCV (r = -0.369, p = 0.05) in goats/26.7 ± 1.2, 22.2 ± 0.2 and 20.9 ± 0.6% PCV (r = -0.251, p = 0.03) in sheep, respectively. The FS 2, 3 and 4 infected goats/sheep measured 6.1 ± 0, 7.9 ± 1.0 and 9.5 ± 0.9 (p < 0.05)/5.8 ± 2.3, 6.9 ± 1.2 and 7.8 ± 0.2% (p < 0.05) mid-granulocyte [(r = 0.928 (goats)/0.834 (sheep), p < 0.05], while the cortisol level was 15.6, 23 ± 4.5 and 42 ± 2.3 (p = 0.23)/12.1 ± 0, 15.9 ± 1.2 and 24 ± 3.4 (p = 0.29) μg/dl, respectively. The infected ruminants recorded low (p < 0.05) level of Hb/PCV while high level of mid-granulocytes/cortisol. Specificity of FAMACHA test was maximized (100%) when FS = 4 was considered anaemic, but sensitivity was low (35.29% in goats; 25% in sheep). The false negatives was 5.9 (goat)/12.5 (sheep)% when FS ≥ 3 was considered anaemic. The small ruminants with FS ≥ 3, BCS ≤ 2.5, Hb ≤ 7.5 g/dl (goats)/8.6 g/dl (sheep), PCV ≤ 19.8% (goats)/22.2% (sheep) and mid-granulocyte ≥7.9% (goats)/6.9 ± 1.2% (sheep) can be subjected to target-selective treatment for haemonchosis in the field simultaneously maximizing the economic benefit to the farmers.

  7. Targeted Learning

    CERN Document Server

    van der Laan, Mark J

    2011-01-01

    The statistics profession is at a unique point in history. The need for valid statistical tools is greater than ever; data sets are massive, often measuring hundreds of thousands of measurements for a single subject. The field is ready to move towards clear objective benchmarks under which tools can be evaluated. Targeted learning allows (1) the full generalization and utilization of cross-validation as an estimator selection tool so that the subjective choices made by humans are now made by the machine, and (2) targeting the fitting of the probability distribution of the data toward the targe

  8. The hemodynamic "target": a visual tool of goal-directed therapy for septic patients Alvo hemodinâmico: uma ferramenta visual de terapia "goal-directed" para pacientes sépticos

    Directory of Open Access Journals (Sweden)

    Fabrice Vallée

    2007-01-01

    Full Text Available OBJECTIVE: To improve understanding of the hemodynamic status of patients with sepsis by nursing teams through the attainment of hemodynamic parameters using a pentaxial "target" diagram as a clinical tool. Parameters include cardiac index (CI, arterial oxygen saturation (SaO2, mean arterial pressure (MAP, arterial blood lactate, and central venous oxygen saturation (ScvO2. METHODS: Design: Prospective descriptive study. Setting: The intensive care unit of a university hospital. Patients: During a 6-month period, 38 intubated septic shock patients were included in the study. Survivors and nonsurvivors were compared. Interventions: MAP, CI, SaO2, ScvO2 and lactate were measured at 0, 6, 12, 24, 36, and 48 h. Measurements were recorded on the target diagram along with the norepinephrine infusion rate and the hemoglobin (Hb level. The number of lactate and ScvO2 measurements achieved during the target period were compared to a 6-month retrospective control period just before starting the protocol. We assessed the nurse knowledge status prior to the introduction of target diagram. We then performed a post-test after implementing the new recording technique. MEASUREMENTS AND RESULTS: The nursing team expressed a positive attitude toward the target concept. The mean number of lactate and ScvO2 measurements performed for each patient during the control period was significantly lower than during the target period, and those values were rarely used as goal values before the introduction of the target diagram. At 24 hours, 46% of the survivors had achieved all the goal parameter values of the target diagram, compared to only 10% of nonsurvivors (P = .01. CONCLUSION: The target diagram is a visual multiparametric tool involving all the medical and nursing team that helps achieve goal-directed therapy for septic patients. The number of goal values reached at each time point during the first 48 hours was closely linked to mortality.OBJETIVO: Melhorar a

  9. THERMAL NEUTRON FLUX MAPPING ON A TARGET CAPSULE AT RABBIT FACILITY OF RSG-GAS REACTOR FOR USE IN k0-INAA

    Directory of Open Access Journals (Sweden)

    Sutisna Sutisna

    2015-03-01

    Full Text Available Instrumental neutron activation analysis based on the k0 method (k0-INAA requires the availability of the accurate reactor parameter data, in particular a thermal neutron flux that interact with a targets inside the target capsule. This research aims to determine and map the thermal neutron flux inside the capsule and irradiation channels used for the elemental quantification using the k0-AANI. Mapping of the thermal neutron flux (фth on two type of irradiation capsule have been done for RS01 and RS02 facilities of RSG-GAS reactor. Thermal neutron flux determined using Al-0,1%Au alloy through 197Au(n,g 198Au nuclear reaction, while the flux mapping done using statistics R. Thermal neutron flux are calculated using k0-IAEA software provided by IAEA. The results showed the average thermal neutron flux is (5.6±0.3×10+13 n.cm-2.s-1; (5.6±0.4×10+13 n.cm-2.s-1; (5.2±0.4×10+13 n.cm-2.s-1 and (5.3±0.4×10+13 n.cm-2.s-1 for Polyethylene capsule of 1st , 2nd, 3rd and 4th layer respectively. In the case of Aluminum capsule, the thermal neutron flux was lower compared to that on Polyethylene capsule. There were (3.0±0.2×10+13 n.cm-2.s-1; (2.8±0.1×10+13 n.cm-2.s-1; (3.2±0.3×10+13 n.cm-2.s-1 for 1st, 2nd and 3rd layers respectively. For each layer in the capsule, the thermal neutron flux is not uniform and it was no degradation flux in the axial direction, both for polyethylene and aluminum capsules. Contour map of eight layer on polyethylene capsule and six layers on aluminum capsule for RS01 and RS02 irradiation channels had a similar pattern with a small diversity for all type of the irradiation capsule. Keywords: thermal neutron, flux, capsule, NAA   Analisis aktivasi neutron instrumental berbasis metode k0 (k0-AANI memerlukan ketersediaan data parameter reaktor yang akurat, khususnya data fluks neutron termal yang berinteraksi dengan inti sasaran di dalam kapsul target. Penelitian ini bertujuan menentukan dan memetakan fluks neutron termal

  10. An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Hongzhi Cao

    Full Text Available The major histocompatibility complex (MHC is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.

  11. An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing.

    Science.gov (United States)

    Cao, Hongzhi; Wu, Jinghua; Wang, Yu; Jiang, Hui; Zhang, Tao; Liu, Xiao; Xu, Yinyin; Liang, Dequan; Gao, Peng; Sun, Yepeng; Gifford, Benjamin; D'Ascenzo, Mark; Liu, Xiaomin; Tellier, Laurent C A M; Yang, Fang; Tong, Xin; Chen, Dan; Zheng, Jing; Li, Weiyang; Richmond, Todd; Xu, Xun; Wang, Jun; Li, Yingrui

    2013-01-01

    The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.

  12. Genetic linkage map of cowpea ( Vigna unguiculata (L.) Walp) using ...

    African Journals Online (AJOL)

    Genetic linkage maps provide a genomic framework for quantitative trait loci identification applied in marker assisted selection breeding in crops with limited resources. It serves as a powerful tool to breeders for analysing the mode of inheritance of genes of interest and monitoring of the transmission of target genes from ...

  13. Planetary Geologic Mapping Handbook - 2010. Appendix

    Science.gov (United States)

    Tanaka, K. L.; Skinner, J. A., Jr.; Hare, T. M.

    2010-01-01

    Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces. Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962. Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by

  14. A spatially encoded dose difference maximal intensity projection map for patient dose evaluation: A new first line patient quality assurance tool

    Energy Technology Data Exchange (ETDEWEB)

    Hu Weigang; Graff, Pierre; Boettger, Thomas; Pouliot, Jean [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94143 (United States); and others

    2011-04-15

    Purpose: To develop a spatially encoded dose difference maximal intensity projection (DD-MIP) as an online patient dose evaluation tool for visualizing the dose differences between the planning dose and dose on the treatment day. Methods: Megavoltage cone-beam CT (MVCBCT) images acquired on the treatment day are used for generating the dose difference index. Each index is represented by different colors for underdose, acceptable, and overdose regions. A maximal intensity projection (MIP) algorithm is developed to compress all the information of an arbitrary 3D dose difference index into a 2D DD-MIP image. In such an algorithm, a distance transformation is generated based on the planning CT. Then, two new volumes representing the overdose and underdose regions of the dose difference index are encoded with the distance transformation map. The distance-encoded indices of each volume are normalized using the skin distance obtained on the planning CT. After that, two MIPs are generated based on the underdose and overdose volumes with green-to-blue and green-to-red lookup tables, respectively. Finally, the two MIPs are merged with an appropriate transparency level and rendered in planning CT images. Results: The spatially encoded DD-MIP was implemented in a dose-guided radiotherapy prototype and tested on 33 MVCBCT images from six patients. The user can easily establish the threshold for the overdose and underdose. A 3% difference between the treatment and planning dose was used as the threshold in the study; hence, the DD-MIP shows red or blue color for the dose difference >3% or {<=}3%, respectively. With such a method, the overdose and underdose regions can be visualized and distinguished without being overshadowed by superficial dose differences. Conclusions: A DD-MIP algorithm was developed that compresses information from 3D into a single or two orthogonal projections while hinting the user whether the dose difference is on the skin surface or deeper.

  15. A spatially encoded dose difference maximal intensity projection map for patient dose evaluation: a new first line patient quality assurance tool.

    Science.gov (United States)

    Hu, Weigang; Graff, Pierre; Boettger, Thomas; Pouliot, Jean

    2011-04-01

    To develop a spatially encoded dose difference maximal intensity projection (DD-MIP) as an online patient dose evaluation tool for visualizing the dose differences between the planning dose and dose on the treatment day. Megavoltage cone-beam CT (MVCBCT) images acquired on the treatment day are used for generating the dose difference index. Each index is represented by different colors for underdose, acceptable, and overdose regions. A maximal intensity projection (MIP) algorithm is developed to compress all the information of an arbitrary 3D dose difference index into a 2D DD-MIP image. In such an algorithm, a distance transformation is generated based on the planning CT. Then, two new volumes representing the overdose and underdose regions of the dose difference index are encoded with the distance transformation map. The distance-encoded indices of each volume are normalized using the skin distance obtained on the planning CT. After that, two MIPs are generated based on the underdose and overdose volumes with green-to-blue and green-to-red lookup tables, respectively. Finally, the two MIPs are merged with an appropriate transparency level and rendered in planning CT images. The spatially encoded DD-MIP was implemented in a dose-guided radiotherapy prototype and tested on 33 MVCBCT images from six patients. The user can easily establish the threshold for the overdose and underdose. A 3% difference between the treatment and planning dose was used as the threshold in the study; hence, the DD-MIP shows red or blue color for the dose difference > 3% or < or = 3%, respectively. With such a method, the overdose and underdose regions can be visualized and distinguished without being overshadowed by superficial dose differences. A DD-MIP algorithm was developed that compresses information from 3D into a single or two orthogonal projections while hinting the user whether the dose difference is on the skin surface or deeper.

  16. Targeted therapies for cancer

    Science.gov (United States)

    ... Kummar S, Murgo AJ, Tomaszewski JE, Doroshow JH. Therapeutic targeting of cancer cells: era of molecularly targeted agents. ... ADAM Health Solutions. About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

  17. The strategy map as a tool to increase the return on learning investments: learning practitioners first impressions at the EAPRIL 2015 conference

    OpenAIRE

    de Schryver, Tom

    2016-01-01

    While strategy maps have their roots in strategic management accounting, they have much to offer to learning departments looking for a good return on learning investments. A strategy map is a visual model that shows which investments are most likely to improve the internal operations of a learning department, which in turn satisfices its customers better and secures that the goals of the learning department are being pursued. A strategy map thus leads to better aligned investments decisions. ...

  18. Mapping in the cloud

    CERN Document Server

    Peterson, Michael P

    2014-01-01

    This engaging text provides a solid introduction to mapmaking in the era of cloud computing. It takes students through both the concepts and technology of modern cartography, geographic information systems (GIS), and Web-based mapping. Conceptual chapters delve into the meaning of maps and how they are developed, covering such topics as map layers, GIS tools, mobile mapping, and map animation. Methods chapters take a learn-by-doing approach to help students master application programming interfaces and build other technical skills for creating maps and making them available on the Internet. Th

  19. OpenStreetMap, the Wikipedia Map

    OpenAIRE

    Maier, Gunther

    2014-01-01

    "This paper presents OpenStreetMap and closely related software as a resource for spatial economic research. The paper demonstrates how information can be extracted from OpenStreetMap, how it can be used as a geographical interface in web-based communication, and illustrates the value of the tools by use of a specific application, the WU campus GIS." (author's abstract)

  20. Poverty alleviation through geographic targeting: How much does disaggregation help?

    NARCIS (Netherlands)

    Elbers, C.T.M.; Fujii, T.; Lanjouw, P.F.; Özler, B; Yin, W

    2007-01-01

    In this paper, we employ recently completed "poverty maps" for three countries as tools for an ex ante evaluation of the distributional incidence of geographic targeting of public resources. We simulate the impact on poverty of transferring an exogenously given budget to geographically defined

  1. Using the soil and water assessment tool to estimate achievable water quality targets through implementation of beneficial management practices in an agricultural watershed.

    Science.gov (United States)

    Yang, Qi; Benoy, Glenn A; Chow, Thien Lien; Daigle, Jean-Louis; Bourque, Charles P-A; Meng, Fan-Rui

    2012-01-01

    Runoff from crop production in agricultural watersheds can cause widespread soil loss and degradation of surface water quality. Beneficial management practices (BMPs) for soil conservation are often implemented as remedial measures because BMPs can reduce soil erosion and improve water quality. However, the efficacy of BMPs may be unknown because it can be affected by many factors, such as farming practices, land-use, soil type, topography, and climatic conditions. As such, it is difficult to estimate the impacts of BMPs on water quality through field experiments alone. In this research, the Soil and Water Assessment Tool was used to estimate achievable performance targets of water quality indicators (sediment and soluble P loadings) after implementation of combinations of selected BMPs in the Black Brook Watershed in northwestern New Brunswick, Canada. Four commonly used BMPs (flow diversion terraces [FDTs], fertilizer reductions, tillage methods, and crop rotations), were considered individually and in different combinations. At the watershed level, the best achievable sediment loading was 1.9 t ha(-1) yr(-1) (89% reduction compared with default scenario), with a BMP combination of crop rotation, FDT, and no-till. The best achievable soluble P loading was 0.5 kg ha(-1) yr(-1) (62% reduction), with a BMP combination of crop rotation and FDT and fertilizer reduction. Targets estimated through nonpoint source water quality modeling can be used to evaluate BMP implementation initiatives and provide milestones for the rehabilitation of streams and rivers in agricultural regions. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  2. The strategy map as a tool to increase the return on learning investments: learning practitioners first impressions at the EAPRIL 2015 conference

    NARCIS (Netherlands)

    de Schryver, Tom

    2016-01-01

    While strategy maps have their roots in strategic management accounting, they have much to offer to learning departments looking for a good return on learning investments. A strategy map is a visual model that shows which investments are most likely to improve the internal operations of a learning

  3. A Tool for Creating Regionally Calibrated High-Resolution Land Cover Data Sets for the West African Sahel: Using Machine Learning to Scale Up Hand-Classified Maps in a Data-Sparse Environment

    Science.gov (United States)

    Van Gordon, M.; Van Gordon, S.; Min, A.; Sullivan, J.; Weiner, Z.; Tappan, G. G.

    2017-12-01

    Using support vector machine (SVM) learning and high-accuracy hand-classified maps, we have developed a publicly available land cover classification tool for the West African Sahel. Our classifier produces high-resolution and regionally calibrated land cover maps for the Sahel, representing a significant contribution to the data available for this region. Global land cover products are unreliable for the Sahel, and accurate land cover data for the region are sparse. To address this gap, the U.S. Geological Survey and the Regional Center for Agriculture, Hydrology and Meteorology (AGRHYMET) in Niger produced high-quality land cover maps for the region via hand-classification of Landsat images. This method produces highly accurate maps, but the time and labor required constrain the spatial and temporal resolution of the data products. By using these hand-classified maps alongside SVM techniques, we successfully increase the resolution of the land cover maps by 1-2 orders of magnitude, from 2km-decadal resolution to 30m-annual resolution. These high-resolution regionally calibrated land cover datasets, along with the classifier we developed to produce them, lay the foundation for major advances in studies of land surface processes in the region. These datasets will provide more accurate inputs for food security modeling, hydrologic modeling, analyses of land cover change and climate change adaptation efforts. The land cover classification tool we have developed will be publicly available for use in creating additional West Africa land cover datasets with future remote sensing data and can be adapted for use in other parts of the world.

  4. How we created a targeted teaching tool using blog architecture for anesthesia and critical care education--the A/e anesthesia exchange blog.

    Science.gov (United States)

    Saichaie, Kem; Benson, Jocelyn; Kumar, Avinash B

    2014-08-01

    The time constraints on a clinical educator have increased immensely over the past decade. Technology has served to significantly bridge the challenge over the past decade. WHAT WE DID: We created a method of delivering targeted educational content for point of care learning in anesthesia and critical care. Our blog platform allows clinician-educators to deliver content as videopodcasts and presentations to learners in a straightforward and easily accessible manner both on the web and through mobile platforms. The A/e Anesthesia exchange "pushed" content at predetermined time intervals to learners and content was based on timely topics that were clinically relevant to their daily practice. The A/e Blog allowed multiple authors across disciplines to contribute content, thus providing learners potentially access to resources of knowledge from the entire team of clinician-educators at an institution. During the pilot phase of A/e blog implementation, the authors gained valuable insights into the use and limitations of web-based technology as a teaching tool. These included challenges with faculty and student participation, managing techno stress of faculty not fluent with the technology, tailoring content based on analytics data and web platform robustness and spam protection. With these insights in hand, we anticipate the launch of an even more robust A/e: Anesthesia Exchange (version 2.0) by the end of 2013.

  5. Transperineal Magnetic Resonance Imaging-targeted Biopsy versus Transperineal Template Prostate Mapping Biopsy in the Detection of Localised Radio-recurrent Prostate Cancer.

    Science.gov (United States)

    Kanthabalan, A; Abd-Alazeez, M; Arya, M; Allen, C; Freeman, A; Jameson, C; Kirkham, A; Mitra, A V; Payne, H; Punwani, S; Ramachandran, N; Walkden, M; Emberton, M; Ahmed, H U

    2016-09-01

    Multi-parametric magnetic resonance imaging (mpMRI) may identify radio-recurrent intra-prostatic cancer accurately. We aimed to compare visually directed MRI-targeted biopsies (MRI-TB) to an accurate reference standard - transperineal prostate mapping (TPM) biopsies with 5 mm sampling - in the detection of clinically significant cancer in men with biochemical failure after radiotherapy. A retrospective registry analysis between 2006 and 2014 identified 77 men who had undergone mpMRI followed by MRI-TB and TPM. Clinical significance was set at two definitions of disease. Definition 1 was Gleason ≥ 4+3 and/or maximum cancer core length ≥ 6 mm. Definition 2 was Gleason ≥ 3+4 and/or maximum cancer core length ≥ 4 mm. Of the 77 patients included, the mean age was 70 years (range 61-82; standard deviation 5.03). The median prostate-specific antigen (PSA) at the time of external beam radiotherapy (EBRT) was 14 ng/ml (interquartile range 7.83-32.50). The most frequent EBRT dose given was 74 Gy over 37 fractions. Eight patients had iodine-seed implant brachytherapy or high dose rate brachytherapy. Neoadjuvant/adjuvant hormonal therapy use was reported in 38. The time from EBRT to biochemical recurrence was a median of 60 months (interquartile range 36.75-85.00). The median PSA at the time of mpMRI was 4.68 ng/ml (interquartile range 2.68-7.60). The median time between mpMRI and biopsy was 2.76 months (interquartile range 1.58-4.34). In total, 2392 TPM and 381 MRI-TB cores were taken with 18% and 50% cancer detection, respectively. Detection rates of definition 1 clinically significant cancer were 52/77 (68%) versus 55/77 (71%) for MRI-TB and TPM, respectively. MRI-TB was more efficient requiring 1 core versus 2.8 cores to detect definition 2 cancer. MRI-TB seems to have encouraging detection rates for clinically significant cancer with fewer cores compared with TPM, although TPM had higher detection rates for smaller lower grade lesions. Copyright © 2016 The

  6. Usability Evaluation of Public Web Mapping Sites

    Science.gov (United States)

    Wang, C.

    2014-04-01

    Web mapping sites are interactive maps that are accessed via Webpages. With the rapid development of Internet and Geographic Information System (GIS) field, public web mapping sites are not foreign to people. Nowadays, people use these web mapping sites for various reasons, in that increasing maps and related map services of web mapping sites are freely available for end users. Thus, increased users of web mapping sites led to more usability studies. Usability Engineering (UE), for instance, is an approach for analyzing and improving the usability of websites through examining and evaluating an interface. In this research, UE method was employed to explore usability problems of four public web mapping sites, analyze the problems quantitatively and provide guidelines for future design based on the test results. Firstly, the development progress for usability studies were described, and simultaneously several usability evaluation methods such as Usability Engineering (UE), User-Centered Design (UCD) and Human-Computer Interaction (HCI) were generally introduced. Then the method and procedure of experiments for the usability test were presented in detail. In this usability evaluation experiment, four public web mapping sites (Google Maps, Bing maps, Mapquest, Yahoo Maps) were chosen as the testing websites. And 42 people, who having different GIS skills (test users or experts), gender (male or female), age and nationality, participated in this test to complete the several test tasks in different teams. The test comprised three parts: a pretest background information questionnaire, several test tasks for quantitative statistics and progress analysis, and a posttest questionnaire. The pretest and posttest questionnaires focused on gaining the verbal explanation of their actions qualitatively. And the design for test tasks targeted at gathering quantitative data for the errors and problems of the websites. Then, the results mainly from the test part were analyzed. The