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1

Site Map  

Cancer.gov

Site Map Programs & Resources Research Groups Foundations of Prevention Biometry Publications Statistical Software About the Research Group Cancer Biomarkers Funding Opportunities Key Programs Meetings and Events Publications About

2

STATE System Interactive Maps  

MedlinePLUS

... Reproductive Health More CDC Sites STATE System Interactive Maps Recommend on Facebook Tweet Share Compartir Highlights 2012 Abstract Highlights 2012 (by section) Highlights 2012 State Map Highlights 2012 Buttons Highlights 2012 Download [Zip–16. ...

3

Site Map  

Cancer.gov

Skip to Content The National Cancer Institute www.cancer.gov The National Institutes of Health Home About BBRB Mission and Goals BBRB Staff Biorepository Coordinating Committee (BCC) Interactive Timeline Related Initiatives International Initiatives Funding

4

Human migrations map, interactive 2D animationSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

The red lines show the possible migration pathway of the ancient human Homo erectus (sometimes known as Homo ergaster). There is little controversy about the travels of H. erectus. This possible path was mapped using fossil evidence that spans more than 1.5 million years. Many researchers believe that H. erectus lived until approximately 300,000 years ago. However, H. erectus may have survived in Indonesia until 40,000 years ago.

2008-10-06

5

Mapping a Study Site  

NSDL National Science Digital Library

In this outdoor activity, learners use a mapping technique to become oriented to the major features of an outdoor site. Learners become aware of both physical and biological features including trees, rocks, water, signs of human activity. After completing this activity, learners can try the OBIS Terrestrial Hi-Lo Hunt and add more detail to their map.

Lawrence Hall of Science

1982-01-01

6

Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites.  

PubMed

Binding sites present well-defined interaction patterns that putative ligands must meet. Knowing them is essential to guide structure-based drug discovery projects. However, complex aspects of molecular recognition-such as protein flexibility or the effect of aqueous solvation-hinder accurate predictions. This is particularly true for polar contacts, which are heavily influenced by the local environment and the behavior of discrete water molecules. Here we present and validate MDmix (Molecular Dynamics simulations with mixed solvents) as a method that provides much more accurate interaction maps than ordinary potentials (e.g., GRID). Additionally, MDmix also affords water displaceability predictions, with advantages over methods that use pure water as solvent (e.g., inhomogeneous fluid solvation theory). With current MD software and hardware solutions, predictions can be obtained in a matter of hours and visualized in a very intuitive manner. Thus, MDmix is an ideal complement in everyday structure-based drug discovery projects. PMID:25275946

Alvarez-Garcia, Daniel; Barril, Xavier

2014-10-23

7

Importance of genetic maps, Mary-Claire KingSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Mary-Claire King DNAi Location:Applications>Genes and medicine>gene hunting>Markers Moving slowly Mary-Claire King talks about the tedious process of hunting for genes in the days before genetic maps (based on thousands of markers) were readily available.

2008-03-26

8

Usability Evaluation of Public Web Mapping Sites  

NASA Astrophysics Data System (ADS)

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 success rate from different public web mapping sites was calculated and compared, and displayed by the means of diagram. And the answers from questionnaires were also classified and organized in this part. Moreover, based on the analysis, this paper expands the discussion about the layout, map visualization, map tools, search logic and etc. Finally, this paper closed with some valuable guidelines and suggestions for the design of public web mapping sites. Also, limitations for this research stated in the end.

Wang, C.

2014-04-01

9

Montana Maps Interactive  

NSDL National Science Digital Library

Montana Maps Interactive is a new tool provided by the state's Natural Resource Information System (NRIS). The program shows a variety of geographic information layers for the state of Montana. Users can view cities, natural and political features, national parks and forests, and various types of land use, among other features. Maps can be zoomed in or out. The feature query allows users to locate features from a layer (e.g. streams or land use) by selecting the layer and then identifying the feature on the map or by letting the program find the feature given its name. The map is then redrawn with the selected feature highlighted in yellow and its attributes listed above the map.

10

NCI: SBIR & STTR - Site Map  

Cancer.gov

Skip to main content Sign Up for Updates | Follow us on Twitter | Connect with us on LinkedIn | Contact Us | Site Map Search About Program Information Program Structure Goals Eligibility Criteria Employment Opportunities Meet the Team Funding Opportunities Find

11

Waste Site Mapping  

NASA Technical Reports Server (NTRS)

Old aircraft considered not restorable are melted down in on-site furnaces to reclaim the aluminum in their airframes. The process produces aluminum ingots and leaves a residue known as "dross." Because dross contains contaminants like lead silver cadmium and copper, Pima County, the dross dumping site, wanted to locate areas where dross had been dumped. Dr. Larry Lepley and Sandra L. Perry used the Landsat Thematic Mapper to screen for dross. A special two-step procedure was developed to separate the dross dumps (typically no larger than 50 meters across) from the desert background. The project has opened the door for similar applications.

1994-01-01

12

Interactive Cardiovascular System Map  

NSDL National Science Digital Library

The cardiovascular portion of the InnerBody website is a road map to the human cardiovascular system. It displays all of the main veins and arteries of the human body allowing the user to click on various parts of body and dozens of links to the many different systems appear. Users can hover over the links to discover what each part is named, or click on the link to be brought to a thorough definition and description of the selected system. Users may also �zoom in� on certain parts to view more detail. In addition to the interactive �map,� InnerBody also has images and descriptions about common issues that arise within the cardiovascular system.

13

3D interactive pictorial maps  

E-print Network

these maps interactive on the Web and have them accessible to a large number of viewers. The results show a number of interactive 3D pictorial maps of different countries and continents. These maps are initially built with Maya, a 3D modeling software..., and converted into web pages using the Viewpoint Technology. For statistical maps, Mel scripts have been used in Maya to take input from the user and change the shape of models accordingly to represent data. These maps are interactive and navigable...

Naz, Asma

2005-02-17

14

Mapping critical interactive sites within the periplasmic domain of the Vibrio cholerae type II secretion protein EpsM.  

PubMed

The type II secretion (T2S) system is present in many gram-negative species, both pathogenic and nonpathogenic, where it supports the delivery of a variety of toxins, proteases, and lipases into the extracellular environment. In Vibrio cholerae, the T2S apparatus is composed of 12 Eps proteins that assemble into a multiprotein complex that spans the entire cell envelope. Two of these proteins, EpsM and EpsL, are key components of the secretion machinery present in the inner membrane. In addition to likely forming homodimers, EpsL and EpsM have been shown to form a stable complex in the inner membrane and to protect each other from proteolytic degradation. To identify and map the specific regions of EpsM involved in protein-protein interactions with both another molecule of EpsM and EpsL, we tested the interactions of deletion constructs of EpsM with full-length EpsM and EpsL by functional characterization and copurification as well as coimmunoprecipitation. Analysis of the truncated EpsM mutants revealed that the region of EpsM from amino acids 100 to 135 is necessary for EpsM to form homo-oligomers, while residues 84 to 99 appear to be critical for a stable interaction with EpsL. PMID:17921296

Johnson, Tanya L; Scott, Maria E; Sandkvist, Maria

2007-12-01

15

Accurately mapping the location of the binding site for the interaction between hepatitis B virus X protein and cytochrome c oxidase III.  

PubMed

The hepatitis B virus (HBV) X protein (HBx) plays an important pathogenetic role in hepatocarcinoma tumorigenesis. As HBx does not have the ability to bind to double-stranded DNA (dsDNA), protein-protein interaction is crucial for HBx functions. In a previous study, we screened a novel HBx-interacting protein, the cytochrome c oxidase subunit III (COXIII). In the present study, we aimed to accurately map the location of the binding site for the interaction of HBx with COXIII. Two fragments of HBx mutants (X1 aa1-72 and X2 aa1-117) were amplified by polymerase chain reaction (PCR) and separately inserted into the pAS2-1 plasmid. PCR and gene sequencing confirmed the correct insertion of the mutant fragments in the plasmid. The transcription of the mutant fragments in yeast cells was demonstrated by RT-PCR and western blot analysis confirmed that they were accurately translated into fusion proteins. Hybridization on solid medium and the detection of ?-galactosidase (?-gal) activity indicated that the binding site for the interaction between HBx and COXIII was located between aa72 and aa117. Specific interactions between the HBxX2 protein and COXIII were verified by co-immunoprecipitation. To the best of our knowledge, this is the first study showing to demonstrate that aa72-117 in HBx is the key region for binding with COXIII. PMID:25483779

Li, Dan; Ding, Jian; Chen, Zhixin; Chen, Yun; Lin, Na; Chen, Fenglin; Wang, Xiaozhong

2015-02-01

16

Dynamic and Interactive Mapping Syllabus  

NSDL National Science Digital Library

From Foothill College and the Using a Web-Based GIS to Teach Problem-Based Science in High School and College project, this pdf contains a syllabus on Dynamic and Interactive Mapping. The objective of the course is to introduce students to "maps for the World-Wide Web, animation, multimedia presentation, and interactive interfaces for presenting geographic information." The syllabus includes lectures, discussions, and laboratory exercises on "computer mapping, GIS, and computer graphics."

17

statement of significance, location map, site plan, landscape plan, site ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

statement of significance, location map, site plan, landscape plan, site sections, evolution of cemetery landscape. - San Francisco National Cemetery, 1 Lincoln Boulevard, San Francisco, San Francisco County, CA

18

Mapping the Major Interaction Between Binding Protein and Ig Light Chains to Sites Within the Variable Domain1  

Microsoft Academic Search

Newly synthesized Ig chains are known to interact in vivo with the binding protein (BiP), a major peptide-binding chaperone in the endoplasmic reticulum. The predominant interactions between the light chain and BiP are observed early in the folding pathway, when the light chain is either completely reduced, or has only one disulfide bond. In this study, we describe the in

David P. Davis; Ritu Khurana; Stephen Meredith; Fred J. Stevens; Yair Argon

19

Kelsey: Clues of the Dig Site Map  

NSDL National Science Digital Library

In this activity, learners explore dinosaur fossils and a dig site. Learners work in groups to analyze a dig site map and match bones to a skeletal drawing of Kelsey (a Triceratops). Learners use colored pencils or markers to color-code bones from the dig site map and the skeleton. This activity is featured on page 33 of the "Dinosphere" unit of study for K-2 learners.

Rick Crosslin

2004-01-01

20

Yellowstone National Park Interactive Map  

NSDL National Science Digital Library

This Yellowstone National Park Map is a handy way to quickly find locations and buildings located in the park. It is currently the most detailed map of Yellowstone national park that can be viewed online. The pull down menu has Yellowstone features such as geyser basins, campgrounds, trails, mountains, and historical points and park structures. Popular geysers, and park locations such as Norris geyser basin, Yellowstone visitor centers, park housing, lodging, and park dining can be easily found. All Yellowstone National Park named structures are indexed so you can easily find the sites that you want to locate.

NPS Source: CENSUS

21

Interactive Geophysical Mapping on the Web  

NASA Astrophysics Data System (ADS)

We have developed a set of interactive, web-based map utilities that make geophysical results accessible to a large number and variety of users. These tools provide access to pre-determined map regions via a simple Html/JavaScript interface or to user-selectable areas using a Java interface to a Generic Mapping Tools (GMT) engine. Users can access a variety of maps, satellite images, and geophysical data at a range of spatial scales for the earth and other planets of the solar system. Developed initially by UNAVCO for study of global-scale geodynamic processes, users can choose from a variety of base maps (satellite mosaics, global topography, geoid, sea-floor age, strain rate and seismic hazard maps, and others) and can then add a number of geographic and geophysical overlays for example coastlines, political boundaries, rivers and lakes, NEIC earthquake and volcano locations, stress axes, and observed and model plate motion and deformation velocity vectors representing a compilation of 2933 geodetic measurements from around the world. The software design is flexible allowing for construction of special editions for different target audiences. Custom maps been implemented for UNAVCO as the "Jules Verne Voyager" and "Voyager Junior", for the International Lithosphere Project's "Global Strain Rate Map", and for EarthScope Education and Outreach as "EarthScope Voyager Jr.". For the later, a number of EarthScope-specific features have been added, including locations of proposed USArray (seismic), Plate Boundary Observatory (geodetic), and San Andreas Fault Observatory at Depth sites plus detailed maps and geographically referenced examples of EarthScope-related scientific investigations. In addition, we are developing a website that incorporates background materials and curricular activities that encourage users to explore Earth processes. A cluster of map processing computers and nearly a terabyte of disk storage has been assembled to power the generation of interactive maps and provide space for a very large collection of map data. A portal to these map tools can be found at: http://jules.unavco.ucar.edu.

Meertens, C.; Hamburger, M.; Estey, L.; Weingroff, M.; Deardorff, R.; Holt, W.

2002-12-01

22

The Interactive Nolli Map of Rome  

NSDL National Science Digital Library

Born in 1701, Giambattista Nolli was an architect who was enamored of Rome in a way that few people have ever experienced. He spent thousands of hours creating his La Pianta Grande di Roma ("the great plan of Rome"), which became his remarkable 1748 map of the Eternal City. The actual map consists of twelve engraved copper plates that measure six feet high and seven feet wide when combined. Nolli was very careful to record the streets, squares, and various other public spaces throughout the city. This website, created by a team of dedicated scholars at the University of Oregon, allows users to examine the map in all its glory, along with a number of interactive layers that document specific building types and census data. First time visitors can launch the map engine from the homepage, and after that, they may wish to look at some of the thematic sections, which include "Natural Features", "Architecture", and "Cartography". The site also includes some fine articles on the map and its legacy, including "The Walls of Rome" and "The Nolli Map as Artifact".

23

1884, 1889 & 1893 Site Maps Brookland Site Development ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1884, 1889 & 1893 Site Maps - Brookland Site Development Study, Brookland, bounded by B&O Railroad Tracks, Rhode Island & Brentwood Avenues on the south, 18th Street & South Dakota Avenue on the east, and Michigan Avenue on the North, Washington, District of Columbia, DC

24

1863, 1880 & 1884 Site Maps Brookland Site Development ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1863, 1880 & 1884 Site Maps - Brookland Site Development Study, Brookland, bounded by B&O Railroad Tracks, Rhode Island & Brentwood Avenues on the south, 18th Street & South Dakota Avenue on the east, and Michigan Avenue on the North, Washington, District of Columbia, DC

25

Site maps and facilities listings  

SciTech Connect

In September 1989, a Memorandum of Agreement among DOE offices regarding the environmental management of DOE facilities was signed by appropriate Assistant Secretaries and Directors. This Memorandum of Agreement established the criteria for EM line responsibility. It stated that EM would be responsible for all DOE facilities, operations, or sites (1) that have been assigned to DOE for environmental restoration and serve or will serve no future production need; (2) that are used for the storage, treatment, or disposal of hazardous, radioactive, and mixed hazardous waste materials that have been properly characterized, packaged, and labelled, but are not used for production; (3) that have been formally transferred to EM by another DOE office for the purpose of environmental restoration and the eventual return to service as a DOE production facility; or (4) that are used exclusively for long-term storage of DOE waste material and are not actively used for production, with the exception of facilities, operations, or sites under the direction of the DOE Office of Civilian Radioactive Waste Management. As part of the implementation of the Memorandum of Agreement, Field Offices within DOE submitted their listings of facilities, systems, operation, and sites for which EM would have line responsibility. It is intended that EM facility listings will be revised on a yearly basis so that managers at all levels will have a valid reference for the planning, programming, budgeting and execution of EM activities.

Not Available

1993-11-01

26

Teacher's Guide Mapping Your Research Site  

E-print Network

the metric system but unfortunately, builders do not). Determine the size of all the important structures of the history of their research site. In the valley some schools actually rest on archaeological sites and so the history of human interactions with the environment at their school site can be quite long. Basic

Hall, Sharon J.

27

Interactive Modelling of Hair with Texture Maps  

Microsoft Academic Search

We present a system for interactively modelling and styling hair on an arbitrary surface using texture maps . Texture maps are used to modulate characteristics of hair strands on the surface, and combinations of these texture maps represent a great deal of information about a hairstyle. We render the scenes in real-time, enabling the user to interactively design and style

Will Baker; Scott A. King

28

Sense of Place Evoked by Interactive Maps  

E-print Network

, spatial cognition, and virtual reality literature, this study constructed a conceptual framework to measure how different interactivity levels of a digital map interface affect potential tourists' experience when exploring maps. In addition, the study...

Go, Hanyoung

2012-07-16

29

Interactive Geophysical Mapping on the Web  

Microsoft Academic Search

We have developed a set of interactive, web-based map utilities that make geophysical results accessible to a large number and variety of users. These tools provide access to pre-determined map regions via a simple Html\\/JavaScript interface or to user-selectable areas using a Java interface to a Generic Mapping Tools (GMT) engine. Users can access a variety of maps, satellite images,

C. Meertens; M. Hamburger; L. Estey; M. Weingroff; R. Deardorff; W. Holt

2002-01-01

30

A Protein Interaction Map of Drosophila melanogaster  

Microsoft Academic Search

Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence

L. Giot; J. S. Bader; C. Brouwer; A. Chaudhuri; B. Kuang; Y. Li; Y. L. Hao; C. E. Ooi; B. Godwin; E. Vitols; G. Vijayadamodar; P. Pochart; H. Machineni; M. Welsh; Y. Kong; B. Zerhusen; R. Malcolm; Z. Varrone; A. Collis; M. Minto; S. Burgess; L. McDaniel; E. Stimpson; F. Spriggs; J. Williams; K. Neurath; N. Ioime; M. Agee; E. Voss; K. Furtak; R. Renzulli; N. Aanensen; S. Carrolla; E. Bickelhaupt; Y. Lazovatsky; A. DaSilva; J. Zhong; C. A. Stanyon; R. L. Finley; K. P. White; M. Braverman; T. Jarvie; S. Gold; M. Leach; J. Knight; R. A. Shimkets; M. P. McKenna; J. Chant; J. M. Rothberg

2003-01-01

31

24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

32

23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 updated to 1931. - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

33

Interactive Map of 1906 Earthquake Photos  

NSDL National Science Digital Library

An interactive map of the city that allows the Bancroft's photographic archive of the quake to be searched by region of the city. The map is divided into regions, and points of interest are highlighted. By comparing photographs taken in each region, it's possible to compare how different areas of the city were affected by the earthquake.

The Bancroft Library

34

Interactive Maps for Community in Online Learning  

ERIC Educational Resources Information Center

The online courses studied here used the visual medium of the interactive geographic map as a form of dialogue to reduce students' sense of transactional distance during the course, build their skills with Web 2.0 media, and increase their motivation. Using the dynamic map and the related online spreadsheet, the course participants created digital…

Cavanaugh, Terence W.; Cavanaugh, Cathy

2008-01-01

35

Mapping of sites in forest stands.  

PubMed

Generally, the forest companies use the total one year planting area as a minimum stratum of the total population and, consequently, the forest inventory processing has been conducted by applying the stratified random sampling to it. This study was carried out in the National Forest of Tres Barras, Brazil, and it aimed to classify and map the sites of Pinus elliottii stands. A systematic sampling was structured into clusters and applied independently by compartments. The clusters, in maltese cross, were composed of four sampling subunits, using Prodan sampling method with a fixed number of six trees. By analysis of the methodology it was possible to confirm the hypothesis: a) the selective thinning cause expressive increase of volumetric variability within compartments; b) the variation of sites within the compartments causes volumetric expansion of variance and this grows proportionally to the quality of the sites; c) the stratification in sites results in minimum variance within them; d) the stratification in sites resulted in until to 91% reduction of variances within them. PMID:25590737

Netto, Sylvio Péllico; Stefanello, Flavio R; Pelissari, Allan L; David, Hassan C

2014-12-01

36

Interactivity on Traditional Media Web Sites  

Microsoft Academic Search

This study compares the radio industry's use of interactivity to that of other traditional media on the Web such as newspapers and television stations, along the dimensions of audience-oriented interactivity and source-oriented interactivity. A content analysis of 112 traditional radio station Web sites, 282 traditional newspaper Web sites, and 128 traditional television station Web sites found that traditional radio station

Michelle Seelig

2008-01-01

37

Topographic Map of Pathfinder Landing Site  

NASA Technical Reports Server (NTRS)

Topographic map of the landing site, to a distance of 60 meters from the lander in the LSC coordinate system. The lander is shown schematically in the center; 2.5 meter radius circle (black) centered on the camera was not mapped. Gentle relief [root mean square (rms) elevation variation 0.5 m; rms a directional slope 4O] and organization of topography into northwest and northeast-trending ridges about 20 meters apart are apparent. Roughly 30% of the illustrated area is hidden from the camera behind these ridges. Contours (0.2 m interval) and color coding of elevations were generated from a digital terrain model, which was interpolated by kriging from approximately 700 measured points. Angular and parallax point coordinates were measured manually on a large (5 m length) anaglyphic uncontrolled mosaic and used to calculate Cartesian (LSC) coordinates. Errors in azimuth on the order of 10 are therefore likely; elevation errors were minimized by referencing elevations to the local horizon. The uncertainty in range measurements increases quadratically with range. Given a measurement error of 1/2 pixel, the expected precision in range is 0.3 meter at 10 meter range, and 10 meters at 60 meter range. Repeated measurements were made, compared, and edited for consistency to improve the range precision. Systematic errors undoubtedly remain and will be corrected in future maps compiled digitally from geometrically controlled images. Cartographic processing by U.S. Geological Survey.

NOTE: original caption as published in Science Magazine

Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California Institute of Technology (Caltech).

1997-01-01

38

Groundwater maps of the Hanford Site, June 1993  

Microsoft Academic Search

The Groundwater Maps of the Hanford Site, June 1993 is an update of the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This report series presents the semiannual water level measurements taken at site groundwater monitoring wells each June and December and the groundwater maps derived from these measurements. These reports document

G. L. Kasza; M. J. Hartman; W. A. Jordan; D. C. Weekes

1994-01-01

39

Geographic Information System Interactive Map Server  

NSDL National Science Digital Library

Cornell University's Institute for the Study of the Continents (INSTOC) has launched this interactive, data-rich Website to provide regional "maps showing major geographic features of a region, along with such information as the location of earthquake faults, a record of earthquake occurrences and technical data about the events." The Geoscience Interactive Database (Java applet with accompanying User Guide) enables users to interact dynamically with "large volumes of organized digital data sets, map and display any parts of selected data," and create unique maps for download (in postscript or JPEG formats). In addition to the database, INSTOC offers information about their current projects, highlighted at the Webpage, including Building the Digital Earth, Active Tectonics Studies in the Dead Sea Fault Zone, and The Saudi Arabia Seismology Project, among others.

40

Outline Map Sites: The Perry-Castaneda Library Map Collection  

NSDL National Science Digital Library

This website provides an extensive list of links to outline maps of the world, continents, countries, and counties, as well as some historical and thematic maps. Maps are presented as they were originally published, and the original publisher/source and date is provided.

41

The public Human Genome Project: mapping the genome, sequencing, and reassembly, 3D animationSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

DNAi location: Genome>The Project>putting it together>Animations>Hierarchical shotgun (public) Mapping the genome AND Sequencing and assembly This animation shows how the human genome was sequenced using the 'hierarchical shotgun' method of the public Human Genome Project. All the base pairs in our DNA are represented as letters on pieces of paper.

2008-10-06

42

Data visualization in interactive maps and time series  

NASA Astrophysics Data System (ADS)

State-of-the-art data visualization has nothing to do with plots and maps we used few years ago. Many opensource tools are now available to provide access to scientific data and implement accessible, interactive, and flexible web applications. Here we will present a web site opened November 2013 to create custom global and regional maps and time series from research models and datasets. For maps, we explore and get access to data sources from a THREDDS Data Server (TDS) with the OGC WMS protocol (using the ncWMS implementation) then create interactive maps with the OpenLayers javascript library and extra information layers from a GeoServer. Maps become dynamic, zoomable, synchroneaously connected to each other, and exportable to Google Earth. For time series, we extract data from a TDS with the Netcdf Subset Service (NCSS) then display interactive graphs with a custom library based on the Data Driven Documents javascript library (D3.js). This time series application provides dynamic functionalities such as interpolation, interactive zoom on different axes, display of point values, and export to different formats. These tools were implemented for the Global Carbon Atlas (http://www.globalcarbonatlas.org): a web portal to explore, visualize, and interpret global and regional carbon fluxes from various model simulations arising from both human activities and natural processes, a work led by the Global Carbon Project.

Maigne, Vanessa; Evano, Pascal; Brockmann, Patrick; Peylin, Philippe; Ciais, Philippe

2014-05-01

43

Dynamic Map: Representation of interactions between robots  

SciTech Connect

As robotics applications become more complex, the need for tools to analyze and explain interactions between robots has become more acute. We introduce the concept of Dynamic Map (DM), which can serve as a generic tool to analyze interactions between robots or with their environment. We show that this concept can be applied to different kinds of applications, like a predator-prey situation, or collision avoidance.

Zanardi, C. [GRPR, Ecole Polytechnique de Montreal (Canada)

1996-12-31

44

Mapping of a yeast G protein betagamma signaling interaction.  

PubMed Central

The mating pathway of Saccharomyces cerevisiae is widely used as a model system for G protein-coupled receptor-mediated signal transduction. Following receptor activation by the binding of mating pheromones, G protein betagamma subunits transmit the signal to a MAP kinase cascade, which involves interaction of Gbeta (Ste4p) with the MAP kinase scaffold protein Ste5p. Here, we identify residues in Ste4p required for the interaction with Ste5p. These residues define a new signaling interface close to the Ste20p binding site within the Gbetagamma coiled-coil. Ste4p mutants defective in the Ste5p interaction interact efficiently with Gpa1p (Galpha) and Ste18p (Ggamma) but cannot function in signal transduction because cells expressing these mutants are sterile. Ste4 L65S is temperature-sensitive for its interaction with Ste5p, and also for signaling. We have identified a Ste5p mutant (L196A) that displays a synthetic interaction defect with Ste4 L65S, providing strong evidence that Ste4p and Ste5p interact directly in vivo through an interface that involves hydrophobic residues. The correlation between disruption of the Ste4p-Ste5p interaction and sterility confirms the importance of this interaction in signal transduction. Identification of the Gbetagamma coiled-coil in Ste5p binding may set a precedent for Gbetagamma-effector interactions in more complex organisms. PMID:9832519

Dowell, S J; Bishop, A L; Dyos, S L; Brown, A J; Whiteway, M S

1998-01-01

45

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2010 CFR

...2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

2010-10-01

46

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2014 CFR

...2014-10-01 2014-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

2014-10-01

47

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2011 CFR

...2011-10-01 2011-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

2011-10-01

48

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2013 CFR

...2013-10-01 2013-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

2013-10-01

49

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2012 CFR

...2012-10-01 2012-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

2012-10-01

50

Surface-material maps of Viking landing sites on Mars  

NASA Technical Reports Server (NTRS)

Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

Moore, H. J.; Keller, J. M.

1991-01-01

51

Seismic hazard mapping of California considering site effects  

USGS Publications Warehouse

In this paper, we have combined the U.S. Geological Survey's National Seismic Hazard Maps model with the California geologic map showing 17 generalized geologic units that can be defined by their VS30. We regrouped these units into seven VS30 values and calculated a probabilistic seismic hazard map for the entire state for each VS30 value. By merging seismic hazard maps based on the seven different V S30 values, a suite of seismic hazard maps was computed for 0.2 and 1.0 s spectral ordinates at 2% probability of exceedance (PE) in 50 years. The improved hazards maps explicitly incorporate the site effects and their spatial variability on ground motion estimates. The spectral acceleration (SA) at 1.0 s map of seismic shaking potential for California has now been published as California Geological Survey Map Sheet 48.

Kalkan, E.; Wills, C.J.; Branum, D.M.

2010-01-01

52

Groundwater maps of the Hanford Site, June 1993  

SciTech Connect

The Groundwater Maps of the Hanford Site, June 1993 is an update of the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This report series presents the semiannual water level measurements taken at site groundwater monitoring wells each June and December and the groundwater maps derived from these measurements. These reports document the changes in the groundwater level at Hanford as the site has transitioned from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. Groundwater Maps of the Hanford Site are prepared for the US Department of Energy, Office of Environmental Restoration and Waste Management, by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC). This document fulfills reporting requirements specified in WHC (1993), Section 8.0 {open_quotes}Water Quality{close_quotes} and also described in the Environmental Monitoring Plan for the Hanford Site (DOE-RL 1991). Maps depicting the water table beneath the Hanford Site south of the Columbia River are presented in this report. Appendix A lists the well identification number, depth to water, casing elevating and the water level elevation for each well measured during June 1993. A summary discussion of the data is included with a well index map, the depth to water map and the contoured map of the water table surface for the Hanford Site and each of the three operational areas (the 100, 200, and 300-1100 Areas).

Kasza, G.L.; Hartman, M.J.; Jordan, W.A.; Weekes, D.C.

1994-02-01

53

Interactive State of Metropolitan America Indicator Map  

NSDL National Science Digital Library

How quickly have the suburbs in the American southeast grown over the past decade? This question, and many others, are answered in fine visual form on this website, created by staff members at The Brookings Institution. Visitors can use the interactive maps to look over population, ethnicity, age, and educational attainment distributions across the United States. Each map contains a zoom feature, and visitors can use the subject indicators to look at different variables. Also, visitors can toggle through different geographic scales of focus, including metro areas, center cities, suburbs, and states. Finally, visitors can also download and read "The State of Metropolitan America" report which provides additional perspective on some of these recent demographic trends.

54

Groundwater maps of the Hanford site, June 1995  

SciTech Connect

The Groundwater Maps of the Hanford Site, June 1995 is a continuation of a series of reports (see Serkowski et al. 1995) that document the configuration of the water table aquifer beneath the Hanford Site (Figure 1). This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. Groundwater Maps of the Hanford Site is prepared for the U.S. Department of Energy by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC). This document fulfills reporting requirements specified in WHC-CM-7-5, Section 8.0 ``Water Quality`` and described in the environmental monitoring plan for the Hanford Site. (DOE-RL 1993a) This document highlights the three major operations areas (the 100, 200 and 300/1100 Areas) where wastes were discharged to the soil. Each area includes a summary discussion of the data, a well index map, and a contoured map of the water table surface. Appendix A contains all of the data collected for this program.

Sweeney, M.D.

1996-03-15

55

Coordinate Map of Rocks at Pathfinder Landing Site  

NASA Technical Reports Server (NTRS)

Mars-local-level (LL frame) coordinate map of rocks counted at the Mars Pathfinder landing site. Positions, apparent diameters (D), and heights (H) were measured to the nearest centimeter in the Mars map virtual reality environment constructed from the 'Monster Pan'

1997-01-01

56

Site Map | Physical Sciences in Oncology  

Cancer.gov

Search site CENTERS Arizona State University Cornell University Dana-Farber Cancer Institute H. Lee Moffitt Cancer Center & Research Institute Johns Hopkins University Massachusetts Institute of Technology The Methodist Hospital Research Institute Northwestern

57

Soil Liquefaction Susceptibility and Site Class Maps of Washington State  

NSDL National Science Digital Library

In response to the Nisqually earthquake of 2001, the Washington State Division of Geology and Earth Resources (DGER) developed two types of earthquake hazard maps for every county in the state: liquefaction susceptibility maps, which outline areas where water-saturated sandy soil loses strength during earthquake shaking, and National Earthquake Hazards Reduction Program (NEHRP) site class maps, which outline areas where soils amplify ground shaking. The maps will be used by state and local governments in Washington to update existing hazard mitigation plans and to delineate geologically hazardous areas for emergency planning and response, planning of local zoning ordinances, and building code enforcement. A link is provided to an ftp site where the maps are stored in folders.

58

Groundwater maps of the Hanford Site, June 1994  

SciTech Connect

This report is a continuation of reports (Kasza et al., 1994) that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and ground water monitoring programs currently in progress on the Hanford Site. This report highlights the three major operations areas (the 100, 200, and 300/1100 Areas) where wastes were discharged to the soil. Each area includes a summary discussion of the data, a well index map, and a contoured map of the water table surface.

Serkowski, J.A.; Jordan, W.A.; Hartman, M.J.

1994-12-01

59

Mapping enzyme active sites in complex proteomes.  

PubMed

Genome sequencing projects have uncovered many novel enzymes and enzyme classes for which knowledge of active site structure and mechanism is limited. To facilitate mechanistic investigations of the numerous enzymes encoded by prokaryotic and eukaryotic genomes, new methods are needed to analyze enzyme function in samples of high biocomplexity. Here, we describe a general strategy for profiling enzyme active sites in whole proteomes that utilizes activity-based chemical probes coupled with a gel-free analysis platform. We apply this gel-free strategy to identify the sites of labeling on enzymes targeted by sulfonate ester probes. For each enzyme examined, probe labeling was found to occur on a conserved active site residue, including catalytic nucleophiles (e.g., C32 in glutathione S-transferase omega) and bases/acids (e.g., E269 in aldehyde dehydrogenase-1; D204 in enoyl CoA hydratase-1), as well as residues of unknown function (e.g., D127 in 3 beta-hydroxysteroid dehydrogenase/isomerase-1). These results reveal that sulfonate ester probes are remarkably versatile activity-based profiling reagents capable of labeling a diversity of catalytic residues in a range of mechanistically distinct enzymes. More generally, the gel-free strategy described herein, by consolidating into a single step the identification of both protein targets of activity-based probes and the specific residues labeled by these reagents, provides a novel platform in which the proteomic comparison of enzymes can be accomplished in unison with a mechanistic analysis of their active sites. PMID:14759193

Adam, Gregory C; Burbaum, Jonathan; Kozarich, John W; Patricelli, Matthew P; Cravatt, Benjamin F

2004-02-11

60

Antibody Recognition of Cancer-Related Gangliosides and Their Mimics Investigated Using in silico Site Mapping  

Microsoft Academic Search

Modified gangliosides may be overexpressed in certain types of cancer, thus, they are considered a valuable target in cancer immunotherapy. Structural knowledge of their interaction with antibodies is currently limited, due to the large size and high flexibility of these ligands. In this study, we apply our previously developed site mapping technique to investigate the recognition of cancer-related gangliosides by

Mark Agostino; Elizabeth Yuriev; Paul A. Ramsland

2012-01-01

61

Groundwater maps of the Hanford Site, June 1992  

SciTech Connect

The Groundwater Maps of the Hanford Site, June 1992 is an update to the series of reports that document the configuration of the water table in the unconsolidated sediments beneath the Hanford Site (Figure 1). Water level measurements for these reports are collected from site groundwater monitoring wells each June and December. The groundwater data are portrayed on a series of maps to illustrate the hydrologic conditions at the Hanford Site and are also tabulated in an appendix. The purpose of this report series is to document the changes in the groundwater level at Hanford as the site transitions from a nuclear material production role to environmental restoration and remediation. In addition, these reports provide water level data in support of the site characterization and groundwater monitoring programs on the Hanford Site. Groundwater maps of the Hanford Site are prepared for the US Department of Energy, Office of Environmental Restoration and Waste Management, by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC).

Kasza, G.L.; Hartman, M.J.; Hodges, F.N.; Weekes, D.C.

1992-12-01

62

Groudwater maps of the Hanford Site Separations Area, June 1989  

SciTech Connect

The groundwater maps of the Hanford Site Separations Area, recorded June 1989, are prepared by the Environmental Engineering and Technology Function, Environmental Division, Westinghouse Hanford Company. This set of groundwater maps consists of Separations Area depth-to-water map, Separations Area water table map, and a map comparing the potentiometric surface of the Rattlesnake Ridge confined aquifer with the water table of the unconfined aquifer. The field measurements for these maps were collected during June 1989. The Separations Area depth-to-water map depicts the measurement well locations and the depths to the water table at these locations. This map supports engineering or environmental studies which may require the approximate depth from the ground surface to the water table. On the third map, the potentiometric surface of the Rattlesnake Ridge confined aquifer is compared with the water table of the unconfined aquifer in the vicinity of West Lake, Gable Mountain Pond, and the B Pond system. The purpose of this map is to monitor the potential for aquifer intercommunication in this area. 3 figs., 1 tab.

Kasza, G.L.; Reidel, S.P.; Schatz, A.L.

1989-09-01

63

Mapping chromatin interactions with 5C technology  

PubMed Central

In eukaryotes, genome organization can be observed on many levels and at different scales. This organization is important not only to reduce chromosome length but also for the proper execution of various biological processes. High-resolution mapping of spatial chromatin structure was made possible by the development of the chromosome conformation capture (3C) technique. 3C uses chemical cross-linking followed by proximity-based ligation of fragmented DNA to capture frequently interacting chromatin segments in cell populations. Several 3C-related methods capable of higher chromosome conformation mapping throughput were reported afterwards. These techniques include the 3C-carbon copy (5C) approach, which offers the advantage of being highly quantitative and reproducible. We provide here a reference protocol for the production of 5C libraries analyzed by next-generation sequencing or onto microarrays. A procedure used to verify that 3C library templates bear the high quality required to produce superior 5C libraries is also described. We believe that this comprehensive detailed protocol will help guide researchers in probing spatial genome organization and its role in various biological processes. PMID:23137922

Ferraiuolo, Maria A.; Sanyal, Amartya; Naumova, Natalia; Dekker, Job; Dostie, Josée

2013-01-01

64

Robotic Mapping of Cultural Heritage Sites  

NASA Astrophysics Data System (ADS)

In archaeological studies the use of new technologies has moved into focus in the past years creating new challenges such as the processing of the massive amounts of data. In this paper we present steps and processes for smart 3D modelling of environments by use of the mobile robot Irma3D. A robot that is equipped with multiple sensors, most importantly a photo camera and a laser scanner, enables the automation of most of the processes, including data acquisition and registration. The robot was tested in two scenarios, Ostia Antica and the Würzburg Residence. The paper describes the steps for creating 3D color reconstructions of these renown cultural heritage sites.

Borrmann, D.; Heß, R.; Houshiar, H. R.; Eck, D.; Schilling, K.; Nüchter, A.

2015-02-01

65

Direct optical mapping of transcription factor binding sites on field-stretched ?-DNA in nanofluidic devices  

PubMed Central

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage ?-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (? 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

2014-01-01

66

INTERACTIVE NAME PLACEMENT FOR PROVISIONAL MAPS.  

USGS Publications Warehouse

Computer generation and placement of map type has been refined into a production mode at Mid-Continent Mapping Center (MCMC) for USGS 1:24,000- and 1:25,000-scale Provisional maps. The map collar program is written in FORTRAN using batch processing that allows the program to work in the background.

Goldberg, Jeffrey L.; Miller, Thomas C.

1983-01-01

67

Groundwater maps of the Hanford Site, December 1993  

SciTech Connect

This report is an update to the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This series presents the latest results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. The three major operations areas (the 100, 200 and 300/1100 Areas) where wastes were discharged to the soil are covered in this update. The water level measurements from the wells in these areas are portrayed on a set of maps to illustrate the hydrologic conditions and are also tabulated in an appendix. A summary discussion of the data is included with the well index map, the depth to water map, and the contoured map of the water table surface for each of the three areas.

Kasza, G.L.; Hartman, M.J.; Jordan, W.A.; Borghese, J.V.

1994-07-01

68

Groundwater maps of the Hanford Site, December 1995  

SciTech Connect

This the latest in a series of reports that document the configuration of the water table aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site.

Sweeney, M.D., Westinghouse Hanford

1996-07-02

69

Groundwater maps of the Hanford Site, December 1994  

SciTech Connect

This report is a continuation of a series of reports (see Serkowski et al 1994) that the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site.

Serkowski, J.A.; Hartman, M.J.; Sweeney, M.D.

1995-06-01

70

24 CFR 3285.103 - Site suitability with design zone maps.  

Code of Federal Regulations, 2010 CFR

...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...

2010-04-01

71

24 CFR 3285.103 - Site suitability with design zone maps.  

Code of Federal Regulations, 2012 CFR

...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...

2012-04-01

72

24 CFR 3285.103 - Site suitability with design zone maps.  

Code of Federal Regulations, 2013 CFR

...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...

2013-04-01

73

24 CFR 3285.103 - Site suitability with design zone maps.  

Code of Federal Regulations, 2011 CFR

...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...

2011-04-01

74

24 CFR 3285.103 - Site suitability with design zone maps.  

Code of Federal Regulations, 2014 CFR

...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...

2014-04-01

75

13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test Area 1-125. Specifications No. ENG (NASA)-04-35363-1; Drawing No. 60-09-34; sheet 11. Ref. No. C-l. D.O. SERIES 1597/1. Approved for siting on 24 April 1962. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Leuhman Ridge near Highways 58 & 395, Boron, Kern County, CA

76

Seismic hazard maps of Italy including site effects  

Microsoft Academic Search

The seismic hazard of Italy was mapped adopting multiple models of seismic sources, recurrence rates and attenuation relationships, and investigating the influence of site effects on assessing the earthquake hazard. This result was achieved by placing all the alternatives in a logic-tree diagram, and performing an uncertainty analysis of the main epistemic variables involved in probabilistic seismic hazard computations. Several

R. Romeo; A. Paciello; D. Rinaldis

2000-01-01

77

Exchange interactions in systems with multiple magnetic sites.  

PubMed

Nonequivalent magnetic interactions in systems with multiple magnetic centers can be explored through a proper description of exchange coupling. The magnetic exchange coupling constant (J) in systems with two magnetic sites is reliably estimated using Heisenberg-Dirac-van Vleck (HDVV) model through broken symmetry approach (BS) within a density functional theory (DFT) framework. However, in case of systems with multiple magnetic centers, exchange coupling constants, evaluated through state-of-the-art techniques, are often found to be inadequate to produce a correct fingerprint of the nature of magnetic interactions therein. This work suggests a new scheme to estimate exchange coupling constants in such systems. In this strategy, distribution of spins on magnetic sites in the ground state of systems with multiple magnetic centers is computed. On the basis of this spin mapping, exchange coupling constants between specific pairs are estimated through BS-DFT approach while keeping all other paramagnetic atoms magnetically inactive. Nonetheless, the effect of magnetically inert paramagnetic sites is already taken into account by the process of spin mapping, which is further justified through expressing the HDVV Hamiltonian in terms of spin density operators. We employ this technique to hypothetical benchmark systems, H(3)He(3) and H(4)He(4) followed by real molecules, cationic manganese trimer, 1,3,5-benzenetriyltris (N-tert-butyl nitroxide), and a pentanuclear manganese complex. Results are found to be concordant with the already established nature of magnetic interaction in these systems. This strategy is different from the most popular scheme to compute J in systems with multiple magnetic centers in the sense that it avoids the formation of a large matrix out of different spin configurations and thus provides a reliable and computationally economic way to address the magnetic interactions in non isotropic systems with multiple magnetic sites. PMID:20496941

Paul, Satadal; Misra, Anirban

2010-06-24

78

Global Mapping of the Yeast Genetic Interaction Network  

Microsoft Academic Search

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to

Amy Hin Yan Tong; Guillaume Lesage; Gary D. Bader; Huiming Ding; Hong Xu; Xiaofeng Xin; James Young; Gabriel F. Berriz; Renee L. Brost; Michael Chang; YiQun Chen; Xin Cheng; Gordon Chua; Helena Friesen; Debra S. Goldberg; Jennifer Haynes; Christine Humphries; Grace He; Shamiza Hussein; Lizhu Ke; Nevan Krogan; Zhijian Li; Joshua N. Levinson; Hong Lu; Patrice Ménard; Christella Munyana; Ainslie B. Parsons; Owen Ryan; Raffi Tonikian; Tania Roberts; Anne-Marie Sdicu; Jesse Shapiro; Bilal Sheikh; Bernhard Suter; Sharyl L. Wong; Lan V. Zhang; Hongwei Zhu; Christopher G. Burd; Sean Munro; Chris Sander; Jasper Rine; Jack Greenblatt; Matthias Peter; Anthony Bretscher; Graham Bell; Frederick P. Roth; Grant W. Brown; Brenda Andrews; Howard Bussey; Charles Boone

2004-01-01

79

Global Land Survey Impervious Mapping Project Web Site  

NASA Technical Reports Server (NTRS)

The Global Land Survey Impervious Mapping Project (GLS-IMP) aims to produce the first global maps of impervious cover at the 30m spatial resolution of Landsat. The project uses Global Land Survey (GLS) Landsat data as its base but incorporates training data generated from very high resolution commercial satellite data and using a Hierarchical segmentation program called Hseg. The web site contains general project information, a high level description of the science, examples of input and output data, as well as links to other relevant projects.

DeColstoun, Eric Brown; Phillips, Jacqueline

2014-01-01

80

Information Flow between Weakly Interacting Lattices of Coupled Maps  

E-print Network

Weakly interacting lattices of coupled maps can be modeled as ordinary coupled map lattices separated from each other by boundary regions with small coupling parameters. We demonstrate that such weakly interacting lattices can nevertheless have unexpected and striking effects on each other. Under specific conditions, particular stability properties of the lattices are significantly influenced by their weak mutual interaction. This observation is tantamount to an efficacious information flow across the boundary. 1

York Dobyns; Harald Atmanspacher

81

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.  

PubMed

Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenesis experiments, and common polymorphisms. Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions. We illustrate the utility of MuPIT interactive in rationalizing the impact of selected polymorphisms in the PharmGKB database, somatic mutations identified in the Cancer Genome Atlas study of invasive breast carcinomas, and rare variants identified in the exome sequencing project. MuPIT interactive is freely available for non-profit use at http://mupit.icm.jhu.edu . PMID:23793516

Niknafs, Noushin; Kim, Dewey; Kim, Ryangguk; Diekhans, Mark; Ryan, Michael; Stenson, Peter D; Cooper, David N; Karchin, Rachel

2013-11-01

82

Access to Space Interactive Design Web Site  

NASA Technical Reports Server (NTRS)

The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

83

From ORFeomes to Protein Interaction Maps in Viruses  

Microsoft Academic Search

Although cloned viral ORFeomes are particularly well suited for genome-wide interaction mapping due to the limited size of viral genomes, only a few such studies have been published. Here, we summarize virus interaction mapping projects involving vaccinia virus, hepatitis C virus (HCV), potato virus A (PVA), pea seed-borne mosaic virus (PSbMV), and bacteriophage T7, as well as some projects in

Peter Uetz; Seesandra V. Rajagopala; Yu-An Dong; Jürgen Haas

2009-01-01

84

Mapping receptor-ligand interactions with synthetic peptide arrays: exploring the structure and function of membrane receptors.  

PubMed

Development of synthetic peptide array technology started in the early 1990s. The technique originally developed by Ronald Frank has become a powerful tool for high throughput approaches in biology and chemistry mapping protein interaction sites. In this review we focus on peptide arrays applied to investigate receptor-ligand interactions, such as peroxisomal membrane receptor proteins, the maltose importer machinery and receptor proteins recognizing short linear motifs of their partners. We present several systematic sets of peptide arrays useful for mapping protein-protein- or receptor-ligand binding sites. Besides a more technical description of the peptide array preparation we discuss in detail the reliability and improvement of mapping protein-protein interactions by synthetic peptide arrays. At least proteomic approaches for mapping protein-protein interactions by peptide arrays are shown especially for the case of protein interaction domains. PMID:21561681

Volkmer, Rudolf; Kretzschmar, Ines; Tapia, Victor

2012-04-01

85

A map of directional genetic interactions in a metazoan cell.  

PubMed

Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations. PMID:25748138

Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

2015-01-01

86

Development and application of site mapping methods for the design of glycosaminoglycans.  

PubMed

Glycosaminoglycans (GAGs) are complex polysaccharides involved in a wide range of biological signaling events, as well as being important as biological structural materials. Despite the ubiquity and importance of GAG-protein interactions in biological systems and potentially as therapeutic targets, detailed structures of such interactions are sparse in availability. Computational methods can provide detailed structural knowledge of these interactions; however, they should be evaluated against suitable test systems prior to their widespread use. In this study, we have investigated the application of automated molecular docking and interaction mapping techniques to characterizing GAG-protein interactions. A series of high-resolution X-ray crystal structures of GAGs in complex with proteins was used to evaluate the approaches. Accurately scoring the pose fitting best with the crystal structure was a challenge for all docking programs evaluated. The site mapping technique offered excellent prediction of the key residues involved in ligand recognition, comparable to the best pose and improved over the top-ranked pose. A design protocol incorporating site- and ligand-based mapping techniques was developed and applied to identify GAGs capable of binding to acidic fibroblast growth factor (aFGF). The protocol was able to identify ligands known to bind to aFGF and accurately able to predict the binding modes of those ligands when using a known ligand-binding conformation of the protein. This study demonstrates the value of mapping-based techniques in identifying specific GAG epitopes recognized by proteins and for GAG-based drug design. PMID:24859723

Agostino, Mark; Gandhi, Neha S; Mancera, Ricardo L

2014-09-01

87

Site classification map for Tbilisi using seismic prospecting methods  

NASA Astrophysics Data System (ADS)

This aspect deserves major attention since it plays considerable role in the definition of the seismic impact to be considered in the design and retrofitting of structures. The most important parameter of soil maps of seismic site conditions, the shear wave velocity in the upper 30 m section of the ground (VS30) on regional scales are relatively rare since they require substantial investment in geological and geotechnical data acquisition and interpretation. Work presented here was initiated by working package wp5 of regional projects EMME (Earthquake Model for Middle East Region). In the frame of the project geophysical field work were done in some parts of Tbilisi. Seismic prospecting measurements were done along some profiles. In seismic= prospecting RAS-24 was used and obtained data is processed by Winsism V.12 (refraction analysis ). Second version of soil classification for Tbilisi city was done on the basis of new geo-engineering map of 1: 25 000 scales. For this the number of engineering-geological researches and generalization on the territory of Tbilisi were processed, All the Geological and Engineer-geological reports, that were collected and processed. Since in the geological reports less attention is paid to the genesis of the quaternary sediments and their lithological description, and in this regard the territory of Tbilisi is very difficult and multi-spectrum, it was necessary to conduct additional field surveys in 10 districts to specify information. Finely combining information that comes from seismoprospecting measurements and geo-engineering map the new site classification map expressed in Vs30 were derived for Tbilisi city.

Goguadze, Nino; Gventcadze, Aleko; Arabidze, Vakhtang; Tsereteli, Emil; Gaphrindashvili, Giorgi

2013-04-01

88

Evaluation of Mapping Methodologies at a Legacy Test Site  

NASA Astrophysics Data System (ADS)

On June 12th, 1985, a nuclear test with an announced yield between 20-150kt was detonated in rhyolitic lava in a vertical emplacement borehole at a depth of 608m below the surface. This test did not collapse to the surface and form a crater, but rather resulted in a subsurface collapse with more subtle surface expressions of deformation, providing an opportunity to evaluate the site using a number of surface mapping methodologies. The site was investigated over a two-year time span by several mapping teams. In order to determine the most time efficient and accurate approach for mapping post-shot surface features at a legacy test site, a number of different techniques were employed. The site was initially divided into four quarters, with teams applying various methodologies, techniques, and instrumentations to each quarter. Early methods included transect lines and site gridding with a Brunton pocket transit, flagging tape, measuring tape, and stakes; surveying using a hand-held personal GPS to locate observed features with an accuracy of × 5-10m; and extensive photo-documentation. More recent methods have incorporated the use of near survey grade GPS devices to allow careful location and mapping of surface features. Initially, gridding was employed along with the high resolution GPS surveys, but this was found to be time consuming and of little observational value. Raw visual observation (VOB) data included GPS coordinates for artifacts or features of interest, field notes, and photographs. A categorization system was used to organize the myriad of items, in order to aid in database searches and for visual presentation of findings. The collected data set was imported into a geographic information system (GIS) as points, lines, or polygons and overlain onto a digital color orthophoto map of the test site. Once these data were mapped, spectral data were collected using a high resolution field spectrometer. In addition to geo-locating the field observations with 10cm resolution GPS, LiDAR and hyperspectral imagery were also acquired. The LiDAR and hyperspectral data are being processed and will be added to the existing geo-referenced database as separate information layers for remote sensing analysis of surface features associated with the legacy test. By consolidating the various components of a VOB data point (coordinates, photo and item description) into a standalone database, searching or querying for other components or collects such as subsurface geophysical and/or airborne imagery is made much easier. Work by Los Alamos National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under Contract No. DE AC52 06NA25946 with the U.S. Department of Energy.

Sussman, A. J.; Schultz-Fellenz, E. S.; Roback, R. C.; Kelley, R. E.; Drellack, S.; Reed, D.; Miller, E.; Cooper, D. I.; Sandoval, M.; Wang, R.

2013-12-01

89

A proteome-wide protein interaction map for Campylobacter jejuni  

PubMed Central

Background Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes. Here we report the systematic identification of protein interactions for the bacterium Campylobacter jejuni, a food-borne pathogen and a major cause of gastroenteritis worldwide. Results Using high-throughput yeast two-hybrid screens we detected and reproduced 11,687 interactions. The resulting interaction map includes 80% of the predicted C. jejuni NCTC11168 proteins and places a large number of poorly characterized proteins into networks that provide initial clues about their functions. We used the map to identify a number of conserved subnetworks by comparison to protein networks from Escherichia coli and Saccharomyces cerevisiae. We also demonstrate the value of the interactome data for mapping biological pathways by identifying the C. jejuni chemotaxis pathway. Finally, the interaction map also includes a large subnetwork of putative essential genes that may be used to identify potential new antimicrobial drug targets for C. jejuni and related organisms. Conclusion The C. jejuni protein interaction map is one of the most comprehensive yet determined for a free-living organism and nearly doubles the binary interactions available for the prokaryotic kingdom. This high level of coverage facilitates pathway mapping and function prediction for a large number of C. jejuni proteins as well as orthologous proteins from other organisms. The broad coverage also facilitates cross-species comparisons for the identification of evolutionarily conserved subnetworks of protein interactions. PMID:17615063

Parrish, Jodi R; Yu, Jingkai; Liu, Guozhen; Hines, Julie A; Chan, Jason E; Mangiola, Bernie A; Zhang, Huamei; Pacifico, Svetlana; Fotouhi, Farshad; DiRita, Victor J; Ideker, Trey; Andrews, Phillip; Finley, Russell L

2007-01-01

90

Global Mapping of the Yeast Genetic Interaction Network  

E-print Network

principles of genetic interaction networks, we conducted a large-scale analysis of synthetic geneticGlobal Mapping of the Yeast Genetic Interaction Network Amy Hin Yan Tong,1,2 * Guillaume Lesage,3 P. Roth,7 Grant W. Brown,5 Brenda Andrews,2 Howard Bussey,3 Charles Boone1,2 A genetic

Mihail, Milena

91

Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems  

E-print Network

Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems Daniel M. Ratner of carbohydrates in biological processes.[1] This includes carbohydrate­carbohy- drate, carbohydrate­protein, and carbohydrate­nu- cleic acid interactions (see Figure 1). Carbohydrates, in the form of glycopeptides

Ratner, Daniel M.

92

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces  

PubMed Central

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors. PMID:22701576

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

93

A geostatistical approach to mapping site response spectral amplifications  

USGS Publications Warehouse

If quantitative estimates of the seismic properties do not exist at a location of interest then the site response spectral amplifications must be estimated from data collected at other locations. Currently, the most common approach employs correlations of site class with maps of surficial geology. Analogously, correlations of site class with topographic slope can be employed where the surficial geology is unknown. Our goal is to identify and validate a method to estimate site response with greater spatial resolution and accuracy for regions where additional effort is warranted. This method consists of three components: region-specific data collection, a spatial model for interpolating seismic properties, and a theoretical method for computing spectral amplifications from the interpolated seismic properties. We consider three spatial interpolation schemes: correlations with surficial geology, termed the geologic trend (GT), ordinary kriging (OK), and kriging with a trend (KT). We estimate the spectral amplifications from seismic properties using the square root of impedance method, thereby linking the frequency-dependent spectral amplifications to the depth-dependent seismic properties. Thus, the range of periods for which this method is applicable is limited by the depth of exploration. A dense survey of near-surface S-wave slowness (Ss) throughout Kobe, Japan shows that the geostatistical methods give more accurate estimates of Ss than the topographic slope and GT methods, and the OK and KT methods perform equally well. We prefer the KT model because it can be seamlessly integrated with geologic maps that cover larger regions. Empirical spectral amplifications show that the region-specific data achieve more accurate estimates of observed median short-period amplifications than the topographic slope method. ?? 2010 Elsevier B.V.

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Tanaka, Y.; Tanaka, H.

2010-01-01

94

R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping  

PubMed Central

Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl’s static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data. PMID:25527287

Broman, Karl W.

2015-01-01

95

Interactive computer methods for generating mineral-resource maps  

USGS Publications Warehouse

Inasmuch as maps are a basic tool of geologists, the U.S. Geological Survey's CRIB (Computerized Resources Information Bank) was constructed so that the data it contains can be used to generate mineral-resource maps. However, by the standard methods used-batch processing and off-line plotting-the production of a finished map commonly takes 2-3 weeks. To produce computer-generated maps more rapidly, cheaply, and easily, and also to provide an effective demonstration tool, we have devised two related methods for plotting maps as alternatives to conventional batch methods. These methods are: 1. Quick-Plot, an interactive program whose output appears on a CRT (cathode-ray-tube) device, and 2. The Interactive CAM (Cartographic Automatic Mapping system), which combines batch and interactive runs. The output of the Interactive CAM system is final compilation (not camera-ready) paper copy. Both methods are designed to use data from the CRIB file in conjunction with a map-plotting program. Quick-Plot retrieves a user-selected subset of data from the CRIB file, immediately produces an image of the desired area on a CRT device, and plots data points according to a limited set of user-selected symbols. This method is useful for immediate evaluation of the map and for demonstrating how trial maps can be made quickly. The Interactive CAM system links the output of an interactive CRIB retrieval to a modified version of the CAM program, which runs in the batch mode and stores plotting instructions on a disk, rather than on a tape. The disk can be accessed by a CRT, and, thus, the user can view and evaluate the map output on a CRT immediately after a batch run, without waiting 1-3 days for an off-line plot. The user can, therefore, do most of the layout and design work in a relatively short time by use of the CRT, before generating a plot tape and having the map plotted on an off-line plotter.

Calkins, James Alfred; Crosby, A.S.; Huffman, T.E.; Clark, A.L.; Mason, G.T.; Bascle, R.J.

1980-01-01

96

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps  

PubMed Central

Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either a high false-discovery rate (interaction sets have low overlap because each set is contaminated by a large number of stochastic false-positive interactions) or a high false-negative rate (interaction sets have low overlap because each misses many true interactions). We extend capture–recapture theory to provide the first unified model for false-positive and false-negative rates for two-hybrid screens. Analysis of yeast, worm, and fly data indicates that 25% to 45% of the reported interactions are likely false positives. Membrane proteins have higher false-discovery rates on average, and signal transduction proteins have lower rates. The overall false-negative rate ranges from 75% for worm to 90% for fly, which arises from a roughly 50% false-negative rate due to statistical undersampling and a 55% to 85% false-negative rate due to proteins that appear to be systematically lost from the assays. Finally, statistical model selection conclusively rejects the Erdös-Rényi network model in favor of the power law model for yeast and the truncated power law for worm and fly degree distributions. Much as genome sequencing coverage estimates were essential for planning the human genome sequencing project, the coverage estimates developed here will be valuable for guiding future proteomic screens. All software and datasets are available in Datasets S1 and S2, Figures S1–S5, and Tables S1?S6, and are also available from our Web site, http://www.baderzone.org. PMID:18039026

Huang, Hailiang; Jedynak, Bruno M; Bader, Joel S

2007-01-01

97

Perry-Castaneda Library Map Collection: Country and Regional Map Sites  

NSDL National Science Digital Library

This map collection covers nearly every country and region from the Adriatic Sea to Zimbabwe. There are also cartographic reference resources (gazetteers, distance calculators, time zone maps, sun and moon rise/set calculators, tidal information, map projections, bibliographies, glossaries and guides), outline maps, city maps, state maps, historic maps, and weather maps.

98

USGS Topographic Maps  

NSDL National Science Digital Library

The United States Geological Survey (USGS) is the primary civilian mapping agency of the United States. Materials available at this site include general information about topographic mapping, and information about USGS map products and how to obtain them. There is also information on digital raster graphics (DRG), scanned images of U.S. Geological Survey (USGS) standard series topographic maps. Other links provide access to data on map revisions, map symbols, mapping standards, and the National Map, a new interactive online mapping application.

99

Interactive Maps from the Great Basin Center for Geothermal Energy  

DOE Data Explorer

The Great Basin Center for Geothermal Energy, part of the University of Nevada, Reno, conducts research towards the establishment of geothermal energy as an economically viable energy source within the Great Basin. The Center specializes in collecting and synthesizing geologic, geochemical, geodetic, geophysical, and tectonic data, and using Geographic Information System (GIS) technology to view and analyze this data and to produce favorability maps of geothermal potential. The interactive maps are built with layers of spatial data that are also available as direct file downloads (see DDE00299). The maps allow analysis of these many layers, with various data sets turned on or off, for determining potential areas that would be favorable for geothermal drilling or other activity. They provide information on current exploration projects and leases, Bureau of Land Management land status, and map presentation of each type of scientific spatial data: geothermal, geophysical, geologic, geodetic, groundwater, and geochemical.

100

Remote Sensing Interactive: Land Cover Map / Image Comparison  

NSDL National Science Digital Library

The Land Cover Map/Image Comparison is one of a number of interactive tools being developed to illustrate basic remote-sensing concepts. Here, the user is able to examine a portion of the Cricahua Mountains in southern Arizona by viewing two sets of images from TM and Modis sensors, and selecting areas within them for closer examination at three magnification levels.

Ned Horning

101

Mapping the interaction site for the tarantula toxin hainantoxin-IV (?-TRTX-Hn2a) in the voltage sensor module of domain II of voltage-gated sodium channels.  

PubMed

Peptide toxins often have pharmacological applications and are powerful tools for investigating the structure-function relationships of voltage-gated sodium channels (VGSCs). Although a group of potential VGSC inhibitors have been reported from tarantula venoms, little is known about the mechanism of their interaction with VGSCs. In this study, we showed that hainantoxin-IV (?-TRTX-Hn2a, HNTX-IV in brief), a 35-residue peptide from Ornithoctonus hainana venom, preferentially inhibited rNav1.2, rNav1.3 and hNav1.7 compared with rNav1.4 and hNav1.5. hNav1.7 was the most sensitive to HNTX-IV (IC50?21nM). In contrast to many other tarantula toxins that affect VGSCs, HNTX-IV at subsaturating concentrations did not alter activation and inactivation kinetics in the physiological range of voltages, while very large depolarization above +70mV could partially activate toxin-bound hNav1.7 channel, indicating that HNTX-IV acts as a gating modifier rather than a pore blocker. Site-directed mutagenesis indicated that the toxin bound to site 4, which was located on the extracellular S3-S4 linker of hNav1.7 domain II. Mutants E753Q, D816N and E818Q of hNav1.7 decreased toxin affinity for hNav1.7 by 2.0-, 3.3- and 130-fold, respectively. In silico docking indicated that a three-toed claw substructure formed by residues with close contacts in the interface between HNTX-IV and hNav1.7 domain II stabilized the toxin-channel complex, impeding movement of the domain II voltage sensor and inhibiting hNav1.7 activation. Our data provide structural details for structure-based drug design and a useful template for the design of highly selective inhibitors of a specific subtype of VGSCs. PMID:25218973

Cai, Tianfu; Luo, Ji; Meng, Er; Ding, Jiuping; Liang, Songping; Wang, Sheng; Liu, Zhonghua

2014-09-10

102

Integrating physical and genetic maps: from genomes to interaction networks  

PubMed Central

Physical and genetic mapping data have become as important to network biology as they once were to the Human Genome Project. Integrating physical and genetic networks currently faces several challenges: increasing the coverage of each type of network; establishing methods to assemble individual interaction measurements into contiguous pathway models; and annotating these pathways with detailed functional information. A particular challenge involves reconciling the wide variety of interaction types that are currently available. For this purpose, recent studies have sought to classify genetic and physical interactions along several complementary dimensions, such as ordered versus unordered, alleviating versus aggravating, and first versus second degree. PMID:17703239

Beyer, Andreas; Bandyopadhyay, Sourav; Ideker, Trey

2009-01-01

103

A map of directional genetic interactions in a metazoan cell  

PubMed Central

Gene–gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene–gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations. DOI: http://dx.doi.org/10.7554/eLife.05464.001 PMID:25748138

Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

2015-01-01

104

Magnetic mapping and interpretation of an archaeological site in Syria  

NASA Astrophysics Data System (ADS)

Among the subsurface methods of exploration that have been developed to meet the new requirements of archaeological research, geophysical methods offer a very wide range of applications in the study of buried deposits. In their latest developments, the prospecting method based on the measurement of the magnetic field is particularly effective at very different types of sites, ranging from prehistoric times to the most recent. The measured magnetic field observed at a place and at a time, results from the vector sum of the main regional field, the effect of subsurface structures, local disturbances such as power lines, buildings, fences, and the diurnal variation (solar influence). The principle of the magnetic method is, from magnetic measurements on a flat plane above the prospected surface, to study the three-dimensional variations of magnetization producing the magnetic anomalies. The use of magnetic surveys for archaeological prospecting is a well-established and versatile technique, and wide ranges of data processing routines are often applied to further enhance acquired data or derive source parameters. The main purpose of this work was to acquire new magnetic data on the field and to propose quantitative interpretations of magnetic maps obtained on three archaeological sites of Bronze Age in Syria (Badiyah ANR program). More precisely, some results are presented concerning one of the three sites, the Tell Al-Rawda-site which corresponds to a circular city of Early Bronze Age with a radius of about 200 m. Several profiles are used to characterize magnetizations. A large portion of archaeological geophysical data are concerned primarily with identifying the location and spatial extent of buried remains, although the data collected are likely to contain further information relating to the depth and geometry of anomalous features. A simple magnetic model corresponding to rectangular structures uniformly magnetized associated to walls cannot explain the magnetic anomalies. On contrary, the shape of the magnetic anomalies implies to propose magnetized or non-magnetized structures with a width of several meters. To fit completely the shape of the magnetic anomaly, an iterative algorithm is used consisting of modifying the shape of the top of the magnetized layer.

khatib alkontar, Rozan AL; Munschy, Marc; Castel, Corinne; Quenet, Philippe

2014-05-01

105

The protein-protein interaction map of Helicobacter pylori.  

PubMed

With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function. As elementary constituents of cellular protein complexes and pathways, protein-protein interactions are key determinants of protein function. Here we have built a large-scale protein-protein interaction map of the human gastric pathogen Helicobacter pylori. We have used a high-throughput strategy of the yeast two-hybrid assay to screen 261 H. pylori proteins against a highly complex library of genome-encoded polypeptides. Over 1,200 interactions were identified between H. pylori proteins, connecting 46.6% of the proteome. The determination of a reliability score for every single protein-protein interaction and the identification of the actual interacting domains permitted the assignment of unannotated proteins to biological pathways. PMID:11196647

Rain, J C; Selig, L; De Reuse, H; Battaglia, V; Reverdy, C; Simon, S; Lenzen, G; Petel, F; Wojcik, J; Schächter, V; Chemama, Y; Labigne, A; Legrain, P

2001-01-11

106

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists  

PubMed Central

A mechanistic understanding of signaling networks requires identification and analysis of phosphorylation sites. Mass spectrometry offers a rapid and highly sensitive approach to mapping phosphorylation sites. However, mass spectrometry has significant limitations that must be considered when planning to carry out phosphorylation-site mapping. Here we provide an overview of key information that should be taken into consideration before beginning phosphorylation-site analysis, as well as a step-by-step guide for carrying out successful experiments. PMID:23447708

Dephoure, Noah; Gould, Kathleen L.; Gygi, Steven P.; Kellogg, Douglas R.

2013-01-01

107

Phylogeny-guided interaction mapping in seven eukaryotes  

PubMed Central

Background The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal. Results We developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more accurate predictions. We apply our framework to reconcile seven eukaryotic interactomes: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae and A. thaliana. Comprehensive GO-based quality assessment indicates a 5% to 44% score increase in predicted interactomes compared to the input data. Further support is provided by gold-standard MIPS, CYC2008 and HPRD datasets. We demonstrate the ability to recover known PPIs in well-characterized yeast and human complexes (26S proteasome, endosome and exosome) and suggest possible new partners interacting with the putative SWI/SNF chromatin remodeling complex in A. thaliana. Conclusion Our phylogeny-guided approach compares favorably to two standard methods for mapping PPIs across species. Detailed analysis of predictions in selected functional modules uncovers specific PPI profiles among homologous proteins, establishing interaction-based partitioning of protein families. Provided evidence also suggests that interactions within core complex subunits are in general more conserved and easier to transfer accurately to other organisms, than interactions between these subunits. PMID:19948065

2009-01-01

108

Interaction sites of DivIVA and RodA from Corynebacterium glutamicum  

PubMed Central

Elongation growth in actinobacteria is localized at the cell poles. This is in contrast to many classical model organisms where insertion of new cell wall material is localized around the lateral site. We previously described a role of RodA from Corynebacterium glutamicum in apical cell growth and morphogenesis. Deletion of rodA had drastic effects on morphology and growth, likely a result from misregulation of penicillin-binding proteins and cell wall precursor delivery. We identified the interaction of RodA with the polar scaffold protein DivIVA, thus explaining subcellular localization of RodA to the cell poles. In this study, we describe this interaction in detail and map the interaction sites of DivIVA and RodA. A single amino acid residue in the N-terminal domain of DivIVA was found to be crucial for the interaction with RodA. The interaction site of RodA was mapped to its cytoplasmic, C-terminal domain, in a region encompassing the last 10 amino acids (AAs). Deletion of these 10 AAs significantly decreased the interaction efficiency with DivIVA. Our results corroborate the interaction of DivIVA and RodA, underscoring the important role of DivIVA as a spatial organizer of the elongation machinery in Corynebacterineae. PMID:25709601

Sieger, Boris; Bramkamp, Marc

2015-01-01

109

Maps  

NSDL National Science Digital Library

This collection presents maps of blast and fire damage to Hiroshima and Nagasaki, Japan, and the radioactive fallout levels from the Trinity and BRAVO tests. The collection also includes maps of Manhattan Project Era Sites (Hanford, Washington, Oak Ridge, Tennessee, and Los Alamos, New Mexico).

Christopher Griffith

110

Methods for Mapping of Interaction Networks Involving Membrane Proteins  

SciTech Connect

Numerous approaches have been taken to study protein interactions, such as tagged protein complex isolation followed by mass spectrometry, yeast two-hybrid methods, fluorescence resonance energy transfer, surface plasmon resonance, site-directed mutagenesis, and crystallography. Membrane protein interactions pose significant challenges due to the need to solubilize membranes without disrupting protein-protein interactions. Traditionally, analysis of isolated protein complexes by high-resolution 2D gel electrophoresis has been the main method used to obtain an overall picture of proteome constituents and interactions. However, this method is time consuming, labor intensive, detects only abundant proteins and is not suitable for the coverage required to elucidate large interaction networks. In this review, we discuss the application of various methods to elucidate interactions involving membrane proteins. These techniques include methods for the direct isolation of single complexes or interactors as well as methods for characterization of entire subcellular and cellular interactomes.

Hooker, Brian S.; Bigelow, Diana J.; Lin, Chiann Tso

2007-11-23

111

Topographic Mapping and Rover Localization in MER 2003 Mission Landing Sites  

Microsoft Academic Search

This presentation illustrates results of topographic mapping and rover localization in Spirit and Opportunity landing sites. MOC\\/NA images, DIMES descent images, and surface Pancam and Navcam images are used to map regional and local topographic features of the landing sites. A new bundle adjustment method builds an image network with improved visual odometric data to supply enhance pointing data that

R. Li; K. di; L. Matthies; M. Maimone; R. Arvidson; L. Crumpler; F. Xu; J. Wang; X. Niu; C. Serafy; D. Ming; L. Richter; D. Marais; M. Golombek; S. Squyres; J. Johnson; J. Bell; J. Maki; M. Malin; T. Parker; L. Edwards; M. Sims; A. Wang; J. Garvin; L. Soderblom

2004-01-01

112

Map Maker  

NSDL National Science Digital Library

This interactive mapping site allows users to build maps of any portion of the United States including overlays of many different kinds of data. Some of the categories of data available include agriculture, biology, climate, environment, geology, and water. The maps are printable and savable and can be shared with others via email.

United States Department of the Interior

113

RNA antisense purification (RAP) for mapping RNA interactions with chromatin.  

PubMed

RNA-centric biochemical purification is a general approach for studying the functions and mechanisms of noncoding RNAs. Here, we describe the experimental procedures for RNA antisense purification (RAP), a method for selective purification of endogenous RNA complexes from cell extracts that enables mapping of RNA interactions with chromatin. In RAP, the user cross-links cells to fix endogenous RNA complexes and purifies these complexes through hybrid capture with biotinylated antisense oligos. DNA loci that interact with the target RNA are identified using high-throughput DNA sequencing. PMID:25555582

Engreitz, Jesse; Lander, Eric S; Guttman, Mitchell

2015-01-01

114

Online Maps and Data  

NSDL National Science Digital Library

From the California Geological Survey, the Online Maps and Data site contains information focused on natural hazards. Topics include minerals, earthquakes, and landslide and erosion hazards. The site also includes the General Location Guide for Ultramafic Rocks in California. The site also has links to a publications page and a new interactive mapping program called the Seismic Hazards Mapping Web page.

115

Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo  

Microsoft Academic Search

A iimdamentdly new moIec&r-biology tech- nology in constructing restriction maps, Optical Mapping, has been developed by Schwartz et al. (1993). Using this method restriction maps are constructed by measuring the relevant fluorescence jnt&ty and length measurements. However, it is &&tilt to directly estimate the restriction site lo- C&XI.S of single DNA molecules based on these optical mapping data because of

Jae Kyu Lee; Vlado Dan?ík; Michael S. Waterman

1998-01-01

116

Integrated Mapping and Imaging at a Legacy Test Site (Invited)  

NASA Astrophysics Data System (ADS)

A team of multi-disciplinary geoscientists was tasked to characterize and evaluate a legacy nuclear detonation site in order to develop research locations with the long-term goal of improving treaty monitoring, verification, and other national security applications. There was a test at the site of interest that was detonated on June 12, 1985 in a vertical emplacement borehole at a depth of 608m below the surface in rhyolites. With announced yield of 20-150 kt, the event did not collapse to the surface and form a crater, but rather experienced a subsurface collapse with more subtle surface expressions of deformation. This result provides the team with an opportunity to evaluate a number of surface and subsurface inspection technologies in a broad context. The team collected ground-based visual observation, ground penetrating radar, electromagnetic, ground-based and airborne LiDAR, ground-based and airborne hyperspectral, gravity and magnetics, dc and induction electrical methods, and active seismic data during field campaigns in the summers of 2012 and 2013. Detection of features was performed using various approaches that were assessed for accuracy, efficiency and diversity of target features. For example, whereas the primary target of the ground-based visual observation survey was to map the surface features, the target of the gravity survey was to attempt the detection of a possible subsurface collapse zone which might be located as little as 200 meters below the surface. The datasets from surveys described above are integrated into a geographical information system (GIS) database for analysis and visualization. Other presentations during this session provide further details as to some of the work conducted. Work by Los Alamos National Laboratory and Lawrence Livermore National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under Contract No. DE AC52 06NA25946 with the U.S. Department of Energy. Sandia National Laboratories, is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Sussman, A. J.; Schultz-Fellenz, E. S.; Kelley, R. E.; Sweeney, J. J.; Vigil, S.; DiBenedetto, J.; Chipman, V.

2013-12-01

117

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions  

E-print Network

of thousands of genetic interactions (GIs) in Saccharomyces cerevisiae. The interpretation of these data synthetic lethality, has first been performed in Saccharomyces cerevisiae using the SGA (Tong et al, 2004

Shamir, Ron

118

Active Site Interactions in Proteolytic Enzymes  

Microsoft Academic Search

The HIV-1 virus encodes a protease essential for the processing of polyprotein precursors into mature viral proteins. This enzyme is a primary target for drug design against AIDS. Concurrent effects of inhibitors targeted to defined regions of the extended active site were investigated using Yonetani-Theorell kinetics to understand its complex specificity requirements. Kinetic data revealed that the simultaneous presence of

Ernest Asante-Appiah

1994-01-01

119

Active site interactions in proteolytic enzymes  

Microsoft Academic Search

The HIV-1 virus encodes a protease essential for the processing of polyprotein precursors into mature viral proteins. This enzyme is a primary target for drug design against AIDS. Concurrent effects of inhibitors targeted to defined regions of the extended active site were investigated using Yonetani-Theorell kinetics to understand its complex specificity requirements. Kinetic data revealed that the simultaneous presence of

Ernest Asante-appiah

1995-01-01

120

Review of interactive safer sex Web sites: practice and potential.  

PubMed

The Internet is increasingly being viewed as a health promotion tool with enormous potential. However, this potential cannot be realized if Web sites do not utilize the features that make the Internet a "hybrid" mass and interpersonal communication medium. The purpose of this study was to examine interactive safer sex Web sites on a number of dimensions. A comprehensive search that included Internet search engines, links from well-known sites, and previously published reviews yielded 21 Web sites that met criteria. Web sites were coded on dimensions including targeting of the Web sites, safer sex messages presented, theoretical strategies utilized, interactivity, and other characteristics. Results indicate that a moderate amount of targeting of Web sites exists, especially on age group (e.g., teenagers); the most prevalent safer sex messages were to "use condoms" and "be sexually abstinent"; raising the perceived threat of sexually transmitted diseases and HIV was the most prevalent theoretical strategy used to motivate safer sex; and finally, a moderate amount of interactivity was found on the Web sites, with most Web sites containing 4 or 5 features out of 15 features examined. Evidence that Web sites were tailoring information or messages to individuals was not found. Implications of these results for improving safer sex Web sites and developing interventions online are discussed. PMID:17137415

Noar, Seth M; Clark, Ashley; Cole, Christi; Lustria, Mia Liza A

2006-01-01

121

Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP.  

PubMed

The photoactivatable ribonucleoside enhanced cross-linking immunoprecipitation (PAR-CLIP) has been increasingly used for the global mapping of RNA-protein interaction sites. There are two key features of the PAR-CLIP experiments: The sequence read tags are likely to form an enriched peak around each RNA-protein interaction site; and the cross-linking procedure is likely to introduce a specific mutation in each sequence read tag at the interaction site. Several ad hoc methods have been developed to identify the RNA-protein interaction sites using either sequence read counts or mutation counts alone; however, rigorous statistical methods for analyzing PAR-CLIP are still lacking. In this article, we propose an integrative model to establish a joint distribution of observed read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we developed a novel modeling approach that adopts non-homogeneous hidden Markov models to incorporate the nucleotide sequence at each genomic location. Both simulation studies and data application showed that our method outperforms the ad hoc methods, and provides reliable inferences for the RNA-protein binding sites from PAR-CLIP data. PMID:24571656

Yun, Jonghyun; Wang, Tao; Xiao, Guanghua

2014-06-01

122

Learning to merge: a new tool for interactive mapping  

NASA Astrophysics Data System (ADS)

The task of turning raw imagery into semantically meaningful maps and overlays is a key area of remote sensing activity. Image analysts, in applications ranging from environmental monitoring to intelligence, use imagery to generate and update maps of terrain, vegetation, road networks, buildings and other relevant features. Often these tasks can be cast as a pixel labeling problem, and several interactive pixel labeling tools have been developed. These tools exploit training data, which is generated by analysts using simple and intuitive paint-program annotation tools, in order to tailor the labeling algorithm for the particular dataset and task. In other cases, the task is best cast as a pixel segmentation problem. Interactive pixel segmentation tools have also been developed, but these tools typically do not learn from training data like the pixel labeling tools do. In this paper we investigate tools for interactive pixel segmentation that also learn from user input. The input has the form of segment merging (or grouping). Merging examples are 1) easily obtained from analysts using vector annotation tools, and 2) more challenging to exploit than traditional labels. We outline the key issues in developing these interactive merging tools, and describe their application to remote sensing.

Porter, Reid B.; Lundquist, Sheng; Ruggiero, Christy

2013-05-01

123

PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps  

PubMed Central

Background The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression. Results Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarity of co-regulators belonging to the same cluster, given their positional binding information. The tool has been tested on experimental collections of human and yeast interactions, identifying modules that coordinate functionally related messages. Conclusions This tool is an original attempt to uncover combinatorial patterns using all the post-transcriptional interaction data available so far. PTRcombiner is available at http://disi.unitn.it/~passerini/software/PTRcombiner/. PMID:24758252

2014-01-01

124

HomozygosityMapper—an interactive approach to homozygosity mapping  

PubMed Central

Homozygosity mapping is a common method for mapping recessive traits in consanguineous families. In most studies, applications for multipoint linkage analyses are applied to determine the genomic region linked to the disease. Unfortunately, these are neither suited for very large families nor for the inclusion of tens of thousands of SNPs. Even if less than 10 000 markers are employed, such an analysis may easily last hours if not days. Here we present a web-based approach to homozygosity mapping. Our application stores marker data in a database into which users can directly upload their own SNP genotype files. Within a few minutes, the database analyses the data, detects homozygous stretches and provides an intuitive graphical interface to the results. The homozygosity in affected individuals is visualized genome-wide with the ability to zoom into single chromosomes and user-defined chromosomal regions. The software also displays the underlying genotypes in all samples. It is integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. They can at any point restrict access to their data or make it public, allowing HomozygosityMapper to be used as a data repository for homozygosity-mapping studies. HomozygosityMapper is available at http://www.homozygositymapper.org/. PMID:19465395

Seelow, Dominik; Schuelke, Markus; Hildebrandt, Friedhelm; Nürnberg, Peter

2009-01-01

125

Genome-wide map of regulatory interactions in the human genome  

PubMed Central

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. PMID:25228660

Heidari, Nastaran; Phanstiel, Douglas H.; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q.

2014-01-01

126

Preliminary analysis of Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) for mineralogic mapping at sites in Nevada and Colorado  

NASA Technical Reports Server (NTRS)

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data for sites in Nevada and Colorado were evaluated to determine their utility for mineralogical mapping in support of geologic investigations. Equal energy normalization is commonly used with imaging spectrometer data to reduce albedo effects. Spectra, profiles, and stacked, color-coded spectra were extracted from the AVIRIS data using an interactive analysis program (QLook) and these derivative data were compared to Airborne Imaging Spectrometer (AIS) results, field and laboratory spectra, and geologic maps. A feature extraction algorithm was used to extract and characterize absorption features from AVIRIS and laboratory spectra, allowing direct comparison of the position and shape of absorption features. Both muscovite and carbonate spectra were identified in the Nevada AVIRIS data by comparison with laboratory and AIS spectra, and an image was made that showed the distribution of these minerals for the entire site. Additional, distinctive spectra were located for an unknown mineral. For the two Colorado sites, the signal-to-noise problem was significantly worse and attempts to extract meaningful spectra were unsuccessful. Problems with the Colorado AVIRIS data were accentuated by the IAR reflectance technique because of moderate vegetation cover. Improved signal-to-noise and alternative calibration procedures will be required to produce satisfactory reflectance spectra from these data. Although the AVIRIS data were useful for mapping strong mineral absorption features and producing mineral maps at the Nevada site, it is clear that significant improvements to the instrument performance are required before AVIRIS will be an operational instrument.

Kruse, Fred A.; Taranik, Dan L.; Kierein-Young, Kathryn S.

1988-01-01

127

Developing a map of geologically defined site-condition categories for California  

USGS Publications Warehouse

Consideration of site conditions is a vital step in analyzing and predicting earthquake ground motion. The importance of amplification by soil conditions has long been recognized, but though many seismic-instrument sites have been characterized by their geologic conditions, there has been no consistent, simple classification applied to all sites. As classification of sites by shear-wave velocity has become more common, the need to go back and provide a simple uniform classification for all stations has become apparent. Within the Pacific Earthquake Engineering Research Center's Next Generation Attenuation equation project, developers of attenuation equations recognized the need to consider site conditions and asked that the California Geological Survey provide site conditions information for all stations that have recorded earthquake ground motion in California. To provide these estimates, we sorted the available shear-wave velocity data by geologic unit, generalized the geologic units, and prepared a map so that we could use the extent of the map units to transfer the velocity characteristics from the sites where they were measured to sites on the same or similar materials. This new map is different from the California Geological Survey "preliminary site-conditions map of California" in that 19 geologically defined categories are used, rather than National Earthquake Hazards Reduction Program categories. Although this map does not yet cover all of California, when completed it may provide a basis for more precise consideration of site conditions in ground-motion calculations.

Wills, C.J.; Clahan, K.B.

2006-01-01

128

MIMO: an efficient tool for molecular interaction maps overlap  

PubMed Central

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

2013-01-01

129

Mapping of mutation-sensitive sites in proteinlike chains M. Skorobogatiy1  

E-print Network

Mapping of mutation-sensitive sites in proteinlike chains M. Skorobogatiy1 and G. Tiana2 1 sensitive to point mutations ``hot'' sites in proteinlike chains. It has been found that this pattern is responsible for the distribution pattern of sites sensitive to point mutations in a heteropolymeric chain

Skorobogatiy, Maksim

130

Thermal interaction effect on nucleation site distribution in subcooled boiling  

SciTech Connect

An experimental work on subcooled boiling of refrigerant, R134a, to examine nucleation site distributions on both copper and stainless steel heating surfaces was performed. In order to obtain high fidelity active nucleation site density and distribution data, a high-speed digital camera was utilized to record bubble emission images from a view normal to heating surfaces. Statistical analyses on nucleation site data were done and their statistical distributions were obtained. Those experimentally observed nucleation site distributions were compared to the random spatial Poisson distribution. The comparisons showed that, rather than purely random, active nucleation site distributions on boiling surfaces are relatively more uniform. Experimental results also showed that on the copper heating surface, nucleation site distributions are slightly more uniform than on the stainless steel surface. This was concluded as the results of thermal interactions between nucleation sites with different solid thermal conductivities. A two dimensional thermal interaction model was then developed to quantitatively examine the thermal interactions between nucleation sites. The results give a reasonable explanation to the experimental observation on nucleation site distributions.

Ling Zou; Barclay Joned

2012-05-01

131

Prediction protein--protein interaction sites heterocomplexes with neural networks  

E-print Network

Prediction protein--protein interaction sites heterocomplexes with neural networks Piero Fariselli neural network based system, which a cross validation proce­ dure and allows correct detection 73 face. However neural networks trained a reduced representation of interacting patch sequence profile su

Pazos, Florencio

132

Prediction of proteinprotein interaction sites in heterocomplexes with neural networks  

E-print Network

Prediction of protein­protein interaction sites in heterocomplexes with neural networks Piero on information about evolutionary con- servation and surface disposition. We implement a neural network based protein sur- face. However neural networks trained with a reduced representation of the interacting patch

Pazos, Florencio

133

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data  

Microsoft Academic Search

Mammalian RNA complexity is regulated through interactions of RNA-binding proteins (RBPs) with their target transcripts. High-throughput sequencing together with UV-crosslinking and immunoprecipitation (HITS-CLIP) is able to globally map RBP-binding footprint regions at a resolution of ?30-60 nucleotides. Here we describe a systematic way to analyze HITS-CLIP data to identify exact crosslink sites, and thereby determine protein-RNA interactions at single-nucleotide resolution.

Chaolin Zhang; Robert B Darnell

2011-01-01

134

Ecoregions of North Dakota and South Dakota: Interactive Map  

NSDL National Science Digital Library

Ecoregions denote areas of general similarity in ecosystems and in the type, quality, and quantity of environmental resources. They are designed to serve as a spatial framework for the research, assessment, management, and monitoring of ecosystems and ecosystem components. This interactive map shows the ecoregions of North and South Dakota in increasing levels of detail (from level III to level IV). Clicking on the legend shows information for each type of ecoregion, including a photo and description, physiography, geology, soils type, climate, natural vegetation types, and land use/land cover. A downloadable version is available.

135

NMR Mapping of the IFNAR1-EC binding site on IFN?2 reveals allosteric changes in the IFNAR2-EC binding site  

PubMed Central

All type I interferons (IFNs) bind to a common cell-surface receptor consisting of two subunits. IFNs initiate intracellular signal transduction cascades by simultaneous interaction with the extracellular domains of its receptor subunits IFNAR1 and IFNAR2. In this study we mapped the surface of IFN?2 interacting with the extracellular domain of IFNAR1 (IFNAR1-EC) by following changes in or the disappearance of the [1H,15N]-TROSY-HSQC cross peaks of IFN?2 caused by the binding of the extracellular domain of IFNAR1 (IFNAR1-EC) to the binary complex of IFN?2 with IFNAR2-EC. The NMR study on the 89 kDa complex was conducted at pH 8 and 308 K using an 800 MHz spectrometer. IFNAR1 binding affected a total of 47 out of 165 IFN?2 residues contained in two large patches on the face of the protein opposing the binding site for IFNAR2 and in a third patch located on the face containing the IFNAR2 binding site. The first two patches form the IFNAR1 binding site and one of these matches the IFNAR1 binding site previously identified by site-directed mutagenesis. The third patch partially matches the IFN?2 binding site for IFNAR2-EC indicating allosteric communication between the binding sites for the two receptor subunits. PMID:20047337

Akabayov, Sabine Ruth; Biron, Zohar; Lamken, Peter; Piehler, Jacob; Anglister, Jacob

2010-01-01

136

Web GIS in practice III: creating a simple interactive map of England's Strategic Health Authorities using Google Maps API, Google Earth KML, and MSN Virtual Earth Map Control  

Microsoft Academic Search

This eye-opener article aims at introducing the health GIS community to the emerging online consumer geoinformatics services from Google and Microsoft (MSN), and their potential utility in creating custom online interactive health maps. Using the programmable interfaces provided by Google and MSN, we created three interactive demonstrator maps of England's Strategic Health Authorities. These can be browsed online at http:\\/\\/www.healthcybermap.org\\/GoogleMapsAPI\\/

Maged N Kamel Boulos

2005-01-01

137

Mapping the FEN1 interaction domain with hTERT  

PubMed Central

The activity of telomerase in cancer cells is tightly regulated by numerous proteins including DNA replication factors. However, it is unclear how replication proteins regulate telomerase action in higher eukaryotic cells. Previously we have demonstrated that the multifunctional DNA replication and repair protein flap endonuclease 1 (FEN1) is in complex with telomerase and may regulate telomerase activity in mammalian cells. In this study, we further analyzed the nature of this association. Our results show that FEN1 and telomerase association occurs throughout the S phase, with the maximum association in the mid S phase. We further mapped the physical domains in FEN1 required for this association and found that the C terminus and the nuclease domain of FEN1 are involved in this interaction, whereas the PCNA binding ability of FEN1 is dispensable for the interaction. These results provide insights into the nature of possible protein-protein associations that telomerase participates in for maintaining functional telomeres. PMID:21345332

Sampathi, Shilpa; Chai, Weihang

2011-01-01

138

Final report for the project "Improving the understanding of surface-atmosphere radiative interactions by mapping surface reflectance over the ARM CART site" (award DE-FG02-02ER63351)  

SciTech Connect

Surface spectral reflectance (albedo) is a fundamental variable affecting the transfer of solar radiation and the Earth’s climate. It determines the proportion of solar energy absorbed by the surface and reflected back to the atmosphere. The International Panel on Climate Change (IPCC) identified surface albedo among key factors influencing climate radiative forcing. Accurate knowledge of surface reflective properties is important for advancing weather forecasting and climate change impact studies. It is also important for determining radiative impact and acceptable levels of greenhouse gases in the atmosphere, which makes this work strongly linked to major scientific objectives of the Climate Change Research Division (CCRD) and Atmospheric Radiation Measurement (ARM) Program. Most significant accomplishments of eth project are listed below. I) Surface albedo/BRDF datasets from 1995 to the end of 2004 have been produced. They were made available to the ARM community and other interested users through the CCRS public ftp site ftp://ftp.ccrs.nrcan.gc.ca/ad/CCRS_ARM/ and ARM IOP data archive under “PI data Trishchenko”. II) Surface albedo properties over the ARM SGP area have been described for 10-year period. Comparison with ECMWF data product showed some deficiencies in the ECMWF surface scheme, such as missing some seasonal variability and no dependence on sky-conditions which biases surface energy budget and has some influence of the diurnal cycle of upward radiation and atmospheric absorption. III) Four surface albedo Intensive Observation Period (IOP) Field Campaigns have been conducted for every season (August, 2002, May 2003, February 2004 and October 2004). Data have been prepared, documented and transferred to ARM IOP archive. Nine peer-reviewed journal papers and 26 conference papers have been published.

Alexander P. Trishchenko; Yi Luo; Konstantin V. Khlopenkov, William M. Park; Zhanqing Li; Maureen Cribb

2008-11-28

139

Depicting combinatorial complexity with the molecular interaction map notation  

PubMed Central

To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to electronic circuit diagrams. Such diagrams must surmount the difficulties posed by complex patterns of protein modifications and multiprotein complexes. To meet that challenge, we have designed the molecular interaction map (MIM) notation (http://discover.nci.nih.gov/mim/). Here we show the advantages of the MIM notation for three important types of diagrams: (1) explicit diagrams that define specific pathway models for computer simulation; (2) heuristic maps that organize the available information about molecular interactions and encompass the possible processes or pathways; and (3) diagrams of combinatorially complex models. We focus on signaling from the epidermal growth factor receptor family (EGFR, ErbB), a network that reflects the major challenges of representing in a compact manner the combinatorial complexity of multimolecular complexes. By comparing MIMs with other diagrams of this network that have recently been published, we show the utility of the MIM notation. These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and generally understood. PMID:17016517

Kohn, Kurt W; Aladjem, Mirit I; Kim, Sohyoung; Weinstein, John N; Pommier, Yves

2006-01-01

140

Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps  

PubMed Central

SUMMARY To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 differential measurements. Each agent was associated with a distinct interaction pattern, which, unlike single-mutant phenotypes or gene expression data, has high statistical power to pinpoint the specific repair mechanisms at work. The agent-specific networks revealed roles for the histone acetyltranferase Rtt109 in the mutagenic bypass of DNA lesions and the neddylation machinery in cell-cycle regulation and genome stability, while the network induced by multiple agents implicates Irc21, an uncharacterized protein, in checkpoint control and DNA repair. Our multiconditional genetic interaction map provides a unique resource that identifies agent-specific and general DNA damage response pathways. PMID:23273983

Guénolé, Aude; Srivas, Rohith; Vreeken, Kees; Wang, Ze Zhong; Wang, Shuyi; Krogan, Nevan J.; Ideker, Trey; van Attikum, Haico

2013-01-01

141

Validation of Innovative Exploration Technologies for Newberry Volcano: Drill Site Location Map 2010  

DOE Data Explorer

Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop “blind” geothermal resources.

Jaffe, Todd

142

Constraint-based simulation of biological systems described by Molecular Interaction Maps  

E-print Network

Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca of biochemical networks de- scribed by the graphical notation of Molecular Interaction Maps. Such maps generating the full list of reactions. 1 Introduction The aim of this work is the simulation of biological

Bortolussi, Luca

143

Towards a proteome-scale map of the human protein-protein interaction network  

Microsoft Academic Search

Systematic mapping of protein-protein interactions, or `interactome' mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting that a human interactome map will provide insight into development

Jean-François Rual; Kavitha Venkatesan; Tong Hao; Tomoko Hirozane-Kishikawa; Amélie Dricot; Ning Li; Gabriel F. Berriz; Francis D. Gibbons; Matija Dreze; Nono Ayivi-Guedehoussou; Niels Klitgord; Christophe Simon; Mike Boxem; Stuart Milstein; Jennifer Rosenberg; Debra S. Goldberg; Lan V. Zhang; Sharyl L. Wong; Giovanni Franklin; Siming Li; Joanna S. Albala; Janghoo Lim; Carlene Fraughton; Estelle Llamosas; Sebiha Cevik; Camille Bex; Philippe Lamesch; Robert S. Sikorski; Jean Vandenhaute; Huda Y. Zoghbi; Alex Smolyar; Stephanie Bosak; Reynaldo Sequerra; Lynn Doucette-Stamm; Michael E. Cusick; David E. Hill; Frederick P. Roth; Marc Vidal

2005-01-01

144

Entanglement increase from local interactions and not completely positive maps  

SciTech Connect

Simple examples are constructed that show the entanglement of two qubits being both increased and decreased by interactions on just one of them. One of the two qubits interacts with a third qubit, a control, that is never entangled or correlated with either of the two entangled qubits, and is never entangled, but becomes correlated, with the system of those two qubits. The two entangled qubits do not interact, but their state can change from maximally entangled to separable or from separable to maximally entangled. Similar changes for the two qubits are made with a SWAP operation between one of the qubits and a control; then there are compensating changes of entanglement that involve the control. When the entanglement increases, the map that describes the change of the state of the two entangled qubits is not completely positive. The combination of two independent interactions that individually give exponential decay of the entanglement can cause the entanglement to not decay exponentially but, instead, go to zero at a finite time.

Jordan, Thomas F.; Shaji, Anil; Sudarshan, E. C. G. [Physics Department, University of Minnesota, Duluth, Minnesota 55812 (United States); Department of Physics and Astronomy, University of New Mexico, 800 Yale Boulevard NE, Albuquerque, New Mexico 87131 (United States); Center for Statistical Mechanics, University of Texas at Austin, 1 University Station C1609, Austin, Texas 78712 (United States)

2007-08-15

145

The Shark-Search Algorithm. An Application: Tailored Web Site Mapping  

Microsoft Academic Search

This paper introduces the “shark search” algorithm, a refined version of one of the first dynamic Web search algorithms, the “fish search”. The shark-search has been embodied into a dynamic Web site mapping that enables users to tailor Web maps to their interests. Preliminary experiments show significant improvements over the original fish-search algorithm.

Michael Herscovici; Michal Jacovi; Yoëlle S. Maarek; Dan Pelleg; Menachem Shtalhaim; Ur Sigalit

1998-01-01

146

Preliminary Correlation Map of Geomorphic Surfaces in North-Central Frenchman Flat, Nevada Test Site  

SciTech Connect

This correlation map (scale = 1:12,000) presents the results of a mapping initiative that was part of the comprehensive site characterization required to operate the Area 5 Radioactive Waste Management Site, a low-level radioactive waste disposal facility located in northern Frenchman Flat at the Nevada Test Site. Eight primary map units are recognized for Quaternary surfaces: remnants of six alluvial fan or terrace surfaces, one unit that includes colluvial aprons associated with hill slopes, and one unit for anthropogenically disturbed surfaces. This surficial geology map provides fundamental data on natural processes for reconstruction of the Quaternary history of northern Frenchman Flat, which in turn will aid in the understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. The bedrock units identified on this map were derived from previous published mapping efforts and are included for completeness.

Bechtel Nevada

2005-08-01

147

Landing Site Selection and Surface Traverse Planning using the Lunar Mapping & Modeling Portal  

NASA Astrophysics Data System (ADS)

Introduction: The Lunar Mapping and Modeling Portal (LMMP), is a web-based Portal and a suite of interactive visualization and analysis tools for users to access mapped lunar data products (including image mosaics, digital elevation models, etc.) from past and current lunar missions (e.g., Lunar Reconnaissance Orbiter, Apollo, etc.), and to perform in-depth analyses to support lunar surface mission planning and system design for future lunar exploration and science missions. It has been widely used by many scientists mission planners, as well as educators and public outreach (e.g., Google Lunar XPRICE teams, RESOLVE project, museums etc.) This year, LMMP was used by the Lunar and Planetary Institute (LPI)'s Lunar Exploration internship program to perform lighting analysis and local hazard assessments, such as, slope, surface roughness and crater/boulder distribution to research landing sites and surface pathfinding and traversal. Our talk will include an overview of LMMP, a demonstration of the tools as well as a summary of the LPI Lunar Exploration summer interns' experience in using those tools.

Law, E.; Chang, G.; Bui, B.; Sadaqathullah, S.; Kim, R.; Dodge, K.; Malhotra, S.

2013-12-01

148

A blurred interface formulation of The Reference Map Technique for Fluid-Solid Interactions and Fluid-Solid-Solid Interactions  

E-print Network

In this work we present a blurred interface method for Fluid-Solid Interactions (FSI) and multiple solids immersed in a fluid or FSSI (Fluid-Solid-Solid Interactions) based on the reference map technique as presented by ...

Valkov, Boris Ivanov

2014-01-01

149

Heteroduplex formation and S1 digestion for mapping alternative splicing sites.  

PubMed

The identification of alternatively spliced transcripts has contributed to a better comprehension of developmental mechanisms, tissue-specific physiological processes and human diseases. Polymerase chain reaction amplification of alternatively spliced variants commonly leads to the formation of heteroduplexes as a result of base pairing involving exons common between the two variants. S1 nuclease cleaves single-stranded loops of heteroduplexes and also nicks the opposite DNA strand. In order to establish a strategy for mapping alternative splice-prone sites in the whole transcriptome, we developed a method combining the formation of heteroduplexes between 2 distinct splicing variants and S1 nuclease digestion. For 20 consensuses identified here using this methodology, 5 revealed a conserved splice site after inspection of the cDNA alignment against the human genome (exact splice sites). For 8 other consensuses, conserved splice sites were mapped at 2 to 30 bp from the border, called proximal splice sites; for the other 7 consensuses, conserved splice sites were mapped at 40 to 800 bp, called distal splice sites. These latter cases showed a nonspecific activity of S1 nuclease in digesting double-strand DNA. From the 20 consensuses identified here, 5 were selected for reverse transcription-polymerase chain reaction validation, confirming the splice sites. These data showed the potential of the strategy in mapping splice sites. However, the lack of specificity of the S1 nuclease enzyme is a significant obstacle that impedes the use of this strategy in large-scale studies. PMID:18949713

Ferreira, E N; Rangel, M C R; Pineda, P B; Vidal, D O; Camargo, A A; Souza, S J; Carraro, D M

2008-01-01

150

Charting the genetic interaction map of a cell.  

PubMed

Genome sequencing projects have revealed a massive catalog of genes and astounding genetic diversity in a variety of organisms. We are now faced with the formidable challenge of assigning functions to thousands of genes, and how to use this information to understand how genes interact and coordinate cell function. Studies indicate that the majority of eukaryotic genes are dispensable, highlighting the extensive buffering of genomes against genetic and environmental perturbations. Such robustness poses a significant challenge to those seeking to understand the wiring diagram of the cell. Genome-scale screens for genetic interactions are an effective means to chart the network that underlies this functional redundancy. A complete atlas of genetic interactions offers the potential to assign functions to most genes identified by whole genome sequencing projects and to delineate a functional wiring diagram of the cell. Perhaps more importantly, mapping genetic networks on a large-scale will shed light on the general principles and rules governing genetic networks and provide valuable information regarding the important but elusive relationship between genotype and phenotype. PMID:21111604

Costanzo, Michael; Baryshnikova, Anastasia; Myers, Chad L; Andrews, Brenda; Boone, Charles

2011-02-01

151

Complete Bouguer gravity map of the Nevada Test Site and vicinity, Nevada  

SciTech Connect

About 15,000 gravity stations were used to create the gravity map. Gravity studies at the Nevada Test Site were undertaken to help locate geologically favorable areas for underground nuclear tests and to help characterize potential high-level nuclear waste storage sites. 48 refs. (TEM)

Healey, D.L.; Harris, R.N.; Ponce, D.A.; Oliver, H.W.

1987-12-31

152

Location map showing sites MAT1-3 to be drilled in summer 07. The Redbeds  

E-print Network

. Previous drilling offshore the New Jersey coastline has met with limited success: drill sites no closer-1- Location map showing sites MAT1-3 to be drilled in summer 07. The Redbeds The Annual Newsletter. Integrated Ocean Drilling Program Expedition 313 Invades New Jersey Contributed by Gregory S. Mountain

153

Soils maps supplement to soil moisture ground truth, Lafayette, Indiana, site St. Charles, Missouri, site  

NASA Technical Reports Server (NTRS)

A compilation of soils information obtained as the result of a library search of data on the Lafayette, Indiana, site and St. Charles, Missouri, site is presented. Soils data for the Lafayette, Indiana, site are shown in Plates 1 and 2; and soils data for the St. Charles, Missouri, site are shown in Plates 3 and 4.

Jones, E. B.; Olt, S. E.

1975-01-01

154

A Web-Based Interactive Mapping System of State Wide School Performance: Integrating Google Maps API Technology into Educational Achievement Data  

ERIC Educational Resources Information Center

Google Maps API (Application Programming Interface), released in late June 2005 by Google, is an amazing technology that allows users to embed Google Maps in their own Web pages with JavaScript. Google Maps API has accelerated the development of new Google Maps based applications. This article reports a Web-based interactive mapping system…

Wang, Kening; Mulvenon, Sean W.; Stegman, Charles; Anderson, Travis

2008-01-01

155

Generation of Prescription Maps for Curative and Preventative Site-Specific Management of Bean Leaf Beetles (Coleoptera: Chrysomelidae)  

Microsoft Academic Search

Site-specific pest management utilizes spatial information about pest distribution to apply control tactics only where pest density is economically high within a field. This study mapped the spatial distribution of bean leaf beetles and generated prescription maps for site-specific bean leaf beetle management. To characterize and map distributions of bean leaf beetles, geostatistics and spatial analysis with distance indices (SADIE)

Yong-Lak Park; Rayda K. Krell

2005-01-01

156

Mapping a ligand binding site using genetically encoded photoactivatable crosslinkers.  

PubMed

G protein-coupled receptor (GPCR) signaling complexes are important for mediating many different biological processes. Uncovering the mechanism for how a ligand triggers a GPCR to elicit a specific response is an active area of research. One step toward understanding this mechanism is through identifying a ligand's binding site on a GPCR. We have optimized a targeted photocrosslinking technology to detect the residues in a receptor that are within a precise distance from a bound ligand in the receptor-ligand complex. Here, we describe the method for introducing photoactivable crosslinkers into a GPCR using the amber stop codon suppression technology. In addition, we review the steps to identify the binding site of a fluorescein-tagged peptide ligand and a tritium-labeled small molecule ligand. PMID:23332706

Grunbeck, Amy; Huber, Thomas; Sakmar, Thomas P

2013-01-01

157

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites  

DOEpatents

Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

Goodman, Mark M. (Atlanta, GA); Faraj, Bahjat (Lithonia, GA)

1999-01-01

158

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites  

DOEpatents

Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

Goodman, M.M.; Faraj, B.

1999-07-06

159

Digital soil mapping at pilot sites in the northwest coast of Egypt: A multinomial logistic regression approach  

Microsoft Academic Search

The study examines a digital soil mapping approach for the production of soil maps by using multinomial logistic regression on soil and terrain information at pilot sites in the Northwestern Coastal region of Egypt. The aim is to reproduce the original map and predict soil distribution in the adherent landscape. Reference soil maps produced by conventional methods at Omayed and

Fawzy Hassan Abdel-Kader

2011-01-01

160

MotifMap: integrative genome-wide maps of regulatory motif sites for model species  

E-print Network

alignment # of matrices 12 (files only) † Yeast sacCer2 multiz7way Worm Flyfly, mouse, and human (both for a 17-species and 32-species alignment).alignments and estimated phylogenetic trees are avail- able, creating genome-wide maps for the yeast, worm, fly and

Daily, Kenneth; Patel, Vishal R; Rigor, Paul; Xie, Xiaohui; Baldi, Pierre

2011-01-01

161

Mapping substance P binding sites on the neurokinin-1 receptor using genetic incorporation of a photoreactive amino acid.  

PubMed

Substance P (SP) is a neuropeptide that mediates numerous physiological responses, including transmission of pain and inflammation through the neurokinin-1 (NK1) receptor, a G protein-coupled receptor. Previous mutagenesis studies and photoaffinity labeling using ligand analogues suggested that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact with a fluorescently labeled SP analog. Notably, 10 of the receptor variants with BzF in the Nt tail and 4 of those with BzF in ECLII cross-linked efficiently to SP, indicating that these 14 sites are juxtaposed to SP in the ligand-bound receptor. These results show that two distinct regions of the NK1 receptor possess multiple determinants for SP binding and demonstrate the utility of genetically encoded photocross-linking to map complex multitopic binding sites on G protein-coupled receptors in a cell-based assay format. PMID:24831006

Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas; Grunbeck, Amy; Naganathan, Saranga; Schwartz, Thue W; Sakmar, Thomas P

2014-06-27

162

Groundwater vulnerability: interactions of chemical and site properties.  

PubMed

This study brings together extensive, multi-annual groundwater monitoring datasets from the UK and Midwestern US to test the relative importance of site (e.g. land use, soil and aquifer type) and chemical factors (e.g. solubility in water) and between and within year variations in controlling groundwater contamination by pesticides. ANOVA (general linear modelling) was used to test the significance and proportion of variation explained by each factor and their interactions. Results from both the UK and US datasets show that: (i) Chemical and site factors both have a statistically significant influence on groundwater pollution; (ii) Site factors on their own explain a greater proportion of data variance than chemical factors on their own; (iii) Interaction between site and chemical factors represents the most important control on the occurrence of pesticides in groundwater; (iv) Variation within the year was slight but still significant while there was no significant difference between data from consecutive years. The combination of factors analysed in this study were sufficient to explain the majority of the variation in the data save for that ascribable to the analytical detection limit. The results provide statistical evidence that it is viable to develop both molecular methods and groundwater vulnerability as tools to understanding pollution, but that a greater emphasis should be placed on their interaction to fully understand pesticide contamination. PMID:12462580

Worral, Fred; Besien, Tim; Kolpin, Dana W

2002-11-01

163

Integration of sequence tagged microsatellite sites to the chickpea genetic map  

Microsoft Academic Search

Fifty sequence-tagged microsatellite site (STMS) markers and a resistant gene-analog (RGA) locus were integrated into a chickpea (Cicer arietinum L., 2n = 2x = 16 chromosomes) genetic map that was previously constructed using 142 F6-derived recombinant inbred lines (RILs) from a cross of C. arietinum 2 Cicer reticulatum Lad. The map covers 1,174.5 cM with an average distance of 7.0

M. Tekeoglu; P. N. Rajesh; F. J. Muehlbauer

2002-01-01

164

Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces  

PubMed Central

Polar residue hot spots have been observed at protein–protein binding sites. Here we show that hot spots occur predominantly at the interfaces of macromolecular complexes, distinguishing binding sites from the remainder of the surface. Consequently, hot spots can be used to define binding epitopes. We further show a correspondence between energy hot spots and structurally conserved residues. The number of structurally conserved residues, particularly of high ranking energy hot spots, increases with the binding site contact size. This finding may suggest that effectively dispersing hot spots within a large contact area, rather than compactly clustering them, may be a strategy to sustain essential key interactions while still allowing certain protein flexibility at the interface. Thus, most conserved polar residues at the binding interfaces confer rigidity to minimize the entropic cost on binding, whereas surrounding residues form a flexible cushion. Furthermore, our finding that similar residue hot spots occur across different protein families suggests that affinity and specificity are not necessarily coupled: higher affinity does not directly imply greater specificity. Conservation of Trp on the protein surface indicates a highly likely binding site. To a lesser extent, conservation of Phe and Met also imply a binding site. For all three residues, there is a significant conservation in binding sites, whereas there is no conservation on the exposed surface. A hybrid strategy, mapping sequence alignment onto a single structure illustrates the possibility of binding site identification around these three residues. PMID:12730379

Ma, Buyong; Elkayam, Tal; Wolfson, Haim; Nussinov, Ruth

2003-01-01

165

Geomorphic Surface Maps of Northern Frenchman Flat, Nevada Test Site, Southern Nevada  

SciTech Connect

Large-scale (1:6000) surficial geology maps of northern Frenchman Flat were developed in 1995 as part of comprehensive site characterization required to operate a low-level radioactive waste disposal facility in that area. Seven surficial geology maps provide fundamental data on natural processes and are the platform needed to reconstruct the Quaternary history of northern Frenchman Flat. Reconstruction of the Quaternary history provides an understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. Seven geomorphic surfaces (Units 1 through 7) are recognized, spanning from the early Quaternary to present time.

Bechtel Nevada

2005-08-01

166

An Interactive Map Viewer for the Urban Geology of Ottawa (Canada): an Example of Web Publishing  

NASA Astrophysics Data System (ADS)

Developed by the Terrain Sciences Division (TSD) of the Geological Survey of Canada (GSC), an interactive map viewer, called GEOSERV (www.geoserv.org), is now available on the Internet. The purpose of this viewer is to provide engineers, planners, decision makers, and the general public with the geoscience information required for sound regional planning in densely populated areas, such as Canada's national capital, Ottawa (Ontario). Urban geology studies rely on diverse branches of earth sciences such as hydrology, engineering geology, geochemistry, stratigraphy, and geomorphology in order to build a three-dimensional model of the character of the land and to explain the geological processes involved in the dynamic equilibrium of the local environment. Over the past few years, TSD has compiled geoscientific information derived from various sources such as borehole logs, geological maps, hydrological reports and digital elevation models, compiled it in digital format and stored it in georeferenced databases in the form of point, linear, and polygonal data. This information constitutes the geoscience knowledge base which is then processed by Geographic Information Systems (GIS) to integrate the various sources of information and produce derived graphics, maps and models describing the geological infrastructure and response of the geological environment to human activities. Urban Geology of Canada's National Capital Area is a pilot project aiming at developing approaches, methodologies and standards that can be applied to other major urban centres of the country, while providing the geoscience knowledge required for sound regional planning and environmental protection of the National Capital Area. Based on an application developed by ESRI (Environmental System Research Institute), namely ArcIMS, the TSD has customized this web application to give free access to geoscience information of the Ottawa/Outaouais (Ontario/Québec) area including geological history, subsurface database, stratigraphy, bedrock, surficial and hydrogeology maps, and a few others. At present, each layer of geospatial information in TSD's interactive map viewer is connected to simple independent flat files (i.e. shapefiles), but it is also possible to connect GEOSERV to other types of (relational) databases (e.g. Microsoft SQL Server, Oracle). Frequent updating of shapefiles could be a cumbersome task, when new records are added, since we have to completely rebuild the updated shapefiles. However, new attributes can be added to existing shapefiles easily. At present, the updating process can not be done on-the-fly; we must stop and restart the updated MapService if one of its shapefiles is changed. The public can access seventeen MapServices that provide interactive tools that users can use to query, zoom, pan, select, and so on, or print the map displayed on their monitor. The map viewer is light-weight as it uses HTML and Javascript, so end users do not have to download and install any plug-ins. A free CD and a companion web site were also developed to give access to complementary information, like high resolution raster maps and reports. Some of the datasets are available free of charge, on-line.

Giroux, D.; Bélanger, R.

2003-04-01

167

Satellite Power System (SPS) mapping of exclusion areas for rectenna sites  

NASA Technical Reports Server (NTRS)

The areas of the United States that were not available as potential sites for receiving antennas that are an integral part of the Satellite Power System concept are presented. Thirty-six variables with the potential to exclude the rectenna were mapped and coded in a computer. Some of these variables exclude a rectenna from locating within the area of its spatial influence, and other variables potentially exclude the rectenna. These maps of variables were assembled from existing data and were mapped on a grid system.

Blackburn, J. B., Jr.; Bavinger, B. A.

1978-01-01

168

Constraint-based simulation of biological systems described by Molecular Interaction Maps  

E-print Network

Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca to simulate biochemical networks de- scribed by the graphical notation of Molecular Interaction Maps within The aim of this work is the simulation of biological regulatory networks described by the graphical

Bortolussi, Luca

169

EFFECTS OF INTERACTIVITY IN A WEB SITE The Moderating Effect of Need for Cognition  

Microsoft Academic Search

This paper examines how consumers process the information available, and what their experiences are, when exposed to an interactive Web site as compared with a noninteractive Web site. The experiment developed analyzes two versions of a Web site in which the capacity to interact with the message has been manipulated. The results show that the interactive Web site leads to

Maria Sicilia; Salvador Ruiz; Jose L. Munuera

170

Transparency laws and interactive public relations: An analysis of Latin American government Web sites  

Microsoft Academic Search

A content analysis of 50 Latin American government Web sites was conducted to assess whether new transparency laws in the hemisphere impacted the interactivity, usability, technological expertise, and national symbolism manifest on the sites. Web sites were found to be generally usable but limited in interactivity. There was no difference in Web site interactivity between countries with transparency laws and

Eileen M. Searson; Melissa A. Johnson

2010-01-01

171

Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites  

PubMed Central

Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3? of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3? have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3? interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM. PMID:25238155

Summerton, Jean C.; Martin, Gregory M.; Evanseck, Jeffrey D.; Chapman, Michael S.

2014-01-01

172

FLS2-BAK1 Extracellular Domain Interaction Sites Required for Defense Signaling Activation  

PubMed Central

Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function. PMID:25356676

Koller, Teresa; Bent, Andrew F

2014-01-01

173

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching  

PubMed Central

Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5?-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus. PMID:24288369

Robinson, Kirsten E.; Orans, Jillian; Kovach, Alexander R.; Link, Todd M.; Brennan, Richard G.

2014-01-01

174

Environmental Research Translation: enhancing interactions with communities at contaminated sites.  

PubMed

The characterization and remediation of contaminated sites are complex endeavors fraught with numerous challenges. One particular challenge that is receiving increased attention is the development and encouragement of full participation by communities and community members affected by a given site in all facets of decision-making. Many disciplines have been grappling with the challenges associated with environmental and risk communication, public participation in environmental data generation, and decision-making and increasing community capacity. The concepts and methods developed by these disciplines are reviewed, with a focus on their relevance to the specific dynamics associated with environmental contamination sites. The contributions of these disciplines are then synthesized and integrated to help develop Environmental Research Translation (ERT), a proposed framework for environmental scientists to promote interaction and communication among involved parties at contaminated sites. This holistic approach is rooted in public participation approaches to science, which includes: a transdisciplinary team, effective collaboration, information transfer, public participation in environmental projects, and a cultural model of risk communication. Although there are challenges associated with the implementation of ERT, it is anticipated that application of this proposed translational science method could promote more robust community participation at contaminated sites. PMID:25173762

Ramirez-Andreotta, Monica D; Brusseau, Mark L; Artiola, Janick F; Maier, Raina M; Gandolfi, A Jay

2014-11-01

175

Home | Register | Home Delivery | Site Map | Archives | Print Edition | Advertise | Feedback jobs * cars * homes * rentals  

E-print Network

Home | Register | Home Delivery | Site Map | Archives | Print Edition | Advertise | Feedback jobs California Business Politics Sports August 11, 2001 Talk about it E-mail story Print THE REGION Second Source Rights," with Frost's article, titled "The Developing Human Rights Discourse: A History of the Human

Elkan, Charles

176

Global mapping of c-Myc binding sites and target gene networks in human B cells  

E-print Network

Global mapping of c-Myc binding sites and target gene networks in human B cells Karen I. Zeller) The protooncogene MYC encodes the c-Myc transcription factor that regulates cell growth, cell proliferation, cell what direct Myc-induced transcriptomes promote cell transformation. Here we provide a snapshot

Weng, Zhiping

177

Implementation of Action Sequences by a Neostriatal Site: A Lesion Mapping Study of Grooming Syntax  

E-print Network

Implementation of Action Sequences by a Neostriatal Site: A Lesion Mapping Study of Grooming Syntax ("action syntax") as well as simpler as- pects of movement. This study focused on sequential organi- zation of rodent grooming. Grooming syntax provides an op- portunity to study how neural systems coordinate natural

Berridge, Kent

178

RBPmap: a web server for mapping binding sites of RNA-binding proteins  

PubMed Central

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5’ and 3’ UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. PMID:24829458

Paz, Inbal; Kosti, Idit; Ares, Manuel; Cline, Melissa; Mandel-Gutfreund, Yael

2014-01-01

179

An approach to mapping haplotype-specific recombination sites in human MHC class III  

SciTech Connect

Studies of the major histocompatibility complex (MHC) in mouse indicate that the recombination sites are not randomly distributed and their occurrence is haplotype-dependent. No data concerning haplotype-specific recombination sites in human are available due to the low number of informative families. To investigate haplotype-specific recombination sites in human MHC, we describe an approach based on identification of recombinant haplotypes derived from one conserved haplotype at the population level. The recombination sites were mapped by comparing polymorphic markers between the recombinant and assumed original haplotypes. We tested this approach on the extended haplotype HLA A3; B47; Bf{sup *}F; C4A{sup *}1; C4B{sup *}Q0; DR7, which is most suitable for this analysis. First, it carries a number of rare markers, and second, the haplotype, albeit rare in the general population, is frequent in patients with 21-hydroxylase (21OH) defect. We observed recombinants derived from this haplotype in patients with 21OH defect. All these haplotypes had the centromeric part (from Bf to DR) identical to the original haplotype, but they differed in HLA A and B. We therefore assumed that they underwent recombinations in the segment that separates the Bf and HLA B genes. Polymorphic markers indicated that all break points mapped to two segments near the TNF locus. This approach makes possible the mapping of preferential recombination sites in different haplotypes. 20 refs., 1 fig., 1 tab.

Levo, A.; Westman, P.; Partanen, J. [Finnish Red Cross Blood Transfusion Service, Helsinki (Finland)

1996-12-31

180

High precision landing site mapping and rover localization for Chang'e-3 mission  

NASA Astrophysics Data System (ADS)

This paper presents the comprehensive results of landing site topographic mapping and rover localization in Chang'e-3 mission. High-precision topographic products of the landing site with extremely high resolutions (up to 0.05 m) were generated from descent images and registered to CE-2 DOM. Local DEM and DOM with 0.02 m resolution were produced routinely at each waypoint along the rover traverse. The lander location was determined to be (19.51256°W, 44.11884°N, -2615.451 m) using a method of DOM matching. In order to reduce error accumulation caused by wheel slippage and IMU drift in dead reckoning, cross-site visual localization and DOM matching localization methods were developed to localize the rover at waypoints; the overall traveled distance from the lander is 114.8 m from cross-site visual localization and 111.2 m from DOM matching localization. The latter is of highest accuracy and has been verified using a LRO NAC image where the rover trajeactory is directly identifiable. During CE-3 mission operations, landing site mapping and rover localization products including DEMs and DOMs, traverse maps, vertical traverse profiles were generated timely to support teleoperation tasks such as obstacle avoidance and rover path planning.

Liu, ZhaoQin; Di, KaiChang; Peng, Man; Wan, WenHui; Liu, Bin; Li, LiChun; Yu, TianYi; Wang, BaoFeng; Zhou, JianLiang; Chen, HongMin

2015-01-01

181

Extended DFT + U + V method with on-site and inter-site electronic interactions  

NASA Astrophysics Data System (ADS)

In this paper we introduce a generalization of the popular DFT + U method based on the extended Hubbard model that includes on-site and inter-site electronic interactions. The novel corrective Hamiltonian is designed to study systems for which electrons are not completely localized on atomic states (according to the general scheme of Mott localization) and hybridization between orbitals from different sites plays an important role. The application of the extended functional to archetypal Mott-charge-transfer (NiO) and covalently bonded insulators (Si and GaAs) demonstrates its accuracy and versatility and the possibility to obtain a unifying and equally accurate description for a broad range of very diverse systems.

Leiria Campo, Vivaldo, Jr.; Cococcioni, Matteo

2010-02-01

182

Matrix model maps and reconstruction of AdS supergravity interactions  

SciTech Connect

We consider the question of reconstructing (cubic) SUGRA interactions in AdS/CFT. The method we introduce is based on the matrix model maps (MMP) which were previously successfully employed at the linearized level. The strategy is to start with the map for 1/2 BPS configurations, which is exactly known (to all orders) in the Hamiltonian framework. We then use the extension of the matrix model map with the corresponding Ward identities to completely specify the interaction. A central point in this construction is the nonvanishing of off-shell interactions (even for highest-weight states)

Cremonini, Sera; Mello Koch, Robert de; Jevicki, Antal [Michigan Center for Theoretical Physics, Randall Laboratory of Physics, University of Michigan, Ann Arbor, MI 48109 (United States); Department of Physics, University of Witwatersrand, Wits, 2050 (South Africa); Department of Physics, Brown University, Providence, RI 02912 (United States)

2008-05-15

183

Mapping interactions between complement C3 and regulators using mutations in atypical hemolytic uremic syndrome.  

PubMed

The pathogenesis of atypical hemolytic uremic syndrome (aHUS) is strongly linked to dysregulation of the alternative pathway of the complement system. Mutations in complement genes have been identified in about two-thirds of cases, with 5% to 15% being in C3. In this study, 23 aHUS-associated genetic changes in C3 were characterized relative to their interaction with the control proteins factor H (FH), membrane cofactor protein (MCP; CD46), and complement receptor 1 (CR1; CD35). In surface plasmon resonance experiments, 17 mutant recombinant proteins demonstrated a defect in binding to FH and/or MCP, whereas 2 demonstrated reduced binding to CR1. In the majority of cases, decreased binding affinity translated to a decrease in proteolytic inactivation (known as cofactor activity) of C3b via FH and MCP. These results were used to map the putative binding regions of C3b involved in the interaction with MCP and CR1 and interrogated relative to known FH binding sites. Seventy-six percent of patients with C3 mutations had low C3 levels that correlated with disease severity. This study expands our knowledge of the functional consequences of aHUS-associated C3 mutations relative to the interaction of C3 with complement regulatory proteins mediating cofactor activity. PMID:25608561

Schramm, Elizabeth C; Roumenina, Lubka T; Rybkine, Tania; Chauvet, Sophie; Vieira-Martins, Paula; Hue, Christophe; Maga, Tara; Valoti, Elisabetta; Wilson, Valerie; Jokiranta, Sakari; Smith, Richard J H; Noris, Marina; Goodship, Tim; Atkinson, John P; Fremeaux-Bacchi, Veronique

2015-04-01

184

Mapping Control and Affiliation in Teacher-Student Interaction with State Space Grids  

ERIC Educational Resources Information Center

This paper explores how State Space Grids (SSG), a dynamic systems research method, can be used to map teacher-student interactions from moment-to-moment and thereby to incorporate temporal aspects of interaction. Interactions in two secondary school classrooms are described in terms of level of interpersonal control and affiliation, and of…

Mainhard, M. Tim; Pennings, Helena J. M.; Wubbels, Theo; Brekelmans, Mieke

2012-01-01

185

Shear wave velocity mapping of Hat Yai district, southern Thailand: implication for seismic site classification  

NASA Astrophysics Data System (ADS)

Soil characteristics play an important role in the degree of ground shaking due to local site amplification during an earthquake. The objectives of this work are to study shear wave velocity (Vs) distribution in the near surface, and to develop a seismic site classification map for soil effect characterization and seismic hazard assessment in Hat Yai district, southern Thailand. The Vs determination based on the multichannel analysis of surface waves technique, has been carried out and analyzed at 70 measuring sites throughout the district. On the basis of the weighted-average Vs in the upper 30?m depth (Vs30), a seismic site classification map, based on the National Earthquake Hazards Reduction Program (NEHRP) standard has been developed. It is found that the NEHRP site class in Hat Yai can be classified into four groups in accordance with the value of Vs30 within the range of about 150 to 1160?m?s?1. Most parts of the study area are typically classified as site class C and D. Site class C is mostly found within the colluvial and terrace deposits in the western and eastern part of the area, whereas site class D is concentrated in the alluvial sediment of the middle and northern flood plain areas. A small portion of site class B is observed in the western mountain ranges, where there is a thin overburden on the firm rock. There is a remarkably low Vs30 value at only one site, located near the main stream in the northern part of the study area. The results imply that the soil characteristics in the central and northern Hat Yai district pose a medium to high amplification rate with respect to the other regions. Although Vs data alone are insufficient to verify the potential of the amplification of ground shaking, this study provides an initial attempt to understand seismic hazards in the study area.

Yordkayhun, Sawasdee; Sujitapan, Chedtaporn; Chalermyanont, Tanit

2015-02-01

186

Reproductive parameters in female yellow-blotched map turtles (Graptemys flavimaculata) from a historically contaminated site vs. a reference site.  

PubMed

Graptemys flavimaculata, the yellow-blotched map turtle, is a long-lived, threatened, species, endemic to the Pascagoula River drainage in Mississippi. During the 1980s, one branch of the drainage (i.e. the Leaf River) was impacted by effluent from a wood pulp processing plant known to contain endocrine disrupters. A decade later, we examined seasonal reproductive parameters (i.e. monthly plasma estradiol-17beta (E(2)), testosterone (T), vitellogenin (VTG) and follicular development) in adult female turtles from historically polluted and reference sites in the drainage to determine if legacy exposure to pollution impacts reproduction . We found no seasonal patterns in E(2) or T and these patterns did not differ between sites. However, E(2) differed significantly among ovarian stages for the reference, but not pollutant exposed females. A significantly greater percentage of reference site females were able to produce a second clutch than females from the historically polluted site (50% and 17%). Additionally, there was a significant positive correlation between E(2) with VTG levels for reference, but not pollutant exposed females. Body and yolk tissue contaminant analysis indicated that exposure to pollutants is presently minimal and unlikely the cause of the reproductive differences observed between sites; instead, differences are potentially due to exposure history. PMID:19651226

Shelby-Walker, Jennifer A; Ward, Chelsea K; Mendonça, Mary T

2009-11-01

187

Repeated mapping of reefs constructed by Sabellaria spinulosa Leuckart 1849 at an offshore wind farm site  

NASA Astrophysics Data System (ADS)

Sabellaria spinulosa reefs are considered to be sensitive and of high conservation status. This article evaluates the feasibility of using remote sensing technology to delineate S. spinulosa reefs. S. spinulosa reef habitats associated with the Thanet Offshore Windfarm site were mapped using high resolution sidescan sonar (410 kHz) and multibeam echo sounder (<1 m2) data in 2005 (baseline), 2007 (pre-construction baseline) and 2012 (post-construction). The S. spinulosa reefs were identified in the acoustic data as areas of distinct irregular texturing. Maps created using acoustic data were validated using quantitative measures of reef quality, namely tube density (as a proxy for the density of live S. spinulosa), percentage cover of S. spinulosa structures (both living and dead) and associated macrofauna derived from seabed images taken across the development site. Statistically significant differences were observed in all physical measures of S. spinulosa as well the number (S) and diversity (H') of associated species, derived from seabed images classified according to the presence or absence of reef, validating the use of high resolution sidescan sonar to map these important biogenic habitats. High precision mapping in the early stages allowed for the micro-siting of wind turbines in a way that caused minimal damage to S. spinulosa reefs during construction. These habitats have since recovered and expanded in extent. The surveys undertaken at the Thanet Offshore Windfarm site demonstrate the importance of repeat mapping for this emerging industry, allowing habitat enhancement to be attributed to the development whilst preventing background habitat degradation from being wrongly attributed to the development.

Pearce, Bryony; Fariñas-Franco, Jose M.; Wilson, Christian; Pitts, Jack; deBurgh, Angela; Somerfield, Paul J.

2014-07-01

188

Catalonia Maps  

NSDL National Science Digital Library

As an autonomous community within the kingdom of Spain, Catalonia has a rich and diverse history. It includes the cosmopolitan city of Barcelona and also has a rather diverse agricultural base that includes crops like maize, potatoes, and olives. Maps of this lovely region of Spain may be found in abundance on this site, which is provided courtesy of the Institut Cartografica de Catalunya. Visitors can search the collection by place name or they can also search the collection through an interactive map of the entire region which will return individual geological and topographic maps. Finally, it is worth noting that the site is also available in Spanish and Catalan.

2006-01-01

189

Optimized strategies for sequence-tagged-site selection in genome mapping.  

PubMed Central

The physical mapping of complex genomes is based on the construction of a genomic library and the determination of the overlaps between the inserts of the mapping clones in order to generate an ordered, cloned representation of nearly all the sequences present in the target genome. Evaluation of the relative efficiency of experimental procedures used to accomplish this goal must minimally include a comparison of the fraction of the genome covered by the ordered arrays (or "contigs"), the average size of the contigs, and the cost, in terms of time and resources, required to generate the map. Sequence-tagged-site (STS) content mapping is one strategy that has been proposed and is being utilized for this type of experiment. This paper describes three STS selection schemes and presents computer simulations of contig-building experiments based on these procedures. The results of these simulations suggest that a nonrandom STS strategy that uses paired probes requires one-third to one-fourth as many STS assays as are required in random and nonpaired approaches, and also results in a map that has both greater genome coverage and a larger average contig size. This strategy promises to reduce the time and cost required to build a high-quality physical map. Images PMID:1896449

Palazzolo, M J; Sawyer, S A; Martin, C H; Smoller, D A; Hartl, D L

1991-01-01

190

Molecular mapping of restriction-site associated DNA markers in allotetraploid upland cotton.  

PubMed

Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits. PMID:25894395

Wang, Yangkun; Ning, Zhiyuan; Hu, Yan; Chen, Jiedan; Zhao, Rui; Chen, Hong; Ai, Nijiang; Guo, Wangzhen; Zhang, Tianzhen

2015-01-01

191

Shared-Screen Interaction: Engaging Groups in Map-Mediated Nonverbal Communication  

NASA Astrophysics Data System (ADS)

This chapter describes the design and development of an interactive video installation that allows participants to explore a map narrative, and engage in group interactions through a shared screen. For this purpose, several layers of cartographic information were employed in a computer application, which was programmed with motion-tracking libraries in the open source tool processing. The interactive video installation has been chosen as a medium to achieve the following aims: (1) The visualization of urban-conflict as an interactive map narrative, and (2) the encouragement of social encounters through a shared screen. The development process begins with the design of interaction between the system and the participants, as well as between the participants themselves. Then we map the interaction design concepts into multimedia and architectural design. Finally, we provide a discussion on the creative process and the collaboration between different disciplines, such as architecture, urban planning, cartography, computer engineering, and media studies.

Chorianopoulos, Konstantinos; Rieniets, Tim

192

CapsidMaps: Protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.  

PubMed

Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the ?-? Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu. PMID:25697908

Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks, Charles L; Reddy, Vijay S

2015-04-01

193

Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites  

PubMed Central

Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites, a property that has been used to infer the location of these sites from protein homology. In an inter-species complementation experiment, a sequence present in a homologue is substituted into a protein and tested for its ability to support function. Therefore, substitutions that inhibit function can identify interaction sites that changed over evolution. However, most of the sequence differences within a protein family remain unexplored because of the small-scale nature of these complementation approaches. Here we use existing high throughput mutational data on the in vivo function of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein, Pab1, to analyze its sites of interaction. Of 197 single amino acid differences in 52 Pab1 homologues, 17 reduce the function of Pab1 when substituted into the yeast protein. The majority of these deleterious mutations interfere with the binding of the RRM2 domain to eIF4G1 and eIF4G2, isoforms of a translation initiation factor. A large-scale mutational analysis of the RRM2 domain in a two-hybrid assay for eIF4G1 binding supports these findings and identifies peripheral residues that make a smaller contribution to eIF4G1 binding. Three single amino acid substitutions in yeast Pab1 corresponding to residues from the human orthologue are deleterious and eliminate binding to the yeast eIF4G isoforms. We create a triple mutant that carries these substitutions and other humanizing substitutions that collectively support a switch in binding specificity of RRM2 from the yeast eIF4G1 to its human orthologue. Finally, we map other deleterious substitutions in Pab1 to inter-domain (RRM2–RRM1) or protein-RNA (RRM2–poly(A)) interaction sites. Thus, the combined approach of large-scale mutational data and evolutionary conservation can be used to characterize interaction sites at single amino acid resolution. PMID:25671604

Melamed, Daniel; Young, David L.; Miller, Christina R.; Fields, Stanley

2015-01-01

194

CARTOGRAPHIC ANIMATION AND LEGENDS FOR TEMPORAL MAPS: EXPLORATION AND OR INTERACTION  

E-print Network

animations. The approach focuses on matching legend styles to the context for map use. Specifically, we argueCARTOGRAPHIC ANIMATION AND LEGENDS FOR TEMPORAL MAPS: EXPLORATION AND OR INTERACTION Menno@geog.psu.edu & alan@essc.psu.edu Abstract Temporal cartographic animations are increasingly common. For users

Klippel, Alexander

195

Constraint-based simulation of biological systems described by Molecular Interaction Maps  

E-print Network

Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca networks described by the graphical notation of Molecular Inter- action Maps within stochastic Concurrent of this work is the simulation of biological regulatory networks described by the graphical notation

Bortolussi, Luca

196

UBC Social Ecological Economic Development Studies (SEEDS) Student Report Interactive Map of the UBC Food System  

E-print Network

the Industrial Revolution have forever changed the global climate and landscape- arguably for the worse. Global a number of interactive food system maps from other North American universities and drew from those implications of the significance of the map are also discussed. Introduction Industrialization, development

197

Interactive 2D 3D Digital Maps for the support of emergency teams during rescue operations  

E-print Network

the environment of the incident. The SHARE system will incorporate an enhanced Tele Atlas 2D-3D digital mapInteractive 2D ­ 3D Digital Maps for the support of emergency teams during rescue operations Linde Vande Velde1* , Symeon Chatzinotas3 , Martha Larson2 , Jobst Löffler2 , Georgios Paliouras3 1 Tele Atlas

Paliouras, George

198

Site specific endonucleases for human genome mapping. Final report, April 1, 1992--March 31, 1994  

SciTech Connect

Current large scale genome mapping methodology suffers from a lack of tools for generating specific DNA fragments in the megabase size range. While technology such as pulsed field gel electrophoresis can resolve DNA fragments greater than 10 megabases in size, current methods for cleaving mammalian DNA using bacterial restriction enzymes are incapable of producing such fragments. Though several multidimensional approaches are underway to overcome this limitation, there currently is no single step procedure to generate specific DNA fragments in the 2-100 megabase size range. In order to overcome these limitations, we proposed to develop a family of site-specific endonucleases capable of generating DNA fragments in the 2-100 megabase size range in a single step. Additionally, we proposed to accomplish this by relaxing the specificity of a very-rare cutting intron-encoded endonucleases, I-Ppo I, and potentially using the process as a model for development of other enzymes. Our research has uncovered a great deal of information about intron-encoded endonucleases. We have found that I-Ppo I has a remarkable ability to tolerate degeneracy within its recognition sequence, and we have shown that the recognition sequence is larger than 15 base pairs. These findings suggest that a detailed study of the mechanism by which intron-encoded endonucleases recognize their target sequences should provide new sights into DNA-protein interactions; this had led to a continuation of the study of I-Ppo I in Dr. Raines` laboratory and we expect a more detailed understanding of the mechanism of I-Ppo I action to result.

Knoche, K.; Selman, S.; Hung, L. [and others

1994-06-01

199

Posterior insular cortex – a site of vestibular–somatosensory interaction?  

PubMed Central

Background In previous imaging studies the insular cortex (IC) has been identified as an essential part of the processing of a wide spectrum of perception and sensorimotor integration. Yet, there are no systematic lesion studies in a sufficient number of patients examining whether processing of vestibular and the interaction of somatosensory and vestibular signals take place in the IC. Methods We investigated acute stroke patients with lesions affecting the IC in order to fill this gap. In detail, we explored signs of a vestibular tone imbalance such as the deviation of the subjective visual vertical (SVV). We applied voxel-lesion behaviour mapping analysis in 27 patients with acute unilateral stroke. Results Our data demonstrate that patients with lesions of the posterior IC have an abnormal tilt of SVV. Furthermore, re-analysing data of 20 patients from a previous study, we found a positive correlation between thermal perception contralateral to the stroke and the severity of the SVV tilt. Conclusions We conclude that the IC is a sensory brain region where different modalities might interact. PMID:24392273

Baier, Bernhard; zu Eulenburg, Peter; Best, Christoph; Geber, Christian; Müller-Forell, Wibke; Birklein, Frank; Dieterich, Marianne

2013-01-01

200

NATCARB Interactive Maps and the National Carbon Explorer: a National Look at Carbon Sequestration  

DOE Data Explorer

NATCARB is a national look at carbon sequestration. The NATCARB home page, National Carbon Explorer (http://www.natcarb.org/) provides access to information and interactive maps on a national scale about climate change, DOE's carbon sequestration program and its partnerships, CO2 emissions, and sinks. This portal provides access to interactive maps based on the Carbon Sequestration Atlas of the United States and Canada.

201

[Genetic mapping of T-DNA integration sites in Xa21 transgenic rice].  

PubMed

The transformation mediated by Agrobacterium has been successfully applied to rice in recent years. In the previous research we have transferred the Xa21 gene into five rice varieties of China, using Agrobacterium-mediated trasformation. In this study, T-DNA flanking sequences of Xa21 transgenic rice lines were obtained by using thermal asymmetric interlaced PCR (TAIL-PCR). The flanking sequences which are actual rice DNA were identified and located on molecular linkage map developed from a ZYQ8/JX17 double haploid (DH) population. A total of 22 T-DNA flanking rice sequences were isolated. Nineteen of them displayed RFLPs between the two parents, ZYQ8 and JX17, and were mapped on the rice chromosomes, 3, 4, 7, 9, 10, 11 and 12, respectively. The genetic mapping of T-DNA integration sites in Xa21 transgenic rice will benefit the study of position effect and stable inheritance of the transgene Xa21. PMID:12561472

Zhu, Xue-Feng; Chen, Xue-Wei; Li, Xiao-Bing; Qian, Qian; Huang, Da-Nian; Zhu, Li-Huang; Zhai, Wen-Xue

2002-10-01

202

Interactive flare sites within an active region complex  

NASA Technical Reports Server (NTRS)

We examine here a set of images of an active region complex, acquired on June 24-25, 1980, by the Hard X-ray Imaging Spectrometer on SMM, with the purpose of establishing whether there was any interplay between the frequent activity observed at different sites in the activity center and, in such a case, how the interaction was established. By analyzing both quiet and active orbits we show that, as a rule, activity originating in one region triggers the other region's activity. However, we find little unambiguous evidence for the presence of large-scale interconnecting loops. A comparison of X-ray images with magnetic field observations suggested that we interpret the active region behavior in terms of the interaction between different loop systems, in a scenario quite analogous to the interacting bipole representation of individual flares. We conclude that active region interplay provides an easily observable case to study the time-dependent topology and the mechanisms for the spreading of activity in transient events over all energy scales.

Poletto, G.; Gary, G. A.; Machado, M. E.

1993-01-01

203

Mapping the interactions of selected antibiotics and their Cu2+ complexes with the antigenomic ? ribozyme.  

PubMed

The interactions of selected antibiotics with the trans-acting antigenomic delta ribozyme were mapped. Ribozyme with two oligonucleotide substrates was used, one uncleavable with deoxycytidine at the cleavage site, mimicking the initial state of ribozyme, and the other with an all-RNA substrate mimicking, after cleavage, the product state. Mapping was performed with a set of RNA structural probing methods: Pb(2+) -induced cleavage, nuclease digestion, and the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) approach. The experimental results combined with molecular modeling revealed different binding sites for neomycin B, amikacin and actinomycin D inside the ribozyme structure. Neomycin B, an aminoglycoside antibiotic, which strongly inhibited the catalytic properties of delta ribozyme, was bound to the pocket formed by the P1 stem, the P1.1 pseudoknot, and the J4/2 junction. Amikacin showed less effective binding to the ribozyme catalytic core, resulting in weak inhibition. Complexes of these aminoglycosides with Cu(2+) ions were bound to the same ribozyme regions, but more effectively, showing lower Kd values. On the other hand, the Cu(2+) complex of the cyclopeptide antibiotic actinonomycin D was preferentially intercalated into the P2 and the P4 double-stranded region, and was three times more potent in ribozyme inhibition than the free antibiotic. In addition, some differences in SHAPE reactivities between the ribozyme forms containing all-RNA and deoxycytidine-modified substrates in the J4/2 region were detected, pointing to different ribozyme conformations before and after the cleavage event. PMID:23527582

Wrzesinski, Jan; B?aszczyk, Leszek; Wro?ska, Magdalena; Kasprowicz, Aleksandra; Stokowa-So?tys, Kamila; Nagaj, Justyna; Szafraniec, Milena; Kulinski, Tadeusz; Je?owska-Bojczuk, Ma?gorzata; Ciesio?ka, Jerzy

2013-06-01

204

Training site statistics from Landsat and Seasat satellite imagery registered to a common map base  

NASA Technical Reports Server (NTRS)

Landsat and Seasat satellite imagery and training site boundary coordinates were registered to a common Universal Transverse Mercator map base in the Newport Beach area of Orange County, California. The purpose was to establish a spatially-registered, multi-sensor data base which would test the use of Seasat synthetic aperture radar imagery to improve spectral separability of channels used for land use classification of an urban area. Digital image processing techniques originally developed for the digital mosaics of the California Desert and the State of Arizona were adapted to spatially register multispectral and radar data. Techniques included control point selection from imagery and USGS topographic quadrangle maps, control point cataloguing with the Image Based Information System, and spatial and spectral rectifications of the imagery. The radar imagery was pre-processed to reduce its tendency toward uniform data distributions, so that training site statistics for selected Landsat and pre-processed Seasat imagery indicated good spectral separation between channels.

Clark, J.

1981-01-01

205

High-resolution physical and functional mapping of the template adjacent DNA binding site in catalytically active telomerase.  

PubMed

Telomerase is a cellular reverse transcriptase, which utilizes an integral RNA template to extend single-stranded telomeric DNA. We used site-specific photocrosslinking to map interactions between DNA primers and the catalytic protein subunit (tTERT) of Tetrahymena thermophila telomerase in functional enzyme complexes. Our assays reveal contact of the single-stranded DNA adjacent to the primer-template hybrid and tTERT residue W187 at the periphery of the N-terminal domain. This contact was detected in complexes with three different registers of template in the active site, suggesting that it is maintained throughout synthesis of a complete telomeric repeat. Substitution of nearby residue Q168, but not W187, alters the K(m) for primer elongation, implying that it plays a role in the DNA recognition. These findings are the first to directly demonstrate the physical location of TERT-DNA contacts in catalytically active telomerase and to identify amino acid determinants of DNA binding affinity. Our data also suggest a movement of the TERT active site relative to the template-adjacent single-stranded DNA binding site within a cycle of repeat synthesis. PMID:17494734

Romi, Erez; Baran, Nava; Gantman, Marina; Shmoish, Michael; Min, Bosun; Collins, Kathleen; Manor, Haim

2007-05-22

206

Covariance of biophysical data with digital topograpic and land use maps over the FIFE site  

SciTech Connect

This paper discusses the biophysical stratification of the FIFE site, implementation of the stratification utilizing geographic information system methods, and validation of the stratification with respect to field measurements of biomass, Bowen ratio, soil moisture, and the greenness vegetation index (GVI) derived from TM satellite data. Maps of burning and topographic position were significantly associated with variation in GVI, biomass, and Bowen ratio. The stratified design did not significantly alter the estimated site-wide means for surface climate parameters but accounted for between 25 and 45 percent of the sample variance depending on the variable. 30 refs.

Davis, F.W.; Schimel, D.S.; Friedl, M.A.; Michaelsen, J.C.; Kittel, T.G.F.; Dubayah, R.; Dozier, J. (California Univ., Santa Barbara (United States) Colorado State Univ., Fort Collins (United States) Cooperative Inst. for Research in the Atmosphere, Fort Collins, CO (United States) Maryland Univ., College Park (United States) NASA, Goddard Space Flight Center, Greenbelt, MD (United States))

1992-11-01

207

Covariance of biophysical data with digital topograpic and land use maps over the FIFE site  

NASA Technical Reports Server (NTRS)

This paper discusses the biophysical stratification of the FIFE site, implementation of the stratification utilizing geographic information system methods, and validation of the stratification with respect to field measurements of biomass, Bowen ratio, soil moisture, and the greenness vegetation index (GVI) derived from TM satellite data. Maps of burning and topographic position were significantly associated with variation in GVI, biomass, and Bowen ratio. The stratified design did not significantly alter the estimated site-wide means for surface climate parameters but accounted for between 25 and 45 percent of the sample variance depending on the variable.

Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

1992-01-01

208

Demonstration of three different subtypes of adenovirus type 7 by DNA restriction site mapping.  

PubMed Central

Restriction site mapping of the genomes of eight different isolates of adenovirus serotype 7 (Ad7) has been performed with six different restriction endonucleases. In this analysis, 37 different restriction sites were localized. Three distinctly different cleavage patterns of the genomes of the Ad7 strains were observed. These strains could not be distinguished by serological techniques. The following three subtypes were defined on the basis of their restriction site patterns: the Ad7 prototype, represented by strain Gomen originally isolated from a case of pharyngitis; subtype Ad7a, represented by the Ad7 vaccine strain and strains isolated from undifferentiated respiratory disease and from a healthy carrier; and a third subtype of Ad7, represented by three strains which were isolated from Swedish patients, all having pronounced clinical symptoms indicating severe systemic infection. A comparison of the restriction site maps of the protype of Ad3 and the three subtypes of Ad7 indicated greater differences in the position of restriction sites between strains of Ad7 than between strains of the two serotypes. This technique is consequently recommended to obtain a more precise definition of distinct entities of viruses. Images PMID:711317

Wadell, G; Varsanyi, T M

1978-01-01

209

Salt Repository Project site study plan for surface geological mapping: Revision 1, December 22, 1987  

SciTech Connect

This site study plan describes the Surface Geological Mapping field activities to be conducted during early stages of Site Characterization for the Deaf Smith County Site, Texas. The field program has been designed to provide data useful in addressing information and design data needs resulting from Federal/State/local regulatory requirements and repository program requirements. Air and ground surveys and an extensive literature search will be conducted to map areas within and hear proposed nuclear waste repository site in the Deaf Smith County. Findings from this study may identify additional areas requiring further investigation, for which a new site study plan will be prepared. The Salt Repository Project (SRP) Networks specify the schedule under which the program will operate. The Technical and Field Services Contractor (TFSC) is responsible for conducting the field program. Data will be handled and reported in accordance with established SRP procedures. A quality assurance program will be utilized to assure that activities affecting quality are performed correctly and the appropriate documentation is maintained. 27 refs., 13 figs., 5 tabs.

Not Available

1988-03-01

210

Rapid Mapping and Prioritisation of Wetland Sites in the Manawatu-Wanganui Region, New Zealand  

NASA Astrophysics Data System (ADS)

The extent of wetland in New Zealand has decreased by approximately 90% since European settlement began in 1840. Remaining wetlands continue to be threatened by drainage, weeds, and pest invasion. This article presents a rapid method for broad-scale mapping and prioritising palustrine and estuarine wetlands for conservation. Classes of wetland (lacustrine, estuarine, riverine, marine, and palustrine) were mapped using Landsat ETM+ imagery and centre-points of palustrine and estuarine sites as ancillary data. The results shown are for the Manawatu-Wanganui region, which was found to have 3060 ha of palustrine and 250 ha of estuarine wetlands. To set conservation priorities, landscape indicators were computed from a land-cover map and a digital terrain model. Four global indicators were used (representativeness, area, surrounding naturalness, and connectivity), and each was assigned a value to score wetland sites in the region. The final score is an additive function that weights the relative importance of each indicator (i.e., multicriteria decision analysis). The whole process of mapping and ranking wetlands in the Manawatu-Wanganui region took only 6 weeks. The rapid methodology means that consistent wetland inventories and ranking can now actually be produced at reasonable cost, and conservation resources may therefore be better targeted. With complete inventories and priority lists of wetlands, managers will be able to plan for conservation without having to wait for the collection of detailed biologic information, which may now also be prioritised.

Ausseil, Anne-Gaelle E.; Dymond, John R.; Shepherd, James D.

2007-03-01

211

Competition between heavy fermion and Kondo interaction in isoelectronic A-site-ordered perovskites  

NASA Astrophysics Data System (ADS)

With current research efforts shifting towards the 4d and 5d transition metal oxides, understanding the evolution of the electronic and magnetic structure as one moves away from 3d materials is of critical importance. Here we perform X-ray spectroscopy and electronic structure calculations on A-site-ordered perovskites with Cu in the A-site and the B-sites descending along the ninth group of the periodic table to elucidate the emerging properties as d-orbitals change from partially filled 3d to 4d to 5d. The results show that when descending from Co to Ir, the charge transfers from the cuprate-like Zhang-Rice state on Cu to the t2g orbital of the B site. As the Cu d-orbital occupation approaches the Cu2+ limit, a mixed valence state in CaCu3Rh4O12 and heavy fermion state in CaCu3Ir4O12 are obtained. The investigated d-electron compounds are mapped onto the Doniach phase diagram of the competing RKKY and Kondo interactions developed for the f-electron systems.

Meyers, D.; Middey, S.; Cheng, J.-G.; Mukherjee, Swarnakamal; Gray, B. A.; Cao, Yanwei; Zhou, J.-S.; Goodenough, J. B.; Choi, Yongseong; Haskel, D.; Freeland, J. W.; Saha-Dasgupta, T.; Chakhalian, J.

2014-12-01

212

Competition between heavy fermion and Kondo interaction in isoelectronic A-site-ordered perovskites.  

PubMed

With current research efforts shifting towards the 4d and 5d transition metal oxides, understanding the evolution of the electronic and magnetic structure as one moves away from 3d materials is of critical importance. Here we perform X-ray spectroscopy and electronic structure calculations on A-site-ordered perovskites with Cu in the A-site and the B-sites descending along the ninth group of the periodic table to elucidate the emerging properties as d-orbitals change from partially filled 3d to 4d to 5d. The results show that when descending from Co to Ir, the charge transfers from the cuprate-like Zhang-Rice state on Cu to the t(2g) orbital of the B site. As the Cu d-orbital occupation approaches the Cu(2+) limit, a mixed valence state in CaCu(3)Rh(4)O(12) and heavy fermion state in CaCu(3)Ir(4)O(12) are obtained. The investigated d-electron compounds are mapped onto the Doniach phase diagram of the competing RKKY and Kondo interactions developed for the f-electron systems. PMID:25517129

Meyers, D; Middey, S; Cheng, J-G; Mukherjee, Swarnakamal; Gray, B A; Cao, Yanwei; Zhou, J-S; Goodenough, J B; Choi, Yongseong; Haskel, D; Freeland, J W; Saha-Dasgupta, T; Chakhalian, J

2014-01-01

213

Validation of Innovative Exploration Technologies for Newberry Volcano: Drill Site Location Map 2010  

SciTech Connect

Newberry seeks to explore "blind" (no surface evidence) convective hydrothermal systems associated with a young silicic pluton on the flanks of Newberry Volcano. This project will employ a combination of innovative and conventional techniques to identify the location of subsurface geothermal fluids associated with the hot pluton. Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop “blind” geothermal resources.

Jaffe, Todd

2012-01-01

214

Mapping the Specific Cytoprotective Interaction of Humanin with the Pro-apoptotic Protein Bid  

PubMed Central

Humanin is a short endogenous peptide, which can provide protection from cell death through its association with various receptors, including the pro-apoptotic Bcl-2 family proteins Bid, Bim, and Bax. By using NMR chemical shift mapping experiments, we demonstrate that the interaction between Humanin-derived peptides and Bid is specific, and we localize the binding site to a region on the surface of Bid, which includes residues from the conserved helical BH3 domain of the protein. The BH3 domain mediates the association of Bid with other Bcl-2 family members and is essential for the protein's cytotoxic activity. The data suggest that Humanin exerts its cytoprotective activity by engaging the Bid BH3 domain; this would hinder the association of Bid with other Bcl-2 family proteins, thereby mitigating its toxicity. The identification of a Humanin-specific binding site on the surface of Bid reinforces its importance as a direct modulator of programmed cell death, and suggests a strategy for the design of cytoprotective peptide inhibitors of Bid. PMID:17927731

Choi, Jungyuen; Zhai, Dayong; Zhou, Xin; Satterthwait, Arnold; Reed, John C.; Marassi, Francesca M.

2010-01-01

215

Interactive Decal Compositing with Discrete Exponential Maps Ryan Schmidt  

E-print Network

approximation to the exponential map which requires only a sin- gle additional step in Dijkstra's graph-mail: {rms|blob}@cpsc.ucalgary.ca e-mail: cmg@cs.wustl.edu in most animation projects. Constrained combined with a digital camera or image database, realistic textures can be created very quickly (Figure 1

Grimm, Cindy

216

Interactive Computer Programs for Sorting and Mapping Dialect Data.  

ERIC Educational Resources Information Center

This computer program, a mechanization of the handsorted techniques which geographical dialectology has been using, increases the number of hypotheses that can be explored and the various correlations that can be made. It can draw several of the kinds of maps that dialectologists have used in direct atlases. The hardware, software, and program…

Herrick, Earl M.

217

Interactive photogrammetric system for mapping 3D objects  

NASA Astrophysics Data System (ADS)

A new system, FOTO-G, has been developed for 3D photogrammetric applications. It is a production-oriented software system designed to work with highly unconventional photogrammetric image configurations which result when photographing 3D objects. A demonstration with imagery from an actual 3D-mapping project is reported.

Knopp, Dave E.

1990-08-01

218

The lambda phage att site: functional limits and interaction with Int protein  

Microsoft Academic Search

Site-specific integrative recombination of bacteriophage lambda involves unequal partners. The minimal phage att site is composed of approximately 240-base pairs and four distinct binding sites for Int protein, at least three of which are crucial for function. This `donor site' recombines efficiently with a smalle `recipient site' that lacks the extensive interactions with Int protein.

Pei-Ling Hsu; Wilma Ross; Arthur Landy

1980-01-01

219

A genome-wide map of hyper-edited RNA reveals numerous new sites.  

PubMed

Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

2014-01-01

220

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis  

NASA Technical Reports Server (NTRS)

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa; Karr, Laurel J.; Nadarajah, Arunan; Pusey, Marc

1999-01-01

221

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis  

NASA Technical Reports Server (NTRS)

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa; Karr, Laurel; Pusey, Marc

1998-01-01

222

HABITAT AND BIODIVERSITY MAPPING, FOR THE DETERMINATION OF ALGAL BIOMASS AQUACULTURE SITES IN THE COSTAL AREAS OF PUERTO RICO  

E-print Network

HABITAT AND BIODIVERSITY MAPPING, FOR THE DETERMINATION OF ALGAL BIOMASS AQUACULTURE SITES for Puerto Rico. Two models were developed to analyze possible aquaculture sites. The first model evaluates conflict areas and the second model incorporates optimal areas for aquaculture sites. The union

Gilbes, Fernando

223

Mapping Out Atom-Wall Interaction with Atomic Clocks  

SciTech Connect

We explore the feasibility of probing atom-wall interaction with atomic clocks based on atoms trapped in engineered optical lattices. Optical lattice is normal to the wall. By monitoring the wall-induced clock shift at individual wells of the lattice, one would measure the dependence of the atom-wall interaction on the atom-wall separation. We find that the induced clock shifts are large and observable at already experimentally demonstrated levels of accuracy. We show that this scheme may uniquely probe the long-range atom-wall interaction in all three qualitatively distinct regimes of the interaction: van der Waals (image-charge interaction), Casimir-Polder (QED vacuum fluctuations), and Lifshitz (thermal-bath fluctuations) regimes.

Derevianko, A.; Obreshkov, B. [Department of Physics, University of Nevada, Reno, Nevada 89557 (United States); Dzuba, V. A. [Department of Physics, University of Nevada, Reno, Nevada 89557 (United States); School of Physics, University of New South Wales, Sydney, 2052 (Australia)

2009-09-25

224

Mapping Haplotype-haplotype Interactions with Adaptive LASSO  

PubMed Central

Background The genetic etiology of complex diseases in human has been commonly viewed as a complex process involving both genetic and environmental factors functioning in a complicated manner. Quite often the interactions among genetic variants play major roles in determining the susceptibility of an individual to a particular disease. Statistical methods for modeling interactions underlying complex diseases between single genetic variants (e.g. single nucleotide polymorphisms or SNPs) have been extensively studied. Recently, haplotype-based analysis has gained its popularity among genetic association studies. When multiple sequence or haplotype interactions are involved in determining an individual's susceptibility to a disease, it presents daunting challenges in statistical modeling and testing of the interaction effects, largely due to the complicated higher order epistatic complexity. Results In this article, we propose a new strategy in modeling haplotype-haplotype interactions under the penalized logistic regression framework with adaptive L1-penalty. We consider interactions of sequence variants between haplotype blocks. The adaptive L1-penalty allows simultaneous effect estimation and variable selection in a single model. We propose a new parameter estimation method which estimates and selects parameters by the modified Gauss-Seidel method nested within the EM algorithm. Simulation studies show that it has low false positive rate and reasonable power in detecting haplotype interactions. The method is applied to test haplotype interactions involved in mother and offspring genome in a small for gestational age (SGA) neonates data set, and significant interactions between different genomes are detected. Conclusions As demonstrated by the simulation studies and real data analysis, the approach developed provides an efficient tool for the modeling and testing of haplotype interactions. The implementation of the method in R codes can be freely downloaded from http://www.stt.msu.edu/~cui/software.html. PMID:20799953

2010-01-01

225

The go-go interaction technique: non-linear mapping for direct manipulation in VR  

Microsoft Academic Search

The Go-Go immersive interaction technique uses the meta- phor of interactively growing the user's arm and non-linear mapping for reaching and manipulating distant objects. Un- like others, our technique allows for seamless direct ma- nipulation of both nearby objects and those at a distance.

Ivan Poupyrev; Mark Billinghurst; Suzanne Weghorst; Tadao Ichikawa

1996-01-01

226

Linking learning goals and educational resources through interactive concept map visualizations  

Microsoft Academic Search

Concept browsing interfaces can help educators and learners to locate and use learning resources that are aligned with recognized learning goals. The Strand Map Service enables users to navigate interactive visualizations of related learning goals and to request digital library resources aligned with learning goals. These interfaces are created using a programmatic web service interface that dynamically generates interactive visual

Tamara Sumner; Faisal Ahmad; Sonal Bhushan; Qianyi Gu; Francis Javier Molina; Stedman Willard; Michael Wright; Lynne Davis; Greg Janee

2005-01-01

227

Site-response maps for the Los Angeles region based on earthquake ground motions  

USGS Publications Warehouse

Ground-motion records from aftershocks of the 1994 Northridge earthquake and main-shock records from the 1971 San Fernando, 1987 Whittier Narrows, 1991 Sierra Madre, and 1994 Northridge earthquakes are used to estimate site response in the urban Los Angeles, California, area. Two frequency bands are considered, 0.5-1.5 Hz and 2.0-6.0 Hz. Instrument characteristics prevented going to lower frequencies, and frequencies above 6.0 Hz are less important to the building inventory. Site response determined at the instrumented locations is associated with the surficial geology and contoured to produce a continuous spatial estimation of site response. The maps in this report are preliminary and will evolve as more data become available and more analysis is done.

Hartzell, Stephen H.; Harmsen, Stephen C.; Frankel, Arthur D.; Carver, David L.; Cranswick, Edward; Meremonte, Mark E.; Michael, John A.

1996-01-01

228

Protein-Binding RNA Aptamers Affect Molecular Interactions Distantly from Their Binding Sites  

PubMed Central

Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal ?-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the ?-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site. PMID:25793507

Dupont, Daniel M.; Thuesen, Cathrine K.; Bøtkjær, Kenneth A.; Behrens, Manja A.; Dam, Karen; Sørensen, Hans P.; Pedersen, Jan S.; Ploug, Michael; Jensen, Jan K.; Andreasen, Peter A.

2015-01-01

229

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

Microsoft Academic Search

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.

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

2006-01-01

230

The protein-protein interaction map of Helicobacter pylori  

Microsoft Academic Search

With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function. As elementary constituents of cellular protein complexes and pathways, protein-protein interactions are key determinants of protein function. Here we have built a large-scale protein-protein interaction

Jean-Christophe Rain; Luc Selig; Hilde De Reuse; Véronique Battaglia; Céline Reverdy; Stéphane Simon; Gerlinde Lenzen; Fabien Petel; Jérôme Wojcik; Vincent Schächter; Y. Chemama; Agnès Labigne; Pierre Legrain

2001-01-01

231

Identifying Potential Areas for Siting Interim Nuclear Waste Facilities Using Map Algebra and Optimization Approaches  

SciTech Connect

The renewed interest in siting new nuclear power plants in the United States has brought to the center stage, the need to site interim facilities for long-term management of spent nuclear fuel (SNF). In this paper, a two-stage approach for identifying potential areas for siting interim SNF facilities is presented. In the first stage, the land area is discretized into grids of uniform size (e.g., 100m x 100m grids). For the continental United States, this process resulted in a data matrix of about 700 million cells. Each cell of the matrix is then characterized as a binary decision variable to indicate whether an exclusion criterion is satisfied or not. A binary data matrix is created for each of the 25 siting criteria considered in this study. Using map algebra approach, cells that satisfy all criteria are clustered and regarded as potential siting areas. In the second stage, an optimization problem is formulated as a p-median problem on a rail network such that the sum of the shortest distance between nuclear power plants with SNF and the potential storage sites from the first stage is minimized. The implications of obtained results for energy policies are presented and discussed.

Omitaomu, Olufemi A [ORNL; Liu, Cheng [ORNL; Cetiner, Mustafa Sacit [ORNL; Belles, Randy [ORNL; Mays, Gary T [ORNL; Tuttle, Mark A [ORNL

2013-01-01

232

Depth-to-Ice Map of an Arctic Site on Mars  

NASA Technical Reports Server (NTRS)

Color coding in this map of a far-northern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies.

The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow.

The depth to the top of the icy layer estimated from these observations, as little as 5 centimeters (2 inches), matches modeling of where it would be if Mars has an active cycle of water being exchanged by diffusion between atmospheric water vapor and subsurface water ice.

This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67.5 degrees north latitude, 132 degrees east longitude, in the Martian arctic plains called Vastitas Borealis. It was formerly a candidate landing site for NASA's Phoenix Mars Lander mission. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice.

The Thermal Emission Imaging System observed the site in infrared wavelengths during night time, providing surface-temperature information, once on March 13, 2005, during summer in Mars' northern hemisphere, and again on April 8, 2005, during autumn there. The colors on this map signify relative differences in how much the surface temperature changed between those two observations. Blue indicates the locations with the least change. Red indicates areas with most change. Modeling provides estimates that the range of temperature changes shown in this map corresponds to a range in depth-to-ice of 5 centimeters (2 inches) to more than 18 centimeters (more than 7 inches). The sensitivity of this method for estimating the depth is not good for depths greater than about 20 centimeters (8 inches).

The temperature-change data are overlaid on a mosaic of black-and-white, daytime images taken in visible-light wavelengths by the same camera, providing information about shapes in the landscape. The 10-kilometer scale bar is 6.2 miles long.

NASA's Jet Propulsion Laboratory manages the Mars Odyssey mission for NASA's Science Mission Directorate, Washington, D.C. The Thermal Emission Imaging System was developed by Arizona State University in collaboration with Raytheon Santa Barbara Remote Sensing. Lockheed Martin Space Systems, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

2007-01-01

233

Seismic Hazard Maps for Seattle, Washington, Incorporating 3D Sedimentary Basin Effects, Nonlinear Site Response, and Rupture Directivity  

USGS Publications Warehouse

This report presents probabilistic seismic hazard maps for Seattle, Washington, based on over 500 3D simulations of ground motions from scenario earthquakes. These maps include 3D sedimentary basin effects and rupture directivity. Nonlinear site response for soft-soil sites of fill and alluvium was also applied in the maps. The report describes the methodology for incorporating source and site dependent amplification factors into a probabilistic seismic hazard calculation. 3D simulations were conducted for the various earthquake sources that can affect Seattle: Seattle fault zone, Cascadia subduction zone, South Whidbey Island fault, and background shallow and deep earthquakes. The maps presented in this document used essentially the same set of faults and distributed-earthquake sources as in the 2002 national seismic hazard maps. The 3D velocity model utilized in the simulations was validated by modeling the amplitudes and waveforms of observed seismograms from five earthquakes in the region, including the 2001 M6.8 Nisqually earthquake. The probabilistic seismic hazard maps presented here depict 1 Hz response spectral accelerations with 10%, 5%, and 2% probabilities of exceedance in 50 years. The maps are based on determinations of seismic hazard for 7236 sites with a spacing of 280 m. The maps show that the most hazardous locations for this frequency band (around 1 Hz) are soft-soil sites (fill and alluvium) within the Seattle basin and along the inferred trace of the frontal fault of the Seattle fault zone. The next highest hazard is typically found for soft-soil sites in the Duwamish Valley south of the Seattle basin. In general, stiff-soil sites in the Seattle basin exhibit higher hazard than stiff-soil sites outside the basin. Sites with shallow bedrock outside the Seattle basin have the lowest estimated hazard for this frequency band.

Frankel, Arthur D.; Stephenson, William J.; Carver, David L.; Williams, Robert A.; Odum, Jack K.; Rhea, Susan

2007-01-01

234

Physical map of infectious baboon type C viral DNA and sites of integration in infected cells.  

PubMed Central

Three species of unintegrated viral DNAs were found in permissive cells infected with baboon type C virus. The major species was a 9.0-kilobase (kb) linear DNA that was infectious. A restriction endonuclease map of this DNA was constructed and oriented with respect to the viral RNA. The linear DNA had a 0.6-kb sequence repeated at each terminus. These terminal repeat sequences were required for infectivity of the viral DNA. The minor species of the unintegrated viral DNAs were covalently closed circles of 9.0 and 8.4 kb. The smaller circle was in two- to threefold excess over the larger circle. The difference appeared to be that the smaller circle lacked one of the two 0.6-kb repeat sequences found in the larger circle. Restriction endonuclease maps of the integrated viral DNAs were constructed, and the sequences on both viral DNA and cellular DNA that are involved in integration were determined. The integrated viral DNA map was identical to that of the unintegrated infectious 9.0-kb linear DNA. Therefore, a specific site in the terminal repeat sequence of the viral DNA was used to integrate with the host cell DNA. The sizes of the cellular DNA fragments were different from clone to clone but stable with cell passage. Therefore, many sites in the cell DNA can recombine with the viral DNA. Images PMID:6257922

Battula, N; Todaro, G J

1980-01-01

235

The Potential for Mapping Nematode Distributions for Site-specific Management  

PubMed Central

The success of site-specific nematode management depends on a grower or advisor being able to afford to make a map of an infestation that is accurate enough for management decisions. The spatial dependence of nematode infestations and correlation of soil attributes with nematode density were assessed to investigate the scale of sampling required to obtain correlated observations of density and the use of soils data to reduce the cost of sampling. Nematodes and soil were sampled on a 76.2 × 76.2-m grid in two irrigated corn (Zea mays) fields for 2 years. Nematodes of each of three species were found in 36% to 77% of the cores from a field. Spatial dependence was detected for 10 of 16 distributions, and 22% to 67% of the variation in density within a field could be attributed to spatial correlation. Density was correlated to distances of 115 to 649 m in the directions of 0, 45, 90, and 135° from the crop row, and distances varied with direction. Correlations between nematode density and soil attributes were inconsistent between species and fields. These results indicate a potential for mapping nematode infestations for site-specific management, but provide no evidence for reducing the cost of sampling by substituting soils data for nematode counts when making a map. PMID:19265913

Wyse-Pester, Dawn Y.; Wiles, Lori J.; Westra, Philip

2002-01-01

236

RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites.  

PubMed

Intermolecular RNA-RNA interactions are used by many noncoding RNAs (ncRNAs) to achieve their diverse functions. To identify these contacts, we developed a method based on RNA antisense purification to systematically map RNA-RNA interactions (RAP-RNA) and applied it to investigate two ncRNAs implicated in RNA processing: U1 small nuclear RNA, a component of the spliceosome, and Malat1, a large ncRNA that localizes to nuclear speckles. U1 and Malat1 interact with nascent transcripts through distinct targeting mechanisms. Using differential crosslinking, we confirmed that U1 directly hybridizes to 5' splice sites and 5' splice site motifs throughout introns and found that Malat1 interacts with pre-mRNAs indirectly through protein intermediates. Interactions with nascent pre-mRNAs cause U1 and Malat1 to localize proximally to chromatin at active genes, demonstrating that ncRNAs can use RNA-RNA interactions to target specific pre-mRNAs and genomic sites. RAP-RNA is sensitive to lower abundance RNAs as well, making it generally applicable for investigating ncRNAs. PMID:25259926

Engreitz, Jesse M; Sirokman, Klara; McDonel, Patrick; Shishkin, Alexander A; Surka, Christine; Russell, Pamela; Grossman, Sharon R; Chow, Amy Y; Guttman, Mitchell; Lander, Eric S

2014-09-25

237

Functional mapping of protein-protein interactions in an enzyme complex by directed evolution.  

PubMed

The shikimate pathway enzyme chorismate mutase converts chorismate into prephenate, a precursor of Tyr and Phe. The intracellular chorismate mutase (MtCM) of Mycobacterium tuberculosis is poorly active on its own, but becomes >100-fold more efficient upon formation of a complex with the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (MtDS). The crystal structure of the enzyme complex revealed involvement of C-terminal MtCM residues with the MtDS interface. Here we employed evolutionary strategies to probe the tolerance to substitution of the C-terminal MtCM residues from positions 84-90. Variants with randomized positions were subjected to stringent selection in vivo requiring productive interactions with MtDS for survival. Sequence patterns identified in active library members coincide with residue conservation in natural chorismate mutases of the AroQ? subclass to which MtCM belongs. An Arg-Gly dyad at positions 85 and 86, invariant in AroQ? sequences, was intolerant to mutation, whereas Leu88 and Gly89 exhibited a preference for small and hydrophobic residues in functional MtCM-MtDS complexes. In the absence of MtDS, selection under relaxed conditions identifies positions 84-86 as MtCM integrity determinants, suggesting that the more C-terminal residues function in the activation by MtDS. Several MtCM variants, purified using a novel plasmid-based T7 RNA polymerase gene expression system, showed that a diminished ability to physically interact with MtDS correlates with reduced activatability and feedback regulatory control by Tyr and Phe. Mapping critical protein-protein interaction sites by evolutionary strategies may pinpoint promising targets for drugs that interfere with the activity of protein complexes. PMID:25551646

Roderer, Kathrin; Neuenschwander, Martin; Codoni, Giosiana; Sasso, Severin; Gamper, Marianne; Kast, Peter

2014-01-01

238

Functional Mapping of Protein-Protein Interactions in an Enzyme Complex by Directed Evolution  

PubMed Central

The shikimate pathway enzyme chorismate mutase converts chorismate into prephenate, a precursor of Tyr and Phe. The intracellular chorismate mutase (MtCM) of Mycobacterium tuberculosis is poorly active on its own, but becomes >100-fold more efficient upon formation of a complex with the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (MtDS). The crystal structure of the enzyme complex revealed involvement of C-terminal MtCM residues with the MtDS interface. Here we employed evolutionary strategies to probe the tolerance to substitution of the C-terminal MtCM residues from positions 84–90. Variants with randomized positions were subjected to stringent selection in vivo requiring productive interactions with MtDS for survival. Sequence patterns identified in active library members coincide with residue conservation in natural chorismate mutases of the AroQ? subclass to which MtCM belongs. An Arg-Gly dyad at positions 85 and 86, invariant in AroQ? sequences, was intolerant to mutation, whereas Leu88 and Gly89 exhibited a preference for small and hydrophobic residues in functional MtCM-MtDS complexes. In the absence of MtDS, selection under relaxed conditions identifies positions 84–86 as MtCM integrity determinants, suggesting that the more C-terminal residues function in the activation by MtDS. Several MtCM variants, purified using a novel plasmid-based T7 RNA polymerase gene expression system, showed that a diminished ability to physically interact with MtDS correlates with reduced activatability and feedback regulatory control by Tyr and Phe. Mapping critical protein-protein interaction sites by evolutionary strategies may pinpoint promising targets for drugs that interfere with the activity of protein complexes. PMID:25551646

Roderer, Kathrin; Neuenschwander, Martin; Codoni, Giosiana; Sasso, Severin; Gamper, Marianne; Kast, Peter

2014-01-01

239

Microarray Profiling of Phage-Display Selections for Rapid Mapping of Transcription Factor–DNA Interactions  

Microsoft Academic Search

Modern computational methods are revealing putative transcription-factor (TF) binding sites at an extraordinary rate. However, the major challenge in studying transcriptional networks is to map these regulatory element predictions to the protein transcription factors that bind them. We have developed a microarray-based profiling of phage-display selection (MaPS) strategy that allows rapid and global survey of an organism's proteome for sequence-specific

Gordon Freckleton; Soyeon I. Lippman; James R. Broach; Saeed Tavazoie

2009-01-01

240

Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale  

Microsoft Academic Search

Motivation: Protein-protein interaction, mediated by protein interac- tion sites, is intrinsic to many functional processes in the cell. In this paper, we propose a novel method to discover patterns in protein interaction sites. We observed from protein interaction networks that there exist a kind of significant substructures called interacting protein group pairs, which exhibit an all-versus-all interaction between the two

Haiquan Li; Jinyan Li; Limsoon Wong

2006-01-01

241

Protein interaction mapping with ribosome-displayed using PLATO ORF libraries  

PubMed Central

Identifying physical interactions between proteins and other molecules is a critical aspect of biological analysis. Here we describe PLATO, an in vitro method for mapping such interactions by affinity enrichment of a library of full-length open reading frames displayed on ribosomes, followed by massively parallel analysis using DNA sequencing. We demonstrate the broad utility of the method by identifying known and new interacting partners of LYN kinase, patient autoantibodies and the small molecules gefitinib and dasatinib. PMID:24336473

Zhu, Jian; Larman, H. Benjamin; Gao, Geng; Somwar, Romel; Zhang, Zijuan; Laserson, Uri; Ciccia, Alberto; Pavlova, Natalya; Church, George; Zhang, Wei; Kesari, Santosh; Elledge, Stephen J.

2013-01-01

242

MAP Kinase Phosphatase 2 Regulates Macrophage-Adipocyte Interaction  

PubMed Central

Objective Inflammation is critical for the development of obesity-associated metabolic disorders. This study aims to investigate the role of mitogen-activated protein kinase phosphatase 2 (MKP-2) in inflammation during macrophage-adipocyte interaction. Methods White adipose tissues (WAT) from mice either on a high-fat diet (HFD) or normal chow (NC) were isolated to examine the expression of MKP-2. Murine macrophage cell line RAW264.7 stably expressing MKP-2 was used to study the regulation of MKP-2 in macrophages in response to saturated free fatty acid (FFA) and its role in macrophage M1/M2 activation. Macrophage-adipocyte co-culture system was employed to investigate the role of MKP-2 in regulating inflammation during adipocyte-macrophage interaction. c-Jun N-terminal kinase (JNK)- and p38-specific inhibitors were used to examine the mechanisms by which MKP-2 regulates macrophage activation and macrophage-adipocytes interaction. Results HFD changed the expression of MKP-2 in WAT, and MKP-2 was highly expressed in the stromal vascular cells (SVCs). MKP-2 inhibited the production of proinflammatory cytokines in response to FFA stimulation in macrophages. MKP-2 inhibited macrophage M1 activation through JNK and p38. In addition, overexpression of MKP-2 in macrophages suppressed inflammation during macrophage-adipocyte interaction. Conclusion MKP-2 is a negative regulator of macrophage M1 activation through JNK and p38 and inhibits inflammation during macrophage-adipocyte interaction. PMID:25816341

Jiao, Huipeng; Tang, Peng; Zhang, Yongliang

2015-01-01

243

English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life  

E-print Network

Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services - - - - - - - - - China Business World Sci-Edu Culture/Life Sports Photos Most Popular FM Briefings Search About China

244

Detecting cell-adhesive sites in extracellular matrix using force spectroscopy mapping  

NASA Astrophysics Data System (ADS)

The cell microenvironment is composed of extracellular matrix (ECM), which contains specific binding sites that allow the cell to adhere to its surroundings. Cells employ focal adhesion proteins, which must be able to resist a variety of forces to bind to ECM. Current techniques for detecting the spatial arrangement of these adhesions, however, have limited resolution and those that detect adhesive forces lack sufficient spatial characterization or resolution. Using a unique application of force spectroscopy, we demonstrate here the ability to determine local changes in the adhesive property of a fibronectin substrate down to the resolution of the fibronectin antibody-functionalized tip diameter, ~ 20 nm. To verify the detection capabilities of force spectroscopy mapping (FSM), changes in loading rate and temperature were used to alter the bond dynamics and change the adhesion force. Microcontact printing was also used to pattern fluorescein isothiocyanate-conjugated fibronectin in order to mimic the discontinuous adhesion domains of native ECM. Fluorescent detection was used to identify the pattern while FSM was used to map cell adhesion sites in registry with the initial fluorescent image. The results show that FSM can be used to detect the adhesion domains at high resolution and may subsequently be applied to native ECM with randomly distributed cell adhesion sites.

Chirasatitsin, Somyot; Engler, Adam J.

2010-05-01

245

Depth-to-Ice Map of a Southern Mars Site Near Melea Planum  

NASA Technical Reports Server (NTRS)

Color coding in this map of a far-southern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies.

The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow.

The depth to the top of the icy layer estimated from these observations suggests that in some areas, but not others, water is being exchanged by diffusion between atmospheric water vapor and subsurface water ice. Differences in what type of material lies above the ice appear to affect the depth to the ice. The area in this image with the greatest seasonal change in surface temperature corresponds to an area of sand dunes.

This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67 degrees south latitude, 36.5 degrees east longitude, near a plain named Melea Planum. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice.

The Thermal Emission Imaging System observed the site in infrared wavelengths during night time, providing surface-temperature information. It did so once on Dec. 27, 2005, during late summer in Mars' southern hemisphere, and again on Jan. 22, 2006, the first day of autumn there. The colors on this map signify relative differences in how much the surface temperature changed between those two observations. Blue indicates the locations with the least change. Red indicates areas with most change. Modeling provides estimates that the range of temperature changes shown in this map corresponds to a range in depth-to-ice of less than 1 centimeter (0.4 inch) to more than 19 centimeters (more than 7.5 inches). The sensitivity of this method for estimating the depth is not good for depths greater than about 20 centimeters (8 inches).

The temperature-change data are overlaid on a mosaic of black-and-white, daytime images taken in infrared wavelengths by the same camera, providing information about shapes in the landscape. The 20-kilometer scale bar is 12.4 miles long.

NASA's Jet Propulsion Laboratory manages the Mars Odyssey mission for NASA's Science Mission Directorate, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University in collaboration with Raytheon Santa Barbara Remote Sensing. Lockheed Martin Space Systems, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

2007-01-01

246

Interactive Web-based Access and Analysis Tools for the Western Climate Mapping Initiative (WestMap)  

NASA Astrophysics Data System (ADS)

The Western Climate Mapping Consortium (WestMap) has developed a prototype web-based interactive access and resource interface to optimize public dissemination and usage of fine-scale spatial climate time series for the western United States. The western U.S. focus reflects the complex climate interactions and diverse geography that make resource management, policy considerations, and climate research challenging in this region. WestMap was conceived by a consortium comprised of the University of Arizona/CLIMAS, the Western Regional Climate Center (WRCC)/Desert Research Institute, and the PRISM group at Oregon State University, along with collaborators at Scripps Institute of Oceanography/California Applications Project, NOAA Climate Diagnostics Center, and the USDA Natural Resource Conservation Service. WestMap evolved in direct response to a multitude of requests to the WRCC and the RISAs from public and private stakeholder communities for lengthy time series of fine-scale spatial climate aggregated to user-specified domains, and related user-friendly web-based access and analysis tools. The WestMap interface is designed to link three stakeholder-driven components, 1) climate data development and operations (access, maintenance); 2) error assessment, data analysis, diagnostics, and related tools; and (3) data access, visualization, and educational resources. The 100-year PRISM 4km monthly temperature and precipitation series serve as the initial data archive, updating automatically once in operational mode. Operational user components are being designed to allow direct stakeholder access to user-specified data and resources most relevant to current needs in a timely manner. Requested resources currently in development and limited testing stages include clickable maps, regional aggregate capabilities, basic statistical analysis, time series visualization, error assessment, and download/print capability. Phased prototype testing, currently underway internally, will continue with broader stakeholder participation into Spring 2007. Operational release of the prototype interface is planned for late Summer 2007. At this meeting, we will share the latest developmental version of the WestMap interface with participants and invite feedback to help maximize the utility of the interface for the greater interdisciplinary climate community having interests in the western United States.

Comrie, A. C.; Redmond, K.; Glueck, M. F.; Reinbold, H.

2006-12-01

247

Mapping Site Remediation with Electrical Resistivity Tomography Explored via Coupled-Model Simulations  

NASA Astrophysics Data System (ADS)

Remediation programs for sites contaminated with dense non-aqueous phase liquids (DNAPLs) would benefit from an ability to non-intrusively map the evolving volume and extent of the DNAPL source zone. Electrical resistivity tomography (ERT) is a well-established geophysical tool, widely used outside the remediation industry, that has significant potential for mapping DNAPL source zones. However, that potential has not been realized due to challenges in data interpretation from contaminated sites - in either a qualitative or quantitative way. The objective of this study is to evaluate the potential of ERT to map realistic, evolving DNAPL source zones within complex subsurface environments during remedial efforts. For this purpose, a novel coupled model was developed that integrates a multiphase flow model (DNAPL3D-MT), which generates realistic DNAPL release scenarios, with 3DINV, an ERT model which calculates the corresponding resistivity response. This presentation will describe the developed model coupling methodology, which integrates published petrophysical relationships to generate an electrical resistivity field that accounts for both the spatial heterogeneity of subsurface soils and the evolving spatial distribution of fluids (including permeability, porosity, clay content and air/water/DNAPL saturation). It will also present an example in which the coupled model was employed to explore the ability of ERT to track the remediation of a DNAPL source zone. A field-scale, three-dimensional release of chlorinated solvent DNAPL into heterogeneous clayey sand was simulated, including the subsurface migration and subsequent removal of the DNAPL source zone via dissolution in groundwater. Periodic surveys of this site via ERT applied at the surface were then simulated and inversion programs were used to calculate the subsurface distribution of electrical properties. This presentation will summarize this approach and its potential as a research tool exploring the range of site conditions under which ERT may prove useful in aiding DNAPL site remediation. Moreover, it is expected to provide a cost-effective avenue to test optimum ERT data acquisition, inversion and interpretative tools at contaminated sites.

Power, C.; Gerhard, J. I.; Tsourlos, P.; Giannopoulos, A.

2011-12-01

248

A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis  

Microsoft Academic Search

BackgroundComputational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine - the scientific approach to medicine in tight relation with basic science -, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions

Gang Wu; Lisha Zhu; Jennifer E. Dent; Christine Nardini; Frank Beier

2010-01-01

249

Network Physiology: Mapping Interactions Between Networks of Physiologic Networks  

NASA Astrophysics Data System (ADS)

The human organism is an integrated network of interconnected and interacting organ systems, each representing a separate regulatory network. The behavior of one physiological system (network) may affect the dynamics of all other systems in the network of physiologic networks. Due to these interactions, failure of one system can trigger a cascade of failures throughout the entire network. We introduce a systematic method to identify a network of interactions between diverse physiologic organ systems, to quantify the hierarchical structure and dynamics of this network, and to track its evolution under different physiologic states. We find a robust relation between network structure and physiologic states: every state is characterized by specific network topology, node connectivity and links strength. Further, we find that transitions from one physiologic state to another trigger a markedly fast reorganization in the network of physiologic interactions on time scales of just a few minutes, indicating high network flexibility in response to perturbations. This reorganization in network topology occurs simultaneously and globally in the entire network as well as at the level of individual physiological systems, while preserving a hierarchical order in the strength of network links. Our findings highlight the need of an integrated network approach to understand physiologic function, since the framework we develop provides new information which can not be obtained by studying individual systems. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology.

Ivanov, Plamen Ch.; Bartsch, Ronny P.

250

Comparison of reproductive parameters in male yellow-blotched map turtles ( Graptemys flavimaculata) from a historically contaminated site and a reference site  

Microsoft Academic Search

From May to September of 1998, we collected monthly plasma samples from male yellow-blotched map turtles captured at two sites in the Pascagoula River drainage, Mississippi. One site (Vancleave) has a documented history of pollution from industrial sources (principally 2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD). Fish consumption advisories at the Vancleave site were lifted in 1996 and current impacts appear minimal. However, the yellow-blotched

J. A. Shelby; M. T. Mendonça

2001-01-01

251

Interactive System for Dynamic Scene Lighting using Captured Video Environment Maps  

Microsoft Academic Search

Abstract We present an interactive system for fully dynamic,scene lighting using captured high dynamic,range (HDR) video environment,maps. The key component,of our system is an algorithm for efcient decomposition,of HDR video environment map captured over hemisphere into a set of representative directional light sources, which can be used for the direct lighting computation,with shadows,using graphics hardware. The resulting lights exhibit good

Vlastimil Havran; Miloslaw Smyk; Grzegorz Krawczyk; Karol Myszkowski; Hans-Peter Seidel

2005-01-01

252

Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci  

Microsoft Academic Search

The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment interaction, which is of great importance in many quantitative traits, can only be approached by separately analyzing the

R. C. Jansen; J. W. van Ooijen; P. Stam; C. Lister; C. Dean

1995-01-01

253

Regional geology of the Venera landing sites: Tentative results of photogeologic mapping  

NASA Technical Reports Server (NTRS)

The regional geology of the five Venera landing sites, where geochemical measurements and TV observations on the Venusian surface were made, was studied based on the photogeologic analysis of the Magellan C1-MIDRP imagery for the large area that we will call the Venera region (38 deg. N to 22.6 deg. S and 268 to 344 deg. E). The results of the analysis were compiled in the form of a synoptical geologic map at about 1:10 M scale. MIT-processed Magellan altimetry was also used for the analysis.

Basilevsky, A. T.; Weitz, C. M.

1993-01-01

254

Reference interaction site model polaron theory of the hydrated electron  

NASA Astrophysics Data System (ADS)

We have extended the reference interaction site model (RISM)-polaron theory of Chandler et al. [J. Chem. Phys. 81, 1975 (1984)] to treat self-trapping and localized states of excess electrons in polar fluids. The extension is based on a new closure of the RISM equation presented herein. The theory is applied to the hydrated electron employing a simple class of electron-water pseudopotentials. Included in this class are models coinciding with those already examined by others using computer simulations. In those cases, the results for both structural and energetic properties compare well with those of simulation. The work function, or equivalently, the excess chemical potential of the hydrated electron are also computed; the theoretical result agrees with experiment to about 1%. Most interesting, however, is that as the parameter characterizing the pseudopotentials is varied, a critical parameter is found where the electron behavior changes essentially discontinuously from a trapped state to a ``super''-trapped state. This transition may have a direct bearing on theoretical efforts to explain the properties of solvated electrons.

Laria, Daniel; Wu, David; Chandler, David

1991-09-01

255

Carbon Sequestration Atlas and Interactive Maps from the Southwest Regional Partnership on Carbon Sequestration  

DOE Data Explorer

In November of 2002, DOE announced a global climate change initiative involving joint government-industry partnerships working together to find sensible, low cost solutions for reducing GHG emissions. As a result, seven regional partnerships were formed; the Southwest Regional Partnership on Carbon Sequestration (SWP) is one of those. These groups are utilizing their expertise to assess sequestration technologies to capture carbon emissions, identify and evaluate appropriate storage locations, and engage a variety of stakeholders in order to increase awareness of carbon sequestration. Stakeholders in this project are made up of private industry, NGOs, the general public, and government entities. There are a total of 44 current organizations represented in the partnership including electric utilities, oil and gas companies, state governments, universities, NGOs, and tribal nations. The SWP is coordinated by New Mexico Tech and encompasses New Mexico, Arizona, Colorado, Oklahoma, Utah, and portions of Kansas, Nevada, Texas, and Wyoming. Field test sites for the region are located in New Mexico (San Juan Basin), Utah (Paradox Basin), and Texas (Permian Basin).[Taken from the SWP C02 Sequestration Atlas] The SWP makes available at this website their CO2 Sequestration Atlas and an interactive data map.

McPherson, Brian

256

High resolution dynamical mapping of social interactions with active RFID  

E-print Network

In this paper we present an experimental framework to gather data on face-to-face social interactions between individuals, with a high spatial and temporal resolution. We use active Radio Frequency Identification (RFID) devices that assess contacts with one another by exchanging low-power radio packets. When individuals wear the beacons as a badge, a persistent radio contact between the RFID devices can be used as a proxy for a social interaction between individuals. We present the results of a pilot study %recently performed during a conference, and a subsequent preliminary data analysis, that provides an assessment of our method and highlights its versatility and applicability in many areas concerned with human dynamics.

Barrat, Alain; Colizza, Vittoria; Pinton, Jean-Francois; Broeck, Wouter Van den; Vespignani, Alessandro

2008-01-01

257

Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli  

PubMed Central

SUMOylation is an essential ubiquitin-like modification involved in important biological processes in eukaryotic cells. Identification of small ubiquitin-related modifier (SUMO)-conjugated residues in proteins is critical for understanding the role of SUMOylation but remains experimentally challenging. We have set up a powerful and high-throughput method combining quantitative proteomics and peptide immunocapture to map SUMOylation sites and have analyzed changes in SUMOylation in response to stimuli. With this technique we identified 295 SUMO1 and 167 SUMO2 sites on endogenous substrates of human cells. We further used this strategy to characterize changes in SUMOylation induced by listeriolysin O, a bacterial toxin that impairs the host cell SUMOylation machinery, and identified several classes of host proteins specifically deSUMOylated in response to this toxin. Our approach constitutes an unprecedented tool, broadly applicable to various SUMO-regulated cellular processes in health and disease. PMID:25114211

Impens, Francis; Radoshevich, Lilliana; Cossart, Pascale; Ribet, David

2014-01-01

258

Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli.  

PubMed

SUMOylation is an essential ubiquitin-like modification involved in important biological processes in eukaryotic cells. Identification of small ubiquitin-related modifier (SUMO)-conjugated residues in proteins is critical for understanding the role of SUMOylation but remains experimentally challenging. We have set up a powerful and high-throughput method combining quantitative proteomics and peptide immunocapture to map SUMOylation sites and have analyzed changes in SUMOylation in response to stimuli. With this technique we identified 295 SUMO1 and 167 SUMO2 sites on endogenous substrates of human cells. We further used this strategy to characterize changes in SUMOylation induced by listeriolysin O, a bacterial toxin that impairs the host cell SUMOylation machinery, and identified several classes of host proteins specifically deSUMOylated in response to this toxin. Our approach constitutes an unprecedented tool, broadly applicable to various SUMO-regulated cellular processes in health and disease. PMID:25114211

Impens, Francis; Radoshevich, Lilliana; Cossart, Pascale; Ribet, David

2014-08-26

259

Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes.  

PubMed

The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized. In this study, we focused on mapping the genome wide Foxo1-binding sites in naïve CD4(+) T cells, CD8(+) T cells, and Foxp3(+) regulatory T (Treg) cells. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq), we identified Foxo1 binding sites that were shared among or specific to the three T cell populations. Here we describe the experiments, quality controls, as well as the deep sequencing data. Part of the data analysis has been published by Ouyang W et al. in Nature 2012[1] and Kim MV et al. in Immunity 2013[2], and the associated data set were uploaded to NCBI Gene Expression Omnibus. PMID:25302145

Liao, Will; Ouyang, Weiming; Zhang, Michael Q; Li, Ming O

2014-12-01

260

C-B4-01: Educator Experience with Group Interactive Dialogue to Educate and Activate (IDEA) Using Conversation Maps  

PubMed Central

Aims: In order to improve self- efficacy and clinical outcomes for people with diabetes, new approaches using more interactive methods of group education are being promoted. We report results of an educator evaluation of IDEA to assist others who may be interested in starting similar groups in their care settings. Methods: A qualitative analysis was conducted as part of an ongoing randomized trial comparing two different educational interventions (Group IDEA and Individual Education) to Usual Care. As part of the study, educators at HealthPartners clinics in Minneapolis, MN and ABQ Health Partners in Albuquerque, NM were trained on how to use Conversation Maps (CM). All educators completed a Likert scale questionnaire after each CM session with responses from 1–10 (10 being the best). An open- ended evaluation form was also used to solicit positive and negative opinions about the sessions. Analysis: The data consisted of 48 nurse and dietitian evaluations from two sites. The mean Likert scores of the educational experience were calculated and compared for each site and for each of the four CM topics (general information, monitoring, nutrition, and complications). All eight research team members also reviewed answers to the open-ended questions and group consensus was used to describe positive and negative themes. Results: Educator rated Likert scores of map sessions were excellent (mean scores for Maps 1, 2, 3, 4: Overall success 8.3, 7.6, 7.7, 8.8; Ease and comfort levels in facilitation 8.9, 8.9, 9.2, 9.5; Patient motivation to self-manage 7.7, 6.9, 8, 8.8). Scores did not differ significantly across sites or between maps. Positive comments on the maps outweighed the negatives. The challenges identified were: Disruptive (especially angry or negative) people; Distracting topics raised by patients and late arrivals; Variable reading levels among patients (too hard or too easy); and Not enough time to cover the content (especially nutrition). Conclusions: The IDEA method was perceived positively by educators due to its ability to promote patient interaction, sharing, and meaningful discussion. To be successful, however, educators need tips and practice on handling disruptive patients, distractions, variance in literacy, and covering intended nutritional content in a group context.

Sperl-Hillen, JoAnn M; Beaton, Sarah J; Fernandes, Omar; Von Worley, Ann; Hanson, Ann M; Baumer, Dorothy; Lavin-Tompkins, Jodi M

2010-01-01

261

Identification and mapping of natural vegetation on a coastal site using a Worldview-2 satellite image.  

PubMed

Identification and mapping of natural vegetation are major issues for biodiversity management and conservation. Remotely sensed data with very high spatial resolution are currently used to study vegetation, but most satellite sensors are limited to four spectral bands, which is insufficient to identify some natural vegetation formations. The study objectives are to discriminate natural vegetation and identify natural vegetation formations using a Worldview-2 satellite image. The classification of the Worldview-2 image and ancillary thematic data was performed using a hybrid pixel-based and object-oriented approach. A hierarchical scheme using three levels was implemented, from land cover at a field scale to vegetation formation. This method was applied on a 48 km² site located on the French Atlantic coast which includes a classified NATURA 2000 dune and marsh system. The classification accuracy was very high, the Kappa index varying between 0.90 and 0.74 at land cover and vegetation formation levels respectively. These results show that Wordlview-2 images are suitable to identify natural vegetation. Vegetation maps derived from Worldview-2 images are more detailed than existing ones. They provide a useful medium for environmental management of vulnerable areas. The approach used to map natural vegetation is reproducible for a wider application by environmental managers. PMID:24973612

Rapinel, Sébastien; Clément, Bernard; Magnanon, Sylvie; Sellin, Vanessa; Hubert-Moy, Laurence

2014-11-01

262

Noninvasive Localization of Maximal Frequency Sites of Atrial Fibrillation by Body Surface Potential Mapping  

PubMed Central

Background Ablation of high-frequency sources in patients with atrial fibrillation (AF) is an effective therapy to restore sinus rhythm. However, this strategy may be ineffective in patients without a significant dominant frequency (DF) gradient. The aim of this study was to investigate whether sites with high-frequency activity in human AF can be identified noninvasively, which should help intervention planning and therapy. Methods and Results In 14 patients with a history of AF, 67-lead body surface recordings were simultaneously registered with 15 endocardial electrograms from both atria including the highest DF site, which was predetermined by atrial-wide real-time frequency electroanatomical mapping. Power spectra of surface leads and the body surface location of the highest DF site were compared with intracardiac information. Highest DFs found on specific sites of the torso showed a significant correlation with DFs found in the nearest atrium (?=0.96 for right atrium and ?=0.92 for left atrium) and the DF gradient between them (?=0.93). The spatial distribution of power on the surface showed an inverse relationship between the frequencies versus the power spread area, consistent with localized fast sources as the AF mechanism with fibrillatory conduction elsewhere. Conclusions Spectral analysis of body surface recordings during AF allows a noninvasive characterization of the global distribution of the atrial DFs and the identification of the atrium with the highest frequency, opening the possibility for improved noninvasive personalized diagnosis and treatment. PMID:23443619

Guillem, Maria S.; Climent, Andreu M.; Millet, Jose; Arenal, Ángel; Fernández-Avilés, Francisco; Jalife, José; Atienza, Felipe; Berenfeld, Omer

2014-01-01

263

Mapping the Sea Floor of the Historic Area Remediation Site (HARS) Offshore of New York City  

USGS Publications Warehouse

The area offshore of New York City has been used for the disposal of dredged material for over a century. The area has also been used for the disposal of other materials such as acid waste, industrial waste, municipal sewage sludge, cellar dirt, and wood. Between 1976 and 1995, the New York Bight Dredged Material Disposal Site, also known as the Mud Dump Site (MDS), received on average about 6 million cubic yards of dredged material annually. In September 1997 the MDS was closed as a disposal site, and it and the surrounding area were designated as the Historic Area Remediation Site (HARS). The sea floor of the HARS, approximately 9 square nautical miles in area, currently is being remediated by placing a minimum 1-m-thick cap of clean dredged material on top of the surficial sediments that are contaminated from previous disposal of dredged and other materials. The U.S. Geological Survey (USGS) is working cooperatively with the U.S. Army Corps of Engineers (USACE) to map the sea floor geology of the HARS and changes in the characteristics of the surficial sediments over time.

Butman, Bradford

2002-01-01

264

Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomyces cerevisiae  

PubMed Central

In mammalian cells, perturbations in DNA replication result in chromosome breaks in regions termed “fragile sites.” Using DNA microarrays, we mapped recombination events and chromosome rearrangements induced by reduced levels of the replicative DNA polymerase-? in the yeast Saccharomyces cerevisiae. We found that the recombination events were nonrandomly associated with a number of structural/sequence motifs that correlate with paused DNA replication forks, including replication-termination sites (TER sites) and binding sites for the helicase Rrm3p. The pattern of gene-conversion events associated with cross-overs suggests that most of the DNA lesions that initiate recombination between homologs are double-stranded DNA breaks induced during S or G2 of the cell cycle, in contrast to spontaneous recombination events that are initiated by double-stranded DNA breaks formed prior to replication. Low levels of DNA polymerase-? also induced very high rates of aneuploidy, as well as chromosome deletions and duplications. Most of the deletions and duplications had Ty retrotransposons at their breakpoints. PMID:24799712

Song, Wei; Dominska, Margaret; Greenwell, Patricia W.; Petes, Thomas D.

2014-01-01

265

Jules Verne Voyager, Jr: An Interactive Map Tool for Teaching Plate Tectonics  

NASA Astrophysics Data System (ADS)

We present an interactive, web-based map utility that can make new geological and geophysical results accessible to a large number and variety of users. The tool provides a user-friendly interface that allows users to access a variety of maps, satellite images, and geophysical data at a range of spatial scales. The map tool, dubbed 'Jules Verne Voyager, Jr.', allows users to interactively create maps of a variety of study areas around the world. The utility was developed in collaboration with the UNAVCO Consortium for study of global-scale tectonic processes. Users can choose from a variety of base maps (including "Face of the Earth" and "Earth at Night" satellite imagery mosaics, global topography, geoid, sea-floor age, strain rate and seismic hazard maps, and others), add a number of geographic and geophysical overlays (coastlines, political boundaries, rivers and lakes, earthquake and volcano locations, stress axes, etc.), and then superimpose both observed and model velocity vectors representing a compilation of 2933 GPS geodetic measurements from around the world. A remarkable characteristic of the geodetic compilation is that users can select from some 21 plates' frames of reference, allowing a visual representation of both 'absolute' plate motion (in a no-net rotation reference frame) and relative motion along all of the world's plate boundaries. The tool allows users to zoom among at least three map scales. The map tool can be viewed at http://jules.unavco.org/VoyagerJr/Earth. A more detailed version of the map utility, developed in conjunction with the EarthScope initiative, focuses on North America geodynamics, and provides more detailed geophysical and geographic information for the United States, Canada, and Mexico. The ‘EarthScope Voyager’ can be accessed at http://jules.unavco.org/VoyagerJr/EarthScope. Because the system uses pre-constructed gif images and overlays, the system can rapidly create and display maps to a large number of users simultaneously and does not require any special software installation on users' systems. In addition, a javascript-based educational interface, dubbed "Exploring our Dynamic Planet", incorporates the map tool, explanatory material, background scientific material, and curricular activities that encourage users to explore Earth processes using the Jules Verne Voyager, Jr. tool. Exploring our Dynamic Planet can be viewed at http://www.dpc.ucar.edu/VoyagerJr/. Because of its flexibility, the map utilities can be used for hands-on exercises exploring plate interaction in a range of academic settings, from high school science classes to entry-level undergraduate to graduate-level tectonics courses.

Hamburger, M. W.; Meertens, C. M.

2010-12-01

266

Environmental Maps  

NSDL National Science Digital Library

The US Housing and Urban Development (HUD) Environmental Maps Web site is a free Internet service that combines information on HUD's community development and housing programs with Environmental Protection Agency (EPA) environmental data. The maps "provide: location, type, and performance of HUD-funded activities in every neighborhood across the country; and select EPA information on brownfields, hazardous wastes, air pollution and waste water discharges." The Geographic Information Systems (GIS)-based mapping interface is easily manipulated and users can locate theirs, or an interested neighborhood, in no time and browse the information provided. This powerful application is one of the best online interactive GIS mapping sites online for both its content and ease of use, making it a must visit.

267

Copyright 2004 by the Genetics Society of America A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites  

E-print Network

of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton H. Paterson*,,1 *Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster

Wendel, Jonathan F.

268

Acoustic mapping of the regional seafloor geology in and around Hawaiian ocean dredged-material disposal sites  

USGS Publications Warehouse

During January and February 1998 the U.S. Geological Survey Coastal and Marine Geology Team (USGS) conducted regional high-resolution multibeam mapping surveys of the area surrounding EPA-designated ocean disposal sites located offshore of the Hawaiian Islands of Oahu, Kauai, Maui, and Hawaii. The sites are all located within 5 nautical miles of shore on insular shelves or slopes. Regional maps were required of areas much larger than the disposal sites themselves to assess both the regional seafloor geology and the immediate vicinity of the disposal sites. The purpose of the disposal site surveys was to delimit the extent of disposal material by producing detailed bathymetric and backscatter maps of the seafloor with a ± 1 m spatial accuracy and <1% depth error. The advantage of using multibeam over conventional towed, single-beam sidescan sonar is that the multibeam data are accurately georeferenced for precise location of all imaged features. The multibeam produces a coregistered acoustic-backscatter map that is often required to locate individual disposal deposits. These data were collected by the USGS as part of its regional seafloor mapping and in support of ocean disposal site monitoring studies conducted in cooperation with the US Environmental Protection Agency (EPA) and the US Army Corps of Engineers (COE).

Torresan, Michael E.; Gardner, James V.

2000-01-01

269

Quantitative analysis of anthropogenic relief features: automated mapping of charcoal kiln sites from high-resolution ALS data  

NASA Astrophysics Data System (ADS)

High-resolution digital elevation data from airborne laser scanning (ALS) allow for identification and mapping of so far unknown small-scale relief features that are hidden by forest cover. Especially as a result of historic land use, small anthropogenic landforms can occur, e.g., remains of charcoal kilns on sites that were used for charcoal production or ridge and furrow systems in former farmland areas. Mapping such relief features and analyzing their spatial distribution patterns can help to understand past land-use systems and their effects on landscapes. To efficiently detect and quantify small-scale relief features from high-resolution DEMs for larger areas, (semi-) automated mapping routines are required. In order to describe the number and spatial distribution of historic charcoal kiln sites in the area around Cottbus, Germany, we developed a GIS-based routine for the detection and mapping of kiln remnants from ALS elevation models with a resolution of 1 or 2 meters. The method is based on a template matching algorithm, using a combination of morphometric parameters, and is implemented within ArcGIS. The mapping results could be validated against a comprehensive database of kiln sites and diameters recorded from archaeological excavations in the forefield of the opencast mine Jänschwalde and from manual digitization of kiln remnants from Shaded Relief maps for the Jänschwalder Heide and the Tauersche Forst, north of Cottbus. A considerably high number of charcoal kiln sites could be detected in ALS data, and the diameters of the identified charcoal kilns are remarkable large in the area. For the Jänschwalder Heide, more than 5000 kiln sites in an area of 32 km2 were detected by manual digitization, with 1355 kiln sites that are wider than 12 m. These relatively large kiln sites could be mapped with detection rates that are close to those of manual digitization using the automated mapping routine. Detection quality was improved by the combination of several morphometric parameters used for template matching, as compared to a mapping based on elevation values only. In comparison to manual digitization, a combination of the described detection routine and a manual removal of falsely detected sites can considerably facilitate the mapping and distribution analysis of kiln sites or other small-scale relief features.

Schneider, Anna; Takla, Melanie; Nicolay, Alexander; Raab, Alexandra; Raab, Thomas

2014-05-01

270

The FIRST experiment: interaction region and MAPS vertex detector  

NASA Astrophysics Data System (ADS)

The improvement of the precision of the measurement of the nuclear cross-section, in order to fulfill the requirements of the actual Monte Carlo simulations for hadrontherapy and space radioprotection, is the main goal of the FIRST experiment. After a brief introduction on the treatment planning in hadrontherapy, this paper describes main characteristics and components of the experiment. The features of the interaction region detectors and their main needs (low material budget, high angular coverage, two tracks resolution and large trigger rate) are discussed. Special emphasis is devoted in discussing the new silicon pixel vertex detector, in particular its new developed data acquisition and its characterization with the first test results obtained with a prototype of the detector.

Spiriti, E.; de Napoli, M.; Romano, F.; FIRST Collaboration

2011-06-01

271

MAP kinase-interacting kinases--emerging targets against cancer.  

PubMed

Mitogen-activated protein kinase (MAPK)-interacting kinases (Mnks) regulate the initiation of translation through phosphorylation of eukaryotic initiation factor 4E (eIF4E). Mnk-mediated eIF4E activation promotes cancer development and progression. While the phosphorylation of eIF4E is necessary for oncogenic transformation, the kinase activity of Mnks seems dispensable for normal development. For this reason, pharmacological inhibition of Mnks could represent an ideal mechanism-based and nontoxic therapeutic strategy for cancer treatment. In this review, we discuss the current understanding of Mnk biological roles, structures, and functions, as well as clinical implications. Importantly, we propose different strategies for identification of highly selective small molecule inhibitors of Mnks, including exploring a structural feature of their kinase domain, DFD motif, which is unique within the human kinome. We also argue that a combined targeting of Mnks and other pathways should be considered given the complexity of cancer. PMID:24613018

Diab, Sarah; Kumarasiri, Malika; Yu, Mingfeng; Teo, Theodosia; Proud, Christopher; Milne, Robert; Wang, Shudong

2014-04-24

272

Large-scale mapping of human protein–protein interactions by mass spectrometry  

PubMed Central

Mapping protein–protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein–protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24 540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein–protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations. PMID:17353931

Ewing, Rob M; Chu, Peter; Elisma, Fred; Li, Hongyan; Taylor, Paul; Climie, Shane; McBroom-Cerajewski, Linda; Robinson, Mark D; O'Connor, Liam; Li, Michael; Taylor, Rod; Dharsee, Moyez; Ho, Yuen; Heilbut, Adrian; Moore, Lynda; Zhang, Shudong; Ornatsky, Olga; Bukhman, Yury V; Ethier, Martin; Sheng, Yinglun; Vasilescu, Julian; Abu-Farha, Mohamed; Lambert, Jean-Philippe; Duewel, Henry S; Stewart, Ian I; Kuehl, Bonnie; Hogue, Kelly; Colwill, Karen; Gladwish, Katharine; Muskat, Brenda; Kinach, Robert; Adams, Sally-Lin; Moran, Michael F; Morin, Gregg B; Topaloglou, Thodoros; Figeys, Daniel

2007-01-01

273

Interactive marine spatial planning: siting tidal energy arrays around the Mull of Kintyre.  

PubMed

The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the 'ecosystem approach' (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP. PMID:22253865

Alexander, Karen A; Janssen, Ron; Arciniegas, Gustavo; O'Higgins, Timothy G; Eikelboom, Tessa; Wilding, Thomas A

2012-01-01

274

Interactive Marine Spatial Planning: Siting Tidal Energy Arrays around the Mull of Kintyre  

PubMed Central

The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the ‘ecosystem approach’ (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP. PMID:22253865

Alexander, Karen A.; Janssen, Ron; Arciniegas, Gustavo; O'Higgins, Timothy G.; Eikelboom, Tessa; Wilding, Thomas A.

2012-01-01

275

Mapping shallow underground features that influence site-specific agricultural production  

NASA Astrophysics Data System (ADS)

Modern agricultural production practices are rapidly evolving in the United States of America (USA). These new production practices present significant applications for nonintrusive subsurface imaging. One such imaging technology is GPR, and it is now being incorporated within site-specific agriculture in the detection of soil horizons, perched water (episaturation), fragipans, hydrological preferential flow paths, and soil compaction. These features traditionally have been mapped by soil scientists using intrusive measurements (e.g., soil augers, soil pits, coring tools). Rather than developing a tool for soil mapping, our studies are targeting the identification, dimensioning, and position of subsurface features that directly influence agricultural productivity. It is foreseen that this information will allow for an increase in agricultural efficiency through infield machinery automation, and it will also greatly enhance development of highly efficient crop production strategies. The field sensing methodologies that we have developed using existing geophysical technologies are highly dependent upon both the soil and site characteristics due to seasonal variations. The GPR applications presented herein were conducted primarily in a region of loess soil that extends east of the Mississippi River into western Tennessee. GPR studies were also conducted in central Tennessee on the Cumberland Plateau within a region of shallow, sandy loam soils. Additional studies were conducted on the karst area of central Kentucky. Although targeting site-specific agriculture, our results and procedures may benefit the traditional users of GPR technology. We suggest that large-scale agricultural applications of the technology would be enhanced by integrating global positioning (GPS) technology in future hardware and software products.

Freeland, Robert S.; Yoder, Ronald E.; Ammons, John T.

1998-10-01

276

Interaction Techniques for Exploring Historic Sites through Situated Media  

Microsoft Academic Search

We present a set of augmented reality and virtual reality interaction techniques that enable mobile users to visualize and interact virtually with representations of past events. These approaches use historic photographic imagery registered with real and virtual 3D objects to depict events in situ, and to provide interactive timelines. We demonstrate our techniques through examples developed for an important landmark,

Sinem Güven; Steven Feiner

2006-01-01

277

VIMAP: an Interactive Program Providing Radio Spectral Index Maps of Active Galactic Nuclei  

NASA Astrophysics Data System (ADS)

We present a GUI-based interactive Python program, VIMAP, which generates radio spectral index maps of active galactic nuclei (AGN) from Very Long Baseline Interferometry (VLBI) maps obtained at different frequencies. VIMAP is a handy tool for the spectral analysis of synchrotron emission from AGN jets, specifically of spectral index distributions, turn-over frequencies, and core-shifts. In general, the required accurate image alignment is difficult to achieve because of a loss of absolute spatial coordinate information during VLBI data reduction (self-calibration) and/or intrinsic variations of source structure as function of frequency. These issues are overcome by VIMAP which in turn is based on the two-dimensional cross-correlation algorithm of \\citet{croke2008}. In this paper, we briefly review the problem of aligning VLBI AGN maps, describe the workflow of VIMAP, and present an analysis of archival VLBI maps of the active nucleus 3C 120.

Kim, Jae-Young; Trippe, Sascha

2014-10-01

278

Epstein-Barr virus and virus human protein interaction maps Vidal, Elliott Kieff, and Eric Johannsen  

E-print Network

Epstein-Barr virus and virus human protein interaction maps Vidal, Elliott Kieff, and Eric A. Calderwood, Kavitha Venkatesan, Li Xing, Michael R. Chase, Alexei Vazquez, Amy doi:10.1073/pnas. Chase*, Alexei Vazquez , Amy M. Holthaus*, Alexandra E. Ewence*, Ning Li , Tomoko Hirozane

Vazquez, Alexei

279

RE Atlas: The U.S. Atlas of Renewable Resources (Interactive Map, GIS Data)  

DOE Data Explorer

This interactive data map allows a user to explore the locations across the U.S. of many different basic, renewable energy resources. The many layers can be activated one at a time or in multiple combinations and the GIS display draws from a rich combination of data collections.

280

Brief Genetics Report Fine-Mapping Gene-by-Diet Interactions on Chromosome  

E-print Network

Brief Genetics Report Fine-Mapping Gene-by-Diet Interactions on Chromosome 13 in a LG/J SM/J Murine of obesity in humans range as high as 70% based on twin studies (1). However, obesity in the developed world is increasing too rapidly to be caused by changes in genetic background (2). Moreover, some human geno- types

Hrbek, Tomas - Department of Biology, Universidad de Puerto Rico

281

A simple contact mapping algorithm for identifying potential peptide mimetics in protein–protein interaction partners  

PubMed Central

A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, “OpenContact” provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intra-protein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate many of the challenges associated with the development of peptide biomimetics, in general. Proteins 2014; 82:2253–2262. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:24756879

Krall, Alex; Brunn, Jonathan; Kankanala, Spandana; Peters, Michael H

2014-01-01

282

An Interactive Map Viewer for the Urban Geology of Ottawa (Canada): an Example of Web Publishing  

Microsoft Academic Search

Developed by the Terrain Sciences Division (TSD) of the Geological Survey of Canada (GSC), an interactive map viewer, called GEOSERV (www.geoserv.org), is now available on the Internet. The purpose of this viewer is to provide engineers, planners, decision makers, and the general public with the geoscience information required for sound regional planning in densely populated areas, such as Canada's national

D. Giroux; R. Bélanger

2003-01-01

283

Modeling and Mapping of Nanotopography Interactions with CMP , Duane S. Boning1  

E-print Network

, and characteristics of the CMP process including the planarization length or pad stiffness. In this paper we review1 Modeling and Mapping of Nanotopography Interactions with CMP Brian Lee1 , Duane S. Boning1 concern in shallow trench isolation (STI) chemical mechanical polishing (CMP) processes. Previous work has

Boning, Duane S.

284

Enhancements to, and forthcoming developments in the Interactive Multisensor Snow and Ice Mapping System (IMS)  

Microsoft Academic Search

The National Oceanic and Atmospheric Administration's National Environmental Satellite Data and Information Service (NOAA\\/NESDIS) Interactive Multisensor Snow and Ice Mapping System (IMS) has undergone substantial changes since its inception in 1997. These changes include the data sources used to generate the product, methodology of product creation, and even changes in the output. Among the most notable of the past upgrades

Sean R. Helfrich; Donna McNamara; Bruce H. Ramsay; Thomas Baldwin; Tim Kasheta

2007-01-01

285

User-Centric Secure Cross-Site Interaction Framework for Online Social Networking Services  

ERIC Educational Resources Information Center

Social networking service is one of major technological phenomena on Web 2.0. Hundreds of millions of users are posting message, photos, and videos on their profiles and interacting with other users, but the sharing and interaction are limited within the same social networking site. Although users can share some content on a social networking site

Ko, Moo Nam

2011-01-01

286

Digital Geologic Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California  

USGS Publications Warehouse

This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map compilation presents new polygon (geologic map unit contacts), line (fault, fold axis, metamorphic isograd, dike, and caldera wall) and point (structural attitude) vector data for the NTS and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California. The map area covers two 30 x 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7.5-minute quadrangles on the east side-72 quadrangles in all. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area (Wahl and others, 1997) by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. Concurrent publications to this one include a new isostatic gravity map (Ponce and others, 1999) and a new aeromagnetic map (Ponce, 1999).

Slate, Janet L.; Berry, Margaret E.; Rowley, Peter D.; Fridrich, Christopher J.; Morgan, Karen S.; Workman, Jeremiah B.; Young, Owen D.; Dixon, Gary L.; Williams, Van S.; McKee, Edwin H.; Ponce, David A.; Hildenbrand, Thomas G.; Swadley, W.C.; Lundstrom, Scott C.; Ekren, E. Bartlett; Warren, Richard G.; Cole, James C.; Fleck, Robert J.; Lanphere, Marvin A.; Sawyer, David A.; Minor, Scott A.; Grunwald, Daniel J.; Laczniak, Randell J.; Menges, Christopher M.; Yount, James C.; Jayko, Angela S.

1999-01-01

287

Comparison of reproductive parameters in male yellow-blotched map turtles (Graptemys flavimaculata) from a historically contaminated site and a reference site.  

PubMed

From May to September of 1998, we collected monthly plasma samples from male yellow-blotched map turtles captured at two sites in the Pascagoula River drainage, Mississippi. One site (Vancleave) has a documented history of pollution from industrial sources (principally 2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD). Fish consumption advisories at the Vancleave site were lifted in 1996 and current impacts appear minimal. However, the yellow-blotched map turtle, a federally protected species, continues to decline in numbers. To determine if endocrine disruption could be a factor in the low reproductive rates observed in Vancleave turtles, we examined levels of plasma testosterone (T) and estradiol-17beta (E(2)) from males at this site and a second site (Leaksville), which has no known source of industrial pollution. Plasma was also tested for vitellogenin (VTG), which, in males, can be a biomarker of exposure to estrogenic contaminants. No males had detectable plasma VTG nor did mean monthly E(2) levels differ between sites. However, 10% of males from the historically polluted site were found to have high levels of E(2) (equivalent to levels found in females) and T was significantly lower for males captured at this site for 3 of 5 months. Our data suggest that the current impact of contaminants on reproduction in this population is limited. However, a portion of the population may have been affected developmentally, as represented by differences in reproductive parameters detected between sites. PMID:11461839

Shelby, J A; Mendonça, M T

2001-07-01

288

Concept Mapping as a Support for Mars Landing-Site Selection  

NASA Technical Reports Server (NTRS)

The NASA Ames' Center for Mars Exploration (CMEX) serves to coordinate Mars programmatic research at ARC in the sciences, in information technology and in aero-assist and other technologies. Most recently, CMEX has been working with the Institute for Human and Machine Cognition at the University of West Florida to develop a new kind of web browser based on the application of concept maps. These Cmaps, which are demonstrably effective in science teaching, can be used to provide a new kind of information navigation tool that can make web or CD based information more meaningful and more easily navigable. CMEX expects that its 1999 CD-ROM will have this new user interface. CMEX is also engaged with the Mars Surveyor Project Office at JPL in developing an Internet-based source of materials to support the process of selecting landing sites for the next series of Mars landers. This activity -- identifying the most promising sites from which to return samples relevant to the search for evidence of life -- is one that is expected to engage the general public as well as the science community. To make the landing site data easily accessible and meaningful to the public, CMEX is planning to use the IHMC Cmap browser as its user interface.

Cabrol, Nathalie A.; Briggs, Geoffrey A.

1999-01-01

289

Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.  

PubMed

While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type E. coli and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the rnc and rne mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in E. coli and is easily accessible, together with the cDNA coverage plots, in an online genome browser. PMID:25266388

Thomason, Maureen K; Bischler, Thorsten; Eisenbart, Sara K; Förstner, Konrad U; Zhang, Aixia; Herbig, Alexander; Nieselt, Kay; Sharma, Cynthia M; Storz, Gisela

2015-01-01

290

An integrated study of spatial multicriteria analysis and mathematical modelling for managed aquifer recharge site suitability mapping and site ranking at Northern Gaza coastal aquifer.  

PubMed

This paper describes an integrated approach of site suitability mapping and ranking of the most suitable sites, for the implementation of Managed Aquifer Recharge (MAR) projects, using spatial multicriteria decision analysis (SMCDA) techniques and mathematical modelling. The SMCDA procedure contains constraint mapping, site suitability analysis with criteria standardization and weighting, criteria overlay by analytical hierarchy process (AHP) combined with weighted linear combination (WLC) and ordered weighted averaging (OWA), and sensitivity analysis. The hydrogeological impacts of the selected most suitable sites were quantified by using groundwater flow and transport modelling techniques. Finally, ranking of the selected sites was done with the WLC method. The integrated approach is demonstrated by a case study in the coastal aquifer of North Gaza. Constraint mapping shows that 50% of the total study area is suitable for MAR implementation. About 25% of the total area is "very good" and 25% percent is "good" for MAR, according to the site suitability analysis. Six locations were selected and ranked against six representative decision criteria. Long term (year 2003 to year 2040) groundwater flow and transport simulations were performed to quantify the selected criteria under MAR project operation conditions at the selected sites. Finally, the suitability mapping and hydrogeological investigation recommends that the location of the existing infiltration ponds, constructed near the planned North Gaza Wastewater Treatment Plant (NGWWTP) is most suitable for MAR project implementation. This paper concludes that mathematical modelling should be combined with the SMCDA technique in order to select the best location for MAR project implementation. Besides MAR project implementation, the generalised approach can be applicable for any other water resources development project that deals with site selection and implementation. PMID:23603773

Rahman, Mohammad Azizur; Rusteberg, Bernd; Uddin, Mohammad Salah; Lutz, Annegret; Saada, Muath Abu; Sauter, Martin

2013-07-30

291

Exploring 3D Interaction in Alternate Control-Display Space Mappings Jeroen Keijser Sheelagh Carpendale* Mark Hancock* Tobias Isenberg*  

E-print Network

Exploring 3D Interaction in Alternate Control-Display Space Mappings Jeroen Keijser Sheelagh As a culture, we have had fantastical ideas about exploring alter- nate 3D spaces for at least a century ­ take to the display space. To explore alter- nate experiences in 3D interaction, we consider the 3D to 3D map- ping

292

Using Hadoop File System and MapReduce in a small/medium Grid site  

NASA Astrophysics Data System (ADS)

Data storage and data access represent the key of CPU-intensive and data-intensive high performance Grid computing. Hadoop is an open-source data processing framework that includes fault-tolerant and scalable distributed data processing model and execution environment, named MapReduce, and distributed File System, named Hadoop distributed File System (HDFS). HDFS was deployed and tested within the Open Science Grid (OSG) middleware stack. Efforts have been taken to integrate HDFS with gLite middleware. We have tested the File System thoroughly in order to understand its scalability and fault-tolerance while dealing with small/medium site environment constraints. To benefit entirely from this File System, we made it working in conjunction with Hadoop Job scheduler to optimize the executions of the local physics analysis workflows. The performance of the analysis jobs which used such architecture seems to be promising, making it useful to follow up in the future.

Riahi, H.; Donvito, G.; Fanò, L.; Fasi, M.; Marzulli, G.; Spiga, D.; Valentini, A.

2012-12-01

293

Geologic map of the Mine Mountain area, Nevada Test Site, southern Nevada  

SciTech Connect

The Mine Mountain area is a small range of hills on the west side of the central Yucca Flat basin on the Nevada Test Site, Nye County, Nevada. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. Rocks and structures of the Mine Mountain area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds and thrusts formed by hinterland vergence in a general westerly direction; and (3) low-angle normal faulting formed by extension along a northeast-southwest trend. All of these structures are older than the oldest middle Miocene volcanic rocks that were deposited on the flanks of the Mine Mountain terrane. High-angle faults that post-date these volcanic rocks locally show displacements of several hundred meters, but do not strongly affect patterns in the pre-Tertiary rocks.

Cashman, P.H.; Cole, J.C.

1998-10-05

294

Web Mapping for Promoting Interaction and Collaboration in Community Land Planning  

NASA Astrophysics Data System (ADS)

There is an inherent advantage of geographic information Systems (GIS) and mapping in facilitating dialogue between experts and non-experts during land use plan development. Combining visual mapping information and effective user interaction can result in considerable benefits for developing countries like Botswana. Although the adoption of information and communication technologies has lagged behind that for developed countries, initiatives by the Botswana government in providing suitable information infrastructures, including internet and web based communications, are enabling multiple users to interact and collaborate in community land planning. A web mapping application was developed for the Maun Development Plan (MDP) in the Okavango Delta region in Botswana. It was designed according to requirements of land planners and managers and implemented using ArcGIS Viewer for Flex. Land planners and managers from two organisations in Maun involved in the development of the MDP were asked to evaluate the web mapping tools. This paper describes the results of implementation and some preliminary results of the web mapping evaluation.

Veenendaal, B.; Dhliwayo, M.

2013-10-01

295

Mapping air pollution using Earth observation techniques for cultural heritage sites  

NASA Astrophysics Data System (ADS)

Air pollutants, together with climatic parameters, are of major importance for the deterioration of cultural heritage monuments. Atmospheric pollution is widely recognized as one of the major anthropogenic threats to architectural cultural heritage, in particular when associated with water absorption phenomena. Atmospheric particle deposition on surfaces of Monuments (of cultural heritage interest) may cause an aesthetic impact induced by a series of chemical reactions. Therefore there is a need for systematic monitoring and mapping of air pollution for areas where important archaeological sites and monuments are found. observation techniques, such as the use of satellite image for the retrieval of Aerosol Optical Thickness (AOT), are ideal for this purpose. In this paper, all important monuments of the Paphos District, listed by the Department of Antiquities of Cyprus, have been mapped using Geographical Information Systems. Several recent (2012) MODIS satellite images (both Aqua and Terra) have been used to extract the AOT values in this area. Multi-temporal analysis was performed to identify areas of high risk where AOT values are considered to be high. In situ observations have been also carried out to verify the results.

Agapiou, Athos; Nisantzi, Argyro; Lysandrou, Vasiliki; Mamouri, Rodanthi; Alexakis, Dimitrios D.; Themistocleous, Kyriacos; Sarris, Apostolos; Hadjimitsis, Diofantos G.

2013-08-01

296

Application of time domain induced polarization to the mapping of lithotypes in a landfill site  

NASA Astrophysics Data System (ADS)

A direct current (DC) resistivity and time domain induced polarization (TDIP) survey was undertaken at a decommissioned landfill site situated in Hørløkke, Denmark, for the purpose of mapping the waste deposits and to discriminate important geological units that control the hydrology of the surrounding area. It is known that both waste deposits and clay have clear signatures in TDIP data, making it possible to enhance the resolution of geological structures compared to DC surveys alone. Four DC/TDIP profiles were carried out crossing the landfill, and another seven profiles in the surroundings provide a sufficiently dense coverage of the entire area. The whole dataset was inverted using a 1-D laterally constrained inversion scheme, recently implemented for TDIP data, in order to use the entire decay curves for reconstructing the electrical parameters of the soil in terms of the Cole-Cole polarization model. Results show that it is possible to resolve both the geometry of the buried waste body and key geological structures. In particular, it was possible to find a silt/clay lens at depth that correlates with the flow direction of the pollution plume spreading out from the landfill and to map a shallow sandy layer rich in clay that likely has a strong influence on the hydrology of the site. This interpretation of the geophysical findings was constrained by borehole data, in terms of geology and gamma ray logging. The results of this study are important for the impact of the resolved geological units on the hydrology of the area, making it possible to construct more realistic scenarios of the variation of the pollution plume as a function of the climate change.

Gazoty, A.; Fiandaca, G.; Pedersen, J.; Auken, E.; Christiansen, A. V.; Pedersen, J. K.

2012-06-01

297

Application of time domain induced polarization to the mapping of lithotypes in a landfill site  

NASA Astrophysics Data System (ADS)

A DC resistivity (DC) and Time Domain Induced Polarization (TDIP) survey was undertaken at a decommissioned landfill site situated in Hørløkke, Denmark, for the purpose of mapping the waste deposits and to discriminate important geological units that control the hydrology of the surrounding area. It is known that both waste deposits and clay have clear signatures in TDIP data, making possible to enhance the resolution of geological structures, when compared to DC surveys alone. Four DC/TDIP profiles were carried out crossing the landfill and another seven profiles in the surroundings, giving a dense coverage over the entire area. The whole dataset was inverted using a 1-D Laterally Constrained Inversion scheme, recently implemented for IP data, in order to use the entire decay curves for reconstructing the electrical parameters of the soil in terms of the Cole-Cole polarization model. Results show that it is possible to both resolve the geometry of the buried waste body and key geological structures. In particular, it was possible to find a silt/clay lens at depth, which correlates with the flow direction of the pollution plume spreading out from the landfill, and to map a shallow sandy layer rich in clay that likely has a strong influence on the hydrology of the site. This interpretation of the geophysical findings was constrained by boreholes data, in terms of geology and gamma ray logging. The results of this study are important for the impact that the resolved geological units have in the hydrology of the area, making it possible to construct more realistic scenarios of the variation of the pollution plume as a function of the climate change.

Gazoty, A.; Fiandaca, G.; Pedersen, J.; Auken, E.; Christiansen, A. V.; Pedersen, J. K.

2012-01-01

298

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

NASA Astrophysics Data System (ADS)

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.

Lakkaraju, Mahesh

299

Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase  

PubMed Central

MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific for ERK, whereas the D box mediates binding to ERK and JNK MAP kinase, suggesting that the partially overlapping substrate specificities of ERK and JNK result from recognition of shared and unique docking sites. These findings enabled us to predict new ERK substrates and design peptide inhibitors of ERK that functioned in vitro and in vivo. PMID:9925641

Jacobs, Dave; Glossip, Danielle; Xing, Heming; Muslin, Anthony J.; Kornfeld, Kerry

1999-01-01

300

Genotype×environment interaction QTL mapping in plants: lessons from Arabidopsis.  

PubMed

Plant growth and development are influenced by the genetic composition of the plant (G), the environment (E), and the interaction between them (G×E). To produce suitable genotypes for multiple environments, G×E should be accounted for and assessed in plant-breeding programs. Here, we review the genetic basis of G×E and its consequence for quantitative trait loci (QTL) mapping in biparental and genome-wide association (GWA) mapping populations. We also consider the implications of G×E for understanding plant fitness trade-offs and evolutionary ecology. PMID:24491827

El-Soda, Mohamed; Malosetti, Marcos; Zwaan, Bas J; Koornneef, Maarten; Aarts, Mark G M

2014-06-01

301

Improving the Apollo 12 landing site mapping with Chandrayaan M3 data  

NASA Astrophysics Data System (ADS)

The geology of the Apollo 12 landing site has been the subject of many studies, including recently by Korotev et al. (2011) and Snape et al. (2013). This research attempts to bring additional understanding from a remote sensing perspective using the Moon Mineralogy Mapper (M3) sensor data, onboard the Chandrayaan lunar orbiter. This has a higher spatial-spectral resolution sensor than the Clementine UV-Vis sensor and provides the opportunity to study the lunar surface with detailed spectral signatures. Mapping of FeO (wt%) and TiO2 (wt%) is done using the methods of Lucey et al. (2000) and Wilcox et al. (2005). A FeO & TiO2 processing module (i.feotio2) is made specifically for this research within the Free & Open Source Software GRASS GIS. Attempts will be made to estimate the lava flow thickness using the method of Bugiolacchi et al. (2006) and individual lava layers thicknesses (Weider et al., 2010). Integration of this new information will be put in perspective and integrated with previous work. Analysis from the combined higher spatial and spectral resolutions will improve the accuracy of the geological mapping at the Apollo 12 landing site. References Bugiolacchi, R., Spudis, P.D., Guest, J.E., 2006. Stratigraphy and composition of lava flows in Mare Nubium and Mare Cognitum. Meteoritics & Planetary Science. 41(2):285-304. Korotev, R.L., Jolliff, B.L., Zeigler, R.A., Seddio, S.M., Haskin, L.A., 2011. Apollo 12 revisited. Geochimica et Cosmochimica Acta. 75(6):1540-1573. Lucey, P.G., Blewett, D.T., Jolliff, B.L., 2000. Lunar iron and titanium abundance algorithms based on final processing of Clementine ultraviolet-visible images. J. Geophys. Res. 105(E8): 20297-20305. Snape, J.F., Alexander, L., Crawford, I.A., Joy, K.H., 2013. Basaltic Regolith Sample 12003,314: A New Member of the Apollo 12 Feldspathic Basalt Suite? Lunar and Planetary Institute Science Conference Abstracts 44:1044. Weider, S.Z., Crawford, I.A. and Joy, K.H., "Individual lava flow thicknesses in Oceanus Procellarum and Mare Serenitatis determined from Clementine multi-spectral data," Icarus, 209, 323-336, (2010). Wilcox, B.B., Lucey, P.G., Gillis, J.J., 2005. Mapping iron in the lunar mare: An improved approach. J. Geophys. Res. 110(E11):2156-2202.

Chemin, Yann; Crawford, Ian; Bugiolacchi, Roberto; Irfan, Huma; Alexander, Louise

2014-05-01

302

Barbara WeberSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Barbara Weber is Director of the Breast Cancer Program at the Abramson Cancer Center at the University of Pennsylvania. Barbara Weber based her gene-mapping work on studies of families with a high incidence of breast cancer. Dr. Weber was startled to realize that her study had yielded crucial information about whether her patient Vicky��ôs sister Denise was at high risk for developing the disease.

2008-10-06

303

Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation  

PubMed Central

An internal ribosomal entry site (IRES) that directs the initiation of viral protein translation is a potential drug target for enterovirus 71 (EV71). Regulation of internal initiation requires the interaction of IRES trans-acting factors (ITAFs) with the internal ribosomal entry site. Biotinylated RNA-affinity chromatography and proteomic approaches were employed to identify far upstream element (FUSE) binding protein 2 (FBP2) as an ITAF for EV71. The interactions of FBP2 with EV71 IRES were confirmed by competition assay and by mapping the association sites in both viral IRES and FBP2 protein. During EV71 infection, FBP2 was enriched in cytoplasm where viral replication occurs, whereas FBP2 was localized in the nucleus in mock-infected cells. The synthesis of viral proteins increased in FBP2-knockdown cells that were infected by EV71. IRES activity in FBP2-knockdown cells exceeded that in the negative control (NC) siRNA-treated cells. On the other hand, IRES activity decreased when FBP2 was over-expressed in the cells. Results of this study suggest that FBP2 is a novel ITAF that interacts with EV71 IRES and negatively regulates viral translation. PMID:19010963

Lin, Jing-Yi; Li, Mei-Ling; Shih, Shin-Ru

2009-01-01

304

Mapping generalized Jaynes-Cummings interaction into correlated finite-sized systems  

E-print Network

We consider a generalized Jaynes-Cummings model of a two-level atom interacting with a multimode nondegenerate coherent field. The sum of the mode frequencies is equal to the two-level transition frequency, creating the resonance condition. The intermediate levels associated with the multi-photon process are adiabatically eliminated using the non-resonant conditions for these transitions. Under such general conditions, the infinite atom-multiphoton interaction is effectively mapped onto an equivalent reduced \\textit{2}$\\times$\\textit{2} bipartite qubit system that facilitates the study of the nonclassical features of the interaction using known information-theoretic measures. We observe that the bipartite pure system is highly entangled as quantified by its entanglement of formation. Further, it is shown that the dynamics of the mapped system can be generated using optically truncated, quantum scissored states that reduce the infinite atom-multiphoton interaction to a finite \\textit{2}$\\times$\\textit{k} system, where $k$ is a suitable truncation number. This allows us to introduce atomic dephasing and study the mixed state dynamics, characterized by the decay of quantum correlations such as quantum discord, which is observed to be more robust than entanglement. The quantum correlation dynamics of the dissipative system qualitatively complements the behavior of collapse and revival of the Rabi oscillations in the system. The effective mapping of the composite system proves to be an efficient tool for measuring information-theoretic properties.

Himadri Shekhar Dhar; Arpita Chatterjee; Rupamanjari Ghosh

2014-04-23

305

Mapping generalized Jaynes-Cummings interaction into correlated finite-sized systems  

NASA Astrophysics Data System (ADS)

We consider a generalized Jaynes-Cummings model of a two-level atom interacting with a multimode nondegenerate coherent field. The sum of the mode frequencies is equal to the two-level transition frequency, creating the resonance condition. The intermediate levels associated with the multiphoton process are adiabatically eliminated using the non-resonant conditions for these transitions. Under such general conditions, the infinite atom-multiphoton interaction is effectively mapped onto an equivalent reduced 2 ×2 bipartite qubit system that facilitates the study of the nonclassical features of the interaction using known information-theoretic measures. We observe that the bipartite pure system is highly entangled as quantified by its entanglement of formation. Furthermore, it is shown that the dynamics of the mapped system can be generated using optically truncated, quantum scissored states that reduce the infinite atom-multiphoton interaction to a finite 2 × k system, where k is a suitable truncation number. This allows us to introduce atomic dephasing and study the mixed state dynamics, characterized by the decay of quantum correlations such as quantum discord, which is observed to be more robust than entanglement. The quantum correlation dynamics of the dissipative system qualitatively complements the behaviour of collapse and revival of the Rabi oscillations in the system. The effective mapping of the composite system proves to be an efficient tool for measuring information-theoretic properties.

Shekhar Dhar, Himadri; Chatterjee, Arpita; Ghosh, Rupamanjari

2014-07-01

306

Comparison of substructural epitopes in enzyme active sites using self-organizing maps.  

PubMed

This paper presents a new algorithm to compare substructural epitopes in protein binding cavities. Through the comparison of binding cavities accommodating well characterized ligands with cavities whose actual guests are yet unknown, it is possible to draw some conclusions on the required shape of a putative ligand likely to bind to the latter cavities. To detect functional relationships among proteins, their binding-site exposed physicochemical characteristics are described by assigning generic pseudocenters to the functional groups of the amino acids flanking the particular active site. The cavities are divided into small local regions of four pseudocenters having the shape of a pyramid with triangular basis. To find similar local regions, an emergent self-organizing map is used for clustering. Two local regions within the same cluster are similar and form the basis for the superpositioning of the corresponding cavities to score this match. First results show that the similarities between enzymes with the same EC number can be found correctly. Enzymes with different EC numbers are detected to have no common substructures. These results indicate the benefit of this method and motivate further studies. PMID:15865062

Kupas, Katrin; Ultsch, Alfred; Klebe, Gerhard

2004-11-01

307

Odorant binding by a pheromone binding protein: active site mapping by photoaffinity labeling.  

PubMed

The bacterially expressed recombinant pheromone binding protein (PBP) of Antheraea polyphemus was photoaffinity labeled with (6E,11Z)-[3H]hexadecadienyl diazoacetate, a photoactivatable analog of the naturally occurring acetate pheromone. Radiolabeled peptides were separated from an endoproteinase Lys-C digestion by HPLC and characterized by Edman degradation. The label was exclusively found in the Asp39-Lys58 fragment. Cleavage of this peptide (DDYVMTDRLAGCAINCLATK) with Arg-C gave a single radiolabeled peptide (DDYVMTDR), which was predicted to be alpha-helical. The adjoining LAGCAINCLATK fragment, which is highly conserved in PBP sequences, was predicted to be a hydrophobic beta-strand and has been proposed to be important in recognition of the alkadienyl chain. Edman degradation confirmed the location of the covalently attached ligand at Thr44 of the smaller hydrophilic peptide. In addition, the synthesis of the newly identified pheromone component (4E,9Z)-tetradecadienyl acetate and its photoaffinity analog, (4E,9Z)-[3H]tetradecadienyl diazoacetate, is also described. Mapping of PBP photoaffinity labeled by (4E,9Z)-[3H]14:Dza revealed that the hydrophobic region Asp21-Lys38 adjacent to the primary binding domain Asp39-Lys58 contained a second modification site. The 14-carbon odorant molecule thus had two binding positions within the recognition site, while only a single binding position was available to the 16-carbon pheromone. PMID:8161541

Du, G; Ng, C S; Prestwich, G D

1994-04-26

308

Site-specific mapping and quantification of protein S-sulfenylation in cells  

PubMed Central

Cysteine S-sulfenylation provides redox regulation of protein functions, but the global cellular impact of this transient post-translational modification remains unexplored. We describe a chemoproteomic workflow to map and quantify over 1,000 S-sulfenylation sites on more than 700 proteins in intact cells. Quantitative analysis of human cells stimulated with hydrogen peroxide or epidermal growth factor measured hundreds of site selective redox changes. Different cysteines in the same proteins displayed dramatic differences in susceptibility to S-sulfenylation. Newly discovered S-sulfenylations provided mechanistic support for proposed cysteine redox reactions and suggested novel redox mechanisms, including S-sulfenyl-mediated redox regulation of the transcription factor HIF1A by SIRT6. S-sulfenylation is favored at solvent-exposed protein surfaces and is associated with sequence motifs that are distinct from those for other thiol modifications. S-sulfenylations affect regulators of phosphorylation, acetylation and ubiquitylation, which suggests regulatory crosstalk between redox control and signaling pathways. PMID:25175731

Yang, Jing; Gupta, Vinayak; Carroll, Kate S.; Liebler, Daniel C.

2014-01-01

309

Geologic map of Paleozoic rocks in the Calico Hills, Nevada Test Site, southern Nevada  

SciTech Connect

The Calico Hills area in the southwestern part of the Nevada Test Site, Nye County, Nevada, exposes a core of pre-Tertiary rocks surrounded by middle Miocene volcanic strata. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. The Devonian and Mississippian rocks of the Calico Hills are distinct from age-equivalent carbonate-shelf or submarine-fan strata in other parts of the Nevada Test Site. The Calico Hills strata are interpreted to have been deposited beyond the continental shelf edge from alternating silicic and carbonate clastic sources. Structures of the Calico Hills area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds, kink zones, and thrusts formed by hinterland-vergent deformation toward northwesterly and northerly directions; and (3) low-angle normal faults that displaced blocks of Middle Paleozoic carbonate strata across the contractionally deformed terrane. All of these structures are older than any of the middle Miocene volcanic rocks that were erupted across the Calico Hills.

Cole, J.C.; Cashman, P.H.

1998-11-01

310

A chemoenzymatic approach toward the identification of fucosylated glycoproteins and mapping of N-glycan sites.  

PubMed

Fucose (Fuc)-containing glycoconjugates play important roles in numerous physiological and pathological processes. Given the biological importance of post-translational glycosylation, a specific and robust strategy for the identification of fucosylated glycoproteins is highly desirable. In this study, we demonstrate an alternative way of labeling of fucosylated structures by metabolic engineering, using a chemoenzymatic approach. In this approach, the activities of Bacteroides fragilis 9343 L-fucokinase/guanosine-5'-diphosphate-Fuc pyrophosphorylase and human ?1,3-fucosyltransferase 9 are combined in a Namalwa cellular model. Interestingly, this system could be applied to labeling of alkyne-modified fucosylated glycoproteins. N-Glycan site mapping and identification were done using an in vitro selective chemical ligation reaction and isotope-coded glycosylation site-specific tagging, subsequent to liquid chromatography-tandem mass spectrometry analysis. This work illustrates the use of a click chemistry-based strategy combined with a glycoproteomic technique to get further insight into the pattern of Fuc-mediated biological processes and functions. PMID:22203233

Liu, Ta-Wei; Kaji, Hiroyuki; Togayachi, Akira; Ito, Hiromi; Sato, Takashi; Narimatsu, Hisashi

2012-05-01

311

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation  

PubMed Central

Summary The emerging discoveries on the link between polyadenylation and disease states underline the need to fully characterize genome-wide polyadenylation states. Here, we report comprehensive maps of global polyadenylation events in human and yeast generated using refinements to the Direct RNA Sequencing technology. This direct approach provides a quantitative view of genome-wide polyadenylation states in a strand-specific manner and requires only attomole RNA quantities. The polyadenylation profiles revealed an abundance of unannotated polyadenylation sites, alternative polyadenylation patterns, and regulatory element-associated polyA+ RNAs. We observed differences in sequence composition surrounding canonical and non-canonical human polyadenylation sites, suggesting novel non-coding RNA-specific polyadenylation mechanisms in humans. Furthermore, we observed the correlation level between sense and antisense transcripts to depend on gene expression levels, supporting the view that overlapping transcription from opposite strands may play a regulatory role. Our data provide a comprehensive view of the polyadenylation state and overlapping transcription. PMID:21145465

Ozsolak, Fatih; Kapranov, Philipp; Foissac, Sylvain; Kim, Sang Woo; Fishilevich, Elane; Monaghan, A. Paula; John, Bino; Milos, Patrice M.

2010-01-01

312

Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM  

PubMed Central

Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells’ interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412

Jensen, Mikkel R. B.; ?opaci?ska, Joanna; Schmidt, Michael S.; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mølhave, Kristian

2013-01-01

313

Interactive Mapping of the Planets: An Online Activity Using the Google Earth Platform  

NASA Astrophysics Data System (ADS)

With funding from the Natural Sciences and Engineering Research Council of Canada's PromoScience program and support from the Department of Earth Sciences at The University of Western Ontario, the Centre for Planetary Science and Exploration (CPSX) has developed a new web-based initiative called Interactive Mapping of the Planets (IMAPS). Additional components include in person school visits to deliver inquiry-based workshops, week-long summer camps, and pre-prepared impact rock lending kits, all framed around the IMAPS activity. IMAPS will is now in beta testing mode and will be demonstrated in this session. The general objective of the online activity is for participants to plan and design a rover mission to Mars based on a given mission goal - e.g., to find evidence for past water flow. The activity begins with participants receiving image-analysis training to learn about the different landforms on Mars and which ones are potentially caused by water flow. They then need to pass a short test to show they can consistently identify Martian landforms. From there, the participants choose a landing site and plan a traverse - utilizing the free Google Earth plug-in - and taking into account factors such as hazards and their sites of interest. A mission control blog will provide updates on the status of their mission and a 'choose your rover' option provides the opportunity to unlock more advanced rovers by collaborating with other scientists and rating their missions. Indeed, evaluation of missions will be done using a crowd-sourcing method. In addition to being fully accessible online, CPSX will also target primary- and secondary-school grades in which astronomy and space science is taught. Teachers in K-12 classrooms will be able to sign-up for the activity ahead of time in order to receive a workshop package, which will guide them on how to use the IMAPS online activity with their class. Teachers will be able to set up groups for their classroom so that they can evaluate their students based on pre-determined criteria. The IMAPS activities are developed in partnerships with the Department of Earth Sciences at Western University, Sports Western, the Thames Valley District School Board, and Dimentians Web Marketing and Design. We are continually looking for new collaborators to help design or test our inquiry- and web-based activities, provide feedback on our programs, or volunteer with us. Please contact cpsxoutreach@uwo.ca if you are interested.

Osinski, G. R.; Gilbert, A.; Harrison, T. N.; Mader, M. M.; Shankar, B.; Tornabene, L. L.

2013-12-01

314

Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms  

PubMed Central

Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall prediction MCC was 0.49. Independent tests on anti-carbohydrate antibodies showed that the carbohydrate antigen binding sites were predicted with comparable accuracy. These results demonstrate that the predictors are among the best in carbohydrate binding site predictions to date. PMID:22848404

Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

315

Near-surface gas mapping studies of salt geologic features at Weeks Island and other sites  

SciTech Connect

Field sampling and rapid gas analysis techniques were used to survey near-surface soil gases for geotechnical diagnostic purposes at the Weeks Island Strategic Petroleum Reserve (SPR) site and other salt dome locations in southern Louisiana. This report presents the complete data, results and interpretations obtained during 1995. Weeks Island 1994 gas survey results are also briefly summarized; this earlier study did not find a definitive correlation between sinkhole No. 1 and soil gases. During 1995, several hundred soil gas samples were obtained and analyzed in the field by gas chromatography, for profiling low concentrations and gas anomalies at ppm to percent levels. The target gases included hydrogen, methane, ethane and ethylene. To supplement the field data, additional gas samples were collected at various site locations for laboratory analysis of target gases at ppb levels. Gases in the near-surface soil originate predominantly from the oil, from petrogenic sources within the salt, or from surface microbial activity. Surveys were conducted across two Weeks Island sinkholes, several mapped anomalous zones in the salt, and over the SPR repository site and its perimeter. Samples were also taken at other south Louisiana salt dome locations for comparative purposes. Notable results from these studies are that elevated levels of hydrogen and methane (1) were positively associated with anomalous gassy or shear zones in the salt dome(s) and (2) are also associated with suspected salt fracture (dilatant) zones over the edges of the SPR repository. Significantly elevated areas of hydrogen, methane, plus some ethane, were found over anomalous shear zones in the salt, particularly in a location over high pressure gas pockets in the salt, identified in the mine prior to SPR operations. Limited stable isotope ratio analyses, SIRA, were also conducted and determined that methane samples were of petrogenic origin, not biogenic.

Molecke, M.A. [Sandia National Lab., Albuquerque, NM (United States); Carney, K.R.; Autin, W.J.; Overton, E.B. [Louisiana State Univ., Baton Rouge, LA (United States)

1996-10-01

316

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.  

PubMed

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng

2010-01-01

317

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping  

PubMed Central

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

2010-01-01

318

Domains 2 and 3 interact to form critical elements of the group II intron active site.  

PubMed

Group II introns are self-splicing RNA molecules that also behave as mobile genetic elements. The secondary structure of group II intron RNAs is typically described as a series of six domains that project from a central wheel. Most structural and mechanistic analyses of the intron have focused on domains 1 and 5, which contain the residues essential for catalysis, and on domain 6, which contains the branch-point adenosine. Domains 2 and 3 (D2, D3) have been shown to make important contributions to intronic activity; however, information about their function is quite limited. To elucidate the role of D2 and D3 in group II ribozyme catalysis, we built a series of multi-piece ribozyme constructs based on the ai5gamma group II intron. These constructs are designed to shed light on the roles of D2 and D3 in some of the major reactions catalyzed by the intron: 5'-exon cleavage, branching, and substrate hydrolysis. Reactions with these constructs demonstrate that D3 stimulates the chemical rate constant of group II intron reactions, and that it behaves as a form of catalytic effector. However, D3 is unable to associate independently with the ribozyme core. Docking of D3 is mediated by a short duplex that is found at the base of D2. In addition to recruiting D3 into the core, the D2 stem directs the folding of the adjacent j(2/3) linker, which is among the most conserved elements in the group II intron active site. In turn, the D2 stem contributes to 5'-splice site docking and ribozyme conformational change. Nucleotide analog interference mapping suggests an interaction between the D2 stem and D3 that builds on the known theta-theta' interaction and extends it into D3. These results establish that D3 and the base of D2 are key elements of the group II intron core and they suggest a hierarchy for active-site assembly. PMID:12823961

Fedorova, Olga; Mitros, Therese; Pyle, Anna Marie

2003-07-01

319

Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast  

Microsoft Academic Search

In the postgenomic era, one of the most interesting and important chal- lenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist indepen- dently. To study the large-scale patterns and

Jong Park; Michael Lappe; Sarah A. Teichmann

320

Seismic Hazard Mapping and Microzonation in the Sikkim Himalaya through GIS Integration of Site Effects and Strong Ground Motion Attributes  

Microsoft Academic Search

The seismic ground motion hazard is mapped in the Sikkim Himalaya with local and regional site conditions incorporated through geographic information system. A strong motion network in Sikkim comprising of 9 digital accelerographs recorded more than 100 events during 1998–2002, of which 41 events are selected with signal-to-noise ratio =3 for the estimation of site response (SR), peak ground acceleration

Sankar Kumar Nath

2004-01-01

321

Multi-level assessment protocol (MAP) for adoption in multi-site clinical trials  

PubMed Central

The National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) is intended to test promising drug abuse treatment models in multi-site clinical trials, and to support adoption of new interventions into clinical practice. Using qualitative research methods we asked: How might the technology of multi-site clinical trials be modified to better support adoption of tested interventions? A total of 42 participants, representing 8 organizational levels ranging from clinic staff to clinical trial leaders, were interviewed about their role in the clinical trial, its interactions with clinics, and intervention adoption. Among eight clinics participating in the clinical trial, we found adoption of the tested intervention in one clinic only. In analysis of interview data we identified four conceptual themes which are likely to affect adoption and may be informative in future multi-site clinical trials. We offer the conclusion that planning for adoption in the early stages of protocol development will better serve the aim of integrating new interventions into practice. PMID:20890376

Guydish, J.; Manser, S.T.; Jessup, M.; Tajima, B.; Sears, C.; Montini, T.

2010-01-01

322

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing  

PubMed Central

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

2012-01-01

323

Using Mutagenesis and Structural Biology to Map the Binding Site for the Plasmodium falciparum Merozoite Protein PfRh4 on the Human Immune Adherence Receptor*  

PubMed Central

To survive and replicate within the human host, malaria parasites must invade erythrocytes. Invasion can be mediated by the P. falciparum reticulocyte-binding homologue protein 4 (PfRh4) on the merozoite surface interacting with complement receptor type 1 (CR1, CD35) on the erythrocyte membrane. The PfRh4 attachment site lies within the three N-terminal complement control protein modules (CCPs 1–3) of CR1, which intriguingly also accommodate binding and regulatory sites for the key complement activation-specific proteolytic products, C3b and C4b. One of these regulatory activities is decay-accelerating activity. Although PfRh4 does not impact C3b/C4b binding, it does inhibit this convertase disassociating capability. Here, we have employed ELISA, co-immunoprecipitation, and surface plasmon resonance to demonstrate that CCP 1 contains all the critical residues for PfRh4 interaction. We fine mapped by homologous substitution mutagenesis the PfRh4-binding site on CCP 1 and visualized it with a solution structure of CCPs 1–3 derived by NMR and small angle x-ray scattering. We cross-validated these results by creating an artificial PfRh4-binding site through substitution of putative PfRh4-interacting residues from CCP 1 into their homologous positions within CCP 8; strikingly, this engineered binding site had an ?30-fold higher affinity for PfRh4 than the native one in CCP 1. These experiments define a candidate site on CR1 by which P. falciparum merozoites gain access to human erythrocytes in a non-sialic acid-dependent pathway of merozoite invasion. PMID:24214979

Park, Hyon Ju; Guariento, Mara; Maciejewski, Mateusz; Hauhart, Richard; Tham, Wai-Hong; Cowman, Alan F.; Schmidt, Christoph Q.; Mertens, Haydyn D. T.; Liszewski, M. Kathryn; Hourcade, Dennis E.; Barlow, Paul N.; Atkinson, John P.

2014-01-01

324

A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome  

Microsoft Academic Search

The ubiquitin-proteasome proteolytic pathway is pivotal in most biological processes. Despite a great level of information available for the eukaryotic 26S proteasome—the protease responsible for the degradation of ubiquitylated proteins—several structural and functional questions remain unanswered. To gain more insight into the assembly and function of the metazoan 26S proteasome, a two-hybrid-based protein interaction map was generated using 30 Caenorhabditis

Anne Davy; Paul Bello; Nicolas Thierry-Mieg; Philippe Vaglio; Joseph Hitti; Lynn Doucette-Stamm; Danielle Thierry-Mieg; Jérôme Reboul; Simon Boulton; Albertha J. M. Walhout; Olivier Coux; Marc Vidal

2001-01-01

325

NMR Mapping and Functional Confirmation of the Collagen Binding Sites of MMP-2†  

PubMed Central

Interactions of matrix metalloproteinase-2 (MMP-2)1 with native and denatured forms of several types of collagen are mediated by the collagen-binding domain (CBD). CBD positions substrates relative to the catalytic site and is essential for their cleavage. Our previous studies identified an CBD binding site on the ?1(I) collagen chain. The corresponding synthetic collagen peptide P713 bound CBD with high affinity and was used in this study to identify specific collagen binding residues by NMR analysis of 15N-labeled CBD complexed with P713. Results obtained showed that P713 caused chemical shifts perturbations of several surface exposed CBD backbone amide resonances in a concentration dependent manner. The ten residues that underwent the largest chemical shift perturbations (R252 in module 1, R296, F297, Y302, E321, Y323, Y329 in module 2, and R368, W374, and Y381, in module 3), were investigated by site-specific substitution with alanine. The structural integrity of the CBD variants was also analyzed by 1D 1H NMR. Surface plasmon resonance and microwell protein binding assays of control and CBD variants showed that residues in all three CBD modules contributed to collagen binding. Single residue substitutions altered the affinity for peptide P713, as well as native and denatured type I collagen, with the greatest effects observed for residues in modules 2 and 3. Additional alanine substitutions involving residues in two or three modules simultaneously further reduced the binding of CBD to native and denatured type I collagen and demonstrated that all three modules contribute to the substrate binding. These results have localized and confirmed the key collagen binding site residues in the three fibronectin type II-like modules of MMP-2. PMID:19459623

Xu, Xiaoping; Mikhailova, Margarita; Ilangovan, Udayar; Chen, Zhihua; Yu, Agnes; Pal, Sanjay; Hinck, Andrew P.; Steffensen, Bjorn

2009-01-01

326

Mapping intended spinal site of care from the upright to prone position: an interexaminer reliability study  

PubMed Central

Background Upright examination procedures like radiology, thermography, manual muscle testing, and spinal motion palpation may lead to spinal interventions with the patient prone. The reliability and accuracy of mapping upright examination findings to the prone position is unknown. This study had 2 primary goals: (1) investigate how erroneous spine-scapular landmark associations may lead to errors in treating and charting spine levels; and (2) study the interexaminer reliability of a novel method for mapping upright spinal sites to the prone position. Methods Experiment 1 was a thought experiment exploring the consequences of depending on the erroneous landmark association of the inferior scapular tip with the T7 spinous process upright and T6 spinous process prone (relatively recent studies suggest these levels are T8 and T9, respectively). This allowed deduction of targeting and charting errors. In experiment 2, 10 examiners (2 experienced, 8 novice) used an index finger to maintain contact with a mid-thoracic spinous process as each of 2 participants slowly moved from the upright to the prone position. Interexaminer reliability was assessed by computing Intraclass Correlation Coefficient, standard error of the mean, root mean squared error, and the absolute value of the mean difference for each examiner from the 10 examiner mean for each of the 2 participants. Results The thought experiment suggesting that using the (inaccurate) scapular tip landmark rule would result in a 3 level targeting and charting error when radiological findings are mapped to the prone position. Physical upright exam procedures like motion palpation would result in a 2 level targeting error for intervention, and a 3 level error for charting. The reliability experiment showed examiners accurately maintained contact with the same thoracic spinous process as the participant went from upright to prone, ICC (2,1)?=?0.83. Conclusions As manual therapists, the authors have emphasized how targeting errors may impact upon manual care of the spine. Practitioners in other fields that need to accurately locate spinal levels, such as acupuncture and anesthesiology, would also be expected to draw important conclusions from these findings. PMID:24904747

2014-01-01

327

Spa2p functions as a scaffold-like protein to recruit the Mpk1p MAP kinase module to sites of polarized growth.  

PubMed

Scaffold proteins play a major role in regulating MAP kinase pathways. In yeast, the Mpk1p-MAP kinase pathway functions to maintain the integrity of the cytoskeleton and the cell wall. In this module, the MEKK Bck1p functions upstream of the MEKs Mkk1p and Mkk2p, which in turn activate the MAP kinase Mpk1p. Mpk1p regulates several nuclear targets, including the transcription factors Rlm1p and SBF, and the two HMG1-like proteins NHP6A and NHP6B. Here we show that Mpk1p constitutively shuttles between the nucleus and the cytoplasm, and both Mpk1p and Mkk1p localize to sites of polarized growth in a Spa2p-dependent manner. Spa2p belongs to a group of proteins that includes Bni1p, Bud6p, and Pea2p, which are involved in the dynamic organization of the actin cytoskeleton during polarized growth. FRAP analysis shows that Spa2p-GFP is stably anchored at bud tips, whereas Mpk1p binds transiently. Spa2p interacts with Mkk1p and Mpk1p, and membrane bound Spa2p is sufficient to recruit Mkk1p and Mpk1p but not other MAP kinases to the cell cortex. Taken together, these results suggest that Spa2p functions as a scaffold-like protein for the cell wall integrity pathway during polarized growth. PMID:12361575

van Drogen, Frank; Peter, Matthias

2002-10-01

328

English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life  

E-print Network

one liter of sea water will produce energy equivalent to 300 liters of gasoline. If a device Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services fusion device, which aims to generate infinite, clean nuclear-fusion-based energy, will be built in March

329

Integration of landslide hazard maps into probabilistic risk assessment in context of global changes: an alpine test site  

E-print Network

1 Integration of landslide hazard maps into probabilistic risk assessment in context of global climate on landslides activity and impacts of social changes on exposure to provide a complete evaluation site. Mechanical approaches represent a solution to quantify landslide susceptibility and to model

Paris-Sud XI, Université de

330

Geologic map of the MTM 25047 and 20047 quadrangles, central Chryse Planitia/Viking 1 Lander site, Mars  

USGS Publications Warehouse

This map uses Viking Orbiter image data and Viking 1 Lander image data to evaluate the geologic history of a part of Chryse Planitia, Mars. The map area lies at the termini of the Maja and Kasei Valles outwash channels and includes the site of the Viking 1 Lander. The photomosaic base for these quadrangles was assembled from 98 Viking Orbiter frames comprising 1204 pixels per line and 1056 lines and ranging in resolution from 20 to 200 m/pixel. These orbital image data were supplemented with images of the surface as seen from the Viking 1 Lander, one of only three sites on the martian surface where planetary geologic mapping is assisted by ground truth.

Crumpler, L.S.; Craddock, R.A.; Aubele, J.C.

2001-01-01

331

Sites, sacredness, and stories: Interactions of archaeology and contemporary paganism  

Microsoft Academic Search

Folklore has, until very recently, been at the fringes of archaeological research. Post-processual archaeology has promoted plurality in interpretation, however, and archaeology more widely is required to make itself relevant to contemporary society; so, contemporary folkloric practices vis-à-vis archaeological remains are once again receiving attention. In this paper we examine contemporary Pagan understandings of and engagements with 'sacred sites' in

Robert J. Wallis; Jenny Blain

2003-01-01

332

Multiple magnetic interactions in A-site-ordered perovskite-structure oxides  

NASA Astrophysics Data System (ADS)

Multiple magnetic interactions in A-site-ordered perovskite-structure oxides AA?3B2B?2O12 with A?-site Cu and B-site Fe ions are highlighted here. Several new compounds with this structure type were obtained by high-pressure synthesis and have been given unusual magnetic properties due to multiple interactions of Cu and Fe ions (A?–A?, A?–B, A?–B?, B–B, B–B?, and B?–B? interactions). The magnetic interaction is discussed here in light of the results of magnetic structure analysis with neutron powder diffraction data and x-ray magnetic circular dichroism spectra obtained in x-ray absorption experiments. The characteristic structural framework with ordered cation arrangements and the variation in the oxidation state of the ions at the A? and B sites are shown to play roles crucial for the diverse and intriguing physical properties of these new compounds.

Shimakawa, Yuichi; Mizumaki, Masaichiro

2014-11-01

333

Mars Exploration Rover (MER) 2003 Data Maps  

NSDL National Science Digital Library

This NASA website provides links to maps for all potential Mars Exploration Rover landing sites. The site includes maps showing MOC (Mars Orbiter Camera )/MOLA (Mars Orbiting Laser Altimeter) images, TES (Thermal Emission Spectrometer) thermal inertia, Geology/MOLA, TES mineral abundances (basalt, andesite, hematite), vertical roughness, and data from the Viking Infrared Thermal Mapper. These maps can also be viewed using the interactive map and data browser.

Marsoweb

334

California Geological Survey: Geologic Maps  

NSDL National Science Digital Library

This index provides access to a selection of geologic maps of California, as well as an overview of geologic and other mapping activities in the state. The index, which can be accessed by clicking on an interactive map of the state, contains lists of selected geologic maps in California prepared by the Regional Geologic Mapping Project (RGMP). The RGMP staff monitors the literature and collects references that contain geologic mapping that may be useful for future compilations. In addition, the site has information about Caltrans Highway Corridor Mapping, The Mineral Resources and Mineral Hazards Mapping Program, North Coast Watersheds Assessment Program, The Timber Harvesting Plan Enforcement Program, and The Seismic Hazards Mapping Program. A set of links is provided to other sources of geologic maps and map information.

335

Snowpack: Decadal Averages Map  

NSDL National Science Digital Library

This is an interactive map of California and the Sierra Nevada mountains, showing projected variations in water stored in snowpack, from 1950 to 2090, assuming low or high emission scenarios over that period of time. Interactive can be adjusted to show different months of the year and various climate models, graphed by site.

California Energy Commission

336

Mapping the Putative G Protein-coupled Receptor (GPCR) Docking Site on GPCR Kinase 2  

PubMed Central

G protein-coupled receptor kinases (GRKs) phosphorylate agonist-occupied receptors initiating the processes of desensitization and ?-arrestin-dependent signaling. Interaction of GRKs with activated receptors serves to stimulate their kinase activity. The extreme N-terminal helix (?N), the kinase small lobe, and the active site tether (AST) of the AGC kinase domain have previously been implicated in mediating the allosteric activation. Expanded mutagenesis of the ?N and AST allowed us to further assess the role of these two regions in kinase activation and receptor phosphorylation in vitro and in intact cells. We also developed a bioluminescence resonance energy transfer-based assay to monitor the recruitment of GRK2 to activated ?2A-adrenergic receptors (?2AARs) in living cells. The bioluminescence resonance energy transfer signal exhibited a biphasic response to norepinephrine concentration, suggesting that GRK2 is recruited to G?? and ?2AAR with EC50 values of 15 nm and 8 ?m, respectively. We show that mutations in ?N (L4A, V7E, L8E, V11A, S12A, Y13A, and M17A) and AST (G475I, V477D, and I485A) regions impair or potentiate receptor phosphorylation and/or recruitment. We suggest that a surface of GRK2, including Leu4, Val7, Leu8, Val11, and Ser12, directly interacts with receptors, whereas residues such as Asp10, Tyr13, Ala16, Met17, Gly475, Val477, and Ile485 are more important for kinase domain closure and activation. Taken together with data on GRK1 and GRK6, our data suggest that all three GRK subfamilies make conserved interactions with G protein-coupled receptors, but there may be unique interactions that influence selectivity. PMID:25049229

Beautrait, Alexandre; Michalski, Kevin R.; Lopez, Thomas S.; Mannix, Katelynn M.; McDonald, Devin J.; Cutter, Amber R.; Medina, Christopher B.; Hebert, Aaron M.; Francis, Charnelle J.; Bouvier, Michel; Tesmer, John J. G.; Sterne-Marr, Rachel

2014-01-01

337

CYCLOSTREPTIN DERIVATIVES SPECIFICALLY TARGET CELLULAR TUBULIN AND FURTHER MAP THE PACLITAXEL SITE  

PubMed Central

Cyclostreptin is the first microtubule stabilizing agent whose mechanism of action was discovered to involve formation of a covalent bond with tubulin. Treatment of cells with cyclostreptin irreversibly stabilizes their microtubules because cyclostreptin forms a covalent bond to ?-tubulin at either the T220 or the N228 residue, located, respectively, at the microtubule pore and luminal taxoid binding sites. Due to its unique mechanism of action, cyclostreptin overcomes P-glycoprotein-mediated multidrug resistance in tumor cells. We used a series of reactive cyclostreptin analogues, 6-chloroacetyl-cyclostreptin, 8-chloroacetyl-cyclostreptin, and [14C-acetyl]-8-acetyl-cyclostreptin, to characterize the cellular target of the compound and to map the binding site. The three analogues were cytotoxic and stabilized microtubules in both sensitive and multidrug resistant tumor cells. In both types of cells, we identified ?-tubulin as the only or the predominantly labeled cellular protein, indicating that a covalent binding to microtubules is sufficient to prevent drug efflux mediated by P-glycoprotein. 6-chloroacetyl-cyclostreptin, 8-chloroacetyl-cyclostreptin, and 8-acetyl-cyclostreptin labeled both microtubules and unassembled tubulin at a single residue of the same tryptic peptide of ?-tubulin as was labeled by cyclostreptin (219-LTTPTYGDLNHLVSATMSGVTTCLR-243), but labeling with the analogues occurred at different positions of the peptide. 8-Acetyl-cyclostreptin reacted either with T220 or N228, as did the natural product, while 8-chloroacetyl-cyclostreptin formed a cross link to C241. Finally 6-chloroacetyl-cyclostreptin reacted with any one of the three residues, thus labeling the pathway for cyclostreptin-like compounds, leading from the pore where these compounds enter the microtubule to the luminal binding pocket. PMID:22148836

Calvo, Enrique; Barasoain, Isabel; Matesanz, Ruth; Pera, Benet; Camafeita, Emilio; Pineda, Oriol; Hamel, Ernest; Vanderwal, Christopher D.; Andreu, José Manuel; López, Juan A.; Díaz, José Fernando

2012-01-01

338

Solution of reference interaction site model for mixtures of short-chain polyatomic molecules  

SciTech Connect

Mixtures of chain molecules---monomers, dimers, trimers, and tetramers---are studied using the soft interaction site model. The site--site Ornstein--Zernike equations are solved using the Percus--Yevick closure. The site--site potential is of the Lennard-Jones 12-6 type. The method of solution, based on the efficient algorithm of Labik and employing Newton--Raphson accelerations, is shown to be fast, accurate and stable; it also shows good convergence behavior even with inaccurate initial estimates. New symmetrical properties among the atom--atom pairs are used to simplify the Jacobian matrix of solution. Pure as well as mixture systems are investigated. Comparison with simulation data of Banon {ital et al}. and Massobrio {ital et al}. is made. The structure is qualitatively described by the integral equations. The internal energy is well predicted by the reference interaction site model calculations.

Wu, R.; Lee, L.L.; Harwell, J.H. (School of Chemical Engineering and Materials Science, University of Oklahoma, Norman, Oklahoma 73019 (US))

1989-10-01

339

Kentucky Mine Mapping Information System  

NSDL National Science Digital Library

This Geographic Information System (GIS) allows users to view and download all known mined out areas (polygons) digitized by the Kentucky Revenue Cabinet; individual reports from the Mines and Minerals database; and scanned images of engineering drawings (mine maps) submitted since January 2002, plus selected earlier maps. The maps can be viewed directly online with the use of an interactive viewer, or they can be downloaded from an FTP site. The interactive viewer shows all scanned maps and oil/gas wells (where available) for a selected area, overlain on a base map or imagery.

340

The Importance of Synchronous Interaction for Student Satisfaction with Course Web Sites  

ERIC Educational Resources Information Center

As more affordable synchronous communications are becoming available, the use of synchronous interactions has not been noted in course Web sites as often as asynchronous communications. Previous research indicated that the integration of synchronous tools into course Web sites has made a positive impact on students. While most of the previous…

Cao, Qidong; Griffin, Thomas E.; Bai, Xue

2009-01-01

341

Predicting and mapping potential Whooping Crane stopover habitat to guide site selection for wind energy projects.  

PubMed

Migratory stopover habitats are often not part of planning for conservation or new development projects. We identified potential stopover habitats within an avian migratory flyway and demonstrated how this information can guide the site-selection process for new development. We used the random forests modeling approach to map the distribution of predicted stopover habitat for the Whooping Crane (Grus americana), an endangered species whose migratory flyway overlaps with an area where wind energy development is expected to become increasingly important. We then used this information to identify areas for potential wind power development in a U.S. state within the flyway (Nebraska) that minimize conflicts between Whooping Crane stopover habitat and the development of clean, renewable energy sources. Up to 54% of our study area was predicted to be unsuitable as Whooping Crane stopover habitat and could be considered relatively low risk for conflicts between Whooping Cranes and wind energy development. We suggest that this type of analysis be incorporated into the habitat conservation planning process in areas where incidental take permits are being considered for Whooping Cranes or other species of concern. Field surveys should always be conducted prior to construction to verify model predictions and understand baseline conditions. PMID:24372936

Belaire, J Amy; Kreakie, Betty J; Keitt, Timothy; Minor, Emily

2014-04-01

342

A terrain-based site characterization map of California with implications for the contiguous United States  

USGS Publications Warehouse

We present an approach based on geomorphometry to predict material properties and characterize site conditions using the VS30 parameter (time?averaged shear?wave velocity to a depth of 30 m). Our framework consists of an automated terrain classification scheme based on taxonomic criteria (slope gradient, local convexity, and surface texture) that systematically identifies 16 terrain types from 1?km spatial resolution (30 arcsec) Shuttle Radar Topography Mission digital elevation models (SRTM DEMs). Using 853 VS30 values from California, we apply a simulation?based statistical method to determine the mean VS30 for each terrain type in California. We then compare the VS30 values with models based on individual proxies, such as mapped surface geology and topographic slope, and show that our systematic terrain?based approach consistently performs better than semiempirical estimates based on individual proxies. To further evaluate our model, we apply our California?based estimates to terrains of the contiguous United States. Comparisons of our estimates with 325 VS30 measurements outside of California, as well as estimates based on the topographic slope model, indicate our method to be statistically robust and more accurate. Our approach thus provides an objective and robust method for extending estimates of VS30 for regions where in situ measurements are sparse or not readily available.

Yong, Alan K.; Hough, Susan E.; Iwahashi, Junko; Braverman, Amy

2012-01-01

343

Expression patterns of FLAGELLIN SENSING 2 map to bacterial entry sites in plant shoots and roots  

PubMed Central

Pathogens can colonize all plant organs and tissues. To prevent this, each cell must be capable of autonomously triggering defence. Therefore, it is generally assumed that primary sensors of the immune system are constitutively present. One major primary sensor against bacterial infection is the FLAGELLIN SENSING 2 (FLS2) pattern recognition receptor (PRR). To gain insights into its expression pattern, the FLS2 promoter activity in ?-glucuronidase (GUS) reporter lines was monitored. The data show that pFLS2::GUS activity is highest in cells and tissues vulnerable to bacterial entry and colonization, such as stomata, hydathodes, and lateral roots. GUS activity is also high in the vasculature and, by monitoring Ca2+ responses in the vasculature, it was found that this tissue contributes to flg22-induced Ca2+ burst. The FLS2 promoter is also regulated in a tissue- and cell type-specific manner and is responsive to hormones, damage, and biotic stresses. This results in stimulus-dependent expansion of the FLS2 expression domain. In summary, a tissue- and cell type-specific map of FLS2 expression has been created correlating with prominent entry sites and target tissues of plant bacterial pathogens. PMID:25205577

Beck, Martina; Wyrsch, Ines; Strutt, James; Wimalasekera, Rinukshi; Webb, Alex; Boller, Thomas; Robatzek, Silke

2014-01-01

344

Construction and Application of a Protein Interaction Map for White Spot Syndrome Virus (WSSV)*  

PubMed Central

White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ?28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein–protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture. PMID:24217020

Sangsuriya, Pakkakul; Huang, Jiun-Yan; Chu, Yu-Fei; Phiwsaiya, Kornsunee; Leekitcharoenphon, Pimlapas; Meemetta, Watcharachai; Senapin, Saengchan; Huang, Wei-Pang; Withyachumnarnkul, Boonsirm; Flegel, Timothy W.; Lo, Chu-Fang

2014-01-01

345

Mapping of the Lunokhod-1 Landing Site: A Case Study for Future Lunar Exploration  

NASA Astrophysics Data System (ADS)

Introduction. Luna-17 landed on November 17, 1970 and deployed Lunokhod-1, the first remotely operated roving vehicle ever to explore a planetary surface. Within 332 days, the vehicle conquered a traverse of approx. 10 km. The rover was equipped with a navigation camera system as well as a scanner camera with which panoramic images were obtained. From separated stations, stereoscopic views were obtained. The history of the Lunokhods came back into focus recently, when the Lunar Reconnaissance Orbiter [1] obtained images from orbit at highest resolutions of 0.5-0.25 m/pixel. The Luna-17 landing platform as well as the roving vehicles at their final resting positions can clearly be identified. In addition, the rover tracks are clearly visible in most areas. From LRO stereo images, digital elevation model (DEM) of the Lunokhod-1 landing site areas have been derived [2]. These are useful to study the topographic profile and slopes of the traverse. The data are also useful to study the 3-D morphology of craters in the surroundings. Methodology. Lunokhod-1 area mapping have been done using GIS techniques. With CraterTools [3] we digitized craters in the Lunokhod-1 traverse area and created a geodatabase, which consists at this moment of about 45,000 craters including their diameters and depths, obtained from the DEM [4]. The LRO DEM also was used to measure traverse. We used automatic GIS functions for calculating various surface parameters of the Lunokhod-1 area surface including slopes, roughness, crater cumulative and spatial densities, and prepared respective thematic maps. We also measured relative depth (ratio D/H) and inner slopes of craters and classified craters by their morphological type using automatic and visual methods. Vertical profiles through several craters using the high resolution DEM have been done, and the results show good agreement with the topographic models with contours in 10cm that have been obtained from the Lunokhod-1 stereo images [5]. The preliminary results of crater morphology show that highest H/D for studied craters of the Lunokhod 1 area is ~0.14, that is noticeably smaller than that for very fresh well studied small craters, for example, in the Apollo 14 [6]. At present more detailed geomorphology analyses using orthoimages with different illumination is in progress and will be shown at the conference. Conclusions and future works. While new missions to the Lunar surface are being planned, it is of utmost importance to identify and make available for access all Lunar surface data. We show that these data can be used for large-scale mapping and surface studies of landing sites for future lunar missions, for example LUNA-GLOB and LUNA-RESOURCE. Acknowledgments: This research was partly funded by the Ministry of Education and Science of the Russian Federation (MEGA-GRANT, Project name: "Geodesy, cartography and the study of planets and satellites", contract No. 11.G34.31.0021).

Karachevtseva, I.; Oberst, J.; Konopikhin, A.; Shingareva, K.; Gusakova, E.; Kokhanov, A.; Baskakova, M.; Peters, O.; Scholten, F.; Wählisch, M.; Robinson, M.

2012-04-01

346

First-generation site-response maps for the Los Angeles region based on earthquake ground motions  

USGS Publications Warehouse

Ground-motion records from aftershocks of the 1994 Northridge earthquake and mainshock records from the 1971 San Fernando, 1987 Whittier Narrows, 1991 Sierra Madre, and 1994 Northridge earthquakes are used to estimate site response relative to a rock site for the urban Los Angeles area. Site response is estimated at 232 mainshock and 201 aftershock sites relative to a low-amplitude site in the Santa Monica Mountains. Average amplification values are calculated for the frequency bands: 1 to 3, 3 to 5, and 5 to 7 Hz. These bands are chosen based on limitations in aftershock recording equipment at lower frequencies and reduced significance to the building inventory at higher frequencies. Site amplification factors determined at the instrumented locations are grouped by the surficial geology and contoured to produce a continuous spatial estimation of amplification. The maps in this article represent the first attempt to produce estimates of site amplification based on observations of ground motion for such a large areal extent of the Los Angeles region. These maps are expected to evolve as more data become available and more analysis is done.

Hartzell, S.; Harmsen, S.; Frankel, A.; Carver, D.; Cranswick, E.; Meremonte, M.; Michael, J.

1998-01-01

347

Concept mapping One-Carbon Metabolism to model future ontologies for nutrient-gene-phenotype interactions.  

PubMed

Advances in the development of bioinformatic tools continue to improve investigators' ability to interrogate, organize, and derive knowledge from large amounts of heterogeneous information. These tools often require advanced technical skills not possessed by life scientists. User-friendly, low-barrier-to-entry methods of visualizing nutrigenomics information are yet to be developed. We utilized concept mapping software from the Institute for Human and Machine Cognition to create a conceptual model of diet and health-related data that provides a foundation for future nutrigenomics ontologies describing published nutrient-gene/polymorphism-phenotype data. In this model, maps containing phenotype, nutrient, gene product, and genetic polymorphism interactions are visualized as triples of two concepts linked together by a linking phrase. These triples, or "knowledge propositions," contextualize aggregated data and information into easy-to-read knowledge maps. Maps of these triples enable visualization of genes spanning the One-Carbon Metabolism (OCM) pathway, their sequence variants, and multiple literature-mined associations including concepts relevant to nutrition, phenotypes, and health. The concept map development process documents the incongruity of information derived from pathway databases versus literature resources. This conceptual model highlights the importance of incorporating information about genes in upstream pathways that provide substrates, as well as downstream pathways that utilize products of the pathway under investigation, in this case OCM. Other genes and their polymorphisms, such as TCN2 and FUT2, although not directly involved in OCM, potentially alter OCM pathway functionality. These upstream gene products regulate substrates such as B12. Constellations of polymorphisms affecting the functionality of genes along OCM, together with substrate and cofactor availability, may impact resultant phenotypes. These conceptual maps provide a foundational framework for development of nutrient-gene/polymorphism-phenotype ontologies and systems visualization. PMID:25091042

Joslin, A C; Green, R; German, J B; Lange, M C

2014-09-01

348

Interactive Maps on War and Peace: A WebGIS Application for Civic Education  

NASA Astrophysics Data System (ADS)

War and violent conflict are omnipresent-be it war in the Middle East, violent conflicts in failed states or increasing military expenditures and exports/ imports of military goods. To understand certain conflicts or peace processes and their possible interrelation, to conduct a well-founded political discussion and to support or influence decision-making, one matter is of special importance: easily accessible and, in particular, reliable data and information. Against this background, the Bonn International Center for Conversion (BICC) in close cooperation with the German Federal Agency for Civic Education (bpb) has been developing a map-based information portal on war and peace with various thematic modules for the latter's online service (http://sicherheitspolitik.bpb.de). The portal will eventually offer nine of such modules that are intended to give various target groups, such as interested members of the public, teachers and learners, policymakers and representatives of the media access to the required information in form of an interactive and country-based global overview or a comparison of different issues. Five thematic modules have been completed so far: War and conflict, peace and demobilization, military capacities, resources and conflict, conventional weapons. The portal offers a broad spectrum of different data processing and visualization tools. Its central feature is an interactive mapping component based on WebGIS and a relational database. Content and data provided through thematic maps in the form of WebGIS layers are generally supplemented by info graphics, data tables and short articles providing deeper knowledge on the respective issue. All modules and their sub-chapters are introduced by background texts. They put all interactive maps of a module into an appropriate context and help the users to also understand the interrelation between various layers. If a layer is selected, all corresponding texts and graphics are shown automatically below the map. Data tables are offered if the copyright of datasets allows such use. All data of all thematic modules is presented in country profiles in a consolidated manner. The portal has been created with Open Source Software. PostgreSQL and PostGIS, MapServer, OpenLayers, MapProxy and cmsmadesimple are combined to manipulate and transform global data sets into interactive thematic maps. A purpose-programmed layer selection menu enables users to select single layers or to combine up to three matching layers from all possible pre-set layer combinations. This applies both to fields of topics within a module and across various modules. Due to the complexity of the structure and visualization constraints, no more than three layers can be combined. The WebGIS-based information portal on war and peace is an excellent example of how GIS technologies can be used for education and outreach. Not only can they play a crucial role in supporting the educational mandate and mission of certain institutions. They can also directly support various target groups in obtaining the knowledge needed by providing a collection of straight forward designed, ready-to-use data, info graphics and maps.

Wirkus, Lars; Strunck, Alexander

2013-04-01

349

The Internet and Public Participation: State Legislature Web Sites and the Many Definitions of Interactivity  

ERIC Educational Resources Information Center

The interactive nature of the Internet is seen by some as a technological innovation that might boost participation in politics and civic affairs. That potential, however, is clouded by imprecise definitions of interactivity found among scholars and practitioners alike. Evaluation of state legislature Web sites found them to not be very…

Ferber, Paul; Foltz, Franz; Pugliese, Rudy

2005-01-01

350

An Online Interactive Map Service for Displaying Ground-Water Conditions in Arizona  

USGS Publications Warehouse

Monitoring the availability of the nation's ground-water supplies is of critical importance to planners and water managers. The general public also has an interest in understanding the status of ground-water conditions, especially in the semi-arid Southwestern United States where much of the water used by municipalities and agriculture comes from the subsurface. Unlike surface-water indicators such as stage or discharge, ground-water conditions may be more difficult to assess and present. Individual well observations may only represent conditions in a limited area surrounding the well and wells may be screened over single or multiple aquifers, further complicating single-well measurement interpretations. Additionally, changes in ground-water conditions may involve time scales ranging from days to many years, depending on recharge, soil properties and depth to the water table. This lack of an easily identifiable ground-water property indicative of current conditions combined with differing time scales of water-level changes makes the presentation of ground-water conditions a difficult task, particularly on a regional basis. One approach is to spatially present several indicators of ground-water conditions that address different time scales and attributes of the aquifer systems. In this report, we describe a publicly-available online interactive map service that presents several different layers of ground-water-conditions information for the alluvial basins in the Lower Colorado River Basin in Arizona (http://montezuma.wr.usgs.gov/website/azgwconditions/). These data layers include wells experiencing water-level decline, wells experiencing water-level rise, recent trends in ground-water levels, change in water level since predevelopment and change in storage since predevelopment. Recent pumpage totals and projected population numbers are also provided for ground-water basins and counties in the region of the Lower Colorado River in Arizona along with a bibliography of U.S. Geological Survey reports for those seeking further information. The methods used to create these data layers are explained with illustrations of example information available on the Web site.

Tillman, Fred D.; Leake, Stanley A.; Flynn, Marilyn E.; Cordova, Jeffrey T.; Schonauer, Kurt T.

2007-01-01

351

High-resolution mapping of transcription factor binding sites on native chromatin  

PubMed Central

Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) is widely used for profiling of TF binding, but is limited by low resolution and poor specificity and sensitivity. We present a simple protocol that starts with micrococcal nuclease-digested uncross-linked chromatin and is followed by affinity purification of TFs and paired-end sequencing. The resulting ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide highly accurate base-pair resolution maps that are not biased toward accessible chromatin, and do not require input normalization. We also demonstrate the high specificity of our method when applied to larger genomes by profiling Drosophila melanogaster GAGA Factor and Pipsqueak. Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. PMID:24336359

Kasinathan, Sivakanthan; Orsi, Guillermo A.; Zentner, Gabriel E.; Ahmad, Kami; Henikoff, Steven

2014-01-01

352

Ribonuclease PH interacts with an acidic ribonuclease E site through a basic 80-amino acid domain.  

PubMed

In this work, we characterize the domains for the in vivo interaction between ribonuclease E (RNase E) and ribonuclease PH (RNase PH). We initially explored the interaction using pull-down assays with full wild-type proteins expressed from a chromosomal monocopy gene. Once the interaction was confirmed, we narrowed down the sites of interaction in each enzyme to an acidic 16-amino acid region in the carboxy-terminal domain of RNase E and a basic 80-amino acid region in RNase PH including an ?3 helix. Our results suggest two novel functional domains of interaction between ribonucleases. PMID:24766456

Martínez, Víctor Pérez-Medina; Dehò, Gianni; Simons, Robert W; García-Mena, Jaime

2014-06-01

353

Mapping texts through dimensionality reduction and visualization techniques for interactive exploration of document collections  

NASA Astrophysics Data System (ADS)

The current availability of information many times impair the tasks of searching, browsing and analyzing information pertinent to a topic of interest. This paper presents a methodology to create a meaningful graphical representation of documents corpora targeted at supporting exploration of correlated documents. The purpose of such an approach is to produce a map from a document body on a research topic or field based on the analysis of their contents, and similarities amongst articles. The document map is generated, after text pre-processing, by projecting the data in two dimensions using Latent Semantic Indexing. The projection is followed by hierarchical clustering to support sub-area identification. The map can be interactively explored, helping to narrow down the search for relevant articles. Tests were performed using a collection of documents pre-classified into three research subject classes: Case-Based Reasoning, Information Retrieval, and Inductive Logic Programming. The map produced was capable of separating the main areas and approaching documents by their similarity, revealing possible topics, and identifying boundaries between them. The tool can deal with the exploration of inter-topics and intra-topic relationship and is useful in many contexts that need deciding on relevant articles to read, such as scientific research, education, and training.

de Andrade Lopes, Alneu; Minghim, Rosane; Melo, Vinícius; Paulovich, Fernando V.

2006-01-01

354

Digital geologic map of the Nevada Test Site and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California  

SciTech Connect

This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map area covers two 30 {times} 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7 1/2-minute quadrangles on the east side. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. This publication also includes a new isostatic gravity map and a new aeromagnetic map. The primary purpose of the three maps is to provide an updated geologic framework to aid interpretation of ground-water flow through and off the NTS. The NTS is centrally located within the area of the Death Valley regional ground-water flow system of southwestern Nevada and adjacent California. During the last 40 years, DOE and its predecessor agencies have conducted about 900 nuclear tests on the NTS, of which 100 were atmospheric tests and the rest were underground tests. More than 200 of the tests were detonated at or beneath the water table, which commonly is about 500 to 600 m below the surface. Because contaminants introduced by these test may move into water supplies off the NTS, rates and directions of ground-water flow must be determined. Knowledge about the ground water also is needed to properly appraise potential future effects of the possible nuclear waste repository at Yucca Mountain, adjacent to the NTS.

Slate, J.L.; Berry, M.E.; Rowley, P.D.; Fridrich, C.J.; Morgan, K.S.; Workman, J.B.; Young, O.D.; Dixon, G.L.; Williams, V.S.; McKee, E.H.; Ponce, D.A.; Hildenbrand, T.G.; Swadley, W.C.; Lundstrom, S.C.; Ekren, E.B.; Warren, R.G.; Cole, J.C.; Fleck, R.J.; Lanphere, M.A.; Sawyer, D.A.; Minor, S.A.; Grunwald, D.J.; Laczniak, R.J.; Menges, C.M.; Yount, J.C.; Jayko, A.S.

2000-03-08

355

Mapping the lipoylation site of Arabidopsis thaliana plastidial dihydrolipoamide S-acetyltransferase using mass spectrometry and site-directed mutagenesis  

Technology Transfer Automated Retrieval System (TEKTRAN)

Background: The catalytic enhancement achieved by the pyruvate dehydrogenase complex (PDC) results from a combination of substrate channeling plus active-site coupling. The mechanism for active-site coupling involves lipoic acid prosthetic groups covalently attached to Lys residues in the primary ...

356

Lectin Site Interaction with Capsular Polysaccharide Mediates Nonimmune Phagocytosis of Type III Group B Streptococci  

PubMed Central

Group B Streptococcus (GBS) causes substantial morbidity but most individuals exposed to the organism remain healthy. These experiments tested the hypothesis that engagement of the complement receptor 3 (CR3) lectin site would effectively trigger neutrophil-mediated phagocytosis of complement-opsonized type III GBS by nonimmune human sera. Using an opsonophagocytosis assay, saccharides identified as interacting with the CR3 lectin site effectively inhibited neutrophil-mediated killing of type III, strain COH1. Fructose, which does not interact with the lectin site, promoted significantly less inhibition of opsonophagocytosis. Saccharide-mediated inhibition was reversed in a dose-related fashion by addition of type III, GBS capsular polysaccharide-specific immunoglobulin G. When capsule-deficient or asialo mutant type III strains were employed, the lectin site was not required. Structurally defined GBS serotypes with a side chain at least two sugars in length engaged the lectin site, and N-acetyl d-glucosamine was not a required component monosaccharide. Intact type III capsular polysaccharide interacted significantly more efficiently with the lectin site than did oligosaccharides representing approximately 5 or 20 repeating units, respectively. Taken together, these experiments indicate that interaction of type III GBS capsular polysaccharide with the lectin site of CR3 effects phagocytosis of these organisms by nonimmune serum. Use of this mechanism of innate immunity provides a potential explanation for the infrequency with which susceptible individuals exposed to type III GBS develop invasive infection. PMID:10992487

Albanyan, Esam A.; Edwards, Morven S.

2000-01-01

357

Phase resetting reduces theta-gamma rhythmic interaction to a one-dimensional map.  

PubMed

Gamma and theta oscillations of the hippocampus are known to interact, but the mechanisms underlying such interaction are not well understood. We focus on a previously published computational model of hippocampal activity that shows the gamma rhythms nesting in the theta rhythms, and investigate the dynamical mechanisms underlying that interaction. There are three types of neurons in the model: pyramidal cells, fast-spiking interneurons, and "oriens lacunosum-moelculare" (O-LM cells); the latter is an inhibitory cell whose inhibition has a longer time scale, and which has currents associated with intrinsic theta-rhythm behavior. We identify two main modes of interaction among the slow and the fast rhythms in the model, modulated by the strength of the excitatory synapse on the O-LM cells. Using resets of phases after each pyramidal cell and O-LM spike, we extend the use of the phase transition map (PTM) to encode the stability type of spiking patterns in networks where different frequencies interact. The tailored application of the PTM to the model network measures how the interaction between the shape of the phase response curves and the length of the gamma period determines the number of gamma spikes in theta cycles, and provides an explicit formula for the length of theta intervals in nesting regimes. Using the PTM, we also explain the covariance of the gamma and theta rhythms as drive is changed over some intervals. PMID:22526842

Malerba, Paola; Kopell, Nancy

2013-06-01

358

The interaction of high-resolution electrophoresis and computational analysis in genome mapping  

SciTech Connect

The construction of physical maps and the determination of the DNA sequence of chromosome-size segments of the human genome is a complex, multidisciplinary undertaking. The approach we have taken to construct a physical map and sequence of human chromosome 19 typifies these interactions. We exploit the power of both acrylamide and agarose gel electrophoresis to provide a simple and versatile method for DNA fingerprinting and the creation of contigs or sets of overlapping genomic clones. Cosmid libraries are constructed from Yeast Artificial Chromosomes (YAC) clones or from flow-sorted chromosomes. Cosmid DNA isolated from the screened library array is cut with a combination of five restriction enzymes and the fragment ends labeled with one of four different fluorochromes. Our approach to contig construction uses a robotic system to label restriction fragments from cosmids with fluorochromes, use of an automated DNA sequencer to capture fragment mobility data in a high resolution multiplex mode processes the mobility data to determine fragment length and provide a statistical measure of overlap among cosmids; and display the contigs and underlying cosmids for operator interaction and access to a database. Data analyses and interactions are conducted over a network of SUN workstations using a set of software tools that we developed and coupled to a commercially available database. Applying these methods, we have analyzed 5154 cosmid clones and assembled 515 contigs for chromosome 19. Some of these contigs have been identified with known genes and many have been mapped to the chromosome by fluorescence in situ hybridization. Existing contigs are being extended by a combination of walking and fingerprinting. 21 refs., 2 figs.

Carrano, A.V.; Branscomb, E.W.; de Jong, P.J.; Mohrenweiser, H.; Olsen, A.; Slezak, T.

1990-07-26

359

Reproductive parameters in female yellow-blotched map turtles ( Graptemys flavimaculata) from a historically contaminated site vs. a reference site  

Microsoft Academic Search

Graptemys flavimaculata, the yellow-blotched map turtle, is a long-lived, threatened, species, endemic to the Pascagoula River drainage in Mississippi. During the 1980s, one branch of the drainage (i.e. the Leaf River) was impacted by effluent from a wood pulp processing plant known to contain endocrine disrupters. A decade later, we examined seasonal reproductive parameters (i.e. monthly plasma estradiol-17? (E2), testosterone

Jennifer A. Shelby-Walker; Chelsea K. Ward; Mary T. Mendonça

2009-01-01

360

Strain pseudospins with power-law interactions: Glassy textures of a cooled coupled-map lattice  

Microsoft Academic Search

We consider a spin-1 model of strain pseudospins S(r&ar;)=0,±1 that arise from a triple-well Landau free energy for a square\\/rectangle or ``austenite-martensite'' structural transformation of a two-dimensional lattice. The pseudospin model has elastic-compatibility-induced power-law anisotropic (PLA) interactions and no quenched disorder. The iteratively solved local mean-field equations for form a temperature-dependent PLA-coupled nonlinear-map lattice, where t is the iteration ``time.''

S. R. Shenoy; T. Lookman

2008-01-01

361

Mapping the Nucleotide Binding Site of Uncoupling Protein 1 Using Atomic Force Microscopy  

PubMed Central

A tight regulation of proton transport in the inner mitochondrial membrane is crucial for physiological processes such as ATP synthesis, heat production, or regulation of the reactive oxygen species as proposed for the uncoupling protein family members (UCP). Specific regulation of proton transport is thus becoming increasingly important in the therapy of obesity and inflammatory, neurodegenerative, and ischemic diseases. We and other research groups have shown previously that UCP1- and UCP2-mediated proton transport is inhibited by purine nucleotides. Several hypotheses have been proposed to explain the inhibitory effect of ATP, although structural details are still lacking. Moreover, the unresolved mystery is how UCP operates in vivo despite the permanent presence of high (millimolar) concentrations of ATP in mitochondria. Here we use the topographic and recognition (TREC) mode of an atomic force microscope to visualize UCP1 reconstituted into lipid bilayers and to analyze the ATP–protein interaction at a single molecule level. The comparison of recognition patterns obtained with anti-UCP1 antibody and ATP led to the conclusion that the ATP binding site can be accessed from both sides of the membrane. Using cantilever tips with different cross-linker lengths, we determined the location of the nucleotide binding site inside the membrane with 1 Å precision. Together with the recently published NMR structure of a UCP family member (Berardi et al. Nature, 2011, 476, 109–113), our data provide a valuable insight into the mechanism of the nucleotide binding and pave the way for new pharmacological approaches against the diseases mentioned above. PMID:23414455

2013-01-01

362

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis  

PubMed Central

Summary Identifying sites where RNA binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV-crosslinking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from in vivo cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide RNA binding maps with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. Applying CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of crosslinked-induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes approximately eight days to prepare RNA for sequencing. Established pipelines for data analysis, including for CIMS, take 3-4 days. PMID:24407355

Moore, Michael; Zhang, Chaolin; Gantman, Emily Conn; Mele, Aldo; Darnell, Jennifer C.; Darnell, Robert B.

2014-01-01

363

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.  

PubMed

The identification of sites where RNA-binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV cross-linking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from in vivo cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high-throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide maps of RNA binding with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. The application of CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of cross-link-induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes ?8 d to prepare RNA for sequencing. Established pipelines for data analysis, including those for CIMS, take 3-4 d. PMID:24407355

Moore, Michael J; Zhang, Chaolin; Gantman, Emily Conn; Mele, Aldo; Darnell, Jennifer C; Darnell, Robert B

2014-02-01

364

Using a sentiment map for visualizing credibility of news sites on the web  

Microsoft Academic Search

We have developed a visualizing news system that shows the trend of the news site on the Web for credibility. If users know the trend of the news site, users can evaluate the credibility of each news topic. This system detects and uses sentiments of each news article to resolve the trend of Web site. The trend of Web sites

Yukiko Kawai; Yusuke Fujita; Tadahiko Kumamoto; Jianwei Jianwei; Katsumi Tanaka

2008-01-01

365

Mapping of DNA markers close to the fragile site on the human X chromosome at Xq27.3.  

PubMed Central

We report the identification of a new RFLP detected by the DNA probe MN12, which is linked to both the fragile site on the X chromosome at Xq27.3 and the highly polymorphic locus detected by St14 (DXS52). In situ mapping confirms the localisation of MN12 distal to the fragile site. A detailed physical analysis of this region of the X chromosome using pulsed-field gel electrophoresis has shown that MN12, St14 and DX13 (DXS15) are physically linked within a region of 470kb. A long range restriction map around the MN12 locus reveals at least two candidate HTF islands, suggesting the existence of expressed sequences in this region. Images PMID:2882476

Patterson, M; Kenwrick, S; Thibodeau, S; Faulk, K; Mattei, M G; Mattei, J F; Davies, K E

1987-01-01

366

AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping.  

PubMed

We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding. PMID:25466435

Xia, Zhiqiang; Zou, Meiling; Zhang, Shengkui; Feng, Binxiao; Wang, Wenquan

2014-01-01

367

A study of ternary element site substitution in Ni{sub 3}Al using pseudopotential orbital radii based structure maps  

SciTech Connect

It is well known that ternary alloying additions are usually added in small quantities to structural intermetallics with a view to optimize their structural, physical, chemical and mechanical properties. Since structural intermetallics are highly ordered alloys, the added ternary solutes often reveal a preponderant tendency to substitute preferentially one of the sublattices. A knowledge of the basic factors governing the preferential site substitution behavior is useful in elucidating the role of ternary additions in controlling the materials properties. In this paper, the authors apply the concept of structure maps for explaining the site substitution behavior of ternary alloying additions in Ni{sub 3}Al.

Raju, S.; Mohandas, E.; Raghunathan, V.S. [Indira Gandhi Centre for Atomic Research, Kalpakkam (India). Metallurgy Div.] [Indira Gandhi Centre for Atomic Research, Kalpakkam (India). Metallurgy Div.

1996-06-01

368

Superstable cycles for antiferromagnetic Q-state Potts and three-site interaction Ising models on recursive lattices  

NASA Astrophysics Data System (ADS)

We consider the superstable cycles of the Q-state Potts (QSP) and the three-site interaction antiferromagnetic Ising (TSAI) models on recursive lattices. The rational mappings describing the models’ statistical properties are obtained via the recurrence relation technique. We provide analytical solutions for the superstable cycles of the second order for both models. A particular attention is devoted to the period three window. Here we present an exact result for the third order superstable orbit for the QSP and a numerical solution for the TSAI model. Additionally, we point out a non-trivial connection between bifurcations and superstability: in some regions of parameters a superstable cycle is not followed by a doubling bifurcation. Furthermore, we use symbolic dynamics to understand the changes taking place at points of superstability and to distinguish areas between two consecutive superstable orbits.

Ananikian, N.; Artuso, R.; Chakhmakhchyan, L.

2014-10-01

369

Using 15N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy  

PubMed Central

A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. In these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the 1H,15N spin-pair of enzyme-bound 15NH4+ can be probed by 15N-edited heteronuclear NMR experiments. Here, we demonstrate the use of NMR spectroscopy to characterise binding of ammonium ions to two different enzymes: human histone deacetylase 8 (HDAC8), which is activated allosterically by potassium, and the bacterial Hsp70 homologue DnaK, for which potassium is an integral part of the active site. Ammonium activates both enzymes in a similar way to potassium, thus supporting this non-invasive approach. Furthermore, we present an approach to map the observed binding site onto the structure of HDAC8. Our method for mapping the binding site is general and does not require chemical shift assignment of the enzyme resonances. PMID:24520048

Werbeck, Nicolas D; Kirkpatrick, John; Reinstein, Jochen; Hansen, D Flemming

2014-01-01

370

Risk map and spatial determinants of pancreas disease in the marine phase of Norwegian Atlantic salmon farming sites  

PubMed Central

Background Outbreaks of pancreas disease (PD) greatly contribute to economic losses due to high mortality, control measures, interrupted production cycles, reduced feed conversion and flesh quality in the aquaculture industries in European salmon-producing countries. The overall objective of this study was to evaluate an effect of potential factors contributing to PD occurrence accounting for spatial congruity of neighboring infected sites, and then create quantitative risk maps for predicting PD occurrence. The study population included active Atlantic salmon farming sites located in the coastal area of 6 southern counties of Norway (where most of PD outbreaks have been reported so far) from 1 January 2009 to 31 December 2010. Results Using a Bayesian modeling approach, with and without spatial component, the final model included site latitude, site density, PD history, and local biomass density. Clearly, the PD infected sites were spatially clustered; however, the cluster was well explained by the covariates of the final model. Based on the final model, we produced a map presenting the predicted probability of the PD occurrence in the southern part of Norway. Subsequently, the predictive capacity of the final model was validated by comparing the predicted probabilities with the observed PD outbreaks in 2011. Conclusions The framework of the study could be applied for spatial studies of other infectious aquatic animal diseases. PMID:23006469

2012-01-01

371

Geologic structure mapping database Spent Fuel Test - Climax, Nevada Test Site  

SciTech Connect

Information on over 2500 discontinuities mapped at the SFT-C is contained in the geologic structure mapping database. Over 1800 of these features include complete descriptions of their orientations. This database is now available for use by other researchers. 6 references, 3 figures, 2 tables.

Yow, J.L. Jr.

1984-12-04

372

Digital Aeromagnetic Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California  

USGS Publications Warehouse

An aeromagnetic map of the Nevada Test Site area was prepared from publicly available aeromagnetic data described by McCafferty and Grauch (1997). Magnetic surveys were processed using standard techniques. Southwest Nevada is characterized by magnetic anomalies that reflect the distribution of thick sequences of volcanic rocks, magnetic sedimentary rocks, and the occurrence of granitic rocks. In addition, aeromagnetic data reveal the presence of linear features that reflect faulting at both regional and local scales.

Ponce, David A.

2000-01-01

373

Modular Robotics for Delivering On-Site contamination Sensors and Mapping Systems to Difficult-to-Access Locations  

SciTech Connect

Presently, characterization operations are scheduled for thousands of facilities and pieces of equipment throughout DOE sites, each of which requires manual surveying with handheld instruments and manual record keeping. Such work, particularly in difficult-to-access-areas, results in significant amounts of worker exposure, long timelines and additional secondary waste generation. Therefore, a distinct need exists for remote tools that can quickly deploy sensors and automated contamination mapping systems into these areas.

Geisinger, Joseph

2001-05-21

374

CANCER MORTALITY MAPS AND GRAPHS  

EPA Science Inventory

The Cancer Mortality Maps & Graph Web Site provides interactive maps, graphs (which are accessible to the blind and visually-impaired), text, tables and figures showing geographic patterns and time trends of cancer death rates for the time period 1950-1994 for more than 40 cancer...

375

Web GIS in practice V: 3-D interactive and real-time mapping in Second Life  

PubMed Central

This paper describes technologies from Daden Limited for geographically mapping and accessing live news stories/feeds, as well as other real-time, real-world data feeds (e.g., Google Earth KML feeds and GeoRSS feeds) in the 3-D virtual world of Second Life, by plotting and updating the corresponding Earth location points on a globe or some other suitable form (in-world), and further linking those points to relevant information and resources. This approach enables users to visualise, interact with, and even walk or fly through, the plotted data in 3-D. Users can also do the reverse: put pins on a map in the virtual world, and then view the data points on the Web in Google Maps or Google Earth. The technologies presented thus serve as a bridge between mirror worlds like Google Earth and virtual worlds like Second Life. We explore the geo-data display potential of virtual worlds and their likely convergence with mirror worlds in the context of the future 3-D Internet or Metaverse, and reflect on the potential of such technologies and their future possibilities, e.g. their use to develop emergency/public health virtual situation rooms to effectively manage emergencies and disasters in real time. The paper also covers some of the issues associated with these technologies, namely user interface accessibility and individual privacy. PMID:18042275

Boulos, Maged N Kamel; Burden, David

2007-01-01

376

Mapping QTL main and interaction influences on milling quality in elite US rice germplasm.  

PubMed

Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two US locations in 2005-2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year-location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date. PMID:20857082

Nelson, J C; McClung, A M; Fjellstrom, R G; Moldenhauer, K A K; Boza, E; Jodari, F; Oard, J H; Linscombe, S; Scheffler, B E; Yeater, K M

2011-02-01

377

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.  

PubMed

LISE is a web server for a novel method for predicting small molecule binding sites on proteins. It differs from a number of servers currently available for such predictions in two aspects. First, rather than relying on knowledge of similar protein structures, identification of surface cavities or estimation of binding energy, LISE computes a score by counting geometric motifs extracted from sub-structures of interaction networks connecting protein and ligand atoms. These network motifs take into account spatial and physicochemical properties of ligand-interacting protein surface atoms. Second, LISE has now been more thoroughly tested, as, in addition to the evaluation we previously reported using two commonly used small benchmark test sets and targets of two community-based experiments on ligand-binding site predictions, we now report an evaluation using a large non-redundant data set containing >2000 protein-ligand complexes. This unprecedented test, the largest ever reported to our knowledge, demonstrates LISE's overall accuracy and robustness. Furthermore, we have identified some hard to predict protein classes and provided an estimate of the performance that can be expected from a state-of-the-art binding site prediction server, such as LISE, on a proteome scale. The server is freely available at http://lise.ibms.sinica.edu.tw. PMID:23609546

Xie, Zhong-Ru; Liu, Chuan-Kun; Hsiao, Fang-Chih; Yao, Adam; Hwang, Ming-Jing

2013-07-01

378

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites  

PubMed Central

LISE is a web server for a novel method for predicting small molecule binding sites on proteins. It differs from a number of servers currently available for such predictions in two aspects. First, rather than relying on knowledge of similar protein structures, identification of surface cavities or estimation of binding energy, LISE computes a score by counting geometric motifs extracted from sub-structures of interaction networks connecting protein and ligand atoms. These network motifs take into account spatial and physicochemical properties of ligand-interacting protein surface atoms. Second, LISE has now been more thoroughly tested, as, in addition to the evaluation we previously reported using two commonly used small benchmark test sets and targets of two community-based experiments on ligand-binding site predictions, we now report an evaluation using a large non-redundant data set containing >2000 protein–ligand complexes. This unprecedented test, the largest ever reported to our knowledge, demonstrates LISE’s overall accuracy and robustness. Furthermore, we have identified some hard to predict protein classes and provided an estimate of the performance that can be expected from a state-of-the-art binding site prediction server, such as LISE, on a proteome scale. The server is freely available at http://lise.ibms.sinica.edu.tw. PMID:23609546

Xie, Zhong-Ru; Liu, Chuan-Kun; Hsiao, Fang-Chih; Yao, Adam; Hwang, Ming-Jing

2013-01-01

379

On-site screened Coulomb interactions for localized electrons in transition metal oxides and defect systems  

NASA Astrophysics Data System (ADS)

Electronic and structural properties of strongly correlated material systems are largely determined by the strength of the on-site Coulomb interaction. Theoretical models devised to capture the physics of strongly correlated materials usually involve screened Coulomb interactions as adjustable parameters. We present first-principles results for the screened on-site Coulomb and exchange energy for transition metal oxides. The dielectric screening is calculated within the random phase approximation and the localized electrons are represented by maximally localized Wannier functions. We further extend our study to calculate on-site Coulomb interactions for localized defect states in semiconductors. We acknowledge the computational support provided by the Center for Computational Research at the University at Buffalo, SUNY. This work is supported by the National Science Foundation under Grant No. DMR-0946404 and by the Department of Energy under Grant No. DE-SC0002623.

Shih, Bi-Ching; Zhang, Peihong

2011-03-01

380

USGS - Coastal and Marine Geology Program Internet Map Server  

NSDL National Science Digital Library

This site from the USGS features marine geology resources, including the Coastal and Marine Map Server, the Gloria Mapping Program and data, and the Coastal and Marine Geology Program. Each of these resources presents data, maps, and publications. For example, the GLORIA system was developed specifically to map the morphology and texture of seafloor features in the deep ocean, while the Coastal and Marine Geology program features an interactive map server to view and create maps using available CMGP data sets.

USGS

381

Interaction Sites of Tropomyosin in Muscle Thin Filament as Identified by Site-Directed Spin-Labeling  

PubMed Central

To identify interaction sites we measured the rotational motion of a spin label covalently bound to the side chain of a cysteine genetically incorporated into rabbit skeletal muscle tropomyosin (Tm) at positions 13, 36, 146, 160, 174, 190, 209, 230, 271, and 279. Upon the addition of F-actin, the mobility of all the spin labels, especially at position 13, 271, or 279, of Tm was inhibited significantly. Slow spin-label motion at the C-terminus (at the 230th and 271st residues) was observed upon addition of troponin. The binding of myosin-head S1 fragments without troponin immobilized Tm residues at 146, 160, 190, 209, 230, 271, and 279, suggesting that these residues are involved in a direct interaction between Tm and actin in its open state. As immobilization occurred at substoichiometric amounts of S1 binding to actin (a 1:7 molar ratio), the structural changes induced by S1 binding to one actin subunit must have propagated and influenced interaction sites over seven actin subunits. PMID:21575577

Ueda, Keisuke; Kimura-Sakiyama, Chieko; Aihara, Tomoki; Miki, Masao; Arata, Toshiaki

2011-01-01

382

Lunar Mapping and Modeling On-the-Go: A mobile framework for viewing and interacting with large geospatial datasets  

NASA Astrophysics Data System (ADS)

The Lunar Mapping and Modeling Portal (LMMP, https://www.lmmp.nasa.gov/) is a collaboration between four NASA centers, JPL, Marshall, Goddard, and Ames, along with the USGS and US Army to provide a centralized geospatial repository for storing processed lunar data collected from the Apollo missions to the latest data acquired by the Lunar Reconnaissance Orbiter (LRO). We offer various scientific and visualization tools to analyze rock and crater densities, lighting maps, thermal measurements, mineral concentrations, slope hazards, and digital elevation maps with the intention of serving not only scientists and lunar mission planners, but also the general public. The project has pioneered in leveraging new technologies and embracing new computing paradigms to create a system that is sophisticated, secure, robust, and scalable all the while being easy to use, streamlined, and modular. We have led innovations through the use of a hybrid cloud infrastructure, authentication through various sources, and utilizing an in-house GIS framework, TWMS (TiledWMS) as well as the commercial ArcGIS product from ESRI. On the client end, we also provide a Flash GUI framework as well as REST web services to interact with the portal. We have also developed a visualization framework on mobile devices, specifically Apple's iOS, which allows anyone from anywhere to interact with LMMP. At the most basic level, the framework allows users to browse LMMP's entire catalog of over 600 data imagery products ranging from global basemaps to LRO's Narrow Angle Camera (NAC) images that provide details of up to .5 meters/pixel. Users are able to view map metadata and can zoom in and out as well as pan around the entire lunar surface with the appropriate basemap. They can arbitrarily stack the maps and images on top of each other to show a layered view of the surface with layer transparency adjusted to suit the user's desired look. Once the user has selected a combination of layers, he can also bookmark those layers for quick access in subsequent sessions. A search tool is also provided to allow users to quickly find points of interests on the moon and to view the auxiliary data associated with that feature. More advanced features include the ability to interact with the data. Using the services provided by the portal, users will be able to log in and access the same scientific analysis tools provided on the web site including measuring between two points, generating subsets, and running other analysis tools, all by using a customized touch interface that are immediately familiar to users of these smart mobile devices. Users can also access their own storage on the portal and view or send the data to other users. Finally, there are features that will utilize functionality that can only be enabled by mobile devices. This includes the use of the gyroscopes and motion sensors to provide a haptic interface visualize lunar data in 3D, on the device as well as potentially on a large screen. The mobile framework that we have developed for LMMP provides a glimpse of what is possible in visualizing and manipulating large geospatial data on small portable devices. While the framework is currently tuned to our portal, we hope that we can generalize the tool to use data sources from any type of GIS services.

Chang, G.; Kim, R.; Bui, B.; Sadaqathullah, S.; Law, E.; Malhotra, S.

2012-12-01

383

Active Learning Centre: utilization patterns of an interactive educational World Wide Web site.  

PubMed Central

The advent of the World Wide Web (WWW) provides unique opportunities to transform medical education. Interactive computer assisted instruction has shown promising results but its growth has been impeded by logistical barriers. We designed an interactive WWW site--Active Learning Centre (ALC)--that offers a novel approach to these problems, combining remotely authored databases with computer-generated self-assessment tests. This study analyzes utilization and user assessment of the site. The site was found to be patronized mostly by students and health professionals from English-speaking countries. Users have been pleased with their experience and suggest further expansion of the ALC. Our data have also tentatively shown that their knowledge improved with repeated visits to the site. PMID:10566435

Turchin, A.; Lehmann, C. U.

1999-01-01

384

Multiphase Micro-Drop Interaction in Inkjet Printing of 3d Structures for Tactile Maps  

NASA Astrophysics Data System (ADS)

Ink-jet technology is a novel method for rapid deposition of accurately measured material with high precision. Consequently it has been used for applications such as, deposition of light emitting polymers and more recently for fabricating 3D objects and micro-mechanical structures. Ink-jet technology is also being applied to produce tactile maps for the visually impaired. The efficiency of the tactile maps, as outlined by psychophysical and cartographic studies of haptics, depends on its 3D features. To comprehend and control these features, detailed understanding of interaction amongst micro-drops, which are typically 50?m in diameter, is imperative. Multiphase interaction takes place between each liquid drop at impact with liquid or solid cured drops (deposited previously) and the solid substrate in an envelop of air. The behavior of micro-drops with regards to surface tension, drop coalescence among liquid and solid drops, drop impact kinetics, wettability, surface energy and drop spread has been analyzed using a computational model.

Ahmed, Kafeel; McCallum, Don; Sheldon, Derek F.

385

Mapping the lipoylation site of Arabidopsis thaliana plastidial dihydrolipoamide S-acetyltransferase using mass spectrometry and site-directed mutagenesis.  

PubMed

Catalytic enhancement achieved by the pyruvate dehydrogenase complex (PDC) results from a combination of substrate channeling plus active-site coupling. The mechanism for active-site coupling involves lipoic acid prosthetic groups covalently attached to Lys in the primary sequence of the dihydrolipoyl S-acetyltransferase (E2) component. Arabidopsis thaliana plastidial E2 (AtplE2-1A-His(6)) was expressed in Escherichia coli. Analysis of recombinant protein by SDS-PAGE revealed a Mr 59,000 band. Supplementation of bacterial culture medium with l-lipoic acid (LA) shifted the band to Mr 57,000. Intact mass determinations using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) revealed the faster migrating E2 species was 189 Da larger than the slower migrating form, exactly the difference that would result from addition of a single lipoamide group. Results from systematic MALDI-TOF analysis of Lys-containing tryptic peptides derived from purified recombinant AtplE2-1A indicate that Lys96 is the site of lipoyl-addition. Analysis of Lys96 site-directed mutant proteins showed that they migrated as single species during SDS-PAGE when expressed in either the absence or presence of supplemental LA. Results from both intact and tryptic peptide mass determinations by MALDI-TOF MS confirmed that the mutant proteins were not lipoylated. The A. thaliana plastidial E2 subunit includes a single lipoyl-prosthetic group covalently attached to Lys96. Despite low primary sequence identity with bacterial E2, the plant E2 protein was recognized and modified by E. coli E2 lipoyl-addition system. Results from meta-genomic analysis suggest a ?-turn is more important in defining the site for LA addition than a conserved sequence motif. PMID:21798751

Casteel, Jill; Miernyk, Ján A; Thelen, Jay J

2011-11-01

386

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities  

PubMed Central

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN?/? DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model. PMID:24104479

Vizeacoumar, Franco J; Arnold, Roland; Vizeacoumar, Frederick S; Chandrashekhar, Megha; Buzina, Alla; Young, Jordan T F; Kwan, Julian H M; Sayad, Azin; Mero, Patricia; Lawo, Steffen; Tanaka, Hiromasa; Brown, Kevin R; Baryshnikova, Anastasia; Mak, Anthony B; Fedyshyn, Yaroslav; Wang, Yadong; Brito, Glauber C; Kasimer, Dahlia; Makhnevych, Taras; Ketela, Troy; Datti, Alessandro; Babu, Mohan; Emili, Andrew; Pelletier, Laurence; Wrana, Jeff; Wainberg, Zev; Kim, Philip M; Rottapel, Robert; O'Brien, Catherine A; Andrews, Brenda; Boone, Charles; Moffat, Jason

2013-01-01

387

Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain  

NASA Astrophysics Data System (ADS)

Ligand binding sites within proteins can interact by allosteric mechanisms to modulate binding affinities and control protein function. Here we present crystal structures of the regulator of K+ conductance (RCK) domain from a K+ channel, MthK, which reveal the structural basis of allosteric coupling between two Ca2+ regulatory sites within the domain. Comparison of RCK domain crystal structures in a range of conformations and with different numbers of regulatory Ca2+ ions bound, combined with complementary electrophysiological analysis of channel gating, suggests chemical interactions that are important for modulation of ligand binding and subsequent channel opening.

Smith, Frank J.; Pau, Victor P. T.; Cingolani, Gino; Rothberg, Brad S.

2013-10-01

388

WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN  

SciTech Connect

The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

Rangaraj, K.; Cooper, P.K.; Trego, K.S.

2009-01-01

389

Mapping Minerals at a Potential Mars Analog Site on the Tibetan Plateau  

Microsoft Academic Search

A new mineral facies map of lacustrine deposits from the cold, arid Qaidam Basin, China shows hydrated sulfates, carbonates, chlorides and phyllosilicates. This area may offer insight into the history of evaporite deposits identified on Mars.

D. P. Mayer; R. E. Arvidson; A. Wang; P. Sobron; M. P. Zheng

2009-01-01

390

High-Density Epicardial Activation Mapping to Optimize the Site for Video-Thoracoscopic Left Ventricular Lead Implant  

PubMed Central

Optimization of Left Ventricular Lead Position Background The left ventricular (LV) lead local electrogram (EGM) delay from the beginning of the QRS complex (QLV) is considered a strong predictor of response to cardiac resynchronization therapy. We have developed a method for fast epicardial QLV mapping during video-thoracoscopic surgery to guide LV lead placement. Methods A three-port, video-thoracoscopic approach was used for LV free wall epicardial mapping and lead implantation. A decapolar electrophysiological catheter was introduced through one port and systematically attached to multiple accessible LV sites. The pacing lead was targeted to the site with maximum QLV. The LV free wall activation pattern was analyzed in 16 pre-specified anatomical segments. Results We implanted LV leads in 13 patients with LBBB or IVCD. The procedural and mapping times were 142 ± 39 minutes and 20 ± 9 minutes, respectively. A total of 15.0 ± 2.2 LV segments were mappable with variable spatial distribution of QLV-optimum. The QLV ratio (QLV/QRSd) at the optimum segment was significantly higher (by 0.17 ± 0.08, p < 0.00001) as compared to an empirical midventricular lateral segment. The LV lead was implanted at the optimum segment in 11 patients (at an adjacent segment in 2 patients) achieving a QLV ratio of 0.82 ± 0.09 (range 0.63–0.93) and 99.5 ± 0.6% match with intraprocedural mapping. Conclusion Video-thoracoscopic LV lead implantation can be effectively and safely guided by epicardial QLV mapping. This strategy was highly successful in targeting the selected LV segment and resulted in significantly higher QLV ratios compared to an empirical midventricular lateral segment. PMID:24724625

Polasek, Rostislav; Skalsky, Ivo; Wichterle, Dan; Martinca, Tomas; Hanuliakova, Jana; Roubicek, Tomas; Bahnik, Jan; Jansova, Helena; Pirk, Jan; Kautzner, Josef

2014-01-01

391

Predicting target-ligand interactions using protein ligand-binding site and ligand substructures  

PubMed Central

Background Cell proliferation, differentiation, Gene expression, metabolism, immunization and signal transduction require the participation of ligands and targets. It is a great challenge to identify rules governing molecular recognition between chemical topological substructures of ligands and the binding sites of the targets. Methods We suppose that the ligand-target interactions are determined by ligand substructures as well as the physical-chemical properties of the binding sites. Therefore, we propose a fragment interaction model (FIM) to describe the interactions between ligands and targets, with the purpose of facilitating the chemical interpretation of ligand-target binding. First we extract target-ligand complexes from sc-PDB database, based on which, we get the target binding sites and the ligands. Then we represent each binding site as a fragment vector based on a target fragment dictionary that is composed of 199 clusters (denoted as fragements in this work) obtained by clustering 4200 trimers according to their physical-chemical properties. And then, we represent each ligand as a substructure vector based on a dictionary containing 747 substructures. Finally, we build the FIM by generating the interaction matrix M (representing the fragment interaction network), and the FIM can later be used for predicting unknown ligand-target interactions as well as providing the binding details of the interactions. Results The five-fold cross validation results show that the proposed model can get higher AUC score (92%) than three prevalence algorithms CS-PD (80%), BLM-NII (85%) and RF (85%), demonstrating the remarkable predictive ability of FIM. We also show that the ligand binding sites (local information) overweight the sequence similarities (global information) in ligand-target binding, and introducing too much global information would be harmful to the predictive ability. Moreover, The derived fragment interaction network can provide the chemical insights on the interactions. Conclusions The target and ligand bindings are local events, and the local information dominate the binding ability. Though integrating of the global information can promote the predictive ability, the role is very limited. The fragment interaction network is helpful for understanding the mechanism of the ligand-target interaction. PMID:25707321

2015-01-01

392

Analysis of the Interaction of the Eg5 Loop5 with the Nucleotide Site  

SciTech Connect

Loop 5 (L5) is a conserved loop that projects from the ?2-helix adjacent to the nucleotide site of all kinesin-family motors. L5 is critical to the function of the mito tickinesin-5 family motors and is the binding site for several kinesin-5 inhibitors that are currently in clinical trials. Its conformational dynamics and its role in motor function are not fully understood. Our previous work using EPR spectroscopy suggested that L5 alters the nucleotide pocket conformation of the kinesin-5 motor Eg5 (Larsonetal.,2010). EPR spectra of a spin-labeled nucleotide analog bound at the nucleotide site of Eg5 display a highly immobilized component that is absent if L5 is shortened or if the inhibitor STLC is added (Larson etal.,2010), which X-ray structures suggest stabilizes an L5 conformation pointing away from the nucleotide site. These data, coupled with the proximity of L5 to the nucleotide site suggest L5 could interact with a bound nucleotide, modulating function. Here we use molecular dynamics (MD) simulations of Eg5 to explore the interaction of L5 with the nucleotide site in greater detail. We performed MD simulations in which the L5-domain of the Eg5•ADP X-ray structure was manually deformed via backbone bond rotations. The L5-domain of Eg5 was sufficiently lengthy that portions of L5 could belocated in proximity to bound ADP. The MD simulations evolved to thermodynamically stable structures at 300K showing that L5 can interact directly with bound nucleotide with significant impingement on the ribosehydroxyls, consistent with the EPR spectroscopy results. Taken together, these data provide support for the hypothes is that L5 modulates Eg5 function via interaction with the nucleotide-binding site.

Harrington, Timothy D.; Naber, Nariman; Larson, Adam G.; Cooke, Roger; Rice, Sarah E.; Pate, Edward F.

2011-11-21

393

Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions  

PubMed Central

Cell signaling networks propagate information from extracellular cues via dynamic modulation of protein–protein interactions in a context-dependent manner. Networks based on receptor tyrosine kinases (RTKs), for example, phosphorylate intracellular proteins in response to extracellular ligands, resulting in dynamic protein–protein interactions that drive phenotypic changes. Most commonly used methods for discovering these protein–protein interactions, however, are optimized for detecting stable, longer-lived complexes, rather than the type of transient interactions that are essential components of dynamic signaling networks such as those mediated by RTKs. Substrate phosphorylation downstream of RTK activation modifies substrate activity and induces phospho-specific binding interactions, resulting in the formation of large transient macromolecular signaling complexes. Since protein complex formation should follow the trajectory of events that drive it, we reasoned that mining phosphoproteomic datasets for highly similar dynamic behavior of measured phosphorylation sites on different proteins could be used to predict novel, transient protein–protein interactions that had not been previously identified. We applied this method to explore signaling events downstream of EGFR stimulation. Our computational analysis of robustly co-regulated phosphorylation sites, based on multiple clustering analysis of quantitative time-resolved mass-spectrometry phosphoproteomic data, not only identified known sitewise-specific recruitment of proteins to EGFR, but also predicted novel, a priori interactions. A particularly intriguing prediction of EGFR interaction with the cytoskeleton-associated protein PDLIM1 was verified within cells using co-immunoprecipitation and in situ proximity ligation assays. Our approach thus offers a new way to discover protein–protein interactions in a dynamic context- and phosphorylation site-specific manner. PMID:22851037

Naegle, Kristen M.; White, Forest M.; Lauffenburger, Douglas A.; Yaffe, Michael B.

2012-01-01

394

Historic Maps  

NSDL National Science Digital Library

The first site about historical maps is the US Military Academy at West Point's History Department's Map Library (1). The page contains links to dozens of maps related to warfare from ancient times, the American Revolution, and the Napoleonic wars to the World Wars and other modern conflicts. Although map descriptions are not given and the main page seemed to have a problem loading correctly, the site does give a very interesting glimpse into the geography and history of conflict. The second offering is from The Dalton School called Maps of the Roman Empire (2). Visitors will find dozens of interesting maps with titles such as the Roman Empire circa 120 AD; Trade Routes; 18 Centuries of Roman Empire; and maps of how the empire expanded, barbarian migrations, and more. Next, the History of Cartography (3) Web site is maintained by the University of Wisconsin Geography Department. The well designed page contains six volumes of information relating to cartographic changes from ancient times to the twentieth century. Full descriptions and images are available from this unique research, editorial, and publishing project. The fourth site from the Library of Congress Historical Collections is entitled American Memory Collections (4). The page contains various links to civil war maps, panoramic maps, revolutionary era maps, and other very impressive collections. The Perry-Castañeda Library Map Collection: Historical Maps Web site (5) of the University of Texas at Austin is the next offering. This extensive site contains a well organized collection of historical maps of Africa, the Americas, Asia, Australia and the Pacific, Europe, the Middle East, Polar Regions and Oceans, Russia and the Former Soviet Republics, Texas, the US, and the World. The sixth site is maintained by John Hopkins University called Color Landforms Atlas of the United States (6). The main page contains links to maps from all fifty states, which include large historical maps from 1895, county maps, and shaded relief maps. The next site, old-maps.co.uk (7), is provided by Britain's national mapping agency and the Landmark Information Group. The site gives online access to Britain's most extensive digital historical map archive, which can be searched and browsed by a variety of subjects to view maps of Buckingham Palace, Edinburgh Castle, and Oxford University, among others. The last historical maps Web site is the Maps and Geography (8) search engine from National Geographic online. Users can search by general historical maps, Lewis and Clark maps, New England and New York maps, Civil War, and World Maps to find and view an impressive and interesting collection.

Brieske, Joel A.

2003-01-01

395

Interaction Maps of the Saccharomyces cerevisiae ESCRT-III Protein Snf7  

PubMed Central

The Saccharomyces cerevisiae ESCRT-III protein Snf7 is part of an intricate interaction network at the endosomal membrane. Interaction maps of Snf7 were established by measuring the degree of binding of individual binding partners to putative binding motifs along the Snf7 sequence by glutathione S-transferase (GST) pulldown. For each interaction partner, distinct binding profiles were obtained. The following observations were made. The ESCRT-III subunits Vps20 and Vps24 showed a complementary binding pattern, suggesting a model for the series of events in the ESCRT-III functional cycle. Vps4 bound to individual Snf7 motifs but not to full-length Snf7. This suggests that Vps4 does not bind to the closed conformation of Snf7. We also demonstrate for the first time that the ALIX/Bro1 homologue Rim20 binds to the ?6 helix of Snf7. Analysis of a Snf7 ?6 deletion mutant showed that the ?6 helix is crucial for binding of Bro1 and Rim20 in vivo and is indispensable for the multivesicular body (MVB)-sorting and Rim-signaling functions of Snf7. The Snf7??6 protein still appeared to be incorporated into ESCRT-III complexes at the endosomal membrane, but disassembly of the complex seemed to be defective. In summary, our study argues against the view that the ESCRT cycle is governed by single one-to-one interactions between individual components and emphasizes the network character of the ESCRT interactions. PMID:24058170

Sciskala, Barbara

2013-01-01

396

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein  

NASA Technical Reports Server (NTRS)

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

Gaucher, Eric A.; Miyamoto, Michael M.; Benner, Steven A.

2003-01-01

397

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein.  

PubMed Central

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals. PMID:12702697

Gaucher, Eric A; Miyamoto, Michael M; Benner, Steven A

2003-01-01

398

Interactions of anthrax lethal factor with protective antigen defined by site-directed spin labeling  

E-print Network

Interactions of anthrax lethal factor with protective antigen defined by site-directed spin, 2010 (sent for review October 29, 2010) The protective antigen (PA) moiety of anthrax toxin forms oligo the PA pore. Anthrax toxin, in addition to its importance in regard to the pathogenesis of Bacillus

McQuade, D. Tyler

399

Identifying protein-protein interaction sites on a genome-wide scale  

E-print Network

Identifying protein-protein interaction sites on a genome-wide scale Haidong Wang Eran Segal Asa}@cs.stanford.edu Dept. of Biochemistry {asa.benhur, brutlag}@stanford.edu Stanford University, CA 94305 Abstract Protein on proteins, with red denoting active and gray denoting inactive motifs. (b) A fragment of our probabilistic

Ben-hur, Asa

400

Predicting Protein-Protein Interaction Sites Using Radial Basis Function Neural Networks  

E-print Network

, Hau San Wong, Peng Chen, Hong-Qiang Wang and De-Shuang Huang, Senior Member, IEEE Abstract and 60405002). B.Wang and P.Chen are with Intelligent Computing Lab, Hefei Institute of Intelligent Machines & Evans [7] proposed predicting protein interaction sites by detecting the presence of "proline brackets

Hefei Institute of Intelligent Machines

401

WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures  

E-print Network

1 WebFEATURE: An interactive web tool for identifying and visualizing functional sites University, Stanford CA 94305 USA Abstract WebFEATURE (http://feature.stanford.edu/webfeature/) is a web and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package

Brutlag, Doug

402

BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska  

NASA Astrophysics Data System (ADS)

In 2013, the Barrow Area Information Database (BAID, www.baid.utep.edu) project resumed field operations in Barrow, AK. The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 11,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Highlights for the 2013 season include the addition of more than 2000 additional research sites, providing differential global position system (dGPS) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal, deployment of a wireless sensor network, and substantial upgrades to the BAID website and web mapping applications.

Cody, R. P.; Kassin, A.; Gaylord, A. G.; Tweedie, C. E.

2013-12-01

403

Interactive segmentation of tongue contours in ultrasound video sequences using quality maps  

NASA Astrophysics Data System (ADS)

Ultrasound (US) imaging is an effective and non invasive way of studying the tongue motions involved in normal and pathological speech, and the results of US studies are of interest for the development of new strategies in speech therapy. State-of-the-art tongue shape analysis techniques based on US images depend on semi-automated tongue segmentation and tracking techniques. Recent work has mostly focused on improving the accuracy of the tracking techniques themselves. However, occasional errors remain inevitable, regardless of the technique used, and the tongue tracking process must thus be supervised by a speech scientist who will correct these errors manually or semi-automatically. This paper proposes an interactive framework to facilitate this process. In this framework, the user is guided towards potentially problematic portions of the US image sequence by a segmentation quality map that is based on the normalized energy of an active contour model and automatically produced during tracking. When a problematic segmentation is identified, corrections to the segmented contour can be made on one image and propagated both forward and backward in the problematic subsequence, thereby improving the user experience. The interactive tools were tested in combination with two different tracking algorithms. Preliminary results illustrate the potential of the proposed framework, suggesting that the proposed framework generally improves user interaction time, with little change in segmentation repeatability.

Ghrenassia, Sarah; Ménard, Lucie; Laporte, Catherine

2014-03-01

404

Site-directed mutagenesis of active site residues reveals plasticity of human butyrylcholinesterase in substrate and inhibitor interactions.  

PubMed

In search of the molecular mechanisms underlying the broad substrate and inhibitor specificities of butyrylcholinesterase (BuChE), we employed site-directed mutagenesis to modify the catalytic triad residue Ser198, the acyl pocket Leu286 and adjacent Phe329 residues, and Met437 and Tyr440 located near the choline binding site. Mutant proteins were produced in microinjected Xenopus oocytes, and Km values towards butyrylthiocholine and IC50 values for the organophosphates diisopropylfluorophosphonate (DFP), diethoxyphosphinylthiocholine iodide (echothiophate), and tetraisopropylpyrophosphoramide (iso-OMPA) were determined. Substitution of Ser198 by cysteine and Met437 by aspartate nearly abolished activity, and other mutations of Ser198 completely abolished it. Tyr440 and Leu286 mutants remained active, but with higher Km and IC50 values. Rates of inhibition by DFP were roughly parallel to IC50 values for several Leu286 mutants. Both Km and IC50 values increased for Leu286 mutants in the order Asp < Gln < Lys. In contrast, cysteine, leucine, and glutamine mutants of Phe329 displayed unmodified Km values toward butyrylthiocholine, but up to 10-fold decreased IC50 values for DFP, iso-OMPA, and echothiophate. These findings add Tyr440 and Phe329 to the list of residues interacting with substrate and ligands, demonstrate plasticity in the active site region of BuChE, and foreshadow the design of recombinant BuChEs with tailored scavenging properties. PMID:8294937

Gnatt, A; Loewenstein, Y; Yaron, A; Schwarz, M; Soreq, H

1994-02-01

405

GEO 599 Web Mapping & Human Computer Interaction (Credits 4) GEO 568 Interactive Cartography and Geovisualization (Credits 4)  

E-print Network

, objects, event handling; DOM & CSS W3 Web Mapping Framework Leaflet, API structure, geoJSON W4 Custom Map Tiles & Data Sources Map tile services and WMS Services; intro to TileMill, review LiDAR W5 Thematic Web

Jenny, Bernhard

406

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.  

PubMed

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets. PMID:24070451

Haider, Kamran; Huggins, David J

2013-10-28

407

Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules  

PubMed Central

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets. PMID:24070451

2013-01-01

408

A Method for Place Name Display Considering User Locating Habits in Map Sites  

NASA Astrophysics Data System (ADS)

The traditional researches for cartographic lettering and display focus on conflict among labels and overlap between labels and features. But these two issues are not significant in web maps. It is worthwhile to concern about how to improve labels' readability considering user locating habits for enhancing user experience. This paper has established a new method for place name display called "the gravitational field". This method is appropriate for the display of dotted place names from the national level (approximately 1:20 million) to city level (approximately 1:250 thousand) in web maps. We have conducted a usability test which used all nationwide provincial capitals, autonomous regions, municipalities, prefecture-level cities, municipal districts, countries and part of the townships dotted names. The results show that this rule improves web map's legibility, and can significantly enhance the user experience.

Liu, X. C.; Li, X.; Wang, L.; Wang, P.

2013-11-01

409

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast  

PubMed Central

Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ?SWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing. PMID:25825871

Patrick, Kristin L.; Ryan, Colm J.; Xu, Jiewei; Lipp, Jesse J.; Nissen, Kelly E.; Roguev, Assen; Shales, Michael; Krogan, Nevan J.; Guthrie, Christine

2015-01-01

410

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast.  

PubMed

Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ?SWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects-and is affected by-co-transcriptional splicing. PMID:25825871

Patrick, Kristin L; Ryan, Colm J; Xu, Jiewei; Lipp, Jesse J; Nissen, Kelly E; Roguev, Assen; Shales, Michael; Krogan, Nevan J; Guthrie, Christine

2015-02-01

411

An interactive program for computer-aided map design, display, and query: EMAPKGS2  

USGS Publications Warehouse

EMAPKGS2 is a user-friendly, PC-based electronic mapping tool for use in hydrogeologic exploration and appraisal. EMAPKGS2 allows the analyst to construct maps interactively from data stored in a relational database, perform point-oriented spatial queries such as locating all wells within a specified radius, perform geographic overlays, and export the data to other programs for further analysis. EMAPKGS2 runs under Microsoft?? Windows??? 3.1 and compatible operating systems. EMAPKGS2 is a public domain program available from the Kansas Geological Survey. EMAPKGS2 is the centerpiece of WHEAT, the Windows-based Hydrogeologic Exploration and Appraisal Toolkit, a suite of user-friendly Microsoft?? Windows??? programs for natural resource exploration and management. The principal goals in development of WHEAT have been ease of use, hardware independence, low cost, and end-user extensibility. WHEAT'S native data format is a Microsoft?? Access?? database. WHEAT stores a feature's geographic coordinates as attributes so they can be accessed easily by the user. The WHEAT programs are designed to be used in conjunction with other Microsoft?? Windows??? software to allow the natural resource scientist to perform work easily and effectively. WHEAT and EMAPKGS have been used at several of Kansas' Groundwater Management Districts and the Kansas Geological Survey on groundwater management operations, groundwater modeling projects, and geologic exploration projects. ?? 1997 Elsevier Science Ltd.

Pouch, G.W.

1997-01-01

412

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways  

PubMed Central

As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

2011-01-01

413

BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.  

PubMed

BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses. PMID:19129928

Mikula, Shawn; Stone, James M; Jones, Edward G

2008-01-01

414

Geophysical logging and geologic mapping data in the vicinity of the GMH Electronics Superfund site near Roxboro, North Carolina  

USGS Publications Warehouse

Geologic mapping, the collection of borehole geophysical logs and images, and passive diffusion bag sampling were conducted by the U.S. Geological Survey North Carolina Water Science Center in the vicinity of the GMH Electronics Superfund site near Roxboro, North Carolina, during March through October 2011. The study purpose was to assist the U.S. Environmental Protection Agency in the development of a conceptual groundwater model for the assessment of current contaminant distribution and future migration of contaminants. Data compilation efforts included geologic mapping of more than 250 features, including rock type and secondary joints, delineation of more than 1,300 subsurface features (primarily fracture orientations) in 15 open borehole wells, and the collection of passive diffusion-bag samples from 42 fracture zones at various depths in the 15 wells.

Chapman, Melinda J.; Clark, Timothy W.; Williams, John H.

2013-01-01

415

Digital mapping of the Mars Pathfinder landing site: Design, acquisition, and derivation of cartographic products for science applications  

USGS Publications Warehouse

The Imager for Mars Pathfinder (IMP) acquired more than 16,000 images and provided panoramic views of the surface of Mars at the Mars Pathfinder landing site in Ares Vallis. This paper describes the stereoscopic, multispectral IMP imaging sequences and focuses on their use for digital mapping of the landing site and for deriving cartographic products to support science applications of these data. Two-dimensional cartographic processing of IMP data, as performed via techniques and specialized software developed for ISIS (the U.S.Geological Survey image processing software package), is emphasized. Cartographic processing of IMP data includes ingestion, radiometric correction, establishment of geometric control, coregistration of multiple bands, reprojection, and mosaicking. Photogrammetric processing, an integral part of this cartographic work which utilizes the three-dimensional character of the IMP data, supplements standard processing with geometric control and topographic information [Kirk et al., this issue]. Both cartographic and photogrammetric processing are required for producing seamless image mosaics and for coregistering the multispectral IMP data. Final, controlled IMP cartographic products include spectral cubes, panoramic (360?? azimuthal coverage) and planimetric (top view) maps, and topographic data, to be archived on four CD-ROM volumes. Uncontrolled and semicontrolled versions of these products were used to support geologic characterization of the landing site during the nominal and extended missions. Controlled products have allowed determination of the topography of the landing site and environs out to ???60 m, and these data have been used to unravel the history of large- and small-scale geologic processes which shaped the observed landing site. We conclude by summarizing several lessons learned from cartographic processing of IMP data. Copyright 1999 by the American Geophysical Union.

Gaddis, L.R.; Kirk, R.L.; Johnson, J.R.; Soderblom, L.A.; Ward, A.W.; Barrett, J.; Becker, K.; Decker, T.; Blue, J.; Cook, D.; Eliason, E.; Hare, T.; Howington-Kraus, E.; Isbell, C.; Lee, E.M.; Redding, B.; Sucharski, R.; Sucharski, T.; Smith, P.H.; Britt, D.T.

1999-01-01

416

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells  

Microsoft Academic Search

Background: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation. RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows. Results:

Alexander S Brodsky; Clifford A Meyer; Ian A Swinburne; Giles Hall; Benjamin J Keenan; Xiaole S Liu; Edward A Fox; Pamela A Silver

2005-01-01

417

Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design  

PubMed Central

The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study. PMID:25822501

Yi, Can; Wen, Jia; Jinxing, Tu; Zhang, Yuan Ming

2015-01-01

418

An Overview of Tubulin Inhibitors That Interact with the Colchicine Binding Site  

PubMed Central

Tubulin dynamics is a promising target for new chemotherapeutic agents. The colchicine binding site is one of the most important pockets for potential tubulin polymerization destabilizers. Colchicine binding site inhibitors (CBSI) exert their biological effects by inhibiting tubulin assembly and suppressing microtubule formation. A large number of molecules interacting with the colchicine binding site have been designed and synthesized with significant structural diversity. CBSIs have been modified as to chemical structure as well as pharmacokinetic properties, and tested in order to find a highly potent, low toxicity agent for treatment of cancers. CBSIs are believed to act by a common mechanism via binding to the colchicine site on tubulin. The present review is a synopsis of compounds that have been reported in the past decade that have provided an increase in our understanding of the actions of CBSIs. PMID:22814904

Lu, Yan; Chen, Jianjun; Xiao, Min; Li, Wei

2013-01-01

419

Interaction of human immunodeficiency virus type 1 Tat with a unique site of TFIID inhibits negative cofactor Dr1 and stabilizes the TFIID-TFIIA complex.  

PubMed Central

We have previously reported the direct physical interaction between the human immunodeficiency virus (HIV) type I Tat protein and the basal transcription factor TBP/TFIID. Affinity chromatography demonstrated that wild-type Tat, but not a transactivation mutant of Tat, was capable of depleting TBP/TFIID from cell extracts. These experiments represented the first demonstration of a basal transcription factor that binds, in an activation-dependent manner, to Tat. We now report that the Tat-TBP interaction can be detected in HIV type 1-infected cells. The domain of TBP interacting with Tat has been mapped from amino acids 163 to 196 by using deletion and site-specific mutants of TBP. This domain of TBP, which includes the HI and S2 domains, is distinct from the H2 binding site for other activator proteins, such as E1A. The interaction of Tat with TFIID regulates the binding of accessory proteins to TFIID. Tat stabilizes the interaction of TFIID with TFIIA in a gel shift assay. In addition, Tat competes for Dr1 interaction with TBP. Our results suggest that the basal transcription factor TBP/TFIID represents an important regulatory molecule in HIV transcription. PMID:8764062

Kashanchi, F; Khleif, S N; Duvall, J F; Sadaie, M R; Radonovich, M F; Cho, M; Martin, M A; Chen, S Y; Weinmann, R; Brady, J N

1996-01-01

420

Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies.  

PubMed

The identification of BACE-1, a key enzyme in the production of Amyloid-? (A?) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of A? peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus dispersion energies. PMID:21691813

Gueto-Tettay, Carlos; Drosos, Juan Carlos; Vivas-Reyes, Ricardo

2011-06-01