California State Waters Map Series Data Catalog

USGS Publications Warehouse

Golden, Nadine E.

2013-01-01

In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California's State Waters. The CSMP approach is to create highly detailed seafloor maps and associated data layers through the collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. CSMP has divided coastal California into 110 map blocks (fig. 1), each to be published individually as USGS Scientific Investigations Maps (SIMs) at a scale of 1:24,000. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the seafloor geology and shallow (to about 100 m) subsurface geology. This CSMP data catalog contains much of the data used to prepare the SIMs in the California State Waters Map Series. Other data that were used to prepare the maps were compiled from previously published sources (for example, onshore geology) and, thus, are not included herein.

Preliminary geologic map of the Piru 7.5' quadrangle, southern California: a digital database

USGS Publications Warehouse

Yerkes, R.F.; Campbell, Russell H.

1995-01-01

This Open-File report is a digital geologic map database. This pamphlet serves to introduce and describe the digital data. There is no paper map included in the Open-File report. This digital map database is compiled from previously published sources combined with some new mapping and modifications in nomenclature. The geologic map database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U. S. Geological Survey. For detailed descriptions of the units, their stratigraphic relations and sources of geologic mapping consult Yerkes and Campbell (1995). More specific information about the units may be available in the original sources.

Potentiometric maps of the Sparta Sand, northern Louisiana and southern Arkansas, 1900, 1965, 1975, and 1980

USGS Publications Warehouse

Ryals, G.N.

1980-01-01

The potentiometric surface of the Sparta Sand in northern Louisiana is shown by contours on four maps. Maps for 1900, 1965 , and spring 1975 are generalized, small-scale maps from previously published reports. The spring 1980 map (1:500,000) is based on measurements in 144 wells and includes the southern tier of counties in southern Arkansas. The map shows regional effects of pumping from the Sparta Sand and effects of local pumping centers at Magnolia and El Dorado, Ark., and at Minden, Ruston, Jonesboro-Hodge, Winnfield, Bastrop, and in the Monroe area of Louisiana. (USGS)

Agricultural Census 2012: Publishing Mashable GIS Big Data Services

NASA Astrophysics Data System (ADS)

Mueller, R.

2014-12-01

The 2012 Agricultural Census was released by the US Department of Agriculture (USDA) on May 2nd 2014; published on a quinquennial basis covering all facets of American production agriculture. The Agricultural Census is a comprehensive source of uniform published agricultural data for every state and county in the US. This is the first Agricultural Census that is disseminated with web mapping services using REST APIs. USDA developed an open GIS mashable web portal that depicts over 250 maps on Crops and Plants, Economics, Farms, Livestock and Animals, and Operators. These mapping services written in JavaScript replace the traditional static maps published as the Ag Atlas. Web users can now visualize, interact, query, and download the Agricultural Census data in a means not previously discoverable. Stakeholders will now be able to leverage this data for activities such as community planning, agribusiness location suitability analytics, availability of loans/funds, service center locations and staffing, and farm programs and policies. Additional sites serving compatible mashable USDA Big Data web services are as follows: The Food Environment Atlas, The Atlas of Rural and Small-Town America, The Farm Program Atlas, SNAP Data System, CropScape, and VegScape. All portals use a similar data organization scheme of "Categories" and "Maps" providing interactive mashable web services for agricultural stakeholders to exploit.

Data-driven mapping of hypoxia-related tumor heterogeneity using DCE-MRI and OE-MRI.

PubMed

Featherstone, Adam K; O'Connor, James P B; Little, Ross A; Watson, Yvonne; Cheung, Sue; Babur, Muhammad; Williams, Kaye J; Matthews, Julian C; Parker, Geoff J M

2018-04-01

Previous work has shown that combining dynamic contrast-enhanced (DCE)-MRI and oxygen-enhanced (OE)-MRI binary enhancement maps can identify tumor hypoxia. The current work proposes a novel, data-driven method for mapping tissue oxygenation and perfusion heterogeneity, based on clustering DCE/OE-MRI data. DCE-MRI and OE-MRI were performed on nine U87 (glioblastoma) and seven Calu6 (non-small cell lung cancer) murine xenograft tumors. Area under the curve and principal component analysis features were calculated and clustered separately using Gaussian mixture modelling. Evaluation metrics were calculated to determine the optimum feature set and cluster number. Outputs were quantitatively compared with a previous non data-driven approach. The optimum method located six robustly identifiable clusters in the data, yielding tumor region maps with spatially contiguous regions in a rim-core structure, suggesting a biological basis. Mean within-cluster enhancement curves showed physiologically distinct, intuitive kinetics of enhancement. Regions of DCE/OE-MRI enhancement mismatch were located, and voxel categorization agreed well with the previous non data-driven approach (Cohen's kappa = 0.61, proportional agreement = 0.75). The proposed method locates similar regions to the previous published method of binarization of DCE/OE-MRI enhancement, but renders a finer segmentation of intra-tumoral oxygenation and perfusion. This could aid in understanding the tumor microenvironment and its heterogeneity. Magn Reson Med 79:2236-2245, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Digital Mapping Techniques '07 - Workshop Proceedings

USGS Publications Warehouse

Soller, David R.

2008-01-01

The Digital Mapping Techniques '07 (DMT'07) workshop was attended by 85 technical experts from 49 agencies, universities, and private companies, including representatives from 27 state geological surveys. This year's meeting, the tenth in the annual series, was hosted by the South Carolina Geological Survey, from May 20-23, 2007, on the University of South Carolina campus in Columbia, South Carolina. Each DMT workshop has been coordinated by the U.S. Geological Survey's National Geologic Map Database Project and the Association of American State Geologists (AASG). As in previous year's meetings, the objective was to foster informal discussion and exchange of technical information, principally in order to develop more efficient methods for digital mapping, cartography, GIS analysis, and information management. At this meeting, oral and poster presentations and special discussion sessions emphasized: 1) methods for creating and publishing map products (here, 'publishing' includes Web-based release); 2) field data capture software and techniques, including the use of LIDAR; 3) digital cartographic techniques; 4) migration of digital maps into ArcGIS Geodatabase format; 5) analytical GIS techniques; and 6) continued development of the National Geologic Map Database.

Short communication: Passive shedding of Mycobacterium avium ssp. paratuberculosis in commercial dairy goats in Brazil.

PubMed

Schwarz, D G G; Lima, M C; Barros, M; Valente, F L; Scatamburlo, T M; Rosado, N; Oliveira, C T S A M; Oliveira, L L; Moreira, M A S

2017-10-01

Goat farming is a low-cost alternative to dairy production in developing countries. In Brazil, goat production has increased in recent years due in part to the implementation of programs encouraging this activity. Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, a disease that causes chronic granulomatous enteritis in ruminants, but MAP transmission dynamics are still poorly understood in goats. In a previously published study of our research group, 10 dairy goat farms (467 animals) from Minas Gerais state were analyzed for MAP detection; 2 fecal cultures and 11 milk samples tested positive for MAP by conventional PCR and were confirmed by sequencing. Because no clinical signs were observed over 1 yr of monitoring, we hypothesized that these MAP-positive goats could be passive shedders. Thus, in the present study, 4 positive goats (4/13) from the previous study were purchased and feces and milk samples were collected for evaluation (twice, with an interval of 3 mo between tests) by culture of MAP, IS900 PCR, or both. All analyses were negative for MAP. At the last time point, blood samples were collected for ELISA, the animals were killed, and tissues collected for tissue culture and histopathology. At necropsy, no macroscopic lesions related to paratuberculosis were observed. Similarly, no histological changes were observed and MAP in samples stained by Ziehl-Neelsen was not detected. These animals were characterized as potential passive shedders with upward contamination of the teat canal by MAP. This is the first report of the passive shedding phenomenon in goats in Brazil and it highlights the importance of identifying these animals for control programs and to ensure the quality of dairy products. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

NORTH AMERICAN DATUM 1983 IMPLEMENTATION IMPACTS ON THE USGS NATIONAL MAPPING PROGRAM.

USGS Publications Warehouse

Jones, William J.; Needham, Paul E.

1985-01-01

The U. S. Geological Survey has previously experienced the impacts on the National Mapping Program that are associated with implementing a readjustment of the horizontal datum. The impacts of these past readjustments were minimal compared to those of the current readjustment. The Geological Survey currently has produced and published over 60,000 different map products. The 7. 5-minute mapping program is nearing completion with over 85 percent of the conterminous States mapped. The intermediate-scale mapping program of the conterminous United States is scheduled for completion of planimetric editions by the end of 1986. It is apparent that until digital cartographic data are available, implementation of the North American Datum 1983 will primarily consist of cartographic adjustment of existing map products.

Geologic map and map database of northeastern San Francisco Bay region, California, [including] most of Solano County and parts of Napa, Marin, Contra Costa, San Joaquin, Sacramento, Yolo, and Sonoma Counties

USGS Publications Warehouse

Graymer, Russell Walter; Jones, David Lawrence; Brabb, Earl E.

2002-01-01

This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (nesfmf.ps, nesfmf.pdf, nesfmf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller.

Principal components analysis of Jupiter VIMS spectra

USGS Publications Warehouse

Bellucci, G.; Formisano, V.; D'Aversa, E.; Brown, R.H.; Baines, K.H.; Bibring, J.-P.; Buratti, B.J.; Capaccioni, F.; Cerroni, P.; Clark, R.N.; Coradini, A.; Cruikshank, D.P.; Drossart, P.; Jaumann, R.; Langevin, Y.; Matson, D.L.; McCord, T.B.; Mennella, V.; Nelson, R.M.; Nicholson, P.D.; Sicardy, B.; Sotin, Christophe; Chamberlain, M.C.; Hansen, G.; Hibbits, K.; Showalter, M.; Filacchione, G.

2004-01-01

During Cassini - Jupiter flyby occurred in December 2000, Visual-Infrared mapping spectrometer (VIMS) instrument took several image cubes of Jupiter at different phase angles and distances. We have analysed the spectral images acquired by the VIMS visual channel by means of a principal component analysis technique (PCA). The original data set consists of 96 spectral images in the 0.35-1.05 ??m wavelength range. The product of the analysis are new PC bands, which contain all the spectral variance of the original data. These new components have been used to produce a map of Jupiter made of seven coherent spectral classes. The map confirms previously published work done on the Great Red Spot by using NIMS data. Some other new findings, presently under investigation, are presented. ?? 2004 Published by Elsevier Ltd on behalf of COSPAR.

Geologic map of the Priest Rapids 1:100,000 quadrangle, Washington

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reidel, S.P.; Fecht, K.R.

1993-09-01

This map of the Priest Rapids 1:100,000-scale quadrangle, Washington, shows the geology of one of fifteen complete or partial 1:100,000-scale quadrangles that cover the southeast quadrant of Washington. Geologic maps of these quadrangles have been compiled by geologists with the Washington Division of Geology and Earth Resources (DGER) and Washington State University and are the principal data sources for a 1:250,000scale geologic map of the southeast quadrant of Washington, which is in preparation. Eleven of those quadrangles are being released as DGER open-file reports (listed below). The map of the Wenatchee quadrangle has been published by the US Geological Surveymore » (Tabor and others, 1982), and the Moses Lake (Gulick, 1990a), Ritzville (Gulick, 1990b), and Rosalia (Waggoner, 1990) quadrangles have already been released. The geology of the Priest Rapids quadrangle has not previously been compiled at 1:100,000 scale. Furthermore, this is the first 1:100,000 or smaller scale geologic map of the area to incorporate both bedrock and surficial geology. This map was compiled in 1992, using published and unpublished geologic maps as sources of data.« less

Organic carbon accumulation in modern sediments of the Angola basin influenced by the Congo deep-sea fan

NASA Astrophysics Data System (ADS)

Baudin, François; Martinez, Philippe; Dennielou, Bernard; Charlier, Karine; Marsset, Tania; Droz, Laurence; Rabouille, Christophe

2017-08-01

Geochemical data (total organic carbon-TOC content, δ13Corg, C:N, Rock-Eval analyses) were obtained on 150 core tops from the Angola basin, with a special focus on the Congo deep-sea fan. Combined with the previously published data, the resulting dataset (322 stations) shows a good spatial and bathymetric representativeness. TOC content and δ13Corg maps of the Angola basin were generated using this enhanced dataset. The main difference in our map with previously published ones is the high terrestrial organic matter content observed downslope along the active turbidite channel of the Congo deep-sea fan till the distal lobe complex near 5000 m of water-depth. Interpretation of downslope trends in TOC content and organic matter composition indicates that lateral particle transport by turbidity currents is the primary mechanism controlling supply and burial of organic matter in the bathypelagic depths.

Cartographic experiment for Latin America. [Santa Cruz, Bolivia and Concepcion, Paraguay

NASA Technical Reports Server (NTRS)

Staples, J. E. (Principal Investigator)

1974-01-01

The author has identified the following significant results. The two experiments clearly demonstrate the practical application of the Skylab photography to update existing maps at an optimum scale of 1:100,000. The photography can even be used, by employing first order photogrammetric instruments, for updating the cultural features in 1:50,000 scale mapping. The S190A imagery has also shown itself to be most economical in preparing new photomap products over previously unmapped areas, such as Concepcion, Paraguay. These maps indicate that Skylab quality imagery is invaluable to the Latin American cartographers in their efforts to provide the mapping products required to develop their countries. In Latin America, where over 5,000 people are employed in map production and where the Latin American governments are expending over $20 million in this effort, the use of such systems to maintain existing mapping and publish new mapping over previously unmapped areas, is of great economic value and could release the conventional Latin American mapping resources to be utilized to produce large scale 1:25,000 and 1:1,000 scale mapping that is needed for specific development projects.

Geology of the Cape Mendocino, Eureka, Garberville, and Southwestern Part of the Hayfork 30 x 60 Minute Quadrangles and Adjacent Offshore Area, Northern California

USGS Publications Warehouse

McLaughlin, Robert J.; Ellen, S.D.; Blake, M.C.; Jayko, Angela S.; Irwin, W.P.; Aalto, K.R.; Carver, G.A.; Clarke, S.H.; Barnes, J.B.; Cecil, J.D.; Cyr, K.A.

2000-01-01

Introduction These geologic maps and accompanying structure sections depict the geology and structure of much of northwestern California and the adjacent continental margin. The map area includes the Mendocino triple junction, which is the juncture of the North American continental plate with two plates of the Pacific ocean basin. The map area also encompasses major geographic and geologic provinces of northwestern California. The maps incorporate much previously unpublished geologic mapping done between 1980 and 1995, as well as published mapping done between about 1950 and 1978. To construct structure sections to mid-crustal depths, we integrate the surface geology with interpretations of crustal structure based on seismicity, gravity and aeromagnetic data, offshore structure, and seismic reflection and refraction data. In addition to describing major geologic and structural features of northwestern California, the geologic maps have the potential to address a number of societally relevant issues, including hazards from earthquakes, landslides, and floods and problems related to timber harvest, wildlife habitat, and changing land use. All of these topics will continue to be of interest in the region, as changing land uses and population density interact with natural conditions. In these interactions, it is critical that the policies and practices affecting man and the environment integrate an adequate understanding of the geology. This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (ceghmf.ps, ceghmf.pdf, ceghmf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:100,000 or smaller.

Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional chromosome painting.

PubMed

Gomes, Anderson José Baia; Nagamachi, Cleusa Yoshiko; Rodrigues, Luis Reginaldo Ribeiro; Ferguson-Smith, Malcolm Andrew; Yang, Fengtang; O'Brien, Patricia Caroline Mary; Pieczarka, Julio Cesar

2018-04-25

The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use chromosome painting with whole chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole chromosome probes allows us to track some syntenic associations prior to the emergence of this family.

An overview of concept mapping in Dutch mental health care.

PubMed

Nabitz, Udo; van Randeraad-van der Zee, Carlijn; Kok, Ineke; van Bon-Martens, Marja; Serverens, Peter

2017-02-01

About 25 years ago, concept mapping was introduced in the Netherlands and applied in different fields. A collection of concept mapping projects conducted in the Netherlands was identified, in part in the archive of the Netherlands Institute of Mental Health and Addiction (Trimbos Institute). Some of the 90 identified projects are internationally published. The 90 concept mapping projects reflect the changes in mental health care and can be grouped into 5-year periods and into five typologies. The studies range from conceptualizing the problems of the homeless to the specification of quality indicators for treatment programs for patients with cystic fibrosis. The number of concept mapping projects has varied over time. Growth has been considerable in the last 5 years compared to the previous 5 years. Three case studies are described in detail with 12 characteristics and graphical representations. Concept mapping aligns well with the typical Dutch approach of the "Poldermodel." A broad introduction of concept mapping in European countries in cooperation with other countries, such as the United States and Canada, would strengthen the empirical basis for applying this approach in health care policy, quality, and clinical work. Copyright © 2016. Published by Elsevier Ltd.

Digital Mapping Techniques '08—Workshop Proceedings, Moscow, Idaho, May 18–21, 2008

USGS Publications Warehouse

Soller, David R.

2009-01-01

The Digital Mapping Techniques '08 (DMT'08) workshop was attended by more than 100 technical experts from 40 agencies, universities, and private companies, including representatives from 24 State geological surveys. This year's meeting, the twelfth in the annual series, was hosted by the Idaho Geological Survey, from May 18-21, 2008, on the University of Idaho campus in Moscow, Idaho. Each DMT workshop has been coordinated by the U.S. Geological Survey's National Geologic Map Database Project and the Association of American State Geologists (AASG). As in previous years' meetings, the objective was to foster informal discussion and exchange of technical information, principally in order to develop more efficient methods for digital mapping, cartography, GIS analysis, and information management. At this meeting, oral and poster presentations and special discussion sessions emphasized (1) methods for creating and publishing map products (here, "publishing" includes Web-based release); (2) field data capture software and techniques, including the use of LiDAR; (3) digital cartographic techniques; (4) migration of digital maps into ArcGIS Geodatabase format; (5) analytical GIS techniques; and (6) continued development of the National Geologic Map Database.

Assessing groundwater accessibility in the Kharga Basin, Egypt: A remote sensing approach

NASA Astrophysics Data System (ADS)

Parks, Shawna; Byrnes, Jeffrey; Abdelsalam, Mohamed G.; Laó Dávila, Daniel A.; Atekwana, Estella A.; Atya, Magdy A.

2017-12-01

We used multi-map analysis of remote sensing and ancillary data to identify potentially accessible sites for groundwater resources in the Kharga Basin in the Western Desert of Egypt. This basin is dominated by Cretaceous sandstone formations and extends within the Nubian Sandstone Aquifer. It is dissected by N-S and E-W trending faults, possibly acting as conduits for upward migration of groundwater. Analysis of paleo-drainage using Digital Elevation Model (DEM) generated from the Shuttle Radar Topography Mission (SRTM) data shows that the Kharga was a closed basin that might have been the site of a paleo-lake. Lake water recharged the Nubian Sandstone Aquifer during the wetter Holocene time. We generated the following layers for the multi-map analysis: (1) Fracture density map from the interpretation of Landsat Operational Land Imager (OLI), SRTM DEM, and RADARSAT data. (2) Thermal Inertia (TI) map (for moisture content imaging) from the Moderate Resolution Imaging Spectroradiometer (MODIS) data. (3) Hydraulic conductivity map from mapping lithological units using the Landsat OLI and previously published data. (4) Aquifer thickness map from previously published data. We quantitatively ranked the Kharga Basin by considering that regions of high fracture density, high TI, thicker aquifer, and high hydraulic conductivity have higher potential for groundwater accessibility. Our analysis shows that part of the southern Kharga Basin is suitable for groundwater extraction. This region is where N-S and E-W trending faults intersect, has relatively high TI and it is underlain by thick aquifer. However, the suitability of this region for groundwater use will be reduced significantly when considering the changes in land suitability and economic depth to groundwater extraction in the next 50 years.

Evaluation of a novel high-resolution mapping technology for ablation of recurrent scar-related atrial tachycardias.

PubMed

Anter, Elad; McElderry, Thomas H; Contreras-Valdes, Fernando M; Li, Jianqing; Tung, Patricia; Leshem, Eran; Haffajee, Charles I; Nakagawa, Hiroshi; Josephson, Mark E

2016-10-01

Rhythmia is a new technology capable of rapid and high-resolution mapping. However, its potential advantage over existing technologies in mapping complex scar-related atrial tachycardias (ATs) has not yet been evaluated. The purpose of this study was to examine the utility of Rhythmia for mapping scar-related ATs in patients who had failed previous ablation procedure(s). This multicenter study included 20 patients with recurrent ATs within 2 years after a previous ablation procedure (1.8 ± 0.7 per patient). In all cases, the ATs could not be adequately mapped during the index procedure because of scar with fractionated electrograms, precluding accurate time annotation, frequent change in the tachycardia in response to pacing, and/or degeneration into atrial fibrillation. These patients underwent repeat mapping and ablation procedure with Rhythmia. From a total of 28 inducible ATs, 24 were successfully mapped. Eighteen ATs (75%) terminated during radiofrequency ablation and 4 (16.6%) with catheter pressure or entrainment from the site of origin or isthmus. Two ATs that were mapped to the interatrial septum slowed but did not terminate with ablation. In 21 of 24 ATs the mechanism was macroreentry, while in 3 of 24 the mechanism was focal. Interestingly, in 5 patients with previously failed ablation of an allegedly "focal" tachycardia, high-resolution mapping demonstrated macroreentrant arrhythmia. The mean mapping time was 28.6 ± 17 minutes, and the mean radiofrequency ablation time to arrhythmia termination was 3.2 ± 2.6 minutes. During a mean follow-up of 7.5 ± 3.1 months, 15 of 20 patients (75%) were free of AT recurrences. The Rhythmia mapping system may be advantageous for mapping complex scar-related ATs. Copyright © 2016 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Energy map of southwestern Wyoming, Part A - Coal and wind

USGS Publications Warehouse

Biewick, Laura; Jones, Nicholas R.

2012-01-01

To further advance the objectives of the Wyoming Landscape Conservation Initiative (WLCI) the U.S. Geological Survey (USGS) and the Wyoming State Geological Survey (WSGS) have compiled Part A of the Energy Map of Southwestern Wyoming. Focusing primarily on electrical power sources, Part A of the energy map is a compilation of both published and previously unpublished coal (including coalbed gas) and wind energy resources data, presented in a Geographic Information System (GIS) data package. Energy maps, data, documentation and spatial data processing capabilities are available in a geodatabase, published map file (pmf), ArcMap document (mxd), Adobe Acrobat PDF map (plate 1) and other digital formats that can be downloaded at the USGS website. Accompanying the map (plate 1) and the geospatial data are four additional plates that describe the geology, energy resources, and related infrastructure. These tabular plates include coal mine (plate 2), coal field (plate 3), coalbed gas assessment unit (plate 4), and wind farm (plate 5) information with hyperlinks to source publications and data on the internet. The plates can be printed and examined in hardcopy, or accessed digitally. The data represent decades of research by the USGS, WSGS, BLM and others, and can facilitate landscape-level science assessments, and resource management decisionmaking.

Atlas of depth-duration frequency of precipitation annual maxima for Texas

USGS Publications Warehouse

Asquith, William H.; Roussel, Meghan C.

2004-01-01

Ninety-six maps depicting the spatial variation of the depth-duration frequency of precipitation annual maxima for Texas are presented. The recurrence intervals represented are 2, 5, 10, 25, 50, 100, 250, and 500 years. The storm durations represented are 15 and 30 minutes; 1, 2, 3, 6, and 12 hours; and 1, 2, 3, 5, and 7 days. The maps were derived using geographically referenced parameter maps of probability distributions used in previously published research by the U.S. Geological Survey to model the magnitude and frequency of precipitation annual maxima for Texas. The maps in this report apply that research and update depth-duration frequency of precipitation maps available in earlier studies done by the National Weather Service.

The Alaskan Mineral Resource Assessment Program; guide to information contained in the folio of geologic and mineral resource maps of the Chandalar Quadrangle, Alaska

USGS Publications Warehouse

Reiser, H.N.; Brosge, W.P.; DeYoung, J.H.; Marsh, S.P.; Hamilton, T.D.; Cady, J.W.; Albert, N.R.D.

1979-01-01

The Chandalar quadrangle in east-central Alaska was investigated by a multidisciplinary research group to assess the mineral resource potential of the quadrangle. This circular serves as a guide to and integrates with a folio of 10 miscellaneous field study (MF) maps and 2 open-file (OF) reports (table 1) concerned with the geology, geophysics, geochemistry, Landsat imagery, and mineral resources of the area. Revisions to the previously published Chandalar quadrangle geologic map, a new radiometric age determination, and a bibliography are also included.

Small-scale features in the Earth's magnetic field observed by Magsat.

USGS Publications Warehouse

Cain, J.C.; Schmitz, D.R.; Muth, L.

1984-01-01

A spherical harmonic expansion to degree and order 29 is derived using a selected magnetically quiet sample of Magsat data. Global maps representing the contribution due to terms of the expansion above n = 13 at 400 km altitude are compared with previously published residual anomaly maps and shown to be similar, even in polar regions. An expansion with such a high degree and order displays all but the sharpest features seen by the satellite and gives a more consistent picture of the high-order field structure at a constant altitude than do component maps derived independently. -Authors

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-10-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprising six health economists and one Delphi methodologist. A two-round, modified Delphi survey, with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorized within six sections: (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS Explanation and Elaboration paper. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of the reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-08-01

"Mapping" onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite the publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist that aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of 6 health economists and 1 Delphi methodologist. A 2-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies, and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorized within 6 sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency, and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by 7 health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years.

20th century Betula pubescens subsp. czerepanovii tree- and forest lines in Norway.

PubMed

Bryn, Anders; Potthoff, Kerstin

2017-01-01

Georeferenced tree- and forest line data has a wide range of applications and are increasingly used for e.g. monitoring of climate change impacts and range shift modelling. As part of a research project, registrations of previously re-mapped tree- and forest lines have been georeferenced. The data described in this paper contains 100 re-mapped registrations of Betula pubescens subsp. czerepanovii throughout Norway. All of the re-mapped tree- and forest line localities are georeferenced, elevation and aspect are given, elevational and spatial uncertainty are provided, and the re-mapping methods are explained. The published data weremapped for the first time between 1819 and 1963. The same sites were re-mapped between 1928 and 1996, but have until now been missing spatial coordinates. The entries contain 40 x 2 tree lines and 60 x 2 forest lines, most likely presenting the regionally highest registered tree- and forest lines at the given time. The entire material is stored and available for download through the GBIF server. Previously, the entries have been published in journals or reports, partly in Norwegian or German only. Without the provision of the spatial coordinates, the specific locations have been unknown. The material is now available for modelling and monitoring of tree- and forest line range shifts: The recordings are useful for interpretation of climate change impacts on tree- and forest lines, and the locations of re-mapped tree- and forest lines can be implemented in future monitoring projects. Since the recordings most likely provide the highest registered Betula pubescens subsp. czerepanovii locations within their specific regions, they are probably representing the contemporary physiognomic range limits.

Digital mapping techniques '06 - Workshop proceedings

USGS Publications Warehouse

Soller, David R.

2007-01-01

The Digital Mapping Techniques `06 (DMT`06) workshop was attended by more than 110 technical experts from 51 agencies, universities, and private companies, including representatives from 27 state geological surveys (see Appendix A of these Proceedings). This workshop was similar in nature to the previous nine meetings, which were held in Lawrence, Kansas (Soller, 1997), Champaign, Illinois (Soller, 1998), Madison, Wisconsin (Soller, 1999), Lexington, Kentucky (Soller, 2000), Tuscaloosa, Alabama (Soller, 2001), Salt Lake City, Utah (Soller, 2002), Millersville, Pennsylvania (Soller, 2003), Portland, Oregon (Soller, 2004), and Baton Rouge, Louisiana (Soller, 2005). This year?s meeting was hosted by the Ohio Geological Survey, from June 11-14, 2006, on the Ohio State University campus in Columbus, Ohio. As in the previous meetings, the objective was to foster informal discussion and exchange of technical information. It is with great pleasure that I note that the objective was successfully met, as attendees continued to share and exchange knowledge and information, and renew friendships and collegial work begun at past DMT workshops.Each DMT workshop has been coordinated by the Association of American State Geologists (AASG) and U.S. Geological Survey (USGS) Data Capture Working Group, the latter of which was formed in August 1996 to support the AASG and the USGS in their effort to build a National Geologic Map Database (see Soller, this volume, and http://ngmdb.usgs.gov/info/standards/datacapt/). The Working Group was formed because increased production efficiencies, standardization, and quality of digital map products were needed for the database - and for the State and Federal geological surveys - to provide more high-quality digital maps to the public.At the 2006 meeting, oral and poster presentations and special discussion sessions emphasized: 1) methods for creating and publishing map products (here, "publishing" includes Web-based release); 2) field data capture software and techniques, including the use of LIDAR; 3) digital cartographic techniques; 4) migration of digital maps into ArcGIS Geodatabase format; 5) analytical GIS techniques; and 6) continued development of the National Geologic Map Database.

Distortion correction of echo planar images applying the concept of finite rate of innovation to point spread function mapping (FRIP).

PubMed

Nunes, Rita G; Hajnal, Joseph V

2018-06-01

Point spread function (PSF) mapping enables estimating the displacement fields required for distortion correction of echo planar images. Recently, a highly accelerated approach was introduced for estimating displacements from the phase slope of under-sampled PSF mapping data. Sampling schemes with varying spacing were proposed requiring stepwise phase unwrapping. To avoid unwrapping errors, an alternative approach applying the concept of finite rate of innovation to PSF mapping (FRIP) is introduced, using a pattern search strategy to locate the PSF peak, and the two methods are compared. Fully sampled PSF data was acquired in six subjects at 3.0 T, and distortion maps were estimated after retrospective under-sampling. The two methods were compared for both previously published and newly optimized sampling patterns. Prospectively under-sampled data were also acquired. Shift maps were estimated and deviations relative to the fully sampled reference map were calculated. The best performance was achieved when using FRIP with a previously proposed sampling scheme. The two methods were comparable for the remaining schemes. The displacement field errors tended to be lower as the number of samples or their spacing increased. A robust method for estimating the position of the PSF peak has been introduced.

National Agricultural Statistics Service (NASS): Agricultural Chemical Use

Science.gov Websites

Management Agricultural Chemical Use Database Search Tips Usage Search | US Maps | Graphical Reports effort among USDA, the USDA Regional Pest Management Centers and the NSF Center for Integrated Pest Management (CIPM). All data available have been previously published by NASS and have been consolidated at

Ancient science in a digital age.

PubMed

Lehoux, Daryn

2013-03-01

Technology is rapidly changing our understanding of ancient science. New methods of visualization are bringing to light important texts we could not previously read; changes in online publishing are allowing unprecedented access to difficult-to-find materials; and online mapping tools are offering new pictures of lost spaces, connectivities, and physical objects.

VIMS spectral mapping observations of Titan during the Cassini prime mission

USGS Publications Warehouse

Barnes, J.W.; Soderblom, J.M.; Brown, R.H.; Buratti, B.J.; Sotin, Christophe; Baines, K.H.; Clark, R.N.; Jaumann, R.; McCord, T.B.; Nelson, R.; Le, Mouelic S.; Rodriguez, S.; Griffith, C.; Penteado, P.; Tosi, F.; Pitman, K.M.; Soderblom, L.; Stephan, K.; Hayne, P.; Vixie, G.; Bibring, J.-P.; Bellucci, G.; Capaccioni, F.; Cerroni, P.; Coradini, A.; Cruikshank, D.P.; Drossart, P.; Formisano, V.; Langevin, Y.; Matson, D.L.; Nicholson, P.D.; Sicardy, B.

2009-01-01

This is a data paper designed to facilitate the use of and comparisons to Cassini/visual and infrared mapping spectrometer (VIMS) spectral mapping data of Saturn's moon Titan. We present thumbnail orthographic projections of flyby mosaics from each Titan encounter during the Cassini prime mission, 2004 July 1 through 2008 June 30. For each flyby we also describe the encounter geometry, and we discuss the studies that have previously been published using the VIMS dataset. The resulting compliation of metadata provides a complementary big-picture overview of the VIMS data in the public archive, and should be a useful reference for future Titan studies. ?? 2009 Elsevier Ltd.

Quasi-conformal mapping with genetic algorithms applied to coordinate transformations

NASA Astrophysics Data System (ADS)

González-Matesanz, F. J.; Malpica, J. A.

2006-11-01

In this paper, piecewise conformal mapping for the transformation of geodetic coordinates is studied. An algorithm, which is an improved version of a previous algorithm published by Lippus [2004a. On some properties of piecewise conformal mappings. Eesti NSV Teaduste Akademmia Toimetised Füüsika-Matemaakika 53, 92-98; 2004b. Transformation of coordinates using piecewise conformal mapping. Journal of Geodesy 78 (1-2), 40] is presented; the improvement comes from using a genetic algorithm to partition the complex plane into convex polygons, whereas the original one did so manually. As a case study, the method is applied to the transformation of the Spanish datum ED50 and ETRS89, and both its advantages and disadvantages are discussed herein.

Spectral Unmixing Based Construction of Lunar Mineral Abundance Maps

NASA Astrophysics Data System (ADS)

Bernhardt, V.; Grumpe, A.; Wöhler, C.

2017-07-01

In this study we apply a nonlinear spectral unmixing algorithm to a nearly global lunar spectral reflectance mosaic derived from hyper-spectral image data acquired by the Moon Mineralogy Mapper (M3) instrument. Corrections for topographic effects and for thermal emission were performed. A set of 19 laboratory-based reflectance spectra of lunar samples published by the Lunar Soil Characterization Consortium (LSCC) were used as a catalog of potential endmember spectra. For a given spectrum, the multi-population population-based incremental learning (MPBIL) algorithm was used to determine the subset of endmembers actually contained in it. However, as the MPBIL algorithm is computationally expensive, it cannot be applied to all pixels of the reflectance mosaic. Hence, the reflectance mosaic was clustered into a set of 64 prototype spectra, and the MPBIL algorithm was applied to each prototype spectrum. Each pixel of the mosaic was assigned to the most similar prototype, and the set of endmembers previously determined for that prototype was used for pixel-wise nonlinear spectral unmixing using the Hapke model, implemented as linear unmixing of the single-scattering albedo spectrum. This procedure yields maps of the fractional abundances of the 19 endmembers. Based on the known modal abundances of a variety of mineral species in the LSCC samples, a conversion from endmember abundances to mineral abundances was performed. We present maps of the fractional abundances of plagioclase, pyroxene and olivine and compare our results with previously published lunar mineral abundance maps.

Preferred reporting items for studies mapping onto preference-based outcome measures: the MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2016-02-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MApping onto Preference-based measures reporting Standards (MAPS) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of six health economists and one Delphi methodologist. A two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorised within six sections, namely (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

PREFERRED REPORTING ITEMS FOR STUDIES MAPPING ONTO PREFERENCE-BASED OUTCOME MEASURES: THE MAPS STATEMENT.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-01-01

"Mapping" onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of six health economists and one Delphi methodologist. A two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies, and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of twenty-nine candidate items, a set of twenty-three essential reporting items was developed. The items are presented numerically and categorized within six sections, namely: (i) title and abstract, (ii) introduction, (iii) methods, (iv) results, (v) discussion, and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency. and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in five years' time.

Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria × ananassa) and its Applicability

PubMed Central

Isobe, Sachiko N.; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

2013-01-01

The cultivated strawberry (Fragaria× ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA′A′BBB′B′ model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers. PMID:23248204

Updates to the zoonotic niche map of Ebola virus disease in Africa

PubMed Central

Pigott, David M; Millear, Anoushka I; Earl, Lucas; Morozoff, Chloe; Han, Barbara A; Shearer, Freya M; Weiss, Daniel J; Brady, Oliver J; Kraemer, Moritz UG; Moyes, Catherine L; Bhatt, Samir; Gething, Peter W; Golding, Nick; Hay, Simon I

2016-01-01

As the outbreak of Ebola virus disease (EVD) in West Africa is now contained, attention is turning from control to future outbreak prediction and prevention. Building on a previously published zoonotic niche map (Pigott et al., 2014), this study incorporates new human and animal occurrence data and expands upon the way in which potential bat EVD reservoir species are incorporated. This update demonstrates the potential for incorporating and updating data used to generate the predicted suitability map. A new data portal for sharing such maps is discussed. This output represents the most up-to-date estimate of the extent of EVD zoonotic risk in Africa. These maps can assist in strengthening surveillance and response capacity to contain viral haemorrhagic fevers. DOI: http://dx.doi.org/10.7554/eLife.16412.001 PMID:27414263

Contour maps of lunar remanent magnetic fields

NASA Technical Reports Server (NTRS)

Hood, L. L.; Russell, C. T.; Coleman, P. J., Jr.

1981-01-01

The 2605 usable orbits of Apollo 15 and 16 subsatellite magnetometer data have been reexamined for intervals suitable for analysis of crustal magnetic anomalies. To minimize plasma-related disturbances, segments from 274 of these orbits were selected from times when the moon was either in a lobe of the geomagnetic tail or in the solar wind with the subsatellites in the lunar wake. External field contributions which remained in the selected intervals were minimized by (1) quadratic detrending of individual orbit segments with lengths much greater than anomaly wavelengths and (2) two-dimensional filtering with minimum passed wavelengths less than or equal to anomaly wavelengths. Improvements in coverage, accuracy, and resolution of previously published anomaly maps produced from these data are obtained. In addition to improved maps of the Reiner Gamma and Van de Graaff-Aitken anomalies studied previously, a third region of relatively high-amplitude anomalies centered near the crater Gerasimovich on the southeastern far side has been mapped. Both the Van de Graaff-Aitken region and the Gerasimovich region are marked by the general occurrence of extensive groups of Reiner Gamma-type swirls.

Digital Mapping Techniques '05--Workshop Proceedings, Baton Rouge, Louisiana, April 24-27, 2005

USGS Publications Warehouse

Soller, David R.

2005-01-01

Intorduction: The Digital Mapping Techniques '05 (DMT'05) workshop was attended by more than 100 technical experts from 47 agencies, universities, and private companies, including representatives from 25 state geological surveys (see Appendix A). This workshop was similar in nature to the previous eight meetings, held in Lawrence, Kansas (Soller, 1997), in Champaign, Illinois (Soller, 1998), in Madison, Wisconsin (Soller, 1999), in Lexington, Kentucky (Soller, 2000), in Tuscaloosa, Alabama (Soller, 2001), in Salt Lake City, Utah (Soller, 2002), in Millersville, Pennsylvania (Soller, 2003), and in Portland, Oregon (Soller, 2004). This year's meeting was hosted by the Louisiana Geological Survey, from April 24-27, 2005, on the Louisiana State University campus in Baton Rouge, Louisiana. As in the previous meetings, the objective was to foster informal discussion and exchange of technical information. It is with great pleasure I note that the objective was successfully met, as attendees continued to share and exchange knowledge and information, and to renew friendships and collegial work begun at past DMT workshops. Each DMT workshop has been coordinated by the Association of American State Geologists (AASG) and U.S. Geological Survey (USGS) Data Capture Working Group, which was formed in August 1996, to support the AASG and the USGS in their effort to build a National Geologic Map Database (see Soller and Berg, this volume, and http://ngmdb.usgs.gov/info/standards/datacapt/). The Working Group was formed because increased production efficiencies, standardization, and quality of digital map products were needed for the database?and for the State and Federal geological surveys?to provide more high-quality digital maps to the public. At the 2005 meeting, oral and poster presentations and special discussion sessions emphasized: 1) methods for creating and publishing map products (here, 'publishing' includes Web-based release); 2) field data capture software and techniques, including the use of LIDAR; 3) digital cartographic techniques; 4) migration of digital maps into ArcGIS Geodatabase format; 5) analytical GIS techniques; 6) continued development of the National Geologic Map Database; and 7) progress toward building and implementing a standard geologic map data model and standard science language for the U.S. and for North America.

Validation of cryo-EM structure of IP₃R1 channel.

PubMed

Murray, Stephen C; Flanagan, John; Popova, Olga B; Chiu, Wah; Ludtke, Steven J; Serysheva, Irina I

2013-06-04

About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines. Copyright © 2013 Elsevier Ltd. All rights reserved.

Geologic map of the Boulder-Fort Collins-Greeley Area, Colorado

USGS Publications Warehouse

Colton, Roger B.

1978-01-01

This digital map shows the geographic extent of rock stratigraphic units (formations) as compiled by Colton in 1976 under the Front Range Urban Corridor Geology Program. Colton used his own geologic mapping and previously published geologic maps to compile one map having a single classification of geologic units. The resulting published color paper map (USGS Map I-855-G, Colton, 1978) was intended for land-use planning and to depict the regional geology. In 1997-1999, another USGS project designed to address urban growth issues was undertaken. This project, the USGS Front Range Infrastructure Resources Project, undertook to digitize Colton's map at 1:100,000 scale, making it useable in Geographical Information Systems (GIS). That product is described here. In general, the digitized map depicts in its western part Precambrian igneous and metamorphic rocks, Pennsylvanian and younger sedimentary rock units, major faults, and brecciated zones along an eastern strip (5-20 km wide) of the Front Range. The central and eastern parts of the map (Colorado Piedmont) show a mantle of Quaternary unconsolidated deposits and interspersed outcrops of sedimentary rock of Cretaceous or Tertiary age. A surficial mantle of unconsolidated deposits of Quaternary age is differentiated and depicted as eolium (wind-blown sand and silt), alluvium (river gravel, sand, and silt of variable composition), colluvium, and a few landslide deposits. At the mountain front, north-trending, Paleozoic and Mesozoic formations of sandstone, shale, and minor limestone dip mostly eastward and form folds, fault blocks, hogbacks and intervening valleys. Local dikes and sills of Tertiary rhyodacite and basalt intrude rocks near the range front, mostly in the Boulder area.

An unsupervised classification method for inferring original case locations from low-resolution disease maps.

PubMed

Brownstein, John S; Cassa, Christopher A; Kohane, Isaac S; Mandl, Kenneth D

2006-12-08

Widespread availability of geographic information systems software has facilitated the use of disease mapping in academia, government and private sector. Maps that display the address of affected patients are often exchanged in public forums, and published in peer-reviewed journal articles. As previously reported, a search of figure legends in five major medical journals found 19 articles from 1994-2004 that identify over 19,000 patient addresses. In this report, a method is presented to evaluate whether patient privacy is being breached in the publication of low-resolution disease maps. To demonstrate the effect, a hypothetical low-resolution map of geocoded patient addresses was created and the accuracy with which patient addresses can be resolved is described. Through georeferencing and unsupervised classification of the original image, the method precisely re-identified 26% (144/550) of the patient addresses from a presentation quality map and 79% (432/550) from a publication quality map. For the presentation quality map, 99.8% of the addresses were within 70 meters (approximately one city block length) of the predicted patient location, 51.6% of addresses were identified within five buildings, 70.7% within ten buildings and 93% within twenty buildings. For the publication quality map, all addresses were within 14 meters and 11 buildings of the predicted patient location. This study demonstrates that lowering the resolution of a map displaying geocoded patient addresses does not sufficiently protect patient addresses from re-identification. Guidelines to protect patient privacy, including those of medical journals, should reflect policies that ensure privacy protection when spatial data are displayed or published.

Porphyry copper deposit tract definition - A global analysis comparing geologic map scales

USGS Publications Warehouse

Raines, G.L.; Connors, K.A.; Chorlton, L.B.

2007-01-01

Geologic maps are a fundamental data source used to define mineral-resource potential tracts for the first step of a mineral resource assessment. Further, it is generally believed that the scale of the geologic map is a critical consideration. Previously published research has demonstrated that the U.S. Geological Survey porphyry tracts identified for the United States, which are based on 1:500,000-scale geology and larger scale data and published at 1:1,000,000 scale, can be approximated using a more generalized 1:2,500,000-scale geologic map. Comparison of the USGS porphyry tracts for the United States with weights-of-evidence models made using a 1:10,000,000-scale geologic map, which was made for petroleum applications, and a 1:35,000,000-scale geologic map, which was created as context for the distribution of porphyry deposits, demonstrates that, again, the USGS US porphyry tracts identified are similar to tracts defined on features from these small scale maps. In fact, the results using the 1:35,000,000-scale map show a slightly higher correlation with the USGS US tract definition, probably because the conceptual context for this small-scale map is more appropriate for porphyry tract definition than either of the other maps. This finding demonstrates that geologic maps are conceptual maps. The map information shown in each map is selected and generalized for the map to display the concepts deemed important for the map maker's purpose. Some geologic maps of small scale prove to be useful for regional mineral-resource tract definition, despite the decrease in spatial accuracy with decreasing scale. The utility of a particular geologic map for a particular application is critically dependent on the alignment of the intention of the map maker with the application. ?? International Association for Mathematical Geology 2007.

A compilation of K-Ar-ages for southern California

USGS Publications Warehouse

Miller, Fred K.; Morton, Douglas M.; Morton, Janet L.; Miller, David M.

2014-01-01

The purpose of this report is to make available a large body of conventional K-Ar ages for granitic, volcanic, and metamorphic rocks collected in southern California. Although one interpretive map is included, the report consists primarily of a systematic listing, without discussion or interpretation, of published and unpublished ages that may be of value in future regional and other geologic studies. From 1973 to 1979, 468 rock samples from southern California were collected for conventional K-Ar dating under a regional geologic mapping project of Southern California (predecessor of the Southern California Areal Mapping Project). Most samples were collected and dated between 1974 and 1977. For 61 samples (13 percent of those collected), either they were discarded for varying reasons, or the original collection data were lost. For the remaining samples, 518 conventional K-Ar ages are reported here; coexisting mineral pairs were dated from many samples. Of these K-Ar ages, 225 are previously unpublished, and identified as such in table 1. All K-Ar ages are by conventional K-Ar analysis; no 40Ar/39Ar dating was done. Subsequent to the rock samples collected in the 1970s and reported here, 33 samples were collected and 38 conventional K-Ar ages determined under projects directed at (1) characterization of the Mesozoic and Cenozoic igneous rocks in and on both sides of the Transverse Ranges and (2) clarifying the Mesozoic and Cenozoic tectonics of the eastern Mojave Desert. Although previously published (Beckerman et al., 1982), another eight samples and 11 conventional K-Ar ages are included here, because they augment those completed under the previous two projects.

Geologic map of the Reyes Peak quadrangle, Ventura County, California

USGS Publications Warehouse

Minor, Scott A.

2004-01-01

New 1:24,000-scale geologic mapping in the Cuyama 30' x 60' quadrangle, in support of the USGS Southern California Areal Mapping Project (SCAMP), is contributing to a more complete understanding of the stratigraphy, structure, and tectonic evolution of the complex junction area between the NW-trending Coast Ranges and EW-trending western Transverse Ranges. The 1:24,000-scale geologic map of the Reyes Peak quadrangle, located in the eastern part of the Cuyama map area, is the final of six contiguous 7 ?' quadrangle geologic maps compiled for a more detailed portrayal and reevaluation of geologic structures and rock units shown on previous maps of the region (Carman, 1964; Dibblee, 1972; Vedder and others, 1973). SCAMP digital geologic maps of the five other contiguous quadrangles have recently been published (Minor, 1999; Kellogg, 1999, 2003; Stone and Cossette, 2000; Kellogg and Miggins, 2002). This digital compilation presents a new geologic map database for the Reyes Peak 7?' quadrangle, which is located in southern California about 75 km northwest of Los Angeles. The map database is at 1:24,000-scale resolution.

Geologic map and map database of parts of Marin, San Francisco, Alameda, Contra Costa, and Sonoma counties, California

USGS Publications Warehouse

Blake, M.C.; Jones, D.L.; Graymer, R.W.; digital database by Soule, Adam

2000-01-01

This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (mageo.txt, mageo.pdf, or mageo.ps), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (mageo.txt, mageo.pdf, or mageo.ps), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller.

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

PubMed Central

Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun

2017-01-01

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding. PMID:28848588

ELEMENT MASSES IN THE CRAB NEBULA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sibley, Adam R.; Katz, Andrea M.; Satterfield, Timothy J.

Using our previously published element abundance or mass-fraction distributions in the Crab Nebula, we derived actual mass distributions and estimates for overall nebular masses of hydrogen, helium, carbon, nitrogen, oxygen and sulfur. As with the previous work, computations were carried out for photoionization models involving constant hydrogen density and also constant nuclear density. In addition, employing new flux measurements for [Ni ii]  λ 7378, along with combined photoionization models and analytic computations, a nickel abundance distribution was mapped and a nebular stable nickel mass estimate was derived.

Preliminary geologic map of the Oat Mountain 7.5' quadrangle, Southern California: a digital database

USGS Publications Warehouse

Yerkes, R.F.; Campbell, Russell H.

1995-01-01

This database, identified as "Preliminary Geologic Map of the Oat Mountain 7.5' Quadrangle, southern California: A Digital Database," has been approved for release and publication by the Director of the USGS. Although this database has been reviewed and is substantially complete, the USGS reserves the right to revise the data pursuant to further analysis and review. This database is released on condition that neither the USGS nor the U. S. Government may be held liable for any damages resulting from its use. This digital map database is compiled from previously published sources combined with some new mapping and modifications in nomenclature. The geologic map database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U. S. Geological Survey. For detailed descriptions of the units, their stratigraphic relations and sources of geologic mapping consult Yerkes and Campbell (1993). More specific information about the units may be available in the original sources.

Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.).

PubMed

Liu, Dexin; Liu, Fang; Shan, Xiaoru; Zhang, Jian; Tang, Shiyi; Fang, Xiaomei; Liu, Xueying; Wang, Wenwen; Tan, Zhaoyun; Teng, Zhonghua; Zhang, Zhengsheng; Liu, Dajun

2015-10-01

Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

A comparison of infrared, radar, and geologic mapping of lunar craters

USGS Publications Warehouse

Thompson, T.W.; Masursky, H.; Shorthill, R.W.; Tyler, G.L.; Zisk, S.H.

1974-01-01

Between 1000 and 2000 infrared (eclipse) and radar anomalies have been mapped on the nearside hemisphere of the Moon. A study of 52 of these anomalies indicates that most are related to impact craters and that the nature of the infrared and radar responses is compatible with a previously developed geologic model of crater aging processes. The youngest craters are pronounced thermal and radar anomalies; that is, they have enhanced eclipse temperatures and are strong radar scatterers. With increasing crater age, the associated thermal and radar responses become progressively less noticeable until they assume values for the average lunar surface. The last type of anomaly to disappear is radar enhancement at longer wavelengths. A few craters, however, have infrared and radar behaviors not predicted by the aging model. One previously unknown feature - a field strewn with centimeter-sized rock fragments - has been identified by this technique of comparing maps at the infrared, radar, and visual wavelengths. ?? 1974 D. Reidel Publishing Company, Dordrecht-Holland.

Preliminary Geologic Map of the Buxton 7.5' Quadrangle, Washington County, Oregon

USGS Publications Warehouse

Dinterman, Philip A.; Duvall, Alison R.

2009-01-01

This map, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits of the Buxton 7.5-minute quadrangle. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:24,000 or smaller. This plot file and accompanying database depict the distribution of geologic materials and structures at a regional (1:24,000) scale. The report is intended to provide geologic information for the regional study of materials properties, earthquake shaking, landslide potential, mineral hazards, seismic velocity, and earthquake faults. In addition, the report contains new information and interpretations about the regional geologic history and framework. However, the regional scale of this report does not provide sufficient detail for site development purposes.

Usability Assessment of the Missouri Cancer Registry's Published Interactive Mapping Reports: Round One.

PubMed

Ben Ramadan, Awatef Ahmed; Jackson-Thompson, Jeannette; Schmaltz, Chester Lee

2017-08-04

 Many users of spatial data have difficulty interpreting information in health-related spatial reports. The Missouri Cancer Registry and Research Center (MCR-ARC) has produced interactive reports for several years. These reports have never been tested for usability.  The aims of this study were to: (1) conduct a multi-approach usability testing study to understand ease of use (user friendliness) and user satisfaction; and (2) evaluate the usability of MCR-ARC's published InstantAtlas reports.   An institutional review board (IRB) approved mixed methodology usability testing study using a convenience sample of health professionals. A recruiting email was sent to faculty in the Master of Public Health program and to faculty and staff in the Department of Health Management and Informatics at the University of Missouri-Columbia. The study included 7 participants. The test included a pretest questionnaire, a multi-task usability test, and the System Usability Scale (SUS). Also, the researchers collected participants' comments about the tested maps immediately after every trial. Software was used to record the computer screen during the trial and the participants' spoken comments. Several performance and usability metrics were measured to evaluate the usability of MCR-ARC's published mapping reports. Of the 10 assigned tasks, 6 reached a 100% completion success rate, and this outcome was relative to the complexity of the tasks. The simple tasks were handled more efficiently than the complicated tasks. The SUS score ranged between 20-100 points, with an average of 62.7 points and a median of 50.5 points. The tested maps' effectiveness outcomes were better than the efficiency and satisfaction outcomes. There was a statistically significant relationship between the subjects' performance on the study test and the users' previous experience with geographic information system (GIS) tools (P=.03). There were no statistically significant relationships between users' performance and satisfaction and their education level, work type, or previous experience in health care (P>.05). There were strong positive correlations between the three measured usability elements. The tested maps should undergo an extensive refining and updating to overcome all the discovered usability issues and meet the perspectives and needs of the tested maps' potential users. The study results might convey the perspectives of academic health professionals toward GIS health data. We need to conduct a second-round usability study with public health practitioners and cancer professionals who use GIS tools on a routine basis. Usability testing should be conducted before and after releasing MCR-ARC's maps in the future. ©Awatef Ahmed Ben Ramadan, Jeannette Jackson-Thompson, Chester Lee Schmaltz. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 04.08.2017.

Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.

PubMed

Gardiner, Laura-Jayne; Bansept-Basler, Pauline; Olohan, Lisa; Joynson, Ryan; Brenchley, Rachel; Hall, Neil; O'Sullivan, Donal M; Hall, Anthony

2016-08-01

Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

PubMed Central

2010-01-01

Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species. PMID:20712870

Meltwater channel scars and the extent of Mid-Pleistocene glaciation in central Pennsylvania

NASA Astrophysics Data System (ADS)

Marsh, Ben

2017-10-01

High-resolution digital topographic data permit morphological analyses of glacial processes in detail that was previously infeasible. High-level glaciofluvial erosional scars in central Pennsylvania, identified and delimited using LiDAR data, define the approximate ice depth during a pre-Wisconsin advance, > 770,000 BP, on a landscape unaffected by Wisconsin glaciation. Distinctive scars on the prows of anticlinal ridges at 175-350 m above the valley floor locate the levels of subice meltwater channels. A two-component planar GIS model of the ice surface is derived using these features and intersected with a digital model of contemporary topography to create a glacial limit map. The map is compared to published maps, demonstrating the limits of conventional sediment-based mapping. Additional distinctive meltwater features that were cut during deglaciation are modeled in a similar fashion.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

PubMed

Newton, Yulia; Novak, Adam M; Swatloski, Teresa; McColl, Duncan C; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S; Baertsch, Robert; Salama, Sofie R; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C; Haussler, David; Morozova, Olena; Stuart, Joshua M

2017-11-01

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111-4. ©2017 AACR . ©2017 American Association for Cancer Research.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

PubMed Central

Newton, Yulia; Novak, Adam M.; Swatloski, Teresa; McColl, Duncan C.; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S.; Baertsch, Robert; Salama, Sofie R.; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C.; Haussler, David; Morozova, Olena; Stuart, Joshua M.

2017-01-01

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex “omics” data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google’s Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. PMID:29092953

Reconnaissance bedrock geology of the southeastern part of the Kenai quadrangle, Alaska: A section in Geologic studies in Alaska by the U.S. Geological Survey, 1998

USGS Publications Warehouse

Bradley, Dwight C.; Wilson, Frederic H.

2000-01-01

We present a new reconnaissance geologic map of the southeastern part of the Kenai quadrangle that improves on previously published maps. Melange of the McHugh Complex is now known to form a continuous strike belt that can be traced from the Seldovia to the Valdez quadrangle; a problematic 75-km-long gap in the McHugh Complex in the Kenai and Seldovia quadrangles does not exist. An Eocene near-trench pluton underlies a range of nunataks in Harding Icefield.

Review and critical appraisal of studies mapping from quality of life or clinical measures to EQ-5D: an online database and application of the MAPS statement.

PubMed

Dakin, Helen; Abel, Lucy; Burns, Richéal; Yang, Yaling

2018-02-12

The Health Economics Research Centre (HERC) Database of Mapping Studies was established in 2013, based on a systematic review of studies developing mapping algorithms predicting EQ-5D. The Mapping onto Preference-based measures reporting Standards (MAPS) statement was published in 2015 to improve reporting of mapping studies. We aimed to update the systematic review and assess the extent to which recently-published studies mapping condition-specific quality of life or clinical measures to the EQ-5D follow the guidelines published in the MAPS Reporting Statement. A published systematic review was updated using the original inclusion criteria to include studies published by December 2016. We included studies reporting novel algorithms mapping from any clinical measure or patient-reported quality of life measure to either the EQ-5D-3L or EQ-5D-5L. Titles and abstracts of all identified studies and the full text of papers published in 2016 were assessed against the MAPS checklist. The systematic review identified 144 mapping studies reporting 190 algorithms mapping from 110 different source instruments to EQ-5D. Of the 17 studies published in 2016, nine (53%) had titles that followed the MAPS statement guidance, although only two (12%) had abstracts that fully addressed all MAPS items. When the full text of these papers was assessed against the complete MAPS checklist, only two studies (12%) were found to fulfil or partly fulfil all criteria. Of the 141 papers (across all years) that included abstracts, the items on the MAPS statement checklist that were fulfilled by the largest number of studies comprised having a structured abstract (95%) and describing target instruments (91%) and source instruments (88%). The number of published mapping studies continues to increase. Our updated database provides a convenient way to identify mapping studies for use in cost-utility analysis. Most recent studies do not fully address all items on the MAPS checklist.

USGS compilation of geographic information system (GIS) data representing coal mines and coal-bearing areas in China

USGS Publications Warehouse

Trippi, Michael H.; Belkin, Harvey E.; Dai, Shifeng; Tewalt, Susan J.; Chou, Chiu-Jung; Trippi, Michael H.; Belkin, Harvey E.; Dai, Shifeng; Tewalt, Susan J.; Chou, Chiu-Jung

2015-01-01

Geographic information system (GIS) information may facilitate energy studies, which in turn provide input for energy policy decisions. The U.S. Geological Survey (USGS) has compiled geographic information system (GIS) data representing the known coal mine locations and coal-mining areas of China as of 2001. These data are now available for download, and may be used in a GIS for a variety of energy resource and environmental studies of China. Province-scale maps were also created to display the point locations of coal mines and the coal-mining areas. In addition, coal-field outlines from a previously published map by Dai and others (2012) were also digitized and are available for download as a separate GIS data file, and shown in a nation-scale map of China. Chemical data for 332 coal samples from a previous USGS study of China and Taiwan (Tewalt and others, 2010) are included in a downloadable GIS point shapefile, and shown on a nation-scale map of China. A brief report summarizes the methodology used for creation of the shapefiles and the chemical analyses run on the samples.

Atlas of relations between climatic parameters and distributions of important trees and shrubs in North America: Revisions for all taxa from the United States and Canada and new taxa from the western United States

USGS Publications Warehouse

Thompson, Robert S.; Anderson, Katherine H.; Pelltier, Richard T.; Strickland, Laura E.; Shafer, Sarah L.; Bartlein, Patrick J.; McFadden, Andrew K.

2015-01-01

This volume of the atlas provides numerous changes, updates, and enhancements from previous volumes. Its geographic coverage is now restricted to Canada and the continental United States, and the source and time period of the climatic data have changed. New variables were added, including monthly values for temperature and precipitation, and measures of interannual variability. The distribution maps for all previously published species were redigitized, some distribution maps were revised, and 148 new species were added from the arid and semiarid western United States. The graphical displays were expanded to illustrate the new climatic variables, and the data tables were modified to provide more detail on the population distributions of plant taxa relative to climatic variables.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.

PubMed

Edger, Patrick P; VanBuren, Robert; Colle, Marivi; Poorten, Thomas J; Wai, Ching Man; Niederhuth, Chad E; Alger, Elizabeth I; Ou, Shujun; Acharya, Charlotte B; Wang, Jie; Callow, Pete; McKain, Michael R; Shi, Jinghua; Collier, Chad; Xiong, Zhiyong; Mower, Jeffrey P; Slovin, Janet P; Hytönen, Timo; Jiang, Ning; Childs, Kevin L; Knapp, Steven J

2018-02-01

Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions. © The Authors 2017. Published by Oxford University Press.

New Mapping in the Sand Springs Range of Western Nevada Clarifies and Constrains Regional Deformation Sequences of the Luning-Fencemaker Thrust Belt

NASA Astrophysics Data System (ADS)

Czarnecki, S.; Jarvis, J.; Satterfield, J. I.

2016-12-01

The Sand Springs Range in western Nevada exposes Mesozoic through Cenozoic structures of the eastern Sierra Nevada, Luning-Fencemaker Thrust Belt (LFTB), Basin and Range province, and Walker Lane. A recent undergraduate geologic mapping project in the northern Sand Springs Range (nSSR) set out to map igneous intrusions in detail, specifically smaller intrusions which had not been a focus in previous work. This was accomplished using different techniques including mapping at a smaller scale (1:8000 vs. 1:24000), locating contacts and faults using handheld GPS, and focusing on relationships between metamorphic tectonites and igneous units. This revealed key cross-cutting relations between structures and diverse Triassic through Tertiary igneous rocks as well as distinctions between the nSSR and the surrounding LFTB assemblages. During our mapping we identified four metamorphic tectonite map units, Cretaceous granitoid and diorite plutons and sills, Tertiary rhyolite sills and dikes, and interbedded Tertiary basalt and ash flow tuff. The cross-cutting relations of these units overturn previously published sequences of events and constrain the timing of a deformation sequence which differs from the surrounding LFTB assemblages. We found that the nSSR contains three phases of deformation: a pre-LFTB syn-metamorphic event which achieved amphibolite facies that is not described elsewhere in the LFTB (D1), followed by two non-metamorphic folding and thrusting phases characteristic of the LFTB (D2 and D3). Our mapping provided four key timing constraints. First, D1 axial-planar cleavage (S1) deformed Triassic intrusions. Second, Cretaceous granitoid and diorite units cross-cut S1 foliation, D1 folds, and low-angle faults. Third, Cretaceous and Tertiary sills that locally terminate at a low-angle fault actually post-dated faulting. Fourth, cross-cutting relations showed a basaltic lava previously mapped as Jurassic is actually Tertiary. The large Sand Springs Pluton was the only intrusion mapped in detail during previous studies; but our mapping has demonstrated the importance of both small and large intrusions in understanding the overall structural history of a complex area. This project was supported by research grants from Angelo State University and the Southwest Section AAPG.

The MAPS Reporting Statement for Studies Mapping onto Generic Preference-Based Outcome Measures: Explanation and Elaboration.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-10-01

The process of "mapping" is increasingly being used to predict health utilities, for application within health economic evaluations, using data on other indicators or measures of health. Guidance for the reporting of mapping studies is currently lacking. The overall objective of this research was to develop a checklist of essential items, which authors should consider when reporting mapping studies. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a checklist, which aims to promote complete and transparent reporting by researchers. This paper provides a detailed explanation and elaboration of the items contained within the MAPS statement. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items and accompanying explanations was created. A two-round, modified Delphi survey, with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorised within six sections, namely, (i) title and abstract, (ii) introduction, (iii) methods, (iv) results, (v) discussion and (vi) other. For each item, we summarise the recommendation, illustrate it using an exemplar of good reporting practice identified from the published literature, and provide a detailed explanation to accompany the recommendation. It is anticipated that the MAPS statement will promote clarity, transparency and completeness of reporting of mapping studies. It is targeted at researchers developing mapping algorithms, peer reviewers and editors involved in the manuscript review process for mapping studies, and the funders of the research. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

Floods on Roseberry Creek, Wacker Branch, and three unnamed tributaries to Roseberry Creek in the vicinity of Scottsboro, Alabama. Flood report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1982-10-01

The study was requested by the city to provide information reflecting current flood conditions in order for the community to better administer its floodplain management program and to qualify for participation in the regular phase of the National Flood Insurance Program (NFIP). This report updates and expands the coverage of a previous TVA report published in April 1967. Profiles and flooded area and floodway maps are provided for Roseberry Creek, Wacker Branch, and three previously unstudied tributaries to Roseberry Creek.

Global geologic map of Ganymede

USGS Publications Warehouse

Collins, Geoffrey C.; Patterson, G. Wesley; Head, James W.; Pappalardo, Robert T.; Prockter, Louise M.; Lucchitta, Baerbel K.; Kay, Johnathan P.

2014-01-01

Ganymede is the largest satellite of Jupiter, and its icy surface has been formed through a variety of impact cratering, tectonic, and possibly cryovolcanic processes. The history of Ganymede can be divided into three distinct phases: an early phase dominated by impact cratering and mixing of non-ice materials in the icy crust, a phase in the middle of its history marked by great tectonic upheaval, and a late quiescent phase characterized by a gradual drop in heat flow and further impact cratering. Images of Ganymede suitable for geologic mapping were collected during the flybys of Voyager 1 and Voyager 2 (1979), as well as during the Galileo Mission in orbit around Jupiter (1995–2003). This map represents a synthesis of our understanding of Ganymede geology after the conclusion of the Galileo Mission. We summarize the properties of the imaging dataset used to construct the map, previously published maps of Ganymede, our own mapping rationale, and the geologic history of Ganymede. Additional details on these topics, along with detailed descriptions of the type localities for the material units, may be found in the companion paper to this map (Patterson and others, 2010).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willard, H.F.; Cremers, F.; Mandel, J.L.

A high-quality integrated genetic and physical map of the X chromosome from telomere to telomere, based primarily on YACs formatted with probes and STSs, is increasingly close to reality. At the Fifth International X Chromosome Workshop, organized by A.M. Poustka and D. Schlessinger in Heidelberg, Germany, April 24--27, 1994, substantial progress was recorded on extension and refinement of the physical map, on the integration of genetic and cytogenetic data, on attempts to use the map to direct gene searches, and on nascent large-scale sequencing efforts. This report summarizes physical and genetic mapping information presented at the workshop and/or published sincemore » the reports of the fourth International X Chromosome Workshop. The principle aim of the workshop was to derive a consensus map of the chromosome, in terms of physical contigs emphasizing the location of genes and microsatellite markers. The resulting map is presented and updates previous versions. This report also updates the list of highly informative microsatellites. The text highlights the working state of the map, the genes known to reside on the X, and the progress toward integration of various types of data.« less

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

PubMed Central

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

PubMed

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

Status and distribution of mangrove forests of the world using earth observation satellite data

USGS Publications Warehouse

Giri, C.; Ochieng, E.; Tieszen, L.L.; Zhu, Z.; Singh, A.; Loveland, T.; Masek, J.; Duke, N.

2011-01-01

Aim Our scientific understanding of the extent and distribution of mangrove forests of the world is inadequate. The available global mangrove databases, compiled using disparate geospatial data sources and national statistics, need to be improved. Here, we mapped the status and distributions of global mangroves using recently available Global Land Survey (GLS) data and the Landsat archive.Methods We interpreted approximately 1000 Landsat scenes using hybrid supervised and unsupervised digital image classification techniques. Each image was normalized for variation in solar angle and earth-sun distance by converting the digital number values to the top-of-the-atmosphere reflectance. Ground truth data and existing maps and databases were used to select training samples and also for iterative labelling. Results were validated using existing GIS data and the published literature to map 'true mangroves'.Results The total area of mangroves in the year 2000 was 137,760 km2 in 118 countries and territories in the tropical and subtropical regions of the world. Approximately 75% of world's mangroves are found in just 15 countries, and only 6.9% are protected under the existing protected areas network (IUCN I-IV). Our study confirms earlier findings that the biogeographic distribution of mangroves is generally confined to the tropical and subtropical regions and the largest percentage of mangroves is found between 5?? N and 5?? S latitude.Main conclusions We report that the remaining area of mangrove forest in the world is less than previously thought. Our estimate is 12.3% smaller than the most recent estimate by the Food and Agriculture Organization (FAO) of the United Nations. We present the most comprehensive, globally consistent and highest resolution (30 m) global mangrove database ever created. We developed and used better mapping techniques and data sources and mapped mangroves with better spatial and thematic details than previous studies. ?? 2010 Blackwell Publishing Ltd.

Arctic lead detection using a waveform mixture algorithm from CryoSat-2 data

NASA Astrophysics Data System (ADS)

Lee, Sanggyun; Kim, Hyun-cheol; Im, Jungho

2018-05-01

We propose a waveform mixture algorithm to detect leads from CryoSat-2 data, which is novel and different from the existing threshold-based lead detection methods. The waveform mixture algorithm adopts the concept of spectral mixture analysis, which is widely used in the field of hyperspectral image analysis. This lead detection method was evaluated with high-resolution (250 m) MODIS images and showed comparable and promising performance in detecting leads when compared to the previous methods. The robustness of the proposed approach also lies in the fact that it does not require the rescaling of parameters (i.e., stack standard deviation, stack skewness, stack kurtosis, pulse peakiness, and backscatter σ0), as it directly uses L1B waveform data, unlike the existing threshold-based methods. Monthly lead fraction maps were produced by the waveform mixture algorithm, which shows interannual variability of recent sea ice cover during 2011-2016, excluding the summer season (i.e., June to September). We also compared the lead fraction maps to other lead fraction maps generated from previously published data sets, resulting in similar spatiotemporal patterns.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Deutsch, Joseph; Salazar, Walter; Hernandez-Ochoa, Miguel; Grygleski, Edward; Steffan, Shawn; Iorizzo, Massimo; Polashock, James; Vorsa, Nicholi; Zalapa, Juan

2016-06-13

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).

Data-driven cluster reinforcement and visualization in sparsely-matched self-organizing maps.

PubMed

Manukyan, Narine; Eppstein, Margaret J; Rizzo, Donna M

2012-05-01

A self-organizing map (SOM) is a self-organized projection of high-dimensional data onto a typically 2-dimensional (2-D) feature map, wherein vector similarity is implicitly translated into topological closeness in the 2-D projection. However, when there are more neurons than input patterns, it can be challenging to interpret the results, due to diffuse cluster boundaries and limitations of current methods for displaying interneuron distances. In this brief, we introduce a new cluster reinforcement (CR) phase for sparsely-matched SOMs. The CR phase amplifies within-cluster similarity in an unsupervised, data-driven manner. Discontinuities in the resulting map correspond to between-cluster distances and are stored in a boundary (B) matrix. We describe a new hierarchical visualization of cluster boundaries displayed directly on feature maps, which requires no further clustering beyond what was implicitly accomplished during self-organization in SOM training. We use a synthetic benchmark problem and previously published microbial community profile data to demonstrate the benefits of the proposed methods.

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.

PubMed

Kruger, Felix A; Gaulton, Anna; Nowotka, Michal; Overington, John P

2015-03-01

PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mapping heuristic for a subset of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule binding. We have since refined this mapping using a manual procedure. Here, we present a resource that provides up-to-date mappings and the possibility to review assigned mappings as well as to participate in their assignment and curation. We also describe how mappings provided through the PPDMs resource are made accessible through the main schema of the ChEMBL database. The PPDMs resource and curation interface is available at https://www.ebi.ac.uk/chembl/research/ppdms/pfam_maps. The source-code for PPDMs is available under the Apache license at https://github.com/chembl/pfam_maps. Source code is available at https://github.com/chembl/pfam_map_loader to demonstrate the integration process with the main schema of ChEMBL. © The Author 2014. Published by Oxford University Press.

Application of Oxidation to the Structural Characterization of Sic Epitaxial Films

NASA Technical Reports Server (NTRS)

Powell, J. A.; Petit, J. B.; Edgar, J. H.; Jenkins, I. G.; Matus, L. G.

1991-01-01

Both 3C-SiC and 6H-SiC single-crystal films can be grown on vicinal (0001) 6H-SiC wafers. It is found that oxidation can be a powerful diagnostic process for (1) 'color mapping' the 3C and 6H regions of these films, (2) decorating stacking faults in the films, (3) enhancing the decoration of double positioning boundaries, and (4) decorating polishing damage. Contrary to previously published oxidation results, proper oxidation conditions can yield interference colors that provide a definitive map of the polytype distribution for both the Si face and C face of SiC films.

Sample locality map and analytical data for potassium-argon ages in the Port Moller, Stepovak Bay, and Simeonof Island quadrangles, Alaska Peninsula

USGS Publications Warehouse

Wilson, Frederic H.; Shew, Nora B.; DuBois, Gregory D.; Bie, Scott W.

1994-01-01

Potassium-argon age determinations for 84 volcanic, intrusive, and hydrothermally altered rocks from the Port Moller, Stepovak Bay, and Simeonof Island quadrangles are reported here. Of these age determinations, 78 samples were analyzed as part of Alaska Mineral Resource Assessment Program (AMRAP) studies in the Port Moller, Stepovak Bay, and Simeonof Island quadrangles. Age deter- minations for 6 of the samples have been previously published (Burk, 1965; Kienle and Turner, 1976; Wilson and others, 1981). This report consists of a sample location map, analytical data (table 1), and rock descriptions (table 2).

Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations.

PubMed

Feltus, F A; Hart, G E; Schertz, K F; Casa, A M; Kresovich, S; Abraham, S; Klein, P E; Brown, P J; Paterson, A H

2006-05-01

To increase the value of associated molecular tools and also to begin to explore the degree to which interspecific and intraspecific genetic variation in Sorghum is attributable to corresponding genetic loci, we have aligned genetic maps derived from two sorghum populations that share one common parent (Sorghum bicolor L. Moench accession BTx623) but differ in morphological and evolutionarily distant alternate parents (S. propinquum or S. bicolor accession IS3620C). A total of 106 well-distributed DNA markers provide for map alignment, revealing only six nominal differences in marker order that are readily explained by sampling variation or mapping of paralogous loci. We also report a total of 61 new QTLs detected from 17 traits in these crosses. Among eight corresponding traits (some new, some previously published) that could be directly compared between the two maps, QTLs for two (tiller height and tiller number) were found to correspond in a non-random manner (P<0.05). For several other traits, correspondence of subsets of QTLs narrowly missed statistical significance. In particular, several QTLs for leaf senescence were near loci previously mapped for 'stay-green' that have been implicated by others in drought tolerance. These data provide strong validation for the value of molecular tools developed in the interspecific cross for utilization in cultivated sorghum, and begin to separate QTLs that distinguish among Sorghum species from those that are informative within the cultigen (S. bicolor).

Method and system for a network mapping service

DOEpatents

Bynum, Leo

2017-10-17

A method and system of publishing a map includes providing access to a plurality of map data files or mapping services between at least one publisher and at least one subscriber; defining a map in a map context comprising parameters and descriptors to substantially duplicate a map by reference to mutually accessible data or mapping services, publishing a map to a channel in a table file on server; accessing the channel by at least one subscriber, transmitting the mapping context from the server to the at least one subscriber, executing the map context by the at least one subscriber, and generating the map on a display software associated with the at least one subscriber by reconstituting the map from the references and other data in the mapping context.

Description and validation of an automated methodology for mapping mineralogy, vegetation, and hydrothermal alteration type from ASTER satellite imagery with examples from the San Juan Mountains, Colorado

USGS Publications Warehouse

Rockwell, Barnaby W.

2012-01-01

The efficacy of airborne spectroscopic, or "hyperspectral," remote sensing for geoenvironmental watershed evaluations and deposit-scale mapping of exposed mineral deposits has been demonstrated. However, the acquisition, processing, and analysis of such airborne data at regional and national scales can be time and cost prohibitive. The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) sensor carried by the NASA Earth Observing System Terra satellite was designed for mineral mapping and the acquired data can be efficiently used to generate uniform mineral maps over very large areas. Multispectral remote sensing data acquired by the ASTER sensor were analyzed to identify and map minerals, mineral groups, hydrothermal alteration types, and vegetation groups in the western San Juan Mountains, Colorado, including the Silverton and Lake City calderas. This mapping was performed in support of multidisciplinary studies involving the predictive modeling of surface water geochemistry at watershed and regional scales. Detailed maps of minerals, vegetation groups, and water were produced from an ASTER scene using spectroscopic, expert system-based analysis techniques which have been previously described. New methodologies are presented for the modeling of hydrothermal alteration type based on the Boolean combination of the detailed mineral maps, and for the entirely automated mapping of alteration types, mineral groups, and green vegetation. Results of these methodologies are compared with the more detailed maps and with previously published mineral mapping results derived from analysis of high-resolution spectroscopic data acquired by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) sensor. Such comparisons are also presented for other mineralized and (or) altered areas including the Goldfield and Cuprite mining districts, Nevada and the central Marysvale volcanic field, Wah Wah Mountains, and San Francisco Mountains, Utah. The automated mineral group mapping products described in this study are ideal for application to mineral resource and mineral-environmental assessments at regional and national scales.

BatSLAM: Simultaneous localization and mapping using biomimetic sonar.

PubMed

Steckel, Jan; Peremans, Herbert

2013-01-01

We propose to combine a biomimetic navigation model which solves a simultaneous localization and mapping task with a biomimetic sonar mounted on a mobile robot to address two related questions. First, can robotic sonar sensing lead to intelligent interactions with complex environments? Second, can we model sonar based spatial orientation and the construction of spatial maps by bats? To address these questions we adapt the mapping module of RatSLAM, a previously published navigation system based on computational models of the rodent hippocampus. We analyze the performance of the proposed robotic implementation operating in the real world. We conclude that the biomimetic navigation model operating on the information from the biomimetic sonar allows an autonomous agent to map unmodified (office) environments efficiently and consistently. Furthermore, these results also show that successful navigation does not require the readings of the biomimetic sonar to be interpreted in terms of individual objects/landmarks in the environment. We argue that the system has applications in robotics as well as in the field of biology as a simple, first order, model for sonar based spatial orientation and map building.

BatSLAM: Simultaneous Localization and Mapping Using Biomimetic Sonar

PubMed Central

Steckel, Jan; Peremans, Herbert

2013-01-01

We propose to combine a biomimetic navigation model which solves a simultaneous localization and mapping task with a biomimetic sonar mounted on a mobile robot to address two related questions. First, can robotic sonar sensing lead to intelligent interactions with complex environments? Second, can we model sonar based spatial orientation and the construction of spatial maps by bats? To address these questions we adapt the mapping module of RatSLAM, a previously published navigation system based on computational models of the rodent hippocampus. We analyze the performance of the proposed robotic implementation operating in the real world. We conclude that the biomimetic navigation model operating on the information from the biomimetic sonar allows an autonomous agent to map unmodified (office) environments efficiently and consistently. Furthermore, these results also show that successful navigation does not require the readings of the biomimetic sonar to be interpreted in terms of individual objects/landmarks in the environment. We argue that the system has applications in robotics as well as in the field of biology as a simple, first order, model for sonar based spatial orientation and map building. PMID:23365647

Geologic map of the Basque-Cantabrian Basin and a new tectonic interpretation of the Basque Arc

NASA Astrophysics Data System (ADS)

Ábalos, B.

2016-11-01

A new printable 1/200.000 bedrock geological map of the onshore Basque-Cantabrian Basin is presented, aimed to contribute to future geologic developments in the central segment of the Pyrenean-Cantabrian Alpine orogenic system. It is accompanied in separate appendixes by a historic report on the precedent geological maps and by a compilation above 350 bibliographic citations of maps and academic reports (usually overlooked or ignored) that are central to this contribution. Structural scrutiny of the map permits to propose a new tectonic interpretation of the Basque Arc, implementing previously published partial reconstructions. It is presented as a printable 1/400.000 tectonic map. The Basque Arc consists of various thrust slices that can expose at the surface basement rocks (Palaeozoic to Lower Triassic) and their sedimentary cover (uppermost Triassic to Tertiary), from which they are detached by intervening (Upper Triassic) evaporites and associated rocks. The slice-bounding thrusts are in most cases reactivated normal faults active during Meso-Cenozoic sedimentation that can be readily related to basement discontinuities generated during the Hercynian orogeny.

Using hydrogeologic data to evaluate geothermal potential in the eastern Great Basin

USGS Publications Warehouse

Masbruch, Melissa D.; Heilweil, Victor M.; Brooks, Lynette E.

2012-01-01

In support of a larger study to evaluate geothermal resource development of high-permeability stratigraphic units in sedimentary basins, this paper integrates groundwater and thermal data to evaluate heat and fluid flow within the eastern Great Basin. Previously published information from a hydrogeologic framework, a potentiometric-surface map, and groundwater budgets was compared to a surficial heat-flow map. Comparisons between regional groundwater flow patterns and surficial heat flow indicate a strong spatial relation between regional groundwater movement and surficial heat distribution. Combining aquifer geometry and heat-flow maps, a selected group of subareas within the eastern Great Basin are identified that have high surficial heat flow and are underlain by a sequence of thick basin-fill deposits and permeable carbonate aquifers. These regions may have potential for future geothermal resources development.

Testing mapping algorithms of the cancer-specific EORTC QLQ-C30 onto EQ-5D in malignant mesothelioma.

PubMed

Arnold, David T; Rowen, Donna; Versteegh, Matthijs M; Morley, Anna; Hooper, Clare E; Maskell, Nicholas A

2015-01-23

In order to estimate utilities for cancer studies where the EQ-5D was not used, the EORTC QLQ-C30 can be used to estimate EQ-5D using existing mapping algorithms. Several mapping algorithms exist for this transformation, however, algorithms tend to lose accuracy in patients in poor health states. The aim of this study was to test all existing mapping algorithms of QLQ-C30 onto EQ-5D, in a dataset of patients with malignant pleural mesothelioma, an invariably fatal malignancy where no previous mapping estimation has been published. Health related quality of life (HRQoL) data where both the EQ-5D and QLQ-C30 were used simultaneously was obtained from the UK-based prospective observational SWAMP (South West Area Mesothelioma and Pemetrexed) trial. In the original trial 73 patients with pleural mesothelioma were offered palliative chemotherapy and their HRQoL was assessed across five time points. This data was used to test the nine available mapping algorithms found in the literature, comparing predicted against observed EQ-5D values. The ability of algorithms to predict the mean, minimise error and detect clinically significant differences was assessed. The dataset had a total of 250 observations across 5 timepoints. The linear regression mapping algorithms tested generally performed poorly, over-estimating the predicted compared to observed EQ-5D values, especially when observed EQ-5D was below 0.5. The best performing algorithm used a response mapping method and predicted the mean EQ-5D with accuracy with an average root mean squared error of 0.17 (Standard Deviation; 0.22). This algorithm reliably discriminated between clinically distinct subgroups seen in the primary dataset. This study tested mapping algorithms in a population with poor health states, where they have been previously shown to perform poorly. Further research into EQ-5D estimation should be directed at response mapping methods given its superior performance in this study.

Map and digital database of sedimentary basins and indications of petroleum in the Central Alaska Province

USGS Publications Warehouse

Troutman, Sandra M.; Stanley, Richard G.

2003-01-01

This database and accompanying text depict historical and modern reported occurrences of petroleum both in wells and at the surface within the boundaries of the Central Alaska Province. These data were compiled from previously published and unpublished sources and were prepared for use in the 2002 U.S. Geological Survey petroleum assessment of Central Alaska, Yukon Flats region. Indications of petroleum are described as oil or gas shows in wells, oil or gas seeps, or outcrops of oil shale or oil-bearing rock and include confirmed and unconfirmed reports. The scale of the source map limits the spatial resolution (scale) of the database to 1:2,500,000 or smaller.

Vegetation, plant biomass, and net primary productivity patterns in the Canadian Arctic

NASA Astrophysics Data System (ADS)

Gould, W. A.; Raynolds, M.; Walker, D. A.

2003-01-01

We have developed maps of dominant vegetation types, plant functional types, percent vegetation cover, aboveground plant biomass, and above and belowground annual net primary productivity for Canada north of the northern limit of trees. The area mapped covers 2.5 million km2 including glaciers. Ice-free land covers 2.3 million km2 and represents 42% of all ice-free land in the Circumpolar Arctic. The maps combine information on climate, soils, geology, hydrology, remotely sensed vegetation classifications, previous vegetation studies, and regional expertise to define polygons drawn using photo-interpretation of a 1:4,000,000 scale advanced very high resolution radiometer (AVHRR) color infrared image basemap. Polygons are linked to vegetation description, associated properties, and descriptive literature through a series of lookup tables in a graphic information systems (GIS) database developed as a component of the Circumpolar Arctic Vegetation Map (CAVM) project. Polygons are classified into 20 landcover types including 17 vegetation types. Half of the region is sparsely vegetated (<50% vegetation cover), primarily in the High Arctic (bioclimatic subzones A-C). Whereas most (86%) of the estimated aboveground plant biomass (1.5 × 1015 g) and 87% of the estimated above and belowground annual net primary productivity (2.28 × 1014 g yr-1) are concentrated in the Low Arctic (subzones D and E). The maps present more explicit spatial patterns of vegetation and ecosystem attributes than have been previously available, the GIS database is useful in summarizing ecosystem properties and can be easily updated and integrated into circumpolar mapping efforts, and the derived estimates fall within the range of current published estimates.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Spatial analysis of plutonium-239 + 240 and Americium-241 in soils around Rocky Flats, Colorado

DOE Office of Scientific and Technical Information (OSTI.GOV)

Litaor, M.I.

1995-05-01

Plutonium and american contamination of soils around Rocky Flats, Colorado resulted from past outdoor storage practices. Four previous studies produce four different Pu isopleth maps. Spatial estimation techniques were not used in the construction of these maps and were also based on an extremely small number of soil samples. The purpose of this study was to elucidate the magnitude of Pu-239 + 240 and Am-241 dispersion in the soil environment east of Rocky Flats using robust spatial estimation techniques. Soils were sampled from 118 plots of 1.01 and 4.05 ha by compositing 25 evenly spaced samples in each plot frommore » the top 0.64 cm. Plutonium-239 + 240 activity ranged from 1.85 to 53 560 Bq/kg with a mean of 1924 Bq/kg and a standard deviation of 6327 Bq/kg. Americium-241 activity ranged from 0.18 to 9990 Bq/kg with a mean of 321 Bq/kg and a standard deviation of 1143 Bq/kg. Geostatistical techniques were used to model the spatial dependency and construct isopleth maps showing Pu-239 + 240 and Am-241 distribution. The isopleth configuration was consistent with the hypothesis that the dominant dispersal mechanism of Pu-239 + 240 was wind dispersion from west to east. The Pu-239 + 240 isopleth map proposed to this study differed significantly in the direction and distance of dispersal from the previously published maps. This ispleth map as well as the Am-241 map should be used as the primary data for future risk assessment associated with public exposure to Pu-239 + 240 and Am-241. 37 refs., 7 figs., 2 tabs.« less

Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Ying; Wecksler, Aaron T.; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

2017-05-01

We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

Mapping Physiological Suitability Limits for Malaria in Africa Under Climate Change.

PubMed

Ryan, Sadie J; McNally, Amy; Johnson, Leah R; Mordecai, Erin A; Ben-Horin, Tal; Paaijmans, Krijn; Lafferty, Kevin D

2015-12-01

We mapped current and future temperature suitability for malaria transmission in Africa using a published model that incorporates nonlinear physiological responses to temperature of the mosquito vector Anopheles gambiae and the malaria parasite Plasmodium falciparum. We found that a larger area of Africa currently experiences the ideal temperature for transmission than previously supposed. Under future climate projections, we predicted a modest increase in the overall area suitable for malaria transmission, but a net decrease in the most suitable area. Combined with human population density projections, our maps suggest that areas with temperatures suitable for year-round, highest-risk transmission will shift from coastal West Africa to the Albertine Rift between the Democratic Republic of Congo and Uganda, whereas areas with seasonal transmission suitability will shift toward sub-Saharan coastal areas. Mapping temperature suitability places important bounds on malaria transmissibility and, along with local level demographic, socioeconomic, and ecological factors, can indicate where resources may be best spent on malaria control.

Maps of the Southern Millimeter-wave Sky from Combined 2500 deg$^2$ SPT-SZ and Planck Temperature Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chown, R.; et al.

We present three maps of the millimeter-wave sky created by combining data from the South Pole Telescope (SPT) and the Planck satellite. We use data from the SPT-SZ survey, a survey of 2540 deg$^2$ of the the sky with arcminute resolution in three bands centered at 95, 150, and 220 GHz, and the full-mission Planck temperature data in the 100, 143, and 217 GHz bands. A linear combination of the SPT-SZ and Planck data is computed in spherical harmonic space, with weights derived from the noise of both instruments. This weighting scheme results in Planck data providing most of themore » large-angular-scale information in the combined maps, with the smaller-scale information coming from SPT-SZ data. A number of tests have been done on the maps. We find their angular power spectra to agree very well with theoretically predicted spectra and previously published results.« less

Using an ultrasound elasticity microscope to map three-dimensional strain in a porcine cornea.

PubMed

Hollman, Kyle W; Shtein, Roni M; Tripathy, Sakya; Kim, Kang

2013-08-01

An ultrasound elasticity microscope was used to map 3-D strain volume in an ex vivo porcine cornea to illustrate its ability to measure the mechanical properties of this tissue. Mechanical properties of the cornea play an important role in its function and, therefore, also in ophthalmic diseases such as kerataconus and corneal ectasia. The ultrasound elasticity microscope combines a tightly focused high-frequency transducer with confocal scanning to produce high-quality speckle over the entire volume of tissue. This system and the analysis were able to generate volume maps of compressional strain in all three directions for porcine corneal tissue, more information than any previous study has reported. Strain volume maps indicated features of the cornea and mechanical behavior as expected. These results constitute a step toward better understanding of corneal mechanics and better treatment of corneal diseases. Copyright © 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Mapping physiological suitability limits for malaria in Africa under climate change

USGS Publications Warehouse

Ryan, Sadie J.; McNally, Amy; Johnson, Leah R.; Mordecai, Erin A.; Ben-Horin, Tal; Paaijmans, Krijn P.; Lafferty, Kevin D.

2015-01-01

We mapped current and future temperature suitability for malaria transmission in Africa using a published model that incorporates nonlinear physiological responses to temperature of the mosquito vector Anopheles gambiae and the malaria parasite Plasmodium falciparum. We found that a larger area of Africa currently experiences the ideal temperature for transmission than previously supposed. Under future climate projections, we predicted a modest increase in the overall area suitable for malaria transmission, but a net decrease in the most suitable area. Combined with human population density projections, our maps suggest that areas with temperatures suitable for year-round, highest-risk transmission will shift from coastal West Africa to the Albertine Rift between the Democratic Republic of Congo and Uganda, whereas areas with seasonal transmission suitability will shift toward sub-Saharan coastal areas. Mapping temperature suitability places important bounds on malaria transmissibility and, along with local level demographic, socioeconomic, and ecological factors, can indicate where resources may be best spent on malaria control.

Mapping regional livelihood benefits from local ecosystem services assessments in rural Sahel

PubMed Central

Sinare, Hanna; Enfors Kautsky, Elin; Ouedraogo, Issa; Gordon, Line J.

2018-01-01

Most current approaches to landscape scale ecosystem service assessments rely on detailed secondary data. This type of data is seldom available in regions with high levels of poverty and strong local dependence on provisioning ecosystem services for livelihoods. We develop a method to extrapolate results from a previously published village scale ecosystem services assessment to a higher administrative level, relevant for land use decision making. The method combines remote sensing (using a hybrid classification method) and interviews with community members. The resulting landscape scale maps show the spatial distribution of five different livelihood benefits (nutritional diversity, income, insurance/saving, material assets and energy, and crops for consumption) that illustrate the strong multifunctionality of the Sahelian landscapes. The maps highlight the importance of a diverse set of sub-units of the landscape in supporting Sahelian livelihoods. We see a large potential in using the resulting type of livelihood benefit maps for guiding future land use decisions in the Sahel. PMID:29389965

Mapping regional livelihood benefits from local ecosystem services assessments in rural Sahel.

PubMed

Malmborg, Katja; Sinare, Hanna; Enfors Kautsky, Elin; Ouedraogo, Issa; Gordon, Line J

2018-01-01

Most current approaches to landscape scale ecosystem service assessments rely on detailed secondary data. This type of data is seldom available in regions with high levels of poverty and strong local dependence on provisioning ecosystem services for livelihoods. We develop a method to extrapolate results from a previously published village scale ecosystem services assessment to a higher administrative level, relevant for land use decision making. The method combines remote sensing (using a hybrid classification method) and interviews with community members. The resulting landscape scale maps show the spatial distribution of five different livelihood benefits (nutritional diversity, income, insurance/saving, material assets and energy, and crops for consumption) that illustrate the strong multifunctionality of the Sahelian landscapes. The maps highlight the importance of a diverse set of sub-units of the landscape in supporting Sahelian livelihoods. We see a large potential in using the resulting type of livelihood benefit maps for guiding future land use decisions in the Sahel.

New gravity anomaly map of Taiwan and its surrounding regions with some tectonic interpretations

NASA Astrophysics Data System (ADS)

Doo, Wen-Bin; Lo, Chung-Liang; Hsu, Shu-Kun; Tsai, Ching-Hui; Huang, Yin-Sheng; Wang, Hsueh-Fen; Chiu, Shye-Donq; Ma, Yu-Fang; Liang, Chin-Wei

2018-04-01

In this study, we compiled recently collected (from 2005 to 2015) and previously reported (published and open access) gravity data, including land, shipborne and satellite-derived data, for Taiwan and its surrounding regions. Based on the cross-over error analysis, all data were adjusted; and, new Free-air gravity anomalies were obtained, shedding light on the tectonics of the region. To obtain the Bouguer gravity anomalies, the densities of land terrain and marine sediments were assumed to be 2.53 and 1.80 g/cm3, respectively. The updated gravity dataset was gridded with a spacing of one arc-minute. Several previously unnoticed gravity features are revealed by the new maps and can be used in a broad range of applications: (1) An isolated gravity high is located between the Shoushan and the Kaoping Canyon off southwest Taiwan. (2) Along the Luzon Arc, both Free-air and Bouguer gravity anomaly maps reveal a significant gravity discontinuity feature at the latitude of 21°20‧N. (3) In the southwestern Okinawa Trough, the NE-SW trending cross-back-arc volcanic trail (CBVT) marks the low-high gravity anomaly (both Free-air and Bouguer) boundary.

Data Warehouse Design from HL7 Clinical Document Architecture Schema.

PubMed

Pecoraro, Fabrizio; Luzi, Daniela; Ricci, Fabrizio L

2015-01-01

This paper proposes a semi-automatic approach to extract clinical information structured in a HL7 Clinical Document Architecture (CDA) and transform it in a data warehouse dimensional model schema. It is based on a conceptual framework published in a previous work that maps the dimensional model primitives with CDA elements. Its feasibility is demonstrated providing a case study based on the analysis of vital signs gathered during laboratory tests.

Geology of Point Reyes National Seashore and vicinity, California: a digital database

USGS Publications Warehouse

Clark, Jospeh C.; Brabb, Earl E.

1997-01-01

This Open-File report is a digital geologic map database. This pamphlet serves to introduce and describe the digital data. There is no paper map included in the Open-File report. The report does include, however, a PostScript plot file containing an image of the geologic map sheet with explanation, as well as the accompanying text describing the geology of the area. For those interested in a paper plot of information contained in the database or in obtaining the PostScript plot files, please see the section entitled 'For Those Who Aren't Familiar With Digital Geologic Map Databases' below. This digital map database, compiled from previously published and unpublished data and new mapping by the authors, represents the general distribution of surficial deposits and rock units in Point Reyes and surrounding areas. Together with the accompanying text file (pr-geo.txt or pr-geo.ps), it provides current information on the stratigraphy and structural geology of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:48,000 or smaller.

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.

PubMed

Schaefer, Nathan K; Shapiro, Beth; Green, Richard E

2017-04-04

Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage. AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.

Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs.

PubMed

Rajaram, Vengaldas; Nepolean, Thirunavukkarasu; Senthilvel, Senapathy; Varshney, Rajeev K; Vadez, Vincent; Srivastava, Rakesh K; Shah, Trushar M; Supriya, Ambawat; Kumar, Sushil; Ramana Kumari, Basava; Bhanuprakash, Amindala; Narasu, Mangamoori Lakshmi; Riera-Lizarazu, Oscar; Hash, Charles Thomas

2013-03-09

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics and sub-tropics of Africa, South Asia and the Americas. It is considered an orphan crop with relatively few genomic and genetic resources. This study was undertaken to increase the EST-based microsatellite marker and genetic resources for this crop to facilitate marker-assisted breeding. Newly developed EST-SSR markers (99), along with previously mapped EST-SSR (17), genomic SSR (53) and STS (2) markers, were used to construct linkage maps of four F7 recombinant inbred populations (RIP) based on crosses ICMB 841-P3 × 863B-P2 (RIP A), H 77/833-2 × PRLT 2/89-33 (RIP B), 81B-P6 × ICMP 451-P8 (RIP C) and PT 732B-P2 × P1449-2-P1 (RIP D). Mapped loci numbers were greatest for RIP A (104), followed by RIP B (78), RIP C (64) and RIP D (59). Total map lengths (Haldane) were 615 cM, 690 cM, 428 cM and 276 cM, respectively. A total of 176 loci detected by 171 primer pairs were mapped among the four crosses. A consensus map of 174 loci (899 cM) detected by 169 primer pairs was constructed using MergeMap to integrate the individual linkage maps. Locus order in the consensus map was well conserved for nearly all linkage groups. Eighty-nine EST-SSR marker loci from this consensus map had significant BLAST hits (top hits with e-value ≤ 1E-10) on the genome sequences of rice, foxtail millet, sorghum, maize and Brachypodium with 35, 88, 58, 48 and 38 loci, respectively. The consensus map developed in the present study contains the largest set of mapped SSRs reported to date for pearl millet, and represents a major consolidation of existing pearl millet genetic mapping information. This study increased numbers of mapped pearl millet SSR markers by >50%, filling important gaps in previously published SSR-based linkage maps for this species and will greatly facilitate SSR-based QTL mapping and applied marker-assisted selection programs.

Transcriptome Sequencing of Hevea brasiliensis for Development of Microsatellite Markers and Construction of a Genetic Linkage Map

PubMed Central

Triwitayakorn, Kanokporn; Chatkulkawin, Pornsupa; Kanjanawattanawong, Supanath; Sraphet, Supajit; Yoocha, Thippawan; Sangsrakru, Duangjai; Chanprasert, Juntima; Ngamphiw, Chumpol; Jomchai, Nukoon; Therawattanasuk, Kanikar; Tangphatsornruang, Sithichoke

2011-01-01

To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ∼4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection. PMID:22086998

A new catalog of planetary maps

NASA Technical Reports Server (NTRS)

Batson, R. M.; Inge, J. L.

1991-01-01

A single, concise reference to all existing planetary maps, including lunar ones, is being prepared that will allow map users to identify and locate maps of their areas of interest. This will be the first such comprehensive listing of planetary maps. Although the USGS shows index maps on the collar of each map sheet, periodically publishes index maps of Mars, and provides informal listings of the USGS map database, no tabulation exists that identifies all planetary maps, including those published by DMA and other organizations. The catalog will consist of a booklet containing small-scale image maps with superimposed quadrangle boundaries and map data tabulations.

Thermal inactivation profiles of Mycobacterium avium subsp. paratuberculosis in lamb skeletal muscle homogenate fluid.

PubMed

Whittington, Richard J; Waldron, Anna; Warne, Darian

2010-01-31

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease in livestock and there is a debate about its role in humans in chronic inflammatory bowel disorders such as Crohn's disease, but the relationship remains unproven. Nevertheless livestock health authorities in many countries aim to lower the prevalence of this infection to reduce potential contamination of the human food supply. MAP may occur in bovine milk and data on thermal inactivation suggest pasteurisation is an effective process. Recently MAP has been identified in skeletal muscle of cattle and sheep but there are no data on its thermal inactivation in these substrates. In this study the inactivation of MAP was studied in a fluid homogenate of lamb skeletal muscle at temperatures previously identified as being relevant to cooking processes applied by domestic consumers. A PCR thermocycler was used to ensure accurate temperatures and rapid heat exchange, while radiometric culture was used to ensure sensitive detection of viable MAP for determination of D and z values. Among the two predominant strains of MAP, S and C, D(55) ranged from 56 to 89 min, D(60) was 8 to 11 min, D(65) was 26 to 35s while D(70) was 1.5 to 1.8s. Values for z were 4.21C degrees for the S strain and 4.51C degrees for the C strain. At temperatures of 65-70 degrees C, MAP appeared to be less heat tolerant in skeletal muscle fluid than in previous reports using milk as the medium. The total thermal exposure of MAP during baking of a sample of 16 leg-of-lamb roasts in domestic ovens was determined to result in more than 20 log reductions in most cases, that is the product was microbiologically safe. Based on the models used in this study, there is a low probability of survival of MAP provided that red meat is cooked to recommended standards. Crown Copyright 2009. Published by Elsevier B.V. All rights reserved.

Mapping the origins of Imperial Roman workers (1st-4th century CE) at Vagnari, Southern Italy, using 87 Sr/86 Sr and δ18 O variability.

PubMed

Emery, Matthew V; Stark, Robert J; Murchie, Tyler J; Elford, Spencer; Schwarcz, Henry P; Prowse, Tracy L

2018-04-18

We obtained the oxygen and strontium isotope composition of teeth from Roman period (1st to 4th century CE) inhabitants buried in the Vagnari cemetery (Southern Italy), and present the first strontium isotope variation map of the Italian peninsula using previously published data sets and new strontium data. We test the hypothesis that the Vagnari population was predominantly composed of local individuals, instead of migrants originating from abroad. We analyzed the oxygen ( 18 O/ 16 O) and strontium ( 87 Sr/ 86 Sr) isotope composition of 43 teeth. We also report the 87 Sr/ 86 Sr composition of an additional 13 molars, 87 Sr/ 86 Sr values from fauna (n = 10), and soil (n = 5) samples local to the area around Vagnari. The 87 Sr/ 86 Sr variation map of Italy uses 87 Sr/ 86 Sr values obtained from previously published data sources from across Italy (n = 199). Converted tooth carbonate (δ 18 O DW ) and 87 Sr/ 86 Sr data indicate that the majority of individuals buried at Vagnari were local to the region. ArcGIS bounded Inverse Distance Weighting (IDW) interpolation of the pan-Italian 87 Sr/ 86 Sr data set approximates the expected 87 Sr/ 86 Sr range of Italy's geological substratum, producing the first strontium map of the Italian peninsula. Results suggest that only 7% of individuals buried at Vagnari were born elsewhere and migrated to Vagnari, while the remaining individuals were either local to Vagnari (58%), or from the southern Italian peninsula (34%). Our results are consistent with the suggestion that Roman Imperial lower-class populations in southern Italy sustained their numbers through local reproduction measures, and not through large-scale immigration from outside the Italian peninsula. © 2018 Wiley Periodicals, Inc.

Geologic Map and Map Database of the Oakland Metropolitan Area, Alameda, Contra Costa, and San Francisco Counties, California

USGS Publications Warehouse

Graymer, R.W.

2000-01-01

Introduction This report contains a new geologic map at 1:50,000 scale, derived from a set of geologic map databases containing information at a resolution associated with 1:24,000 scale, and a new description of geologic map units and structural relationships in the mapped area. The map database represents the integration of previously published reports and new geologic mapping and field checking by the author (see Sources of Data index map on the map sheet or the Arc-Info coverage pi-so and the textfile pi-so.txt). The descriptive text (below) contains new ideas about the Hayward fault and other faults in the East Bay fault system, as well as new ideas about the geologic units and their relations. These new data are released in digital form in conjunction with the Federal Emergency Management Agency Project Impact in Oakland. The goal of Project Impact is to use geologic information in land-use and emergency services planning to reduce the losses occurring during earthquakes, landslides, and other hazardous geologic events. The USGS, California Division of Mines and Geology, FEMA, California Office of Emergency Services, and City of Oakland participated in the cooperative project. The geologic data in this report were provided in pre-release form to other Project Impact scientists, and served as one of the basic data layers for the analysis of hazard related to earthquake shaking, liquifaction, earthquake induced landsliding, and rainfall induced landsliding. The publication of these data provides an opportunity for regional planners, local, state, and federal agencies, teachers, consultants, and others outside Project Impact who are interested in geologic data to have the new data long before a traditional paper map could be published. Because the database contains information about both the bedrock and surficial deposits, it has practical applications in the study of groundwater and engineering of hillside materials, as well as the study of geologic hazards and the academic research on the geologic history and development of the region.

The use of TIMS for mapping different pahoehoe surfaces: Mauna Iki, Kilauea

NASA Technical Reports Server (NTRS)

Rowland, Scott K.

1992-01-01

S-type and p-type pahoehoe record different mechanisms and vigors of activity within an active flow field. There is some controversy about what these mechanisms are exactly, and this study was undertaken with the idea that an accurate map of the two surfaces within a pahoehoe flow field could be helpful in solving the problem. Thermal Infrared Multispectral Scanner (TIMS) allows discrimination between s-type and p-type pahoehoe, and this ability was used to map the two surface types on the Mauna Iki satellite shield (southwest rift zone, Kilauea Volcano). TIMS was previously used to discriminate a'a from pahoehoe as well as to determine relative age relationships of different flows. Although inter-flow variation was minor in the data published by these authors, a second goal presented is to understand such variations to better constrain intra-flow differences used for age dating.

Carbon isotope compositions of terrestrial C3 plants as indicators of (paleo)ecology and (paleo)climate.

PubMed

Kohn, Matthew J

2010-11-16

A broad compilation of modern carbon isotope compositions in all C3 plant types shows a monotonic increase in δ(13)C with decreasing mean annual precipitation (MAP) that differs from previous models. Corrections for temperature, altitude, or latitude are smaller than previously estimated. As corrected for altitude, latitude, and the δ(13)C of atmospheric CO(2), these data permit refined interpretation of MAP, paleodiet, and paleoecology of ecosystems dominated by C3 plants, either prior to 7-8 million years ago (Ma), or more recently at mid- to high latitudes. Twenty-nine published paleontological studies suggest preservational or scientific bias toward dry ecosystems, although wet ecosystems are also represented. Unambiguous isotopic evidence for C4 plants is lacking prior to 7-8 Ma, and hominid ecosystems at 4.4 Ma show no isotopic evidence for dense forests. Consideration of global plant biomass indicates that average δ(13)C of C3 plants is commonly overestimated by approximately 2‰.

A simple method for serving Web hypermaps with dynamic database drill-down

PubMed Central

Boulos, Maged N Kamel; Roudsari, Abdul V; Carson, Ewart R

2002-01-01

Background HealthCyberMap aims at mapping parts of health information cyberspace in novel ways to deliver a semantically superior user experience. This is achieved through "intelligent" categorisation and interactive hypermedia visualisation of health resources using metadata, clinical codes and GIS. HealthCyberMap is an ArcView 3.1 project. WebView, the Internet extension to ArcView, publishes HealthCyberMap ArcView Views as Web client-side imagemaps. The basic WebView set-up does not support any GIS database connection, and published Web maps become disconnected from the original project. A dedicated Internet map server would be the best way to serve HealthCyberMap database-driven interactive Web maps, but is an expensive and complex solution to acquire, run and maintain. This paper describes HealthCyberMap simple, low-cost method for "patching" WebView to serve hypermaps with dynamic database drill-down functionality on the Web. Results The proposed solution is currently used for publishing HealthCyberMap GIS-generated navigational information maps on the Web while maintaining their links with the underlying resource metadata base. Conclusion The authors believe their map serving approach as adopted in HealthCyberMap has been very successful, especially in cases when only map attribute data change without a corresponding effect on map appearance. It should be also possible to use the same solution to publish other interactive GIS-driven maps on the Web, e.g., maps of real world health problems. PMID:12437788

National Atlas of the United States Maps

USGS Publications Warehouse

,

2001-01-01

The "National Atlas of the United States of America®", published by the U.S. Geological Survey (USGS) in 1970, is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. Maps dated after 1970 and before 1997 are either revisions of original atlas maps or new maps published in the original atlas format. The USGS and its partners in government and industry began work on a new "National Atlas" in 1997. Though most new atlas products are designed for the World Wide Web, we are continuing our tradition of printing high-quality maps of America. In 1998, the first completely redesigned maps of the "National Atlas of the United States®" were published.

Evidence-based risk assessment and communication: a new global dengue-risk map for travellers and clinicians.

PubMed

Jentes, Emily S; Lash, R Ryan; Johansson, Michael A; Sharp, Tyler M; Henry, Ronnie; Brady, Oliver J; Sotir, Mark J; Hay, Simon I; Margolis, Harold S; Brunette, Gary W

2016-06-01

International travel can expose travellers to pathogens not commonly found in their countries of residence, like dengue virus. Travellers and the clinicians who advise and treat them have unique needs for understanding the geographic extent of risk for dengue. Specifically, they should assess the need for prevention measures before travel and ensure appropriate treatment of illness post-travel. Previous dengue-risk maps published in the Centers for Disease Control and Prevention's Yellow Book lacked specificity, as there was a binary (risk, no risk) classification. We developed a process to compile evidence, evaluate it and apply more informative risk classifications. We collected more than 839 observations from official reports, ProMED reports and published scientific research for the period 2005-2014. We classified each location as frequent/continuous risk if there was evidence of more than 10 dengue cases in at least three of the previous 10 years. For locations that did not fit this criterion, we classified locations as sporadic/uncertain risk if the location had evidence of at least one locally acquired dengue case during the last 10 years. We used expert opinion in limited instances to augment available data in areas where data were sparse. Initial categorizations classified 134 areas as frequent/continuous and 140 areas as sporadic/uncertain. CDC subject matter experts reviewed all initial frequent/continuous and sporadic/uncertain categorizations and the previously uncategorized areas. From this review, most categorizations stayed the same; however, 11 categorizations changed from the initial determinations. These new risk classifications enable detailed consideration of dengue risk, with clearer meaning and a direct link to the evidence that supports the specific classification. Since many infectious diseases have dynamic risk, strong geographical heterogeneities and varying data quality and availability, using this approach for other diseases can improve the accuracy, clarity and transparency of risk communication. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Geologic Map and Map Database of Eastern Sonoma and Western Napa Counties, California

USGS Publications Warehouse

Graymer, R.W.; Brabb, E.E.; Jones, D.L.; Barnes, J.; Nicholson, R.S.; Stamski, R.E.

2007-01-01

Introduction This report contains a new 1:100,000-scale geologic map, derived from a set of geologic map databases (Arc-Info coverages) containing information at 1:62,500-scale resolution, and a new description of the geologic map units and structural relations in the map area. Prepared as part of the San Francisco Bay Region Mapping Project, the study area includes the north-central part of the San Francisco Bay region, and forms the final piece of the effort to generate new, digital geologic maps and map databases for an area which includes Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Santa Cruz, Solano, and Sonoma Counties. Geologic mapping in Lake County in the north-central part of the map extent was not within the scope of the Project. The map and map database integrates both previously published reports and new geologic mapping and field checking by the authors (see Sources of Data index map on the map sheet or the Arc-Info coverage eswn-so and the textfile eswn-so.txt). This report contains new ideas about the geologic structures in the map area, including the active San Andreas Fault system, as well as the geologic units and their relations. Together, the map (or map database) and the unit descriptions in this report describe the composition, distribution, and orientation of geologic materials and structures within the study area at regional scale. Regional geologic information is important for analysis of earthquake shaking, liquifaction susceptibility, landslide susceptibility, engineering materials properties, mineral resources and hazards, as well as groundwater resources and hazards. These data also assist in answering questions about the geologic history and development of the California Coast Ranges.

Comprehensive Insights in the Mycobacterium avium subsp. paratuberculosis Genome Using New WGS Data of Sheep Strain JIII-386 from Germany

PubMed Central

Möbius, Petra; Hölzer, Martin; Felder, Marius; Nordsiek, Gabriele; Groth, Marco; Köhler, Heike; Reichwald, Kathrin; Platzer, Matthias; Marz, Manja

2015-01-01

Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP)—the etiologic agent of Johne’s disease—affects cattle, sheep, and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III], respectively, MAP-C [Type-II]), comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. This study presents the so far best assembled genome of a MAP-S-strain: Sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from the United States and Australia, and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI (National Center for Biotechnology Information) annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined by either NCBI or BacProt. A new Shine–Dalgarno sequence motif (5′-AGCTGG-3′) was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 noncoding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four of ten assumed MAP-S-specific large sequence polymorphism regions (LSPSs) are still present in MAP-C strains; new LSPSs were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirms the strong similarity of MAP-C strains and shows higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to Mycobacterium intracellulare. PMID:26384038

Ground-water resources of the lower Niobrara River and Ponca Creek basins, Nebraska and South Dakota

USGS Publications Warehouse

Newport, Thomas G.; Krieger, Robert A.

1959-01-01

 The report contains an annotated bibliography of previous publications on the geology and ground-water resources of the area, brief descriptions of the Cretaceous, Tertiary, and Quaternary rocks, a map showing the contour of the water table, logs of test holes and wells not published elsewhere, results of analyses of ground- and surface-water samples, and records of all wells of large discharge and representative wells of small discharge.

Digital mapping techniques '00, workshop proceedings - May 17-20, 2000, Lexington, Kentucky

USGS Publications Warehouse

Soller, David R.

2000-01-01

Introduction: The Digital Mapping Techniques '00 (DMT'00) workshop was attended by 99 technical experts from 42 agencies, universities, and private companies, including representatives from 28 state geological surveys (see Appendix A). This workshop was similar in nature to the first three meetings, held in June, 1997, in Lawrence, Kansas (Soller, 1997), in May, 1998, in Champaign, Illinois (Soller, 1998a), and in May, 1999, in Madison, Wisconsin (Soller, 1999). This year's meeting was hosted by the Kentucky Geological Survey, from May 17 to 20, 2000, on the University of Kentucky campus in Lexington. As in the previous meetings, the objective was to foster informal discussion and exchange of technical information. When, based on discussions at the workshop, an attendee adopts or modifies a newly learned technique, the workshop clearly has met that objective. Evidence of learning and cooperation among participating agencies continued to be a highlight of the DMT workshops (see example in Soller, 1998b, and various papers in this volume). The meeting's general goal was to help move the state geological surveys and the USGS toward development of more cost-effective, flexible, and useful systems for digital mapping and geographic information systems (GIS) analysis. Through oral and poster presentations and special discussion sessions, emphasis was given to: 1) methods for creating and publishing map products (here, 'publishing' includes Web-based release); 2) continued development of the National Geologic Map Database; 3) progress toward building a standard geologic map data model; 4) field data-collection systems; and 5) map citation and authorship guidelines. Four representatives of the GIS hardware and software vendor community were invited to participate. The four annual DMT workshops were coordinated by the AASG/USGS Data Capture Working Group, which was formed in August, 1996, to support the Association of American State Geologists and the USGS in their effort to build a National Geologic Map Database (see Soller and Berg, this volume, and http://ncgmp.usgs.gov/ngmdbproject/standards/datacapt/). The Working Group was formed because increased production efficiencies, standardization, and quality of digital map products were needed to help the Database, and the State and Federal geological surveys, provide more high-quality digital maps to the public.

Labeling Projections on Published Maps

USGS Publications Warehouse

Snyder, John P.

1987-01-01

To permit accurate scaling on a map, and to use the map as a source of accurate positions in the transfer of data, certain parameters - such as the standard parallels selected for a conic projection - must be stated on the map. This information is often missing on published maps. Three current major world atlases are evaluated with respect to map projection identification. The parameters essential for the projections used in these three atlases are discussed and listed. These parameters should be stated on any map based on the same projection.

Geologic map of the MTM 85080 Quadrangle, Chasma Boreale Region of Mars

USGS Publications Warehouse

Herkenhoff, K. E.

2003-01-01

The polar deposits on Mars probably record martian climate history over the last 107 to 109 years (for example, Thomas and others, 1992). The area shown on this map includes polar layered deposits and polar ice, as well as some outcrops of older, underlying terrain. This quadrangle was mapped using Viking Orbiter images in order to study the relations among erosional and depositional processes on the north polar layered deposits and to compare them with the results of previous 1:500,000-scale mapping of the south polar layered deposits. Published geologic maps of the north polar region of Mars are based on images acquired by Mariner 9 and the Viking Orbiters. The extent of the layered deposits and other units varies among previous maps, in particular within Chasma Boreale. The present map agrees most closely with the map by Dial and Dohm (1994): the mantle material is exposed farther north than mapped by Tanaka and Scott (1987). The polar ice cap, areas of partial frost cover, the layered deposits, and two nonvolatile surface units-dust mantle and dark material-were mapped in the south polar region by Herkenhoff and Murray (1990a) at 1:2,000,000 scale using a color mosaic of Viking Orbiter images. Viking Orbiter rev 726, 768, and 771 color mosaics (taken during the northern summer of 1978) were constructed and used to identify similar color/albedo units in the north polar region, including the dark, saltating material that appears to have sources within the layered deposits. However, no dark material has been recognized in this map area. No significant difference in color exists between the layered deposits and the mantle material mapped by Dial and Dohm (1994), indicating that they are either composed of the same materials or are both covered by eolian debris. Therefore, in this map area the color mosaics are most useful for identifying areas of partial frost cover. Because the resolution of the color mosaics is not sufficient to map the color/albedo units in detail at 1:500,000-scale, contacts between them were recognized and mapped using higher resolution black-and-white Viking Orbiter images. The Viking Orbiter 2 images used to construct the map base were taken during the northern summer of 1976 (mostly Ls=133?-135?), with resolutions typically around 60 m/pixel. As noted on the published base, errors of up to 5 km exist in the placement of images in the base map; such errors are evident upon comparison of sheet 1 (summer) and sheet 2 (spring). Therefore, a new photomosaic base was created during map production and the linework was edited to match the new base. No craters have been found in the north polar layered deposits or polar ice cap. The observed lack of craters larger than 300 m implies that the surfaces of these units are no more than 100,000 years old or that they have been resurfaced at a rate of at least 2.3 mm/yr. The recent cratering flux on Mars is poorly constrained, so inferred resurfacing rates and ages of surface units are uncertain by at least a factor of 2.

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

PubMed

Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Mapping the Galilean satellites of Jupiter with Voyager data.

USGS Publications Warehouse

Batson, R.M.

1980-01-01

The four Galilean satellites of Jupiter are being mapped using image data from the Voyager 1 and 2 spacecraft. The maps are published at several scales and in several versions. Preliminary maps at 1:25,000,000-required for mission planning and preliminary science reports-were compiled within three weeks of data acquisition and have been published. Later maps incorporate Rand Corporation photogrammetric triangulations. - from Authors

Cardiovascular tolerance of intravenous bupivacaine in broiler chickens (Gallus gallus domesticus) anesthetized with isoflurane.

PubMed

DiGeronimo, Peter M; da Cunha, Anderson F; Pypendop, Bruno; Brandão, João; Stout, Rhett; Rinaldi, Max; Tully, Thomas N

2017-03-01

To determine the median effective dose (ED 50 ) of intravenous (IV) bupivacaine associated with a 50% probability of causing clinically relevant cardiovascular effects [defined as 30% change in heart rate (HR) or mean arterial pressure (MAP)] in chickens anesthetized with isoflurane. Randomized up-and-down study. A total of 14 Ross-708 broiler chickens (Gallus gallus domesticus) weighing 1.70-2.75 kg. Anesthesia was induced and maintained with isoflurane. Monitoring included the electrocardiogram and invasive arterial pressures. Chickens were administered bupivacaine IV over 2 minutes using a dose based on the response of the previous animal. Dose was decreased when HR and/or MAP in the previous animal increased or decreased ≥30% after bupivacaine administration, or increased when HR or MAP changed <30%. The ED 50 was defined as the dose resulting in ≥30% variation in HR or MAP in 50% of the population studied. The IV ED 50 of bupivacaine was 1.94 mg kg -1 using Dixon's up-and-down method and 1.96 mg kg -1 by logistic regression. These results suggest that 1.33 and 1.96 mg kg -1 of IV bupivacaine are associated with a respective 1 or 50% probability of a clinically significant change in MAP in isoflurane-anesthetized chickens. Identification of the cardiovascular changes associated with different doses of bupivacaine can be used as the basis for studies of therapeutic applications in the domestic chicken. Further studies are required to determine interspecies variation. Published by Elsevier Ltd.

Influence of water stress on the carbon isotopic composition of modern plants: Implications for C4 plant appearance in Indian subcontinent

NASA Astrophysics Data System (ADS)

Basu, S.; Ghosh, S.; Sanyal, P.

2016-12-01

The carbon isotopic composition (d13C) of modern terrestrial plants (C3 and C4) provides the baseline to understand past vegetation composition, paleodietary changes and animal migration etc. Accuracy of past environment reconstruction is dependent on the end-member d13C values of plants which found to vary in regional scale. For instance, the d13C values of Indian C3 plants (d13CC3) are 1 to 2‰ more negative compared to global mean. As observed, most of the previous database is devoid of samples from tropical monsoon realm (like India) and the difference between global and regional mean may introduce errors in vegetation reconstruction. To constrain end-member d13CC3 value, published and newly generated results from wide range of mean annual precipitation (MAP: 1-11,700 mm) are compiled which is ca. 1.5 higher in sample size (n=2440) compared to previous database. Using logarithmic function, new relationship between d13C value and MAP (d13CC3 (‰) =20.1585(0.3061)-1.1276(0.0489)ln(MAP+700)) is proposed. The modeled mean d13CC3 value (-28.9‰) is close to average d13CC3 value for Indian plants (-29.1‰) and suggests the importance of vegetation from low-latitudinal tropical region in global compilation. It was observed that C3 plants, on a global scale, are less sensitive to wet climate relative to dry condition. This inference is in agreement with the paleoclimatic data from Indian subcontinent for the late Quaternary period. Despite well established correlation between d13CC3 value and MAP, previous investigation from Indian subcontinent used fixed end-member values to reconstruct past vegetation and total change in the d13C value of proxies was attributed to changes in relative abundance of C3 and C4 plants. Using region-specific mean d13C value of plants, after correcting for changing MAP and error propagation, existence of C4 before ca. 11 Ma plant is observed; earlier to previous reported timing.

Second generation genetic linkage map for the gilthead sea bream Sparus aurata L.

PubMed

Tsigenopoulos, Costas S; Louro, Bruno; Chatziplis, Dimitrios; Lagnel, Jacques; Vogiatzi, Emmanouella; Loukovitis, Dimitrios; Franch, Rafaella; Sarropoulou, Elena; Power, Deborah M; Patarnello, Tomaso; Mylonas, Constantinos C; Magoulas, Antonios; Bargelloni, Luca; Canario, Adelino; Kotoulas, Georgios

2014-12-01

An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6cM, with an average of 5.75cM. The male and female maps have a length of 1349.2 and 2172.1cM, respectively, and the average distance between markers is 4.38 and 7.05cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. Copyright © 2014 Elsevier B.V. All rights reserved.

High-Resolution Regional Biomass Map of Siberia from Glas, Palsar L-Band Radar and Landsat Vcf Data

NASA Astrophysics Data System (ADS)

Sun, G.; Ranson, K.; Montesano, P.; Zhang, Z.; Kharuk, V.

2015-12-01

The Arctic-Boreal zone is known be warming at an accelerated rate relative to other biomes. The taiga or boreal forest covers over 16 x106 km2 of Arctic North America, Scandinavia, and Eurasia. A large part of the northern Boreal forests are in Russia's Siberia, as area with recent accelerated climate warming. During the last two decades we have been working on characterization of boreal forests in north-central Siberia using field and satellite measurements. We have published results of circumpolar biomass using field plots, airborne (PALS, ACTM) and spaceborne (GLAS) lidar data with ASTER DEM, LANDSAT and MODIS land cover classification, MODIS burned area and WWF's ecoregion map. Researchers from ESA and Russia have also been working on biomass (or growing stock) mapping in Siberia. For example, they developed a pan-boreal growing stock volume map at 1-kilometer scale using hyper-temporal ENVISAT ASAR ScanSAR backscatter data. Using the annual PALSAR mosaics from 2007 to 2010 growing stock volume maps were retrieved based on a supervised random forest regression approach. This method is being used in the ESA/Russia ZAPAS project for Central Siberia Biomass mapping. Spatially specific biomass maps of this region at higher resolution are desired for carbon cycle and climate change studies. In this study, our work focused on improving resolution ( 50 m) of a biomass map based on PALSAR L-band data and Landsat Vegetation Canopy Fraction products. GLAS data were carefully processed and screened using land cover classification, local slope, and acquisition dates. The biomass at remaining footprints was estimated using a model developed from field measurements at GLAS footprints. The GLAS biomass samples were then aggregated into 1 Mg/ha bins of biomass and mean VCF and PALSAR backscatter and textures were calculated for each of these biomass bins. The resulted biomass/signature data was used to train a random forest model for biomass mapping of entire region from 50oN to 75oN, and 80oE to 145oE. The spatial patterns of the new biomass map is much better than the previous maps due to spatially specific mapping in high resolution. The uncertainties of field/GLAS and GLAS/imagery models were investigated using bootstrap procedure, and the final biomass map was compared with previous maps.

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

PubMed Central

Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J.; Neale, David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Echt, Craig S.

2015-01-01

A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

A faunistic study on the leafhoppers of northwestern Iran (Hemiptera, Cicadellidae)

PubMed Central

Abdollahi, Tandis; Jalalizand, Ali Reza; Mozaffarian, Fariba; Wilson, Michael

2015-01-01

Abstract The leafhopper fauna of northwestern Iran: Azarbaijan-e-Sharghi, Azarbaijan-e-Gharbi and Ardabil provinces is listed from previously published records and from our current work. Sixty-nine species are included with four species (Mogangella straminea Dlabola, 1957, Doratura stylata (Boheman, 1847), Macrosteles sordidipennis (Stål, 1858) and Psammotettix seriphidii Emeljanov, 1962) listed as new for Iran and Balclutha punctata (Fabricius, 1775), as a new record for the region. A distribution map of the species in northwestern Iran is given. PMID:25931954

Mineral Mapping with AVIRIS and EO-1 Hyperion

NASA Technical Reports Server (NTRS)

Kruse, Fred A.

2004-01-01

Imaging Spectrometry data or Hyperspectral Imagery (HSI) acquired using airborne systems have been used in the geologic community since the early 1980 s and represent a mature technology (Goetz et al., 1985; Kruse et al., 1999). The solar spectral range, 0.4 to 2.5 m, provides abundant information about many important Earth-surface minerals (Clark et al., 1990). In particular, the 2.0 to 2.5 m (SWIR) spectral range covers spectral features of hydroxyl-bearing minerals, sulfates, and carbonates common to many geologic units and hydrothermal alteration assemblages. Previous research has proven the ability of airborne and spaceborne hyperspectral systems to uniquely identify and map these and other minerals, even in sub-pixel abundances (Kruse and Lefkoff, 1993; Boardman and Kruse, 1994; Boardman et al., 1995; Kruse, et al., 1999). This paper describes a case history for a site in northern Death Valley, California and Nevada along with selected SNR calculations/results for other sites around the world. Various hyperspectral mineral mapping results for this site have previously been presented and published (Kruse, 1988; Kruse et al., 1993, 1999, 2001, 2002, 2003), however, this paper presents a condensed summary of key details for hyperspectral data from 2000 and 2001 and the results of accuracy assessment for satellite hyperspectral data compared to airborne hyperspectral data used as ground truth.

Geologic Map of the Central Marysvale Volcanic Field, Southwestern Utah

USGS Publications Warehouse

Rowley, Peter D.; Cunningham, Charles G.; Steven, Thomas A.; Workman, Jeremiah B.; Anderson, John J.; Theissen, Kevin M.

2002-01-01

The geologic map of the central Marysvale volcanic field, southwestern Utah, shows the geology at 1:100,000 scale of the heart of one of the largest Cenozoic volcanic fields in the Western United States. The map shows the area of 38 degrees 15' to 38 degrees 42'30' N., and 112 degrees to 112 degrees 37'30' W. The Marysvale field occurs mostly in the High Plateaus, a subprovince of the Colorado Plateau and structurally a transition zone between the complexly deformed Great Basin to the west and the stable, little-deformed main part of the Colorado Plateau to the east. The western part of the field is in the Great Basin proper. The volcanic rocks and their source intrusions in the volcanic field range in age from about 31 Ma (Oligocene) to about 0.5 Ma (Pleistocene). These rocks overlie sedimentary rocks exposed in the mapped area that range in age from Ordovician to early Cenozoic. The area has been deformed by thrust faults and folds formed during the late Mesozoic to early Cenozoic Sevier deformational event, and later by mostly normal faults and folds of the Miocene to Quaternary basin-range episode. The map revises and updates knowledge gained during a long-term U.S. Geological Survey investigation of the volcanic field, done in part because of its extensive history of mining. The investigation also was done to provide framework geologic knowledge suitable for defining geologic and hydrologic hazards, for locating hydrologic and mineral resources, and for an understanding of geologic processes in the area. A previous geologic map (Cunningham and others, 1983, U.S. Geological Survey Miscellaneous Investigations Series I-1430-A) covered the same area as this map but was published at 1:50,000 scale and is obsolete due to new data. This new geologic map of the central Marysvale field, here published as U.S. Geological Survey Geologic Investigations Series I-2645-A, is accompanied by gravity and aeromagnetic maps of the same area and the same scale (Campbell and others, 1999, U.S. Geological Survey Geologic Investigations Series I-2645-B).

NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.

PubMed

Costa, Marta; Manton, James D; Ostrovsky, Aaron D; Prohaska, Steffen; Jefferis, Gregory S X E

2016-07-20

Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. VIDEO ABSTRACT. Copyright © 2016 MRC Laboratory of Molecular Biology. Published by Elsevier Inc. All rights reserved.

destiny: diffusion maps for large-scale single-cell data in R.

PubMed

Angerer, Philipp; Haghverdi, Laleh; Büttner, Maren; Theis, Fabian J; Marr, Carsten; Buettner, Florian

2016-04-15

: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming. destiny is an open-source R/Bioconductor package "bioconductor.org/packages/destiny" also available at www.helmholtz-muenchen.de/icb/destiny A detailed vignette describing functions and workflows is provided with the package. carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Effects of altered auditory feedback across effector systems: production of melodies by keyboard and singing.

PubMed

Pfordresher, Peter Q; Mantell, James T

2012-01-01

We report an experiment that tested whether effects of altered auditory feedback (AAF) during piano performance differ from its effects during singing. These effector systems differ with respect to the mapping between motor gestures and pitch content of auditory feedback. Whereas this action-effect mapping is highly reliable during phonation in any vocal motor task (singing or speaking), mapping between finger movements and pitch occurs only in limited situations, such as piano playing. Effects of AAF in both tasks replicated results previously found for keyboard performance (Pfordresher, 2003), in that asynchronous (delayed) feedback slowed timing whereas alterations to feedback pitch increased error rates, and the effect of asynchronous feedback was similar in magnitude across tasks. However, manipulations of feedback pitch had larger effects on singing than on keyboard production, suggesting effector-specific differences in sensitivity to action-effect mapping with respect to feedback content. These results support the view that disruption from AAF is based on abstract, effector independent, response-effect associations but that the strength of associations differs across effector systems. Copyright © 2011. Published by Elsevier B.V.

Water-level altitudes 2001, water-level changes 1977-2001 and 2000-2001, and compaction 1973-2000 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Coplin, L.S.; Houston, Natalie A.; Brown, Dexter W.

2001-01-01

This report is one in an annual series of reports that depicts water-level altitudes and water-level changes since 1977 and compaction since 1973 in the Chicot and Evangeline aquifers in the Houston-Galveston region, Texas. The report, prepared in cooperation with the City of Houston and the Harris-Galveston Coastal Subsidence District, presents maps for the Chicot and Evangeline aquifers showing the approximate water-level altitudes in wells in 2001 (figs 1,4) and approximate water-level changes in wells from 1977 to 2001 and from 2000 to 2001 (figs 2,3,5,6), a map showing extensometer site locations (fig. 7), and graphs showing measured compaction of subserface material at selected sites from 1973 to 2000 (fig. 8). The most recent previously published water-level-altitude maps and water-level-change maps for the two aquifers in the region are by Coplin and Santos. (2000). The Houston-Galveston region comprises Harris and Galveston Counties and adjacent parts of Brazoria, Fort Bend, Waller, Montgomery, Liberty, and Chambers Counties.

Assessment of planetary geologic mapping techniques for Mars using terrestrial analogs: The SP Mountain area of the San Francisco Volcanic Field, Arizona

USGS Publications Warehouse

Tanaka, K.L.; Skinner, J.A.; Crumpler, L.S.; Dohm, J.M.

2009-01-01

We photogeologically mapped the SP Mountain region of the San Francisco Volcanic Field in northern Arizona, USA to evaluate and improve the fidelity of approaches used in geologic mapping of Mars. This test site, which was previously mapped in the field, is chiefly composed of Late Cenozoic cinder cones, lava flows, and alluvium perched on Permian limestone of the Kaibab Formation. Faulting and folding has deformed the older rocks and some of the volcanic materials, and fluvial erosion has carved drainage systems and deposited alluvium. These geologic materials and their formational and modificational histories are similar to those for regions of the Martian surface. We independently prepared four geologic maps using topographic and image data at resolutions that mimic those that are commonly used to map the geology of Mars (where consideration was included for the fact that Martian features such as lava flows are commonly much larger than their terrestrial counterparts). We primarily based our map units and stratigraphic relations on geomorphology, color contrasts, and cross-cutting relationships. Afterward, we compared our results with previously published field-based mapping results, including detailed analyses of the stratigraphy and of the spatial overlap and proximity of the field-based vs. remote-based (photogeologic) map units, contacts, and structures. Results of these analyses provide insights into how to optimize the photogeologic mapping of Mars (and, by extension, other remotely observed planetary surfaces). We recommend the following: (1) photogeologic mapping as an excellent approach to recovering the general geology of a region, along with examination of local, high-resolution datasets to gain insights into the complexity of the geology at outcrop scales; (2) delineating volcanic vents and lava-flow sequences conservatively and understanding that flow abutment and flow overlap are difficult to distinguish in remote data sets; (3) taking care to understand that surficial materials (such as alluvium and volcanic ash deposits) are likely to be under-mapped yet are important because they obscure underlying units and contacts; (4) where possible, mapping multiple contact and structure types based on their varying certainty and exposure that reflect the perceived accuracy of the linework; (5) reviewing the regional context and searching for evidence of geologic activity that may have affected the map area yet for which evidence within the map area may be absent; and (6) for multi-authored maps, collectively analyzing the mapping relations, approaches, and methods throughout the duration of the mapping project with the objective of achieving a solid, harmonious product.

A comprehensive map of the porcine genome.

PubMed

Rohrer, G A; Alexander, L J; Hu, Z; Smith, T P; Keele, J W; Beattie, C W

1996-05-01

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

Coastal erosion and wetland change in Louisiana: selected USGS products

USGS Publications Warehouse

Williams, S. Jeffress; Reid, Jamey M.; Cross, VeeAnn A.; Polloni, Christopher F.

2003-01-01

This Digital Data Series (DDS) report is primarily a selection of USGS science products that were previously published as paper atlases and maps but are no longer available in their original form. We have made an attempt to preserve the paper atlases by having them scanned in an efficient compressed digital format that provides a print-on-demand as well as a programmed viewing capability of the original material. We included additional materials bearing on aspects to enhance the scientific understanding of coastal erosion and wetland loss in Louisiana. In addition, this report contains multimedia-based publications including photographs, a 48-minute video, and map tools to allow the user to experience the many scientifically based research activities that are in progress along the coast of Louisiana.

Geologic Map of the Atlin Quadrangle, Southeastern Alaska

USGS Publications Warehouse

Brew, David A.; Himmelberg, Glen R.; Ford, Arthur B.

2009-01-01

This map presents the results of U.S. Geological Survey (USGS) geologic bedrock mapping studies in the mostly glacier covered Atlin 1:250,000-scale quadrangle, northern southeastern Alaska. These studies are part of a long-term systematic effort by the USGS to provide bedrock geologic and mineral-resource information for all of southeastern Alaska, covering all of the Tongass National Forest (including Wilderness Areas) and Glacier Bay National Park and Preserve. Some contributions to this effort are those concerned with southwesternmost part of the region, the Craig and Dixon Entrance quadrangles (Brew, 1994; 1996) and with the Wrangell-Petersburg area (Brew, 1997a-m; Brew and Grybeck, 1997; Brew and Koch, 1997). As shown on the index map (fig. 1), the study area is almost entirely in the northern Coast Mountains adjacent to British Columbia, Canada. No previous geologic map has been published for the area, although Brew and Ford (1985) included a small part of it in a preliminary compilation of the adjoining Juneau quadrangle; and Brew and others (1991a) showed the geology at 1:500,000 scale. Areas mapped nearby in British Columbia and the United States are also shown on figure 1. All of the map area is in the Coast Mountains Complex as defined by Brew and others (1995a). A comprehensive bibliography is available for this and adjacent areas (Brew, 1997n).

An appraisal of Indonesia's immense peat carbon stock using national peatland maps: uncertainties and potential losses from conversion.

PubMed

Warren, Matthew; Hergoualc'h, Kristell; Kauffman, J Boone; Murdiyarso, Daniel; Kolka, Randall

2017-12-01

A large proportion of the world's tropical peatlands occur in Indonesia where rapid conversion and associated losses of carbon, biodiversity and ecosystem services have brought peatland management to the forefront of Indonesia's climate mitigation efforts. We evaluated peat volume from two commonly referenced maps of peat distribution and depth published by Wetlands International (WI) and the Indonesian Ministry of Agriculture (MoA), and used regionally specific values of carbon density to calculate carbon stocks. Peatland extent and volume published in the MoA maps are lower than those in the WI maps, resulting in lower estimates of carbon storage. We estimate Indonesia's total peat carbon store to be within 13.6 GtC (the low MoA map estimate) and 40.5 GtC (the high WI map estimate) with a best estimate of 28.1 GtC: the midpoint of medium carbon stock estimates derived from WI (30.8 GtC) and MoA (25.3 GtC) maps. This estimate is about half of previous assessments which used an assumed average value of peat thickness for all Indonesian peatlands, and revises the current global tropical peat carbon pool to 75 GtC. Yet, these results do not diminish the significance of Indonesia's peatlands, which store an estimated 30% more carbon than the biomass of all Indonesian forests. The largest discrepancy between maps is for the Papua province, which accounts for 62-71% of the overall differences in peat area, volume and carbon storage. According to the MoA map, 80% of Indonesian peatlands are <300 cm thick and thus vulnerable to conversion outside of protected areas according to environmental regulations. The carbon contained in these shallower peatlands is conservatively estimated to be 10.6 GtC, equivalent to 42% of Indonesia's total peat carbon and about 12 years of global emissions from land use change at current rates. Considering the high uncertainties in peatland extent, volume and carbon storage revealed in this assessment of current maps, a systematic revision of Indonesia's peat maps to produce a single geospatial reference that is universally accepted would improve national peat carbon storage estimates and greatly benefit carbon cycle research, land use management and spatial planning.

Digital Mapping Techniques '11–12 workshop proceedings

USGS Publications Warehouse

Soller, David R.

2014-01-01

At these meetings, oral and poster presentations and special discussion sessions emphasized: (1) methods for creating and publishing map products (here, "publishing" includes Web-based release); (2) field data capture software and techniques, including the use of LiDAR; (3) digital cartographic techniques; (4) migration of digital maps into ArcGIS Geodatabase formats; (5) analytical GIS techniques; and (6) continued development of the National Geologic Map Database.

Preliminary maps showing ground-water resources in the Lower Colorado River region, Arizona, Nevada, New Mexico, and Utah

USGS Publications Warehouse

Brown, S.G.

1976-01-01

This atlas was prepared to meet the need for information on the areal distribution, quantity, and availability of ground water in the lower Colorado River region, an area of about 140,000 square miles in parts of Arizona, Nevada, New Mexico, and Utah. The maps are necessarily generalized in places owing to the lack of sufficient data. In general the geohydrologic information pertains to large areas, and local exceptions occur. Users needing more detailed information for specific areas may address inquiries to the district chief of the U.S. Geological Survey at the addresses given in the section “Selected References.” The maps were prepared using data from previously published reports, data collected by other Federal State, and local agencies, and data from the files of the U.S. Geological Survey offices in Arizona, Nevada, New Mexico, and Utah. The report is the result of the lower Colorado River region Type I framework study made in cooperation with the U.S. Bureau of Reclamation.

Carbon isotope compositions of terrestrial C3 plants as indicators of (paleo)ecology and (paleo)climate

PubMed Central

Kohn, Matthew J.

2010-01-01

A broad compilation of modern carbon isotope compositions in all C3 plant types shows a monotonic increase in δ13C with decreasing mean annual precipitation (MAP) that differs from previous models. Corrections for temperature, altitude, or latitude are smaller than previously estimated. As corrected for altitude, latitude, and the δ13C of atmospheric CO2, these data permit refined interpretation of MAP, paleodiet, and paleoecology of ecosystems dominated by C3 plants, either prior to 7–8 million years ago (Ma), or more recently at mid- to high latitudes. Twenty-nine published paleontological studies suggest preservational or scientific bias toward dry ecosystems, although wet ecosystems are also represented. Unambiguous isotopic evidence for C4 plants is lacking prior to 7–8 Ma, and hominid ecosystems at 4.4 Ma show no isotopic evidence for dense forests. Consideration of global plant biomass indicates that average δ13C of C3 plants is commonly overestimated by approximately 2‰. PMID:21041671

Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification.

PubMed

Cain-Hom, Carol; Splinter, Erik; van Min, Max; Simonis, Marieke; van de Heijning, Monique; Martinez, Maria; Asghari, Vida; Cox, J Colin; Warming, Søren

2017-05-05

Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Remote sensing of potential lunar resources. 2: High spatial resolution mapping of spectral reflectance ratios and implications for nearside mare TiO2 content`

NASA Technical Reports Server (NTRS)

Melendrez, David E.; Johnson, Jeffrey R.; Larson, Stephen M.; Singer, Robert B.

1994-01-01

High spatial resolution maps illustrating variations in spectral reflectance 400/560 nm ratio values have been generated for the following mare regions: (1) the border between southern Mare Serenitatis and northern Mare Tranquillitatis (including the MS-2 standard area and Apollo 17 landing site), (2) central Mare Tranquillitatis, (3) Oceanus Procellarum near Seleucus, and (4) southern Oceanus Procellarum and Flamsteed. We have also obtained 320-1000 nm reflectance spectra of several sites relative to MS-2 to facilitate scaling of the images and provide additional information on surface composition. Inferred TiO2 abundances for these mare regions have been determined using an empirical calibration which relates the weight percent TiO2 in mature mare regolith to the observed 400/560 nm ratio. Mare areas with high TiO2 abundances are probably rich in ilmenite (FeTiO3) a potential lunar resource. The highest potential TiO2 concentrations we have identified in the nearside maria occur in central Mare Tranquillitatis. Inferred TiO2 contents for these areas are greater than 9 wt% and are spatially consistent with the highest-TiO2 regions mapped previously at lower spatial resolution. We note that the morphology of surface units with high 400/560 nm ratio values increases in complexity at higher spatial resolutions. Comparisons have been made with previously published geologic maps, Lunar Orbiter IV, and ground-based images, and some possible morphologic correlatins have been found between our mapped 400/560 nm ratio values and volcanic landforms such as lava flows, mare domes, and collapse pits.

Geologic map of the north polar region of Mars

USGS Publications Warehouse

Tanaka, Kenneth L.; Fortezzo, Corey M.

2012-01-01

The north polar region of Mars occurs within the central and lowest part of the vast northern plains of Mars and is dominated by the roughly circular north polar plateau, Planum Boreum. The northern plains formed very early in Martian time and have collected volcanic flows and sedimentary materials shed from highland sources. Planum Boreum has resulted from the accumulation of water ice and dust particles. Extensive, uncratered dune fields adjacent to Planum Boreum attest to the active and recent transport and accumulation of sand. Our geologic map of Planum Boreum is the first to record its entire observable stratigraphic record using the various post-Viking image and topography datasets released before 2009. We also provide much more detail in the map than previously published, including some substantial revisions based on new data and observations. The available data have increased and improved immensely in quantity, resolution, coverage, positional accuracy, and spectral range, enabling us to resolve previously unrecognized geomorphic features, stratigraphic relations, and compositional information. We also employ more carefully prescribed and effective mapping methodologies and digital techniques, as well as formatting guidelines. The foremost aspect to our mapping approach is how geologic units are discriminated based primarily on their temporal relations with other units as expressed in unit contacts by unconformities or by gradational relations. Whereas timing constraints of such activity in the north polar region are now better defined stratigraphically, they remain poorly constrained chronologically. The end result is a new reconstruction of the sedimentary, erosional, and structural histories of the north polar region and how they may have been driven by climate conditions, available geologic materials, and eolian, periglacial, impact, magmatic, hydrologic, and tectonic activity.

Usability Assessment of the Missouri Cancer Registry’s Published Interactive Mapping Reports: Round One

PubMed Central

Jackson-Thompson, Jeannette; Schmaltz, Chester Lee

2017-01-01

Background  Many users of spatial data have difficulty interpreting information in health-related spatial reports. The Missouri Cancer Registry and Research Center (MCR-ARC) has produced interactive reports for several years. These reports have never been tested for usability. Objective  The aims of this study were to: (1) conduct a multi-approach usability testing study to understand ease of use (user friendliness) and user satisfaction; and (2) evaluate the usability of MCR-ARC’s published InstantAtlas reports. Methods   An institutional review board (IRB) approved mixed methodology usability testing study using a convenience sample of health professionals. A recruiting email was sent to faculty in the Master of Public Health program and to faculty and staff in the Department of Health Management and Informatics at the University of Missouri-Columbia. The study included 7 participants. The test included a pretest questionnaire, a multi-task usability test, and the System Usability Scale (SUS). Also, the researchers collected participants’ comments about the tested maps immediately after every trial. Software was used to record the computer screen during the trial and the participants’ spoken comments. Several performance and usability metrics were measured to evaluate the usability of MCR-ARC’s published mapping reports. Results Of the 10 assigned tasks, 6 reached a 100% completion success rate, and this outcome was relative to the complexity of the tasks. The simple tasks were handled more efficiently than the complicated tasks. The SUS score ranged between 20-100 points, with an average of 62.7 points and a median of 50.5 points. The tested maps’ effectiveness outcomes were better than the efficiency and satisfaction outcomes. There was a statistically significant relationship between the subjects’ performance on the study test and the users’ previous experience with geographic information system (GIS) tools (P=.03). There were no statistically significant relationships between users’ performance and satisfaction and their education level, work type, or previous experience in health care (P>.05). There were strong positive correlations between the three measured usability elements. Conclusions The tested maps should undergo an extensive refining and updating to overcome all the discovered usability issues and meet the perspectives and needs of the tested maps’ potential users. The study results might convey the perspectives of academic health professionals toward GIS health data. We need to conduct a second-round usability study with public health practitioners and cancer professionals who use GIS tools on a routine basis. Usability testing should be conducted before and after releasing MCR-ARC’s maps in the future. PMID:28778842

Water-level altitudes 2008 and water-level changes in the Chicot, Evangeline, and Jasper Aquifers and compaction 1973-2007 in the Chicot and Evangeline Aquifers, Houston-Galveston Region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Houston, Natalie A.

2008-01-01

This report, done in cooperation with the Harris-Galveston Subsidence District, the City of Houston, the Fort Bend Subsidence District, and the Lone Star Groundwater Conservation District, is one in an annual series of reports that depicts water-level altitudes and water-level changes in the Chicot, Evangeline, and Jasper aquifers, and compaction in the Chicot and Evangeline aquifers in the Houston-Galveston region, Texas. The report contains 17 sheets and 16 tables: 3 sheets are maps showing current-year (2008) water-level altitudes for each aquifer, respectively; 3 sheets are maps showing 1-year (2007-08) water-level changes for each aquifer, respectively; 3 sheets are maps showing 5-year (2003-08) water-level changes for each aquifer, respectively; 4 sheets are maps showing long-term (1990-2008 and 1977-2008) water-level changes for the Chicot and Evangeline aquifers, respectively; 1 sheet is a map showing long-term (2000-2008) water-level change for the Jasper aquifer; 1 sheet is a revision of a previously published water-level-altitude map for the Jasper aquifer for 2003; 1 sheet is a map showing site locations of borehole extensometers; and 1 sheet comprises graphs showing measured compaction of subsurface material at the sites from 1973 or later through 2007, respectively. Tables listing the data used to construct the aquifer-data maps and the compaction graphs are included.

Water-level altitudes 2007 and water-level changes in the Chicot, Evangeline, and Jasper Aquifers and compaction 1973-2006 in the Chicot and Evangeline Aquifers, Houston-Galveston Region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Houston, Natalie A.

2007-01-01

This report, done in cooperation with the Harris-Galveston Subsidence District, the City of Houston, the Fort Bend Subsidence District, and the Lone Star Groundwater Conservation District, is one in an annual series of reports that depicts water-level altitudes and water-level changes in the Chicot, Evangeline, and Jasper aquifers, and compaction in the Chicot and Evangeline aquifers in the Houston-Galveston, Texas, region. The report contains 18 sheets and 17 tables: 3 sheets are maps showing current-year (2007) water-level altitudes for each aquifer, respectively; 3 sheets are maps showing 1-year (2006-07) water-level changes for each aquifer, respectively; 3 sheets are maps showing 5-year (2002-07) water-level changes for each aquifer, respectively; 4 sheets are maps showing long-term (1990-2007 and 1977-2007) water-level changes for the Chicot and Evangeline aquifers, respectively; 1 sheet is a map showing long-term (2000-2007) water-level change for the Jasper aquifer; 2 sheets are revisions of previously published water-level-altitude maps for the Jasper aquifer for 2000 and 2002, respectively; 1 sheet is a map showing site locations of borehole extensometers; and 1 sheet comprises graphs showing measured compaction of subsurface material at the sites from 1973 or later through 2006, respectively. Tables listing the data used to construct the aquifer-data maps and the compaction graphs also are included.

Map showing geology, oil and gas fields, and geologic provinces of the Gulf of Mexico region

USGS Publications Warehouse

French, Christopher D.; Schenk, Christopher J.

2006-01-01

This map was created as part of a worldwide series of geologic maps for the U.S. Geological Survey's World Energy Project. These products are available on CD-ROM and the Internet. The goal of the project is to assess the undiscovered, technically recoverable oil and gas resources of the world. Two previously published digital geologic data sets (U.S. and Caribbean) were clipped to the map extent, while the dataset for Mexico was digitized for this project. Original attributes for all data layers were maintained, and in some cases, graphically merged with common symbology for presentation purposes. The world has been divided into geologic provinces that are used for allocation and prioritization of oil and gas assessments. For the World Energy Project, a subset of those provinces is shown on this map. Each province has a set of geologic characteristics that distinguish it from surrounding provinces. These characteristics may include dominant lithologies, the age of the strata, and/or structural type. The World Geographic Coordinate System of 1984 is used for data storage, and the data are presented in a Lambert Conformal Conic Projection on the OFR 97-470-L map product. Other details about the map compilation and data sources are provided in metadata documents in the data section on this CD-ROM. Several software packages were used to create this map including: Environmental Systems Research Institute, Inc. (ESRI) ArcGIS 8.3, ArcInfo software, Adobe Photoshop CS, Illustrator CS, and Acrobat 6.0.

Improving fMRI reliability in presurgical mapping for brain tumours.

PubMed

Stevens, M Tynan R; Clarke, David B; Stroink, Gerhard; Beyea, Steven D; D'Arcy, Ryan Cn

2016-03-01

Functional MRI (fMRI) is becoming increasingly integrated into clinical practice for presurgical mapping. Current efforts are focused on validating data quality, with reliability being a major factor. In this paper, we demonstrate the utility of a recently developed approach that uses receiver operating characteristic-reliability (ROC-r) to: (1) identify reliable versus unreliable data sets; (2) automatically select processing options to enhance data quality; and (3) automatically select individualised thresholds for activation maps. Presurgical fMRI was conducted in 16 patients undergoing surgical treatment for brain tumours. Within-session test-retest fMRI was conducted, and ROC-reliability of the patient group was compared to a previous healthy control cohort. Individually optimised preprocessing pipelines were determined to improve reliability. Spatial correspondence was assessed by comparing the fMRI results to intraoperative cortical stimulation mapping, in terms of the distance to the nearest active fMRI voxel. The average ROC-r reliability for the patients was 0.58±0.03, as compared to 0.72±0.02 in healthy controls. For the patient group, this increased significantly to 0.65±0.02 by adopting optimised preprocessing pipelines. Co-localisation of the fMRI maps with cortical stimulation was significantly better for more reliable versus less reliable data sets (8.3±0.9 vs 29±3 mm, respectively). We demonstrated ROC-r analysis for identifying reliable fMRI data sets, choosing optimal postprocessing pipelines, and selecting patient-specific thresholds. Data sets with higher reliability also showed closer spatial correspondence to cortical stimulation. ROC-r can thus identify poor fMRI data at time of scanning, allowing for repeat scans when necessary. ROC-r analysis provides optimised and automated fMRI processing for improved presurgical mapping. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

PubMed Central

Myśków, Beata; Stojałowski, Stefan; Heller-Uszyńska, Katarzyna; Góralska, Magdalena; Brągoszewski, Piotr; Uszyński, Grzegorz; Kilian, Andrzej; Rakoczy-Trojanowska, Monika

2011-01-01

Background Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers. Methodology/Principal Findings Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers. Conclusions/Significance Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization. PMID:22163026

Geologic Map of Central (Interior) Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Dover, James H.; Bradley, Dwight C.; Weber, Florence R.; Bundtzen, Thomas K.; Haeussler, Peter J.

1998-01-01

Introduction: This map and associated digital databases are the result of a compilation and reinterpretation of published and unpublished 1:250,000- and limited 1:125,000- and 1:63,360-scale mapping. The map area covers approximately 416,000 sq km (134,000 sq mi) and encompasses 25 1:250,000-scale quadrangles in central Alaska. The compilation was done as part of the U.S. Geological Survey National Surveys and Analysis project, whose goal is nationwide assemble geologic, geochemical, geophysical, and other data. This map is an early product of an effort that will eventually encompass all of Alaska, and is the result of an agreement with the Alaska Department of Natural Resources, Division of Oil And Gas, to provide data on interior basins in Alaska. A paper version of the three map sheets has been published as USGS Open-File Report 98-133. Two geophysical maps that cover the identical area have been published earlier: 'Bouguer gravity map of Interior Alaska' (Meyer and others, 1996); and 'Merged aeromagnetic map of Interior Alaska' (Meyer and Saltus, 1995). These two publications are supplied in the 'geophys' directory of this report.

Viable Mycobacterium avium ssp. paratuberculosis isolated from calf milk replacer.

PubMed

Grant, Irene R; Foddai, Antonio C G; Tarrant, James C; Kunkel, Brenna; Hartmann, Faye A; McGuirk, Sheila; Hansen, Chungyi; Talaat, Adel M; Collins, Michael T

2017-12-01

When advising farmers on how to control Johne's disease in an infected herd, one of the main recommendations is to avoid feeding waste milk to calves and instead feed calf milk replacer (CMR). This advice is based on the assumption that CMR is free of viable Mycobacterium avium ssp. paratuberculosis (MAP) cells, an assumption that has not previously been challenged. We tested commercial CMR products (n = 83) obtained from dairy farms around the United States by the peptide-mediated magnetic separation (PMS)-phage assay, PMS followed by liquid culture (PMS-culture), and direct IS900 quantitative PCR (qPCR). Conventional microbiological analyses for total mesophilic bacterial counts, coliforms, Salmonella, coagulase-negative staphylococci, streptococci, nonhemolytic Corynebacterium spp., and Bacillus spp. were also performed to assess the overall microbiological quality of the CMR. Twenty-six (31.3%) of the 83 CMR samples showed evidence of the presence of MAP. Seventeen (20.5%) tested positive for viable MAP by the PMS-phage assay, with plaque counts ranging from 6 to 1,212 pfu/50 mL of reconstituted CMR (average 248.5 pfu/50 mL). Twelve (14.5%) CMR samples tested positive for viable MAP by PMS-culture; isolates from all 12 of these samples were subsequently confirmed by whole-genome sequencing to be different cattle strains of MAP. Seven (8.4%) CMR samples tested positive for MAP DNA by IS900 qPCR. Four CMR samples tested positive by both PMS-based tests and 5 CMR samples tested positive by IS900 qPCR plus one or other of the PMS-based tests, but only one CMR sample tested positive by all 3 MAP detection tests applied. All conventional microbiology results were within current standards for whole milk powders. A significant association existed between higher total bacterial counts and presence of viable MAP indicated by either of the PMS-based assays. This represents the first published report of the isolation of viable MAP from CMR. Our findings raise concerns about the potential ability of MAP to survive manufacture of dried milk-based products. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Making Air Pollution Visible: A Tool for Promoting Environmental Health Literacy.

PubMed

Cleary, Ekaterina Galkina; Patton, Allison P; Wu, Hsin-Ching; Xie, Alan; Stubblefield, Joseph; Mass, William; Grinstein, Georges; Koch-Weser, Susan; Brugge, Doug; Wong, Carolyn

2017-04-12

Digital maps are instrumental in conveying information about environmental hazards geographically. For laypersons, computer-based maps can serve as tools to promote environmental health literacy about invisible traffic-related air pollution and ultrafine particles. Concentrations of these pollutants are higher near major roadways and increasingly linked to adverse health effects. Interactive computer maps provide visualizations that can allow users to build mental models of the spatial distribution of ultrafine particles in a community and learn about the risk of exposure in a geographic context. The objective of this work was to develop a new software tool appropriate for educating members of the Boston Chinatown community (Boston, MA, USA) about the nature and potential health risks of traffic-related air pollution. The tool, the Interactive Map of Chinatown Traffic Pollution ("Air Pollution Map" hereafter), is a prototype that can be adapted for the purpose of educating community members across a range of socioeconomic contexts. We built the educational visualization tool on the open source Weave software platform. We designed the tool as the centerpiece of a multimodal and intergenerational educational intervention about the health risk of traffic-related air pollution. We used a previously published fine resolution (20 m) hourly land-use regression model of ultrafine particles as the algorithm for predicting pollution levels and applied it to one neighborhood, Boston Chinatown. In designing the map, we consulted community experts to help customize the user interface to communication styles prevalent in the target community. The product is a map that displays ultrafine particulate concentrations averaged across census blocks using a color gradation from white to dark red. The interactive features allow users to explore and learn how changing meteorological conditions and traffic volume influence ultrafine particle concentrations. Users can also select from multiple map layers, such as a street map or satellite view. The map legends and labels are available in both Chinese and English, and are thus accessible to immigrants and residents with proficiency in either language. The map can be either Web or desktop based. The Air Pollution Map incorporates relevant language and landmarks to make complex scientific information about ultrafine particles accessible to members of the Boston Chinatown community. In future work, we will test the map in an educational intervention that features intergenerational colearning and the use of supplementary multimedia presentations. ©Ekaterina Galkina Cleary, Allison P Patton, Hsin-Ching Wu, Alan Xie, Joseph Stubblefield, William Mass, Georges Grinstein, Susan Koch-Weser, Doug Brugge, Carolyn Wong. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 12.04.2017.

Geochronologic and geochemical data from Mesozoic rocks in the Black Mountain area northeast of Victorville, San Bernardino County, California

USGS Publications Warehouse

Stone, Paul; Barth, Andrew P.; Wooden, Joseph L.; Fohey-Breting, Nicole K.; Vazquez, Jorge A.; Priest, Susan S.

2013-01-01

We present geochronologic and geochemical data for Mesozoic rocks in the Black Mountain area northeast of Victorville, California, to supplement previous geologic mapping. These data, together with previously published results, limit the depositional age of the sedimentary Fairview Valley Formation to Early Jurassic, refine the ages and chemical compositions of selected units in the overlying Jurassic Sidewinder Volcanics and of related intrusive units, and limit the age of some post-Sidewinder faulting in the Black Mountain area to a brief interval in the Late Jurassic. The new information contributes to a more complete understanding of the Mesozoic magmatic and tectonic evolution of the western Mojave Desert and surrounding regions.

Stratigraphic sections of the Phosphoria formation in Idaho, 1947-48, Part I

USGS Publications Warehouse

McKelvey, Vincent Ellis; Davidson, D.F.; O'Malley, F. W.; Smith, L.E.; Armstrong, F.C.; Sheldon, R.P.

1952-01-01

The Permian Phosphoria formation of the western states contains one of the world's largest reserves of phosphate. Although previous investigations (see especially Mansfield, 1927), including reconnaissance geologic mapping and sampling, established the location of most of the important deposits and their quality of scattered localities, they were not sufficiently detailed to permit a comparison of the merits of individual deposits or an appraisal of the reserves of phosphate rock that might be available under present economic conditions. Because the growing importance of the western phosphate deposits requires a better, more detailed understanding of their distribution and quality, the Geological Survey began in 1947 a comprehensive investigation, including (1) reconnaissance geologic mapping, mostly in Montana, of areas in which the Phosphoria formation could occur but where it had not previously been looked for or found; (2) geologic mapping, mostly in Montana, at a scale no smaller than 1:62,500, of several areas known to contain the Phosphoria formation but not previously mapped except in reconnaissance fashion; (3) geologic and topographic mapping, at a scale of 1:12,000, of some of the richest, thickest, and most accessible deposits; (4) measuring, describing, and sampling all beds of the phosphatic and shaly parts, and in some places the full thickness, of the Phosphoria formation and its stratigraphic equivalents at one or two localities per township over the entire field; (5) chemical and spectrographic analysis of the samples for phosphate, fluorine, minor metals, oil, and rock-forming constituents; and (6) petrologic and geochemical studies of the rocks and minerals of the formation. These studies are designed to define the regional and local geologic structures in which the phosphate bed lie, to provide a basis for the estimation of reserves of the inferred class over the entire region, and to determine the origin of the rocks and the elements contained in them. The data collected are not of the detail required to plan actual mining operations, but it is hoped they will guide industry in the selection of individual deposits worthy of further exploration. Most of the field work contemplated as a part of this investigation is now completed. Although the data will not be compiled or published in final form for some years to come, segments of the data, accompanied by little or no interpretation, will be published as preliminary maps or reports as they are assembled. The present report is the first of a series presenting in abbreviated form the description and analyses of the beds measured and sampled at various localities in southeastern Idaho (pl. 1). Companion reports presenting segments of the data from Montana, Wyoming, and Utah (Swanson and others, 1952, and McKelvey and others, 1952a and 1952b) are being released at the same time as this report, and others are in preparation.

Map showing the distribution and characteristics of plutonic rocks in the Tonopah 1 degree by 2 degrees Quadrangle, central Nevada

USGS Publications Warehouse

John, D.A.

1987-01-01

The accompanying table includes the name (if any) of the pluton and its location, the age of the pluton (either a radiometric age or an age inferred from field relations), modal composition, texture, mineralogy, hydrothermal alteration and mineralization related to the pluton, the source of mapping shown on this map, and published references on the pluton. Radiometric ages are either published K-Ar and fission track ages or new whole-rock Rb-Sr ages determined by A. C. Robinson on samples collected either for this study or as part of regional Sr-isotope studies by R.W. Kistler and A.C. Robinson. K-Ar ages published prior to 1977 are corrected using the new I.U.C.S. constants (Steiger and Jager, 1977). Muscovite alteration ages are reported for several plutons and represent minimum ages for emplacement of these plutons. Compositional classification follows the T. J. G.S. system (“Streckeisen, 1976) and is based either on modal analyses of slabs or estimates from hand specimens. All modes, unless otherwise noted, were measured in this study. The number of modes determined is shown in parentheses, and the range in volume percent of major minerals is given. Where no modal data are available, the color index (percentage of mafic minerals) and major mafic minerals are given for most plutons. Data tabulated on hydrothermal alteration and mineralization related to plutons are based on observations made during field studies for this project. Clear genetic relation between granitic plutonism and several mineral deposits previously attributed to granitic plutonism were not substantiated, and these inconsistencies are noted in the table.

Status of shallow-aquifer mapping in the Northern Front Range Area, Colorado

USGS Publications Warehouse

Robson, Stanley G.

2001-01-01

Mapping of shallow aquifers in the northern Front Range area of Colorado has been completed as part of the U.S. Geological Survey Front Range Infrastructure Resources Project. The aquifer mapping was undertaken as part of a comprehensive effort to better define the mineral, energy, cartographic, biological, and water resources that are critical to the support and development of the area's infrastructure, such as streets. highways, airports, and buildings. The aquifer mapping was undertaken in cooperation with the Colorado Division of Water Resources and the Colorado Water Conservation Board. The shallow aquifers have been mapped in a 2,450-square-mile area extending as an approximately 30-mile-wide band from north of Fort Collins to the Arapahoe-Douglas County line south of Denver (fig. I). The shallow aquifer mapping in the Denver metropolitan area was published in 1996 as Hydrologic Investigations Atlas HA-736 (Robson. 1996). Shallow aquifer mapping in the Greeley-Nunn area was published as HA-746A (Robson, Arnold, and Heiny, 2000a); mapping in the Fort Collins-Loveland area was published as HA-746B (Robson, Arnold, and Heiny, 2000b); mapping in the Fort Lupton-Gilcrest area was published as HA-746C (Robson, Heiny, and Arnold, 2000c); and mapping in the Boulder-Longmont area was published as HA-746D (Robson, Heiny, and Arnold, 2000d). Each of the five atlases contains five map sheets at 1:50,000 scale showing: 1. The thickness and extent of the unconsolidated sediments (loose gravel. sand. silt, and clay) that overlie the bedrock formations in the area (fig. 2). 2. The altitude and configuration of the bedrock surface. 3. The altitude of the water table and direction of ground-water movement. 4. The saturated thickness of the shallow aquifers. 5. The depth to the water table in the shallow aquifers.

Regulation of choroidal blood flow during combined changes in intraocular pressure and arterial blood pressure.

PubMed

Polska, Elzbieta; Simader, Christian; Weigert, Günter; Doelemeyer, Arno; Kolodjaschna, Julia; Scharmann, Ole; Schmetterer, Leopold

2007-08-01

To test the hypothesis that human choroidal blood flow (ChBF) may depend, not only on ocular perfusion pressure (OPP), but also on absolute mean arterial pressure (MAP) and intraocular pressure (IOP). There were two study days in an open design. On the first day, OPP was varied by elevating IOP during a squatting-induced increase in MAP (28 subjects). On the second day, only the IOP was increased (17 subjects). IOP was raised in stepwise increments by using the suction cup Subfoveal ChBF (laser Doppler flowmetry), MAP, and IOP were assessed, and OPP was calculated as (2/3)(MAP - IOP). For correlation analysis, data from all subjects were pooled according to IOP and MAP, and correlation analyses were performed. When data from study day 1 were grouped according to IOP, no correlation was observed between ChBF and MAP; but ChBFs were lower, the higher the IOP (P < 0.001). When data were grouped according to MAP, a significant correlation was found between ChBF and IOP (P < 0.001), but correlations were independent of MAP. When data of study day 2 were pooled according to IOP, a correlation between ChBF and OPP was seen only at IOP > 40 mm Hg (P < 0.05). The data confirm previously published observations that the choroid shows some autoregulatory capacity during changes in OPP. In addition, the data indicate that the choroid regulates its blood flow better during exercise-induced changes in MAP than during an experimental increase in IOP.

Food parenting practices for 5 to 12 year old children: a concept map analysis of parenting and nutrition experts input.

PubMed

O'Connor, Teresia M; Mâsse, Louise C; Tu, Andrew W; Watts, Allison W; Hughes, Sheryl O; Beauchamp, Mark R; Baranowski, Tom; Pham, Truc; Berge, Jerica M; Fiese, Barbara; Golley, Rebecca; Hingle, Melanie; Kremers, Stef P J; Rhee, Kyung E; Skouteris, Helen; Vaughn, Amber

2017-09-11

Parents are an important influence on children's dietary intake and eating behaviors. However, the lack of a conceptual framework and inconsistent assessment of food parenting practices limits our understanding of which food parenting practices are most influential on children. The aim of this study was to develop a food parenting practice conceptual framework using systematic approaches of literature reviews and expert input. A previously completed systematic review of food parenting practice instruments and a qualitative study of parents informed the development of a food parenting practice item bank consisting of 3632 food parenting practice items. The original item bank was further reduced to 110 key food parenting concepts using binning and winnowing techniques. A panel of 32 experts in parenting and nutrition were invited to sort the food parenting practice concepts into categories that reflected their perceptions of a food parenting practice conceptual framework. Multi-dimensional scaling produced a point map of the sorted concepts and hierarchical cluster analysis identified potential solutions. Subjective modifications were used to identify two potential solutions, with additional feedback from the expert panel requested. The experts came from 8 countries and 25 participated in the sorting and 23 provided additional feedback. A parsimonious and a comprehensive concept map were developed based on the clustering of the food parenting practice constructs. The parsimonious concept map contained 7 constructs, while the comprehensive concept map contained 17 constructs and was informed by a previously published content map for food parenting practices. Most of the experts (52%) preferred the comprehensive concept map, while 35% preferred to present both solutions. The comprehensive food parenting practice conceptual map will provide the basis for developing a calibrated Item Response Modeling (IRM) item bank that can be used with computerized adaptive testing. Such an item bank will allow for more consistency in measuring food parenting practices across studies to better assess the impact of food parenting practices on child outcomes and the effect of interventions that target parents as agents of change.

Energy map of southwestern Wyoming - Energy data archived, organized, integrated, and accessible

USGS Publications Warehouse

Biewick, Laura; Jones, Nicholas R.; Wilson, Anna B.

2013-01-01

The Wyoming Landscape Conservation Initiative (WLCI) focuses on conserving world-class wildlife resources while facilitating responsible energy development in southwestern Wyoming. To further advance the objectives of the WLCI long-term, science-based effort, a comprehensive inventory of energy resource and production data is being published in two parts. Energy maps, data, documentation and spatial data processing capabilities are available in geodatabase, published map file (pmf), ArcMap document (mxd), Adobe Acrobat PDF map, and other digital formats that can be downloaded at the USGS website.

Estimating A Reference Standard Segmentation With Spatially Varying Performance Parameters: Local MAP STAPLE

PubMed Central

Commowick, Olivier; Akhondi-Asl, Alireza; Warfield, Simon K.

2012-01-01

We present a new algorithm, called local MAP STAPLE, to estimate from a set of multi-label segmentations both a reference standard segmentation and spatially varying performance parameters. It is based on a sliding window technique to estimate the segmentation and the segmentation performance parameters for each input segmentation. In order to allow for optimal fusion from the small amount of data in each local region, and to account for the possibility of labels not being observed in a local region of some (or all) input segmentations, we introduce prior probabilities for the local performance parameters through a new Maximum A Posteriori formulation of STAPLE. Further, we propose an expression to compute confidence intervals in the estimated local performance parameters. We carried out several experiments with local MAP STAPLE to characterize its performance and value for local segmentation evaluation. First, with simulated segmentations with known reference standard segmentation and spatially varying performance, we show that local MAP STAPLE performs better than both STAPLE and majority voting. Then we present evaluations with data sets from clinical applications. These experiments demonstrate that spatial adaptivity in segmentation performance is an important property to capture. We compared the local MAP STAPLE segmentations to STAPLE, and to previously published fusion techniques and demonstrate the superiority of local MAP STAPLE over other state-of-the- art algorithms. PMID:22562727

Detection of microRNAs in color space.

PubMed

Marco, Antonio; Griffiths-Jones, Sam

2012-02-01

Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs. Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3(') end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs. A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/ antonio.marco@manchester.ac.uk Supplementary data are available at Bioinformatics online.

Genome-Wide Association Study Dissects the Genetic Architecture of Seed Weight and Seed Quality in Rapeseed (Brassica napus L.)

PubMed Central

Li, Feng; Chen, Biyun; Xu, Kun; Wu, Jinfeng; Song, Weilin; Bancroft, Ian; Harper, Andrea L.; Trick, Martin; Liu, Shengyi; Gao, Guizhen; Wang, Nian; Yan, Guixin; Qiao, Jiangwei; Li, Jun; Li, Hao; Xiao, Xin; Zhang, Tianyao; Wu, Xiaoming

2014-01-01

Association mapping can quickly and efficiently dissect complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, although its genome sequence is not yet published. In this study, a recently developed 60K Brassica Infinium® SNP array was used to analyse an association panel with 472 accessions. The single-nucleotide polymorphisms (SNPs) of the array were in silico mapped using ‘pseudomolecules’ representative of the genome of rapeseed to establish their hypothetical order and to perform association mapping of seed weight and seed quality. As a result, two significant associations on A8 and C3 of Brassica napus were detected for erucic acid content, and the peak SNPs were found to be only 233 and 128 kb away from the key genes BnaA.FAE1 and BnaC.FAE1. BnaA.FAE1 was also identified to be significantly associated with the oil content. Orthologues of Arabidopsis thaliana HAG1 were identified close to four clusters of SNPs associated with glucosinolate content on A9, C2, C7 and C9. For seed weight, we detected two association signals on A7 and A9, which were consistent with previous studies of quantitative trait loci mapping. The results indicate that our association mapping approach is suitable for fine mapping of the complex traits in rapeseed. PMID:24510440

Accurate nonlinear mapping between MNI volumetric and FreeSurfer surface coordinate systems.

PubMed

Wu, Jianxiao; Ngo, Gia H; Greve, Douglas; Li, Jingwei; He, Tong; Fischl, Bruce; Eickhoff, Simon B; Yeo, B T Thomas

2018-05-16

The results of most neuroimaging studies are reported in volumetric (e.g., MNI152) or surface (e.g., fsaverage) coordinate systems. Accurate mappings between volumetric and surface coordinate systems can facilitate many applications, such as projecting fMRI group analyses from MNI152/Colin27 to fsaverage for visualization or projecting resting-state fMRI parcellations from fsaverage to MNI152/Colin27 for volumetric analysis of new data. However, there has been surprisingly little research on this topic. Here, we evaluated three approaches for mapping data between MNI152/Colin27 and fsaverage coordinate systems by simulating the above applications: projection of group-average data from MNI152/Colin27 to fsaverage and projection of fsaverage parcellations to MNI152/Colin27. Two of the approaches are currently widely used. A third approach (registration fusion) was previously proposed, but not widely adopted. Two implementations of the registration fusion (RF) approach were considered, with one implementation utilizing the Advanced Normalization Tools (ANTs). We found that RF-ANTs performed the best for mapping between fsaverage and MNI152/Colin27, even for new subjects registered to MNI152/Colin27 using a different software tool (FSL FNIRT). This suggests that RF-ANTs would be useful even for researchers not using ANTs. Finally, it is worth emphasizing that the most optimal approach for mapping data to a coordinate system (e.g., fsaverage) is to register individual subjects directly to the coordinate system, rather than via another coordinate system. Only in scenarios where the optimal approach is not possible (e.g., mapping previously published results from MNI152 to fsaverage), should the approaches evaluated in this manuscript be considered. In these scenarios, we recommend RF-ANTs (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion). © 2018 Wiley Periodicals, Inc.

Publishing Platform for Aerial Orthophoto Maps, the Complete Stack

NASA Astrophysics Data System (ADS)

Čepický, J.; Čapek, L.

2016-06-01

When creating set of orthophoto maps from mosaic compositions, using airborne systems, such as popular drones, we need to publish results of the work to users. Several steps need to be performed in order get large scale raster data published. As first step, data have to be shared as service (OGC WMS as view service, OGC WCS as download service). But for some applications, OGC WMTS is handy as well, for faster view of the data. Finally the data have to become a part of web mapping application, so that they can be used and evaluated by non-technical users. In this talk, we would like to present automated line of those steps, where user puts in orthophoto image and as a result, OGC Open Web Services are published as well as web mapping application with the data. The web mapping application can be used as standard presentation platform for such type of big raster data to generic user. The publishing platform - Geosense online map information system - can be also used for combination of data from various resources and for creating of unique map compositions and as input for better interpretations of photographed phenomenons. The whole process is successfully tested with eBee drone with raster data resolution 1.5-4 cm/px on many areas and result is also used for creation of derived datasets, usually suited for property management - the records of roads, pavements, traffic signs, public lighting, sewage system, grave locations, and others.

Characterization of potential mineralization in Afghanistan: four permissive areas identified using imaging spectroscopy data

USGS Publications Warehouse

King, Trude V.V.; Berger, Byron R.; Johnson, Michaela R.

2014-01-01

As part of the U.S. Geological Survey and Department of Defense Task Force for Business and Stability Operations natural resources revitalization activities in Afghanistan, four permissive areas for mineralization, Bamyan 1, Farah 1, Ghazni 1, and Ghazni 2, have been identified using imaging spectroscopy data. To support economic development, the areas of potential mineralization were selected on the occurrence of selected mineral assemblages mapped using the HyMap™ data (kaolinite, jarosite, hydrated silica, chlorite, epidote, iron-bearing carbonate, buddingtonite, dickite, and alunite) that may be indicative of past mineralization processes in areas with limited or no previous mineral resource studies. Approximately 30 sites were initially determined to be candidates for areas of potential mineralization. Additional criteria and material used to refine the selection and prioritization process included existing geologic maps, Landsat Thematic Mapper data, and published literature. The HyMapTM data were interpreted in the context of the regional geologic and tectonic setting and used the presence of alteration mineral assemblages to identify areas with the potential for undiscovered mineral resources. Further field-sampling, mapping, and supporting geochemical analyses are necessary to fully substantiate and verify the specific deposit types in the four areas of potential mineralization.

Short communication: Investigation into Mycobacterium avium ssp. paratuberculosis in pasteurized milk in Italy.

PubMed

Serraino, A; Bonilauri, P; Giacometti, F; Ricchi, M; Cammi, G; Piva, S; Zambrini, V; Canever, A; Arrigoni, N

2017-01-01

This study investigated the presence of viable Mycobacterium avium ssp. paratuberculosis (MAP) in pasteurized milk produced by Italian industrial dairy plants to verify the prediction of a previously performed risk assessment. The study analyzed 160 one-liter bottles of pasteurized milk from 2 dairy plants located in 2 different regions. Traditional cultural protocols were applied to 500mL of pasteurized milk for each sample. The investigation focused also on the pasteurization parameters and data on the microbiological characteristics of raw milk (total bacterial count) and pasteurized milk (Enterobacteriaceae and Listeria monocytogenes). No sample was positive for MAP, the pasteurization parameters complied with European Union legislation, and the microbiological analysis of raw and pasteurized milk showed good microbiological quality. The results show that a 7-log (or >7) reduction could be a plausible value for commercial pasteurization. The combination of hygiene practices at farm level and commercial pasteurization yield very low or absent levels of MAP contamination in pasteurized milk, suggesting that pasteurized milk is not a significant source of human exposure to MAP in the dairies investigated. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla.

PubMed

Trifonov, Vladimir A; Stanyon, Roscoe; Nesterenko, Anastasia I; Fu, Beiyuan; Perelman, Polina L; O'Brien, Patricia C M; Stone, Gary; Rubtsova, Nadezhda V; Houck, Marlys L; Robinson, Terence J; Ferguson-Smith, Malcolm A; Dobigny, Gauthier; Graphodatsky, Alexander S; Yang, Fengtang

2008-01-01

The order Perissodactyla, the group of odd-toed ungulates, includes three extant families: Equidae, Tapiridae, and Rhinocerotidae. The extremely rapid karyotypic diversification in perissodactyls has so far prevented the establishment of genome-wide homology maps between these three families by traditional cytogenetic approaches. Here we report the first genome-wide comparative chromosome maps of African rhinoceroses, four tapir species, four equine species, and humans. These maps were established by multidirectional chromosome painting, with paint probes derived from flow-sorted chromosomes of Equus grevyi, Tapirus indicus, and Ceratotherium simum as well as painting probes from horse and human. The Malayan tapir (Tapirus indicus), Baird's tapir (T. bairdii), mountain tapir (T. pinchaque), lowland tapir (T. terrestris), and onager (E. hemionus onager), were studied by cross-species chromosome painting for the first time. Our results, when integrated with previously published comparative chromosome maps of the other perissodactyl species, have enabled the reconstruction of perissodactyl, ceratomorph, and equid ancestral karyotypes, and the identification of the defining evolutionary chromosomal rearrangements along each lineage. Our results allow a more reliable estimate of the mode and tempo of evolutionary chromosomal rearrangements, revealing a striking switch between the slowly evolving ceratomorphs and extremely rapidly evolving equids.

A 1.4-Billion Pixel Map of the Seafloor: BOEM's Mission to Visualize Dynamic Geology and Identify Natural Seep Sites in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Kramer, K.; Shedd, W. W.

2017-12-01

In May, 2017, the U.S. Department of the Interior's Bureau of Ocean Energy Management (BOEM) published a high-resolution seafloor map of the northern Gulf of Mexico region. The new map, derived from 3-D seismic surveys, provides the scientific community with enhanced resolution and reveals previously undiscovered and poorly resolved geologic features of the continental slope, salt minibasin province, abyssal plain, Mississippi Fan, and the Florida Shelf and Escarpment. It becomes an even more powerful scientific tool when paired with BOEM's public database of 35,000 seafloor features, identifying natural hydrocarbon seeps, hard grounds, mud volcanoes, sediment flows, pockmarks, slumps, and many others. BOEM has mapped the Gulf of Mexico seafloor since 1998 in a regulatory mission to identify natural oil and gas seeps and protect the coral and chemosynthetic communities growing at those sites. The nineteen-year mapping effort, still ongoing, resulted in the creation of the 1.4-billion pixel map and the seafloor features database. With these tools and continual collaboration with academia, professional scientific institutions, and the offshore energy industry, BOEM will continue to incorporate new data to update and expand these two resources on a regular basis. They can be downloaded for free from BOEM's website at https://www.boem.gov/Gulf-of-Mexico-Deepwater-Bathymetry/ and https://www.boem.gov/Seismic-Water-Bottom-Anomalies-Map-Gallery/.

Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.

PubMed

Lee, Jonghoon; Izzah, Nur Kholilatul; Jayakodi, Murukarthick; Perumal, Sampath; Joh, Ho Jun; Lee, Hyeon Ju; Lee, Sang-Choon; Park, Jee Young; Yang, Ki-Woung; Nou, Il-Sup; Seo, Joodeok; Yoo, Jaeheung; Suh, Youngdeok; Ahn, Kyounggu; Lee, Ji Hyun; Choi, Gyung Ja; Yu, Yeisoo; Kim, Heebal; Yang, Tae-Jin

2015-02-03

Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs. We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

Geologic map of the Calamity Mesa quadrangle, Colorado

USGS Publications Warehouse

Cater, Fred W.

1955-01-01

The series of Geologic Quadrangle Maps of the United States continues the series of quadrangle maps begun with the folios of the Geologic Atlas of the United States, which were published from 1894 to 1945. The present series consists of geologic maps, supplemented where possible by structure sections, columnar sections, and other graphic means of presenting geologic data, and accompanied by a brief explanatory text to make the maps useful for general scientific and economic purposes. Full description and interpretation of the geology of the areas shown on these maps are reserved for publication in other channels, such as the Bulletins and Professional Papers of the Geological Survey. Separate maps of the same areas, covering bedrock, surficial, engineering, and other phases of geology, may be published in the geologic quadrangle map series. 

Geologic Map of the San Luis Hills Area, Conejos and Costilla Counties, Colorado

USGS Publications Warehouse

Thompson, Ren A.; Machette, Michael N.

1989-01-01

This report is a digital image of the U.S. Geological Survey Miscellaneous Investigations Series Map I-1906, 'Geologic map of the San Luis Hills area, Conejos and Costilla Counties, Colorado,' which was published in 1989 by Thompson and Machette, scale 1:50,000 but has been unavailable in a digital version. The map area represents the southwestern portion of the Alamosa 30' x 60' quadrangle, which is currently being remapped by the U.S. Geological Survey. The northern and eastern margins of the San Luis Hills area have been remapped at greater detail and thus small portions of the map area have been updated. The northern margin is shown on U.S. Geological Survey Open-File Report 2005-1392, the northeastern portion is shown on U.S. Geological Survey Open-File Report 2008-1124, and the eastern margin is shown on U.S. Geological Survey Open-File Report 2007-1074. The most significant changes to the 1989 map area are recognition of Lake Alamosa and its deposits (Alamosa Formation), remapping of bedrock in the northeastern San Luis Hills, and redating of volcanic units in the San Luis Hills. Although unpublished, new 40Ar/39Ar ages for volcanic units in the Conejos and Hinsdale Formations add precision to the previous K/Ar-dated rocks, but do not change the basic chronology of the units. The digital version of this map was prepared by Theodore R. Brandt by scanning the original map at 300 pixels per inch, prior to creating the press-quality (96 Mb) and standard (5 Mb) .pdf files.

Geology and mineral resource assessment of the Venezuelan Guayana Shield at 1:500,000 scale; a digital representation of maps published by the U.S. Geological Survey

USGS Publications Warehouse

Schruben, Paul G.; Wynn, J.C.; Gray, Floyd; Cox, D.P.; Sterwart, J.H.; Brooks, W.E.

1997-01-01

This CD-ROM contains vector-based digital maps of the geology and resource assessment of the Venezuela Guayana Shield originally published as paper maps in 1993 in U. S. Geological Survey Bulletin 2062, at a scale of 1:1 million and revised in 1993-95 as separate maps at a scale of 1:500,000. Although the maps on this disc can be displayed at different scales, they are not intended to be used at any scale more detailed than 1:500,000.

Historical Topographic Map Collection bookmark

USGS Publications Warehouse

Fishburn, Kristin A.; Allord, Gregory J.

2017-06-29

The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the historical scanned maps in 2011, is to provide a digital repository of USGS topographic maps, available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of printed topographic maps, and prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic printing process. As the USGS continues the release of a new generation of topographic maps (US Topo) in electronic form, the topographic map remains an indispensable tool for government, science, industry, land management planning, and leisure.

Specification for the U.S. Geological Survey Historical Topographic Map Collection

USGS Publications Warehouse

Allord, Gregory J.; Walter, Jennifer L.; Fishburn, Kristin A.; Shea, Gale A.

2014-01-01

This document provides the detailed requirements for producing, archiving, and disseminating a comprehensive digital collection of topographic maps for the U.S. Geological Survey (USGS) Historical Topographic Map Collection (HTMC). The HTMC is a digital archive of about 190,000 printed topographic maps published by the USGS from the inception of the topographic mapping program in 1884 until the last paper topographic map using lithographic printing technology was published in 2006. The HTMC provides a comprehensive digital repository of all scales and all editions of USGS printed topographic maps that is easily discovered, browsed, and downloaded by the public at no cost. The HTMC provides ready access to maps that are no longer available for distribution in print. A digital file representing the original paper historical topographic map is produced for each historical map in the HTMC in georeferenced PDF (GeoPDF) format (a portable document format [PDF] with a geospatial extension).

Dependence of the cyclization of branched tetraethers on soil moisture in alkaline soils from arid-subhumid China: implications for palaeorainfall reconstructions on the Chinese Loess Plateau

NASA Astrophysics Data System (ADS)

Wang, H.; Liu, W.; Zhang, C. L.

2014-12-01

The use of branched glycerol dialkyl glycerol tetraethers (bGDGTs) in loess-palaeosol sequences (LPSs) has shown promises in continental palaeotemperature reconstructions. Thus far, however, little is known about the effect of soil moisture on their distributions in the water-limited Chinese Loess Plateau (CLP). In this study, the relationships between environmental variables and the cyclization of branched tetraethers (CBT) were investigated in arid-subhumid China using 97 surface soils in the CLP and its vicinity, as well as 78 soils with pH > 7 which have been previously published. We find that CBT correlates best with soil water content (SWC) or mean annual precipitation (MAP) for the overall data set. This indicates that CBT is mainly controlled by soil moisture instead of soil pH in alkaline soils from arid-subhumid regions, where water availability is a limiting factor for the producers of bGDGTs. Therefore, we suggest that CBT can potentially be used as a palaeorainfall proxy on the alkaline CLP. According to the preliminary CBT-MAP relationship for modern CLP soils (CBT = -0.0021 × MAP + 1.7, n = 37, r = -0.93), palaeorainfall history was reconstructed from three LPSs (Yuanbao, Lantian, and Mangshan) with published bGDGT data spanning the past 70 ka. The CBT-derived MAP records of the three sites consistently show precession-driven variation resembling the monsoon record based on speleothem δ18O, supporting CBT as a reasonable proxy for palaeorainfall reconstruction in LPS. The direct application of CBT as a palaeorainfall proxy in corroboration with the bGDGT-based temperature proxy may enable us to further assess the temperature/hydrological association for palaeoclimate studies on the CLP.

Geologic map of the greater Denver area, Front Range urban corridor, Colorado

USGS Publications Warehouse

Trimble, Donald E.; Machette, Michael N.

1979-01-01

This digital map shows the areal extent of surficial deposits and rock stratigraphic units (formations) as compiled by Trimble and Machette from 1973 to 1977 and published in 1979 under the Front Range Urban Corridor Geology Program. Trimble and Machette compiled their geologic map from published geologic maps and unpublished geologic mapping having varied map unit schemes. A convenient feature of the compiled map is its uniform classification of geologic units that mostly matches those of companion maps to the north (USGS I-855-G) and to the south (USGS I-857-F). Published as a color paper map, the Trimble and Machette map was intended for land-use planning in the Front Range Urban Corridor. This map recently (1997-1999) was digitized under the USGS Front Range Infrastructure Resources Project. In general, the mountainous areas in the western part of the map exhibit various igneous and metamorphic bedrock units of Precambrian age, major faults, and fault brecciation zones at the east margin (5-20 km wide) of the Front Range. The eastern and central parts of the map (Colorado Piedmont) depict a mantle of unconsolidated deposits of Quaternary age and interspersed outcroppings of Cretaceous or Tertiary-Cretaceous sedimentary bedrock. The Quaternary mantle comprises eolian deposits (quartz sand and silt), alluvium (gravel, sand, and silt of variable composition), colluvium, and a few landslides. At the mountain front, north-trending, dipping Paleozoic and Mesozoic sandstone, shale, and limestone bedrock formations form hogbacks and intervening valleys.

Energy crop mapping with enhanced TM/MODIS time series in the BCAP agricultural lands

NASA Astrophysics Data System (ADS)

Wang, Cuizhen; Fan, Qian; Li, Qingting; SooHoo, William M.; Lu, Linlin

2017-02-01

Since the mid-2000s, agricultural lands in the United States have been undergoing rapid change to meet the increasing bioenergy demand. In 2009 the USDA Biomass Crop Assistance Program (BCAP) was established. In its Project Area 1, land owners are financially supported to grow perennial prairie grasses (switchgrass) in their row-crop lands. To promote the program, this study tested the feasibility of biomass crop mapping based on unique timings of crop development. With a previously published data fusion algorithm - the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM), a 10-day normalized difference vegetation index (NDVI) time series in 2007 was established by fusing MODIS reflectance into TM image series. Two critical dates - peak growing (PG) and peak drying (PD) - were extracted and a unique "PG-0-PD" timing sequence was defined for each crop. With a knowledge-based decision tree approach, the classification of enhanced TM/MODIS time series reached an overall accuracy of 76% against the USDA Crop Data layer (CDL). Especially, our results showed that winter wheat single cropping and wheat-soybean double cropping were much better classified, which may provide additional information for the CDL product. More importantly, this study extracted the first spatial layer of warm-season prairie grasses that have not been published in any national land cover products, which could serve as a base map for decision making of bioenergy land use in BCAP land.

The vagal ganglia transcriptome identifies candidate therapeutics for airway hyperreactivity.

PubMed

Reznikov, Leah R; Meyerholz, David K; Abou Alaiwa, Mahmoud H; Kuan, Shin-Ping; Liao, Yan-Shin J; Bormann, Nicholas L; Bair, Thomas B; Price, Margaret; Stoltz, David A; Welsh, Michael J

2018-04-05

Mainstay therapeutics are ineffective in some people with asthma, suggesting a need for additional agents. In the current study, we used vagal ganglia transcriptome profiling and connectivity mapping to identify compounds beneficial for alleviating airway hyperreactivity. As a comparison, we also utilized previously published transcriptome data from sensitized mouse lungs and human asthmatic endobronchial biopsies. All transcriptomes revealed agents beneficial for mitigating airway hyperreactivity; however, only the vagal ganglia transcriptome identified agents used clinically to treat asthma (flunisolide, isoetarine). We also tested one compound identified by vagal ganglia transcriptome profiling that had not previously been linked to asthma and found that it had bronchodilator effects in both mouse and pig airways. These data suggest that transcriptome profiling of the vagal ganglia might be a novel strategy to identify potential asthma therapeutics.

The Lunar Source Disk: Old Lunar Datasets on a New CD-ROM

NASA Astrophysics Data System (ADS)

Hiesinger, H.

1998-01-01

A compilation of previously published datasets on CD-ROM is presented. This Lunar Source Disk is intended to be a first step in the improvement/expansion of the Lunar Consortium Disk, in order to create an "image-cube"-like data pool that can be easily accessed and might be useful for a variety of future lunar investigations. All datasets were transformed to a standard map projection that allows direct comparison of different types of information on a pixel-by pixel basis. Lunar observations have a long history and have been important to mankind for centuries, notably since the work of Plutarch and Galileo. As a consequence of centuries of lunar investigations, knowledge of the characteristics and properties of the Moon has accumulated over time. However, a side effect of this accumulation is that it has become more and more complicated for scientists to review all the datasets obtained through different techniques, to interpret them properly, to recognize their weaknesses and strengths in detail, and to combine them synoptically in geologic interpretations. Such synoptic geologic interpretations are crucial for the study of planetary bodies through remote-sensing data in order to avoid misinterpretation. In addition, many of the modem datasets, derived from Earth-based telescopes as well as from spacecraft missions, are acquired at different geometric and radiometric conditions. These differences make it challenging to compare or combine datasets directly or to extract information from different datasets on a pixel-by-pixel basis. Also, as there is no convention for the presentation of lunar datasets, different authors choose different map projections, depending on the location of the investigated areas and their personal interests. Insufficient or incomplete information on the map parameters used by different authors further complicates the reprojection of these datasets to a standard geometry. The goal of our efforts was to transfer previously published lunar datasets to a selected standard geometry in order to create an "image-cube"-like data pool for further interpretation. The starting point was a number of datasets on a CD-ROM published by the Lunar Consortium. The task of creating an uniform data pool was further complicated by some missing or wrong references and keys on the Lunar Consortium CD as well as erroneous reproduction of some datasets in the literature.

Edwin James' and John Hinton's revisions of Maclure's geologic map of the United States

NASA Astrophysics Data System (ADS)

Aalto, K. R.

2012-03-01

William Maclure's pioneering geologic map of the eastern United States, published first in 1809 with Observations on the Geology of the United States, provided a foundation for many later maps - a template from which geologists could extend their mapping westward from the Appalachians. Edwin James, botanist, geologist and surgeon for the 1819/1820 United States Army western exploring expedition under Major Stephen H. Long, published a full account of this expedition with map and geologic sections in 1822-1823. In this he extended Maclure's geology across the Mississippi Valley to the Colorado Rockies. John Howard Hinton (1791-1873) published his widely read text: The History and Topography of the United States in 1832, which included a compilations of Maclure's and James' work in a colored geologic map and vertical sections. All three men were to some degree confounded in their attempts to employ Wernerian rock classification in their mapping and interpretations of geologic history, a common problem in the early 19th Century prior to the demise of Neptunist theory and advent of biostratigraphic techniques of correlation. However, they provided a foundation for the later, more refined mapping and geologic interpretation of the eastern United States.

Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

PubMed Central

2012-01-01

Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium. PMID:23046547

A cellular and regulatory map of the GABAergic nervous system of C. elegans

PubMed Central

Gendrel, Marie; Atlas, Emily G; Hobert, Oliver

2016-01-01

Neurotransmitter maps are important complements to anatomical maps and represent an invaluable resource to understand nervous system function and development. We report here a comprehensive map of neurons in the C. elegans nervous system that contain the neurotransmitter GABA, revealing twice as many GABA-positive neuron classes as previously reported. We define previously unknown glia-like cells that take up GABA, as well as 'GABA uptake neurons' which do not synthesize GABA but take it up from the extracellular environment, and we map the expression of previously uncharacterized ionotropic GABA receptors. We use the map of GABA-positive neurons for a comprehensive analysis of transcriptional regulators that define the GABA phenotype. We synthesize our findings of specification of GABAergic neurons with previous reports on the specification of glutamatergic and cholinergic neurons into a nervous system-wide regulatory map which defines neurotransmitter specification mechanisms for more than half of all neuron classes in C. elegans. DOI: http://dx.doi.org/10.7554/eLife.17686.001 PMID:27740909

Thermal maturity patterns in New York State using CAI and %Ro

USGS Publications Warehouse

Weary, D.J.; Ryder, R.T.; Nyahay, R.E.

2001-01-01

New conodont alteration index (CAI) and vitrinite reflectance (%Ro) data collected from drill holes in the Appalachian basin of New York State allow refinement of thermal maturity maps for Ordovician and Devonian rocks. CAI isotherms on the new maps show a pattern that approximates that published by Harris et al. (1978) in eastern and western New York, but it differs in central New York, where the isotherms are shifted markedly westward by more than 100 km and are more tightly grouped. This close grouping of isograds reflects a steeper thermal gradient than previously noted by Harris et al. (1978) and agrees closely with the abrupt west-to-east increase in thermal maturity across New York noted by Johnsson (1986). These data show, in concordance with previous studies, that thermal maturity levels in these rocks are higher than can be explained by simple burial heating beneath the present thickness of overburden. The Ordovician and Devonian rocks of the Appalachian Basin in New York must have been buried by very thick post-Devonian sediments (4-6 km suggested by Sarwar and Friedman 1995) or were exposed to a higher-than-normal geothermal flux caused by crustal extension, or a combination of the two.

High-resolution mapping of the triangle of Koch: Spatial heterogeneity of fast pathway atrionodal connections.

PubMed

Chua, Kelvin; Upadhyay, Gaurav A; Lee, Elliot; Aziz, Zaid; Beaser, Andrew D; Ozcan, Cevher; Broman, Michael; Nayak, Hemal M; Tung, Roderick

2018-03-01

Dedicated mapping studies of the triangle of Koch to characterize retrograde fast pathway activation have not been previously performed using high-resolution, 3-dimensional, multielectrode mapping technology. To delineate the activation pattern and spatial distribution of the retrograde fast pathway within the triangle of Koch during typical atrioventricular nodal reentrant tachycardia (AVNRT) and right ventricular pacing in a consecutive series of patients using the Rhythmia mapping system (Boston Scientific, Natick, MA). A total of 18 patients with symptomatic typical AVNRT referred for ablation underwent ultra high-density mapping of atrial activation with minielectrode basket configuration during tachycardia. The earliest atrial activation was mapped using automated annotation, with manual overreading by 2 independent observers. The triangle of Koch was classified into 3 anatomic regions: anteroseptal (His), midseptal, and posteroseptal (coronary sinus roof). Thirteen patients underwent mapping of atrial activation during ventricular pacing. A median of 422 mapping points (interquartile range 258-896 points) was acquired within the triangle of Koch during tachycardia. The most common site of earliest atrial activation within the triangle of Koch was anterior in 67% of patients (n = 12). Midseptal early atrial activation was seen in 17% (n = 3), and posteroseptal activation was observed in 11% (n = 2). One patient exhibited broad simultaneous activation of the entire triangle of Koch. Slow pathway potentials were not identified. With high-resolution multielectrode mapping, atrial activation during typical AVNRT exhibited anatomic variability and spatially heterogeneous activation within the triangle of Koch. These findings highlight the limitations of an anatomically based classification of atrioventricular nodal retrograde pathways. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Geologic map of the Oasis Valley basin and vicinity, Nye County, Nevada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fridrich, C.J.; Minor, S.A.; Ryder, P.L.

2000-01-13

This map and accompanying cross sections present an updated synthesis of the geologic framework of the Oasis Valley area, a major groundwater discharge site located about 15 km west of the Nevada Test Site. Most of the data presented in this compilation is new geologic map data, as discussed below. In addition, the cross sections incorporate new geophysical data that have become available in the last three years (Grauch and others, 1997; written comm., 1999; Hildenbrand and others, 1999; Mankinen and others, 1999). Geophysical data are used to estimate the thickness of the Tertiary volcanic and sedimentary rocks on themore » cross sections, and to identify major concealed structures. Large contiguous parts of the map area are covered either by alluvium or by volcanic units deposited after development of the major structures present at the depth of the water table and below. Hence, geophysical data provide critical constraints on our geologic interpretations. A companion paper by Fridrich and others (1999) and the above-cited reports by Hildenbrand and others (1999) and Mankinen and others (1999) provide explanations of the interpretations that are presented graphically on this map. This map covers nine 7.5-minute quadrangles in Nye County, Nevada, centered on the Thirsty Canyon SW quadrangle, and is a compilation of one published quadrangle map (O'Connor and others, 1966) and eight new quadrangle maps, two of which have been previously released (Minor and others, 1997; 1998). The cross sections that accompany this map were drawn to a depth of about 5 km below land surface at the request of hydrologists who are modeling the Death Valley groundwater system.« less

Digital Geologic Map of the Rosalia 1:100,000 Quadrangle, Washington and Idaho: A Digital Database for the 1990 S.Z. Waggoner Map

USGS Publications Warehouse

Derkey, Pamela D.; Johnson, Bruce R.; Lackaff, Beatrice B.; Derkey, Robert E.

1998-01-01

The geologic map of the Rosalia 1:100,000-scale quadrangle was compiled in 1990 by S.Z. Waggoner of the Washington state Division of Geology and Earth Resources. This data was entered into a geographic information system (GIS) as part of a larger effort to create regional digital geology for the Pacific Northwest. The intent was to provide a digital geospatial database for a previously published black and white paper geologic map. This database can be queried in many ways to produce a variety of geologic maps. Digital base map data files are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000) as it has been somewhat generalized to fit the 1:100,000 scale map. The map area is located in eastern Washington and extends across the state border into western Idaho. This open-file report describes the methods used to convert the geologic map data into a digital format, documents the file structures, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. We wish to thank J. Eric Schuster of the Washington Division of Geology and Earth Resources for providing the original stable-base mylar and the funding for it to be scanned. We also thank Dick Blank and Barry Moring of the U.S. Geological Survey for reviewing the manuscript and digital files, respectively.

The Arabidopsis microtubule-associated protein MAP65-3 supports infection by filamentous biotrophic pathogens by down-regulating salicylic acid-dependent defenses.

PubMed

Quentin, Michaël; Baurès, Isabelle; Hoefle, Caroline; Caillaud, Marie-Cécile; Allasia, Valérie; Panabières, Franck; Abad, Pierre; Hückelhoven, Ralph; Keller, Harald; Favery, Bruno

2016-03-01

The oomycete Hyaloperonospora arabidopsidis and the ascomycete Erysiphe cruciferarum are obligate biotrophic pathogens causing downy mildew and powdery mildew, respectively, on Arabidopsis. Upon infection, the filamentous pathogens induce the formation of intracellular bulbous structures called haustoria, which are required for the biotrophic lifestyle. We previously showed that the microtubule-associated protein AtMAP65-3 plays a critical role in organizing cytoskeleton microtubule arrays during mitosis and cytokinesis. This renders the protein essential for the development of giant cells, which are the feeding sites induced by root knot nematodes. Here, we show that AtMAP65-3 expression is also induced in leaves upon infection by the downy mildew oomycete and the powdery mildew fungus. Loss of AtMAP65-3 function in the map65-3 mutant dramatically reduced infection by both pathogens, predominantly at the stages of leaf penetration. Whole-transcriptome analysis showed an over-represented, constitutive activation of genes involved in salicylic acid (SA) biosynthesis, signaling, and defense execution in map65-3, whereas jasmonic acid (JA)-mediated signaling was down-regulated. Preventing SA synthesis and accumulation in map65-3 rescued plant susceptibility to pathogens, but not the developmental phenotype caused by cytoskeleton defaults. AtMAP65-3 thus has a dual role. It positively regulates cytokinesis, thus plant growth and development, and negatively interferes with plant defense against filamentous biotrophs. Our data suggest that downy mildew and powdery mildew stimulate AtMAP65-3 expression to down-regulate SA signaling for infection. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Cross sections showing stratigraphic and depositional lithofacies of upper Cambrian rocks and the relation of lithofacies to potential for Mississippi Valley-type mineralization in the Harrison 1° x 2° quadrangle, Missouri and Arkansas (folio of the Harrison 1 degree by 2 degrees quadrangle, Missouri and Arkansas)

USGS Publications Warehouse

Hayes, Timothy S.; Palmer, James R.; Pratt, Walden P.; Krizanich, Gary; Whitfield, John W.; Seeger, Cheryl M.

1997-01-01

These cross sections are the fifth publication in a folio of maps of the Harrison 1° x 2° quadrangle, Missouri and Arkansas, prepared under the Conterminous United States Mineral Assessment Program (CUSMAP). Previously published maps in this folio relate to the geochemistry of the subsurface carbonate rocks (Erickson and others, 1989), the geophysics of the basement terranes (McCafferty and others, 1989), the sedimentary rocks and mineralization of the Caulfield district (Hayes and others, 1992), the mineral resource potential of the quadrangle (Pratt and others, 1993), and the bedrock geology of the quadrangle (Middendorf and others, 1994 and in press). A final set of maps showing locations of known Mississippi Valley-type deposits and occurrences relative to Late Cambrian shaly lithofacies and other shales in the Harrison and adjoining quadrangle is in preparation (Palmer and Hayes, in press).

An aeromagnetic interpretation of eleven map sheets, scale 1:250,000, in the southern Najd and part of the southern Tuwayq quadrangles, Kingdom of Saudi Arabia

USGS Publications Warehouse

Griscom, Andrew

1983-01-01

Eleven magnetic interpretation maps (scale 1:250,000) have been prepared for the area .of. exposed crystalline rocks in the Southern Najd and part of the Southern Tuwayq quadrangles (scale 1:500,000) from available published data. Boundaries of a variety of rock units that produce distinctive magnetic anomalies .or anomaly patterns are delineated. In some cases these magnetic boundaries correspond with previously mapped geologic contacts, and in other cases they indicate the possibility of additional, as yet unmapped, geologic contacts. The magnetic boundaries also allow the extrapolation of geologic contacts across areas covered by Quaternary deposits. Many boundaries are identified as part of the Najd fault system, and offset magnetic anomalies may be correlated across certain fault zones. Approximate dips were calculated for a few boundaries that represent igneous contacts, faults, or unconformities. Some characteristic anomalies appear to be associated in a general way with areas of gold mineralization and thus provide a guide for further prospecting.

Enhancement and Passive Acoustic Mapping of Cavitation from Fluorescently Tagged Magnetic Resonance-Visible Magnetic Microbubbles In Vivo.

PubMed

Crake, Calum; Owen, Joshua; Smart, Sean; Coviello, Christian; Coussios, Constantin-C; Carlisle, Robert; Stride, Eleanor

2016-12-01

Previous work has indicated the potential of magnetically functionalized microbubbles to localize and enhance cavitation activity under focused ultrasound exposure in vitro. The aim of this study was to investigate magnetic targeting of microbubbles for promotion of cavitation in vivo. Fluorescently labelled magnetic microbubbles were administered intravenously in a murine xenograft model. Cavitation was induced using a 0.5-MHz focused ultrasound transducer at peak negative focal pressures of 1.2-2.0 MPa and monitored in real-time using B-mode imaging and passive acoustic mapping. Magnetic targeting was found to increase the amplitude of the cavitation signal by approximately 50% compared with untargeted bubbles. Post-exposure magnetic resonance imaging indicated deposition of magnetic nanoparticles in tumours. Magnetic targeting was similarly associated with increased fluorescence intensity in the tumours after the experiments. These results suggest that magnetic targeting could potentially be used to improve delivery of cavitation-mediated therapy and that passive acoustic mapping could be used for real-time monitoring of this process. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A method for vreating a three dimensional model from published geologic maps and cross sections

USGS Publications Warehouse

Walsh, Gregory J.

2009-01-01

This brief report presents a relatively inexpensive and rapid method for creating a 3D model of geology from published quadrangle-scale maps and cross sections using Google Earth and Google SketchUp software. An example from the Green Mountains of Vermont, USA, is used to illustrate the step by step methods used to create such a model. A second example is provided from the Jebel Saghro region of the Anti-Atlas Mountains of Morocco. The report was published to help enhance the public?s ability to use and visualize geologic map data.

Scanning and georeferencing historical USGS quadrangles

USGS Publications Warehouse

Fishburn, Kristin A.; Davis, Larry R.; Allord, Gregory J.

2017-06-23

The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the Historical Topographic Map Collection in 2011, is to provide access to a digital repository of USGS topographic maps that is available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of traditional topographic maps, and, prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic process. The next generation of topographic maps, US Topo, is being released by the USGS in digital form, and newer technologies make it possible to also deliver historical maps in the same electronic format that is more publicly accessible.

A spatial database of bedding attitudes to accompany Geologic map of the greater Denver area, Front Range Urban Corridor, Colorado

USGS Publications Warehouse

Trimble, Donald E.; Machette, Michael N.; Brandt, Theodore R.; Moore, David W.; Murray, Kyle E.

2003-01-01

This digital map shows bedding attitude symbols display over the geographic extent of surficial deposits and rock stratigraphic units (formations) as compiled by Trimble and Machette 1973-1977 and published in 1979 (U.S. Geological Survey Map I-856-H) under the Front Range Urban Corridor Geology Program. Trimble and Machette compiled their geologic map from published geologic maps and unpublished geologic mapping having varied map unit schemes. A convenient feature of the compiled map is its uniform classification of geologic units that mostly matches those of companion maps to the north (USGS I-855-G) and to the south (USGS I-857-F). Published as a color paper map, the Trimble and Machette map was intended for land-use planning in the Front Range Urban Corridor. This map recently (1997-1999), was digitized under the USGS Front Range Infrastructure Resources Project (see cross-reference). In general, the mountainous areas in the west part of the map exhibit various igneous and metamorphic bedrock units of Precambrian age, major faults, and fault brecciation zones at the east margin (5-20 km wide) of the Front Range. The eastern and central parts of the map (Colorado Piedmont) depict a mantle of unconsolidated deposits of Quaternary age and interspersed outcroppings of Cretaceous or Tertiary-Cretaceous sedimentary bedrock. The Quaternary mantle is comprised of eolian deposits (quartz sand and silt), alluvium (gravel, sand, and silt of variable composition), colluvium, and few landslides. At the mountain front, north-trending, dipping Paleozoic and Mesozoic sandstone, shale, and limestone bedrock formations form hogbacks and intervening valleys.

VizieR Online Data Catalog: A dust model for bet Pic from 0.58 to 870um (Ballering+, 2016)

NASA Astrophysics Data System (ADS)

Ballering, N. P.; Su, K. Y. L.; Rieke, G. H.; Gaspar, A.

2016-08-01

β Pic was imaged with the HST/STIS CCD in coronagraphic (50CORON) mode under program GO-12551 (PI: Apai), and the results of these observations were published in Apai et al. (2015ApJ...800..136A). The instrument bandpass is set by the response of the CCD and centered at 0.58um. We searched the HST archive and found previously unpublished observations of β Pic with the WFC3 instrument in the IR channel (filter F110W at ~1.16um) from program GO-11150 (PI: Graham). The Spitzer/MIPS observations of β Pic were taken under the Spitzer Guaranteed Time Observing Program 90 (PI: M. Werner). The data at all three bands (24, 70, and 160um) are published here for the first time. Two sets of 24um observations were obtained. The first set was obtained on 2004 March 20, the second set of data was obtained on 2004 April 11. Two sets of 70um observations were obtained. The first set was obtained on 2004 April 12. The second set was obtained on 2005 April 4. Herschel/PACS 70um scan map observations of β Pic (PI G. Olofsson, observation IDs 1342186612 and 1342186613) were published by Vandenbussche et al. (2010A&A...518L.133V). We used the ALMA 870um continuum image previously published by Dent et al. (2014Sci...343.1490D). (1 data file).

Rewiring the connectome: Evidence and effects.

PubMed

Bennett, Sophie H; Kirby, Alastair J; Finnerty, Gerald T

2018-05-01

Neuronal connections form the physical basis for communication in the brain. Recently, there has been much interest in mapping the "connectome" to understand how brain structure gives rise to brain function, and ultimately, to behaviour. These attempts to map the connectome have largely assumed that connections are stable once formed. Recent studies, however, indicate that connections in mammalian brains may undergo rewiring during learning and experience-dependent plasticity. This suggests that the connectome is more dynamic than previously thought. To what extent can neural circuitry be rewired in the healthy adult brain? The connectome has been subdivided into multiple levels of scale, from synapses and microcircuits through to long-range tracts. Here, we examine the evidence for rewiring at each level. We then consider the role played by rewiring during learning. We conclude that harnessing rewiring offers new avenues to treat brain diseases. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach.

PubMed

Korinsak, Siripar; Tangphatsornruang, Sithichoke; Pootakham, Wirulda; Wanchana, Samart; Plabpla, Anucha; Jantasuriyarat, Chatchawan; Patarapuwadol, Sujin; Vanavichit, Apichart; Toojinda, Theerayut

2018-05-15

Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. An association study was performed to identify single nucleotide polymorphisms (SNPs) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations. The division into eight groups was not related to the degree of virulence. Association mapping showed five SNPs associated with fungal virulence on chromosome 1, 2, 3, 4 and 7. The SNP on chromosome 1 was associated with virulence against RD6-Pi7 and IRBL7-M which might be linked to the previously reported AvrPi7. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Measuring iron in the brain using quantitative susceptibility mapping and X-ray fluorescence imaging

PubMed Central

Zheng, Weili; Nichol, Helen; Liu, Saifeng; Cheng, Yu-Chung N.; Haacke, E. Mark

2013-01-01

Measuring iron content in the brain has important implications for a number of neurodegenerative diseases. Quantitative susceptibility mapping (QSM), derived from magnetic resonance images, has been used to measure total iron content in vivo and in post mortem brain. In this paper, we show how magnetic susceptibility from QSM correlates with total iron content measured by X-ray fluorescence (XRF) imaging and by inductively coupled plasma mass spectrometry (ICPMS). The relationship between susceptibility and ferritin iron was estimated at 1.10 ± 0.08 ppb susceptibility per μg iron/g wet tissue, similar to that of iron in fixed (frozen/thawed) cadaveric brain and previously published data from unfixed brains. We conclude that magnetic susceptibility can provide a direct and reliable quantitative measurement of iron content and that it can be used clinically at least in regions with high iron content. PMID:23591072

Comparison of ASTER- and AVIRIS-Derived Mineraland Vegetation Maps of the White Horse Replacement Alunite Deposit and Surrounding Area, Marysvale Volcanic Field, Utah

USGS Publications Warehouse

Rockwell, Barnaby W.

2009-01-01

This report presents and compares mineral and vegetation maps of parts of the Marysvale volcanic field in west-central Utah that were published in a recent paper describing the White Horse replacement alunite deposit. Detailed, field-verified maps of the deposit were produced from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data acquired from a low-altitude Twin Otter turboprop airborne platform. Reconnaissance-level maps of surrounding areas including the central and northern Tushar Mountains, Pahvant Range, and portions of the Sevier Plateau to the east were produced from visible, near-infrared, and shortwave-infrared data acquired by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) sensor carried aboard the Terra satellite platform. These maps are also compared to a previously published mineral map of the same area generated from AVIRIS data acquired from the high-altitude NASA ER-2 jet platform. All of the maps were generated by similar analysis methods, enabling the direct comparison of the spatial scale and mineral composition of surface geologic features that can be identified using the three types of remote sensing data. The high spatial (2-17 meter) and spectral (224 bands) resolution AVIRIS data can be used to generate detailed mineral and vegetation maps suitable for geologic and geoenvironmental studies of individual deposits, mines, and smelters. The lower spatial (15-30 meter) and spectral (9 bands) resolution ASTER data are better suited to less detailed mineralogical studies of lithology and alteration across entire hydrothermal systems and mining districts, including regional mineral resource and geoenvironmental assessments. The results presented here demonstrate that minerals and mineral mixtures can be directly identified using AVIRIS and ASTER data to elucidate spatial patterns of mineralogic zonation; AVIRIS data can enable the generation of maps with significantly greater detail and accuracy. The vegetation mapping results suggest that ASTER data may provide an efficient alternative to spectroscopic data for studies of burn severity after wildland fires. A new, semiautomated methodology for the analysis of ASTER data is presented that is currently being applied to ASTER data coverage of large areas for regional assessments of mineral-resource potential and mineral-environmental effects. All maps are presented in a variety of digital formats, including jpeg, pdf, and ERDAS Imagine (.img). The Imagine format files are georeferenced and suitable for viewing with other geospatial data in Imagine, ArcGIS, and ENVI. The mineral and vegetation maps are attributed so that the material identified for a pixel can be determined easily in ArcMap by using the Identify tool and in Imagine by using the Inquire Cursor tool.

Automatic metro map layout using multicriteria optimization.

PubMed

Stott, Jonathan; Rodgers, Peter; Martínez-Ovando, Juan Carlos; Walker, Stephen G

2011-01-01

This paper describes an automatic mechanism for drawing metro maps. We apply multicriteria optimization to find effective placement of stations with a good line layout and to label the map unambiguously. A number of metrics are defined, which are used in a weighted sum to find a fitness value for a layout of the map. A hill climbing optimizer is used to reduce the fitness value, and find improved map layouts. To avoid local minima, we apply clustering techniques to the map-the hill climber moves both stations and clusters when finding improved layouts. We show the method applied to a number of metro maps, and describe an empirical study that provides some quantitative evidence that automatically-drawn metro maps can help users to find routes more efficiently than either published maps or undistorted maps. Moreover, we have found that, in these cases, study subjects indicate a preference for automatically-drawn maps over the alternatives. © 2011 IEEE Published by the IEEE Computer Society

Evidence-based risk assessment and communication: a new global dengue-risk map for travellers and clinicians#

PubMed Central

Lash, R. Ryan; Johansson, Michael A.; Sharp, Tyler M.; Henry, Ronnie; Brady, Oliver J.; Sotir, Mark J.; Hay, Simon I.; Margolis, Harold S.; Brunette, Gary W.

2016-01-01

Abstract Background: International travel can expose travellers to pathogens not commonly found in their countries of residence, like dengue virus. Travellers and the clinicians who advise and treat them have unique needs for understanding the geographic extent of risk for dengue. Specifically, they should assess the need for prevention measures before travel and ensure appropriate treatment of illness post-travel. Previous dengue-risk maps published in the Centers for Disease Control and Prevention’s Yellow Book lacked specificity, as there was a binary (risk, no risk) classification. We developed a process to compile evidence, evaluate it and apply more informative risk classifications. Methods: We collected more than 839 observations from official reports, ProMED reports and published scientific research for the period 2005–2014. We classified each location as frequent/continuous risk if there was evidence of more than 10 dengue cases in at least three of the previous 10 years. For locations that did not fit this criterion, we classified locations as sporadic/uncertain risk if the location had evidence of at least one locally acquired dengue case during the last 10 years. We used expert opinion in limited instances to augment available data in areas where data were sparse. Results: Initial categorizations classified 134 areas as frequent/continuous and 140 areas as sporadic/uncertain. CDC subject matter experts reviewed all initial frequent/continuous and sporadic/uncertain categorizations and the previously uncategorized areas. From this review, most categorizations stayed the same; however, 11 categorizations changed from the initial determinations. Conclusions: These new risk classifications enable detailed consideration of dengue risk, with clearer meaning and a direct link to the evidence that supports the specific classification. Since many infectious diseases have dynamic risk, strong geographical heterogeneities and varying data quality and availability, using this approach for other diseases can improve the accuracy, clarity and transparency of risk communication. PMID:27625400

County-Scale Distribution of Ixodes scapularis and Ixodes pacificus (Acari: Ixodidae) in the Continental United States

PubMed Central

Eisen, Rebecca J.; Eisen, Lars; Beard, Charles B.

2016-01-01

The blacklegged tick, Ixodes scapularis Say, is the primary vector to humans in the eastern United States of the Lyme disease spirochete Borrelia burgdorferi, as well as causative agents of anaplasmosis and babesiosis. Its close relative in the far western United States, the western blacklegged tick Ixodes pacificus Cooley and Kohls, is the primary vector to humans in that region of the Lyme disease and anaplasmosis agents. Since 1991, when standardized surveillance and reporting began, Lyme disease case counts have increased steadily in number and in geographical distribution in the eastern United States. Similar trends have been observed for anaplasmosis and babesiosis. To better understand the changing landscape of risk of human exposure to disease agents transmitted by I. scapularis and I. pacificus, and to document changes in their recorded distribution over the past two decades, we updated the distribution of these species from a map published in 1998. The presence of I. scapularis has now been documented from 1,420 (45.7%) of the 3,110 continental United States counties, as compared with 111 (3.6%) counties for I. pacificus. Combined, these vectors of B. burgdorferi and other disease agents now have been identified in a total of 1,531 (49.2%) counties spread across 43 states. This marks a 44.7% increase in the number of counties that have recorded the presence of these ticks since the previous map was presented in 1998, when 1,058 counties in 41 states reported the ticks to be present. Notably, the number of counties in which I. scapularis is considered established (six or more individuals or one or more life stages identified in a single year) has more than doubled since the previous national distribution map was published nearly two decades ago. The majority of county status changes occurred in the North-Central and Northeastern states, whereas the distribution in the South remained fairly stable. Two previously distinct foci for I. scapularis in the Northeast and North-Central states appear to be merging in the Ohio River Valley to form a single contiguous focus. Here we document a shifting landscape of risk for human exposure to medically important ticks and point to areas of re-emergence where enhanced vector surveillance and control may be warranted. PMID:26783367

Annual regression-based estimates of evapotranspiration for the contiguous United States based on climate, remote sensing, and stream gage data

NASA Astrophysics Data System (ADS)

Reitz, M. D.; Sanford, W. E.; Senay, G. B.; Cazenas, J.

2015-12-01

Evapotranspiration (ET) is a key quantity in the hydrologic cycle, accounting for ~70% of precipitation across the contiguous United States (CONUS). However, it is a challenge to estimate, due to difficulty in making direct measurements and gaps in our theoretical understanding. Here we present a new data-driven, ~1km2 resolution map of long-term average actual evapotranspiration rates across the CONUS. The new ET map is a function of the USGS Landsat-derived National Land Cover Database (NLCD), precipitation, temperature, and daily average temperature range (from the PRISM climate dataset), and is calibrated to long-term water balance data from 679 watersheds. It is unique from previously presented ET maps in that (1) it was co-developed with estimates of runoff and recharge; (2) the regression equation was chosen from among many tested, previously published and newly proposed functional forms for its optimal description of long-term water balance ET data; (3) it has values over open-water areas that are derived from separate mass-transfer and humidity equations; and (4) the data include additional precipitation representing amounts converted from 2005 USGS water-use census irrigation data. The regression equation is calibrated using data from 2000-2013, but can also be applied to individual years with their corresponding input datasets. Comparisons among this new map, the more detailed remote-sensing-based estimates of MOD16 and SSEBop, and AmeriFlux ET tower measurements shows encouraging consistency, and indicates that the empirical ET estimate approach presented here produces closer agreement with independent flux tower data for annual average actual ET than other more complex remote sensing approaches.

Strain screen and haplotype association mapping of wheel running in inbred mouse strains.

PubMed

Lightfoot, J Timothy; Leamy, Larry; Pomp, Daniel; Turner, Michael J; Fodor, Anthony A; Knab, Amy; Bowen, Robert S; Ferguson, David; Moore-Harrison, Trudy; Hamilton, Alicia

2010-09-01

Previous genetic association studies of physical activity, in both animal and human models, have been limited in number of subjects and genetically homozygous strains used as well as number of genomic markers available for analysis. Expansion of the available mouse physical activity strain screens and the recently published dense single-nucleotide polymorphism (SNP) map of the mouse genome (approximately 8.3 million SNPs) and associated statistical methods allowed us to construct a more generalizable map of the quantitative trait loci (QTL) associated with physical activity. Specifically, we measured wheel running activity in male and female mice (average age 9 wk) in 41 inbred strains and used activity data from 38 of these strains in a haplotype association mapping analysis to determine QTL associated with activity. As seen previously, there was a large range of activity patterns among the strains, with the highest and lowest strains differing significantly in daily distance run (27.4-fold), duration of activity (23.6-fold), and speed (2.9-fold). On a daily basis, female mice ran further (24%), longer (13%), and faster (11%). Twelve QTL were identified, with three (on Chr. 12, 18, and 19) in both male and female mice, five specific to males, and four specific to females. Eight of the 12 QTL, including the 3 general QTL found for both sexes, fell into intergenic areas. The results of this study further support the findings of a moderate to high heritability of physical activity and add general genomic areas applicable to a large number of mouse strains that can be further mined for candidate genes associated with regulation of physical activity. Additionally, results suggest that potential genetic mechanisms arising from traditional noncoding regions of the genome may be involved in regulation of physical activity.

Temporal reliability of ultra-high field resting-state MRI for single-subject sensorimotor and language mapping.

PubMed

Branco, Paulo; Seixas, Daniela; Castro, São Luís

2018-03-01

Resting-state fMRI is a well-suited technique to map functional networks in the brain because unlike task-based approaches it requires little collaboration from subjects. This is especially relevant in clinical settings where a number of subjects cannot comply with task demands. Previous studies using conventional scanner fields have shown that resting-state fMRI is able to map functional networks in single subjects, albeit with moderate temporal reliability. Ultra-high resolution (7T) imaging provides higher signal-to-noise ratio and better spatial resolution and is thus well suited to assess the temporal reliability of mapping results, and to determine if resting-state fMRI can be applied in clinical decision making including preoperative planning. We used resting-state fMRI at ultra-high resolution to examine whether the sensorimotor and language networks are reliable over time - same session and one week after. Resting-state networks were identified for all subjects and sessions with good accuracy. Both networks were well delimited within classical regions of interest. Mapping was temporally reliable at short and medium time-scales as demonstrated by high values of overlap in the same session and one week after for both networks. Results were stable independently of data quality metrics and physiological variables. Taken together, these findings provide strong support for the suitability of ultra-high field resting-state fMRI mapping at the single-subject level. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluating Continuous-Time Slam Using a Predefined Trajectory Provided by a Robotic Arm

NASA Astrophysics Data System (ADS)

Koch, B.; Leblebici, R.; Martell, A.; Jörissen, S.; Schilling, K.; Nüchter, A.

2017-09-01

Recently published approaches to SLAM algorithms process laser sensor measurements and output a map as a point cloud of the environment. Often the actual precision of the map remains unclear, since SLAMalgorithms apply local improvements to the resulting map. Unfortunately, it is not trivial to compare the performance of SLAMalgorithms objectively, especially without an accurate ground truth. This paper presents a novel benchmarking technique that allows to compare a precise map generated with an accurate ground truth trajectory to a map with a manipulated trajectory which was distorted by different forms of noise. The accurate ground truth is acquired by mounting a laser scanner on an industrial robotic arm. The robotic arm is moved on a predefined path while the position and orientation of the end-effector tool are monitored. During this process the 2D profile measurements of the laser scanner are recorded in six degrees of freedom and afterwards used to generate a precise point cloud of the test environment. For benchmarking, an offline continuous-time SLAM algorithm is subsequently applied to remove the inserted distortions. Finally, it is shown that the manipulated point cloud is reversible to its previous state and is slightly improved compared to the original version, since small errors that came into account by imprecise assumptions, sensor noise and calibration errors are removed as well.

Standard for the U.S. Geological Survey Historical Topographic Map Collection

USGS Publications Warehouse

Allord, Gregory J.; Fishburn, Kristin A.; Walter, Jennifer L.

2014-01-01

This document defines the digital map product of the U.S. Geological Survey (USGS) Historical Topographic Map Collection (HTMC). The HTMC is a digital archive of about 190,000 printed topographic quadrangle maps published by the USGS from the inception of the topographic mapping program in 1884 until the last paper topographic map using lithographic printing technology was published in 2006. The HTMC provides a comprehensive digital repository of all scales and all editions of USGS printed topographic maps that is easily discovered, browsed, and downloaded by the public at no cost. Each printed topographic map is scanned “as is” and captures the content and condition of each map. The HTMC provides ready access to maps that are no longer available for distribution in print. A new generation of topographic maps called “US Topo” was defined in 2009. US Topo maps, though modeled on the legacy 7.5-minute topographic maps, conform to different standards. For more information on the HTMC, see the project Web site at: http://nationalmap.gov/historical/.

STS map of genes and anonymous DNA fragments on human chromosome 18 using a panel of somatic cell hybrids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Overhauser, J.; Mewar, R.; Rojas, K.

1993-02-01

Somatic cell hybrids containing different deleted regions of chromosome 18 derived form patients with balanced translocations or terminal deletions were used to create a deletion mapping panel. Twenty-four sequence-tagged sites (STSs) for 17 genes and 7 anonymous polymorphic DNA fragments were identified. These STSs were used to map the 24 loci to 18 defined regions of chromosome 18. Both ERV1, previously mapped to 18q22-q23, and YES1, previously mapped to 18q21.3, were found to map to 18p11.21-pter. Several genes previously mapped to 18q21 were found to be in the order cen-SSAV1-DCC-FECH-GRP-BCL2-PLANH2-tel. The precise mapping of genes to chromosome 18 should helpmore » in determining whether these genes may be involved in the etiology of specific chromosomal syndromes associated with chromosome 18. The mapping of the poloymorphic loci will assist in the integration of the physical map with the recombination map of chromosome 18. 43 refs., 2 figs., 1 tab.« less

PUBLISHING SPILL IMPACT MAPS OVER THE WEB

EPA Science Inventory

This paper discusses the implementaiton of a web-based map publishing technology within a USEPA GIS laboratory. A sophisticated spill travel prediction model for the Ohio River has been installed within the GIS laboratory, and is used by personnel from the NRMRL. The spill simul...

Status and distribution of mangrove forests of the world using earth observation satellite data

USGS Publications Warehouse

Giri, Chandra; Ochieng, E.; Tieszen, Larry L.; Zhu, Zhi-Liang; Singh, Ashbindu; Loveland, Thomas R.; Masek, Jeffery G.; Duke, Norm

2011-01-01

Aim  Our scientific understanding of the extent and distribution of mangrove forests of the world is inadequate. The available global mangrove databases, compiled using disparate geospatial data sources and national statistics, need to be improved. Here, we mapped the status and distributions of global mangroves using recently available Global Land Survey (GLS) data and the Landsat archive. Methods  We interpreted approximately 1000 Landsat scenes using hybrid supervised and unsupervised digital image classification techniques. Each image was normalized for variation in solar angle and earth–sun distance by converting the digital number values to the top-of-the-atmosphere reflectance. Ground truth data and existing maps and databases were used to select training samples and also for iterative labelling. Results were validated using existing GIS data and the published literature to map ‘true mangroves’. Results  The total area of mangroves in the year 2000 was 137,760 km2 in 118 countries and territories in the tropical and subtropical regions of the world. Approximately 75% of world's mangroves are found in just 15 countries, and only 6.9% are protected under the existing protected areas network (IUCN I-IV). Our study confirms earlier findings that the biogeographic distribution of mangroves is generally confined to the tropical and subtropical regions and the largest percentage of mangroves is found between 5° N and 5° S latitude. Main conclusions  We report that the remaining area of mangrove forest in the world is less than previously thought. Our estimate is 12.3% smaller than the most recent estimate by the Food and Agriculture Organization (FAO) of the United Nations. We present the most comprehensive, globally consistent and highest resolution (30 m) global mangrove database ever created. We developed and used better mapping techniques and data sources and mapped mangroves with better spatial and thematic details than previous studies.

Petroleum systems of the San Joaquin Basin Province, California -- geochemical characteristics of oil types: Chapter 9 in Petroleum systems and geologic assessment of oil and gas in the San Joaquin Basin Province, California

USGS Publications Warehouse

Lillis, Paul G.; Magoon, Leslie B.

2007-01-01

New analyses of 120 oil samples combined with 139 previously published oil analyses were used to characterize and map the distribution of oil types in the San Joaquin Basin, California. The results show that there are at least four oil types designated MM, ET, EK, and CM. Most of the oil from the basin has low to moderate sulfur content (less than 1 weight percent sulfur), although a few unaltered MM oils have as much as 1.2 weight percent sulfur. Reevaluation of source rock data from the literature indicate that the EK oil type is derived from the Eocene Kreyenhagen Formation, and the MM oil type is derived, in part, from the Miocene to Pliocene Monterey Formation and its equivalent units. The ET oil type is tentatively correlated to the Eocene Tumey formation of Atwill (1935). Previous studies suggest that the CM oil type is derived from the Late Cretaceous to Paleocene Moreno Formation. Maps of the distribution of the oil types show that the MM oil type is restricted to the southern third of the San Joaquin Basin Province. The composition of MM oils along the southern and eastern margins of the basin reflects the increased contribution of terrigenous organic matter to the marine basin near the Miocene paleoshoreline. EK oils are widely distributed along the western half of the basin, and ET oils are present in the central and west-central areas of the basin. The CM oil type has only been found in the Coalinga area in southwestern Fresno County. The oil type maps provide the basis for petroleum system maps that incorporate source rock distribution and burial history, migration pathways, and geologic relationships between hydrocarbon source and reservoir rocks. These petroleum system maps were used for the 2003 U.S. Geological Survey resource assessment of the San Joaquin Basin Province.

Geologic map of the upper Arkansas River valley region, north-central Colorado

USGS Publications Warehouse

Kellogg, Karl S.; Shroba, Ralph R.; Ruleman, Chester A.; Bohannon, Robert G.; McIntosh, William C.; Premo, Wayne R.; Cosca, Michael A.; Moscati, Richard J.; Brandt, Theodore R.

2017-11-17

This 1:50,000-scale U.S. Geological Survey geologic map represents a compilation of the most recent geologic studies of the upper Arkansas River valley between Leadville and Salida, Colorado. The valley is structurally controlled by an extensional fault system that forms part of the prominent northern Rio Grande rift, an intra-continental region of crustal extension. This report also incorporates new detailed geologic mapping of previously poorly understood areas within the map area and reinterprets previously studied areas. The mapped region extends into the Proterozoic metamorphic and intrusive rocks in the Sawatch Range west of the valley and the Mosquito Range to the east. Paleozoic rocks are preserved along the crest of the Mosquito Range, but most of them have been eroded from the Sawatch Range. Numerous new isotopic ages better constrain the timing of both Proterozoic intrusive events, Late Cretaceous to early Tertiary intrusive events, and Eocene and Miocene volcanic episodes, including widespread ignimbrite eruptions. The uranium-lead ages document extensive about 1,440-million years (Ma) granitic plutonism mostly north of Buena Vista that produced batholiths that intruded an older suite of about 1,760-Ma metamorphic rocks and about 1,700-Ma plutonic rocks. As a result of extension during the Neogene and possibly latest Paleogene, the graben underlying the valley is filled with thick basin-fill deposits (Dry Union Formation and older sediments), which occupy two sub-basins separated by a bedrock high near the town of Granite. The Dry Union Formation has undergone deep erosion since the late Miocene or early Pliocene. During the Pleistocene, ongoing steam incision by the Arkansas River and its major tributaries has been interrupted by periodic aggradation. From Leadville south to Salida as many as seven mapped alluvial depositional units, which range in age from early to late Pleistocene, record periodic aggradational events along these streams that are commonly associated with deposition of glacial outwash or bouldery glacial-flood deposits. Many previously unrecognized Neogene and Quaternary faults, some of the latter with possible Holocene displacement, have been identified on lidar (light detection and ranging) imagery which covers 59 percent of the map area. This imagery has also permitted more accurate remapping of glacial, fluvial, and mass-movement deposits and aided in the determination of their relative ages. Recently published 10beryllium cosmogenic surface-exposure ages, coupled with our new geologic mapping, have revealed the timing and rates of late Pleistocene deglaciation. Glacial dams that impounded the Arkansas River at Clear Creek and possibly at Pine Creek failed at least three times during the middle and late Pleistocene, resulting in catastrophic floods and deposition of enormous boulders and bouldery alluvium downstream; at least two failures occurred during the late Pleistocene during the Pinedale glaciation.

Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height.

PubMed

Gupta, Shefali; Kumar, Tapan; Verma, Subodh; Bharadwaj, Chellapilla; Bhatia, Sabhyata

2015-11-01

Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight--48 g and plant height--53 cm) and BGD112 (100-seed weight--15 g and plant height--65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64%) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24% of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17% of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.

Clinical high-resolution mapping of the proteoglycan-bound water fraction in articular cartilage of the human knee joint.

PubMed

Bouhrara, Mustapha; Reiter, David A; Sexton, Kyle W; Bergeron, Christopher M; Zukley, Linda M; Spencer, Richard G

2017-11-01

We applied our recently introduced Bayesian analytic method to achieve clinically-feasible in-vivo mapping of the proteoglycan water fraction (PgWF) of human knee cartilage with improved spatial resolution and stability as compared to existing methods. Multicomponent driven equilibrium single-pulse observation of T 1 and T 2 (mcDESPOT) datasets were acquired from the knees of two healthy young subjects and one older subject with previous knee injury. Each dataset was processed using Bayesian Monte Carlo (BMC) analysis incorporating a two-component tissue model. We assessed the performance and reproducibility of BMC and of the conventional analysis of stochastic region contraction (SRC) in the estimation of PgWF. Stability of the BMC analysis of PgWF was tested by comparing independent high-resolution (HR) datasets from each of the two young subjects. Unlike SRC, the BMC-derived maps from the two HR datasets were essentially identical. Furthermore, SRC maps showed substantial random variation in estimated PgWF, and mean values that differed from those obtained using BMC. In addition, PgWF maps derived from conventional low-resolution (LR) datasets exhibited partial volume and magnetic susceptibility effects. These artifacts were absent in HR PgWF images. Finally, our analysis showed regional variation in PgWF estimates, and substantially higher values in the younger subjects as compared to the older subject. BMC-mcDESPOT permits HR in-vivo mapping of PgWF in human knee cartilage in a clinically-feasible acquisition time. HR mapping reduces the impact of partial volume and magnetic susceptibility artifacts compared to LR mapping. Finally, BMC-mcDESPOT demonstrated excellent reproducibility in the determination of PgWF. Published by Elsevier Inc.

Linkage map of Escherichia coli K-12, edition 8.

PubMed Central

Bachmann, B J

1990-01-01

The linkage map of Escherichia coli K-12 depicts the arrangement of genes on the circular chromosome of this organism. The basic units of the map are minutes, determined by the time-of-entry of markers from Hfr into F- strains in interrupted-conjugation experiments. The time-of-entry distances have been refined over the years by determination of the frequency of cotransduction of loci in transduction experiments utilizing bacteriophage P1, which transduces segments of DNA approximately 2 min in length. In recent years, the relative positions of many genes have been determined even more precisely by physical techniques, including the mapping of restriction fragments and the sequencing of many small regions of the chromosome. On the whole, the agreement between results obtained by genetic and physical methods has been remarkably good considering the different levels of accuracy to be expected of the methods used. There are now few regions of the map whose length is still in some doubt. In some regions, genetic experiments utilizing different mutant strains give different map distances. In other regions, the genetic markers available have not been close enough to give accurate cotransduction data. The chromosome is now known to contain several inserted elements apparently derived from lambdoid phages and other sources. The nature of the region in which the termination of replication of the chromosome occurs is now known to be much more complex than the picture given in the previous map. The present map is based upon the published literature through June of 1988. There are now 1,403 loci placed on the linkage group, which may represent between one-third and one-half of the genes in this organism. PMID:2194094

Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

PubMed

Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

2017-05-12

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Mapping gullies, dunes, lava fields, and landslides via surface roughness

NASA Astrophysics Data System (ADS)

Korzeniowska, Karolina; Pfeifer, Norbert; Landtwing, Stephan

2018-01-01

Gully erosion is a widespread and significant process involved in soil and land degradation. Mapping gullies helps to quantify past, and anticipate future, soil losses. Digital terrain models offer promising data for automatically detecting and mapping gullies especially in vegetated areas, although methods vary widely measures of local terrain roughness are the most varied and debated among these methods. Rarely do studies test the performance of roughness metrics for mapping gullies, limiting their applicability to small training areas. To this end, we systematically explored how local terrain roughness derived from high-resolution Light Detection And Ranging (LiDAR) data can aid in the unsupervised detection of gullies over a large area. We also tested expanding this method for other landforms diagnostic of similarly abrupt land-surface changes, including lava fields, dunes, and landslides, as well as investigating the influence of different roughness thresholds, resolutions of kernels, and input data resolution, and comparing our method with previously published roughness algorithms. Our results show that total curvature is a suitable metric for recognising analysed gullies and lava fields from LiDAR data, with comparable success to that of more sophisticated roughness metrics. Tested dunes or landslides remain difficult to distinguish from the surrounding landscape, partly because they are not easily defined in terms of their topographic signature.

Isostatic Gravity Map with Geology of the Santa Ana 30' x 60' Quadrangle, Southern California

USGS Publications Warehouse

Langenheim, V.E.; Lee, Tien-Chang; Biehler, Shawn; Jachens, R.C.; Morton, D.M.

2006-01-01

This report presents an updated isostatic gravity map, with an accompanying discussion of the geologic significance of gravity anomalies in the Santa Ana 30 by 60 minute quadrangle, southern California. Comparison and analysis of the gravity field with mapped geology indicates the configuration of structures bounding the Los Angeles Basin, geometry of basins developed within the Elsinore and San Jacinto Fault zones, and a probable Pliocene drainage network carved into the bedrock of the Perris block. Total cumulative horizontal displacement on the Elsinore Fault derived from analysis of the length of strike-slip basins within the fault zone is about 5-12 km and is consistent with previously published estimates derived from other sources of information. This report also presents a map of density variations within pre-Cenozoic metamorphic and igneous basement rocks. Analysis of basement gravity patterns across the Elsinore Fault zone suggests 6-10 km of right-lateral displacement. A high-amplitude basement gravity high is present over the San Joaquin Hills and is most likely caused by Peninsular Ranges gabbro and/or Tertiary mafic intrusion. A major basement gravity gradient coincides with the San Jacinto Fault zone and marked magnetic, seismic-velocity, and isotopic gradients that reflect a discontinuity within the Peninsular Ranges batholith in the northeast corner of the quadrangle.

Estimating the Health and Economic Impacts of Changes in Local Air Quality

PubMed Central

Carvour, Martha L.; Hughes, Amy E.; Fann, Neal

2018-01-01

Objectives. To demonstrate the benefits-mapping software Environmental Benefits Mapping and Analysis Program-Community Edition (BenMAP-CE), which integrates local air quality data with previously published concentration–response and health–economic valuation functions to estimate the health effects of changes in air pollution levels and their economic consequences. Methods. We illustrate a local health impact assessment of ozone changes in the 10-county nonattainment area of the Dallas–Fort Worth region of Texas, estimating the short-term effects on mortality predicted by 2 scenarios for 3 years (2008, 2011, and 2013): an incremental rollback of the daily 8-hour maximum ozone levels of all area monitors by 10 parts per billion and a rollback-to-a-standard ambient level of 65 parts per billion at only monitors above that level. Results. Estimates of preventable premature deaths attributable to ozone air pollution obtained by the incremental rollback method varied little by year, whereas those obtained by the rollback-to-a-standard method varied by year and were sensitive to the choice of ordinality and the use of preloaded or imported data. Conclusions. BenMAP-CE allows local and regional public health analysts to generate timely, evidence-based estimates of the health impacts and economic consequences of potential policy options in their communities. PMID:29698094

The digital global geologic map of Mars: chronostratigraphic ages, topographic and crater morphologic characteristics, and updated resurfacing history

USGS Publications Warehouse

Tanaka, K.L.; Robbins, S.J.; Fortezzo, C.M.; Skinner, J.A.; Hare, T.M.

2014-01-01

A new global geologic map of Mars has been completed in a digital, geographic information system (GIS) format using geospatially controlled altimetry and image data sets. The map reconstructs the geologic history of Mars, which includes many new findings collated in the quarter century since the previous, Viking-based global maps were published, as well as other discoveries that were made during the course of the mapping using new data sets. The technical approach enabled consistent and regulated mapping that is appropriate not only for the map's 1:20,000,000 scale but also for its widespread use by diverse audiences. Each geologic unit outcrop includes basic attributes regarding identity, location, area, crater densities, and chronostratigraphic age. In turn, units are grouped by geographic and lithologic types, which provide synoptic global views of material ages and resurfacing character for the Noachian, Hesperian, and Amazonian periods. As a consequence of more precise and better quality topographic and morphologic data and more complete crater-density dating, our statistical comparisons identify significant refinements for how Martian geologic terrains are characterized. Unit groups show trends in mean elevation and slope that relate to geographic occurrence and geologic origin. In comparison with the previous global geologic map series based on Viking data, the new mapping consists of half the number of units due to simpler, more conservative and globally based approaches to discriminating units. In particular, Noachian highland surfaces overall have high percentages of their areas now dated as an epoch older than in the Viking mapping. Minimally eroded (i.e., pristine) impact craters ≥3 km in diameter occur in greater proportion on Hesperian surfaces. This observation contrasts with a deficit of similarly sized craters on heavily cratered and otherwise degraded Noachian terrain as well as on young Amazonian surfaces. We interpret these as reflecting the relatively stronger, lava-rich, yet less-impacted materials making up much of the younger units. Reconstructions of resurfacing of Mars by its eight geologic epochs using the Hartmann and Neukum chronology models indicate high rates of highland resurfacing during the Noachian (peaking at 0.3 km2/yr during the Middle Noachian), modest rates of volcanism and transition zone and lowland resurfacing during the Hesperian (∼0.1 km2/yr), and low rates of mainly volcanic and polar resurfacing (∼0.01 km2/yr) for most of the Amazonian. Apparent resurfacing increased in the Late Amazonian (∼0.03 km2/yr), perhaps due to better preservation of this latest record.

44 CFR 70.7 - Notice of Letter of Map Amendment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Notice of Letter of Map... FOR MAP CORRECTION Mapping Deficiencies Unrelated to Community-Wide Elevation Determinations § 70.7 Notice of Letter of Map Amendment. (a) The Federal Insurance Administrator, shall not publish a notice in...

Rapid Assessment Procedure for Loiasis and Mapping Lymphatic Filariasis: Two Perfect Illustrations of “To Be in English or Not to Be”

PubMed Central

Carme, Bernard

2012-01-01

Interest in filariasis has found a new impetus now that neglected tropical diseases have their own journal. However, some of the advances published in renowned international journals have completely ignored previous publications on the subject, particularly those in languages other than English. The rapid assessment procedure for loiasis and the mapping of lymphatic filariasis provide two perfect illustrations of this. This problem may seem a bit outdated, given that all “good authors” now publish exclusively in English. It certainly is outdated for most areas of medicine. But, surely, this should not be the case for neglected tropical diseases, for which certain long-standing findings are every bit as important as what may be presented as new discoveries. One possibility would be for certain journals, such as PLOS Neglected Tropical Diseases, to include a specific heading permitting the publication in English of older studies that initially appeared in a language other than English. The texts would be English versions respecting the entirety of the original text. Submission should be accompanied by a presentation of the problem, with details and explanatory comments, with submission at the initiative of the authors of the former article in question or their students or sympathizers. PMID:23272254

A seismic hazard uncertainty analysis for the New Madrid seismic zone

USGS Publications Warehouse

Cramer, C.H.

2001-01-01

A review of the scientific issues relevant to characterizing earthquake sources in the New Madrid seismic zone has led to the development of a logic tree of possible alternative parameters. A variability analysis, using Monte Carlo sampling of this consensus logic tree, is presented and discussed. The analysis shows that for 2%-exceedence-in-50-year hazard, the best-estimate seismic hazard map is similar to previously published seismic hazard maps for the area. For peak ground acceleration (PGA) and spectral acceleration at 0.2 and 1.0 s (0.2 and 1.0 s Sa), the coefficient of variation (COV) representing the knowledge-based uncertainty in seismic hazard can exceed 0.6 over the New Madrid seismic zone and diminishes to about 0.1 away from areas of seismic activity. Sensitivity analyses show that the largest contributor to PGA, 0.2 and 1.0 s Sa seismic hazard variability is the uncertainty in the location of future 1811-1812 New Madrid sized earthquakes. This is followed by the variability due to the choice of ground motion attenuation relation, the magnitude for the 1811-1812 New Madrid earthquakes, and the recurrence interval for M>6.5 events. Seismic hazard is not very sensitive to the variability in seismogenic width and length. Published by Elsevier Science B.V.

Advances in Exercise, Fitness, and Performance Genomics in 2011

PubMed Central

Roth, Stephen M.; Rankinen, Tuomo; Hagberg, James M.; Loos, Ruth J. F.; Pérusse, Louis; Sarzynski, Mark A.; Wolfarth, Bernd; Bouchard, Claude

2014-01-01

This review of the exercise genomics literature emphasizes the highest quality papers published in 2011. Given this emphasis on the best publications, only a small number of published papers are reviewed. One study found that physical activity levels were significantly lower in patients with mitochondrial DNA mutations compared to controls. A two-stage fine mapping follow-up of a previous linkage peak found strong associations between sequence variation in the activin A receptor, type-1B (ACVR1B) gene and knee extensor strength, with rs2854464 emerging as the most promising candidate polymorphism. The association of higher muscular strength with the rs2854464 A-allele was confirmed in two separate cohorts. A study using a combination of transcriptomic and genomic data identified a comprehensive map of the transcriptomic features important for aerobic exercise training-induced improvements in maximal oxygen consumption, but no genetic variants derived from candidate transcripts were associated with trainability. A large-scale de novo meta-analysis confirmed that the effect of sequence variation in the fat mass and obesity-associated (FTO) gene on the risk of obesity differs between sedentary and physically active adults. Evidence for gene-physical activity interactions on type 2 diabetes risk was found in two separate studies. A large study of women found that physical activity modified the effect of polymorphisms in the lipoprotein lipase (LPL), hepatic lipase (LIPC), and cholesteryl ester transfer protein (CETP) genes, identified in previous genome-wide association study (GWAS) reports, on HDL-C. We conclude that a strong exercise genomics corpus of evidence would not only translate into powerful genomic predictors but would also have a major impact on exercise biology and exercise behavior research. PMID:22330029

Comparative genomics of Toll-like receptor signalling in five species

PubMed Central

Jann, Oliver C; King, Annemarie; Corrales, Nestor Lopez; Anderson, Susan I; Jensen, Kirsty; Ait-ali, Tahar; Tang, Haizhou; Wu, Chunhua; Cockett, Noelle E; Archibald, Alan L; Glass, Elizabeth J

2009-01-01

Background Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions. Results We report the genomic localisation of TLR1-10 and ten associated signalling molecules in sheep and pig using in-silico and/or radiation hybrid (RH) mapping techniques and compare their positions with their annotated homologues in the human, cattle and mouse whole genome sequences. We also report medium-density RH maps for porcine chromosomes 8 and 13. A comparative analysis of the positions of previously published relevant QTLs allowed the identification of homologous regions that are associated with similar health traits in several species and which contain TLR related and other immunologically relevant genes. Additional evidence was gathered by examining relevant gene expression and association studies. Conclusion This comparative genomic approach identified eight genes as potentially causative genes for variations of health related traits. These include susceptibility to clinical mastitis in dairy cattle, general disease resistance in sheep, cattle, humans and mice, and tolerance to protozoan infection in cattle and mice. Four TLR-related genes (TLR1, 6, MyD88, IRF3) appear to be the most likely candidate genes underlying QTL regions which control the resistance to the same or similar pathogens in several species. Further studies are required to investigate the potential role of polymorphisms within these genes. PMID:19432955

Compilation of Moho boundary map for northern Fennoscandian shield

NASA Astrophysics Data System (ADS)

Silvennoinen, H.; Kozlovskaya, E.; Kissling, E.; Kosarev, G.

2012-04-01

POLENET/LAPNET project is a passive seismic array experiment in north-western Fennoscandian Shield. It is centered in northern Finland with some stations also in Sweden, Norway and Russia. The experiment was a part of International Polar Year (IPY) 2007-2009. One of the main targets of the project is to obtain a seismic model of the upper mantle using tomographic inversion of teleseismic travel times. To correct teleseismic travel times for crustal effect we present a new Moho map of POLENET/LAPNET study area located between 64˚ - 70˚ N and 18˚ - 34˚ E. The new Moho map is based on published models of previous 2-D controlled source seismic experiments and previous and new receiver function inversion results. There are four major seismic profiles crossing our research area. In addition there are some shorter profiles, but also quite large areas with no previous controlled source seismic information at all. These regions of data gaps were filled by a new analysis of receiver functions obtained from POLENET/LAPNET data. CRUST3D program was used for compiling these different types of 1-D and 2-D data to a 3-D crustal model. The program is designed to take advantage of the different methodological strengths and to compile a 3-D crustal model that fits all available data within its appropriate individual and methodological uncertainty limits. The original data leading to the published models were carefully analyzed to ascertain only information is used from locations where Moho reflectors/refractors were actually observed. The Moho interface is obtained by application of the principle of simplicity: the aim is to find a smoothest Moho interface that satisfies all reflector data within their a priori estimated error bars. On our Moho map we can see three main units in Moho, which suggests presence of three major crustal terrains. In south-western part of our study area the Moho is quite flat and shallow with average Moho depth of 44 km, which suggests that the crust there was formed in Achaean. In northern part of our study area the Moho is also quite flat and the average Moho depth is about 47 km, suggesting that the crust there has been reworked in Proterozoic. Two deepest Moho depressions were found in the north-eastern and south-eastern parts of study area, where it is reaching the depths of almost 60 km. The latter Moho depression appears to be limitation of the thin crust of the Karelian Craton not only from the West, but also from the East and is spatially coincident with the cluster of mineral deposits.

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

PubMed Central

2011-01-01

Background The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/. PMID:21854616

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii).

PubMed

Wang, Chenwei; Webley, Lee; Wei, Ke-jun; Wakefield, Matthew J; Patel, Hardip R; Deakin, Janine E; Alsop, Amber; Marshall Graves, Jennifer A; Cooper, Desmond W; Nicholas, Frank W; Zenger, Kyall R

2011-08-19

The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/.

Mapping publication status and exploring hotspots in a research field: chronic disease self-management.

PubMed

Lu, Yang; Li, Zheng; Arthur, David

2014-08-01

To provide insight into the characteristics of chronic disease self-management by mapping publication status and exploring hotspots. Chronic disease is becoming a major public health issue worldwide, highlighting the importance of self-management in this area. Despite the volume and variety of publications, little is known about how 'chronic disease self-management' has developed, since the first publication 40 years ago. Such is the number of publications in the area, that there is a need for a systematic bibliographic examination to enable clinicians and researchers to navigate this literature. A bibliometric analysis of publications was used. Publication status was achieved using BICOMB software, whereas hotspots were identified with Ucinet software. A search of PubMed was conducted for papers published between 1971-2012. By 2011, the number of publications reached 696, a fourfold increase from the previous 10 years, of which 75% came from the USA and UK. There were 1284 journals, which published chronic disease self-management research, involving various disciplines. The research hotspots highlighted various self-management strategies for the following: diabetes; cardiac vascular and pulmonary chronic disease; pain relief for neoplasms; and obesity. Psychological adjustment was a permeating theme in self-management processes as was using internet-based interventions. Self-management in chronic disease publication has been most evident in developed countries. The bibliographic mapping and identification of publication hotspots provides scholars and practitioners with key target journals, as well as a rigorous overview of the field for use in further research, evidence-based practice and health policy development. © 2014 John Wiley & Sons Ltd.

Mapping the core journals of the physical therapy literature*

PubMed Central

Fell, Dennis W; Buchanan, Melanie J; Horchen, Heidi A; Scherr, Joel A

2011-01-01

Objectives: The purpose of this study was to identify (1) core journals in the literature of physical therapy, (2) currency of references cited in that literature, and (3) online databases providing the highest coverage rate of core journals. Method: Data for each cited reference in each article of four source journals for three years were recorded, including type of literature, year of publication, and journal title. The journal titles were ranked in descending order according to the frequency of citations and divided into three zones using Bradford's Law of Scattering. Four databases were analyzed for coverage rates of articles published in the Zone 1 and Zone 2 journals in 2007. Results: Journal articles were the most frequently cited type of literature, with sixteen journals supplying one-third of the cited journal references. Physical Therapy was the most commonly cited title. There were more cited articles published from 2000 to 2007 than in any previous full decade. Of the databases analyzed, CINAHL provided the highest coverage rate for Zone 1 2007 publications. Conclusions: Results were similar to a previous study, except for changes in the order of Zone 1 journals. Results can help physical therapists and librarians determine important journals in this discipline. PMID:21753912

Surficial Geologic Map of the Worcester North-Oxford- Wrentham-Attleboro Nine-Quadrangle Area in South- Central Massachusetts

USGS Publications Warehouse

Stone, Byron D.; Stone, Janet R.; DiGiacomo-Cohen, Mary L.

2008-01-01

The surficial geologic map layer shows the distribution of nonlithified earth materials at land surface in an area of nine 7.5-minute quadrangles (417 mi2 total) in south-central Massachusetts (fig. 1). Across Massachusetts, these materials range from a few feet to more than 500 ft in thickness. They overlie bedrock, which crops out in upland hills and in resistant ledges in valley areas. The geologic map differentiates surficial materials of Quaternary age on the basis of their lithologic characteristics (such as grain size and sedimentary structures), constructional geomorphic features, stratigraphic relationships, and age. Surficial materials also are known in engineering classifications as unconsolidated soils, which include coarse-grained soils, fine-grained soils, or organic fine-grained soils. Surficial materials underlie and are the parent materials of modern pedogenic soils, which have developed in them at the land surface. Surficial earth materials significantly affect human use of the land, and an accurate description of their distribution is particularly important for water resources, construction aggregate resources, earth-surface hazards assessments, and land-use decisions. The mapped distribution of surficial materials that lie between the land surface and the bedrock surface is based on detailed geologic mapping of 7.5-minute topographic quadrangles, produced as part of an earlier (1938-1982) cooperative statewide mapping program between the U.S. Geological Survey and the Massachusetts Department of Public Works (now Massachusetts Highway Department) (Page, 1967; Stone, 1982). Each published geologic map presents a detailed description of local geologic map units, the genesis of the deposits, and age correlations among units. Previously unpublished field compilation maps exist on paper or mylar sheets and these have been digitally rendered for the present map compilation. Regional summaries based on the Massachusetts surficial geologic mapping studies discuss the ages of multiple glaciations, the nature of glaciofluvial, glaciolacustrine, and glaciomarine deposits, and the processes of ice advance and retreat across Massachusetts (Koteff and Pessl, 1981; papers in Larson and Stone, 1982; Oldale and Barlow, 1986; Stone and Borns, 1986; Warren and Stone, 1986). This compilation of surficial geologic materials is an interim product that defines the areas of exposed bedrock and the boundaries between glacial till, glacial stratified deposits, and overlying postglacial deposits. This work is part of a comprehensive study to produce a statewide digital map of the surficial geology at a 1:24,000-scale level of accuracy. This surficial geologic map layer covering nine quadrangles revises previous digital surficial geologic maps (Stone and others, 1993; MassGIS, 1999) that were compiled on base maps at regional scales of 1:125,000 and 1:250,000. The purpose of this study is to provide fundamental geologic data for the evaluation of natural resources, hazards, and land information within the Commonwealth of Massachusetts.

ERTS-1 MSS imagery: Its use in delineating soil associations and as a base map for publishing soils information. [South Dakota

NASA Technical Reports Server (NTRS)

Westin, F. C.

1974-01-01

ERTS 1 imagery is a useful tool in the identification and refinement of soil association areas and an excellent base map upon which soil association information can be published. Prints of bands 5 and 7 were found to be most useful to help delineate major soil and vegetation areas. After delineating major soil areas, over 4800 land sale prices covering a period of 1967-72 were located in the soil areas and averaged. The soil association then were described as soil association value areas and published on a 1:1,000,000 scale ERTS mosaic of South Dakota constructed using negative prints of band 7. The map is intended for use by state and county revenue officers, by individual buyers and sellers of land and lending institutions, and as a reference map by those planning road routes and cable lines and pipelines.

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

Data Mining of Determinants of Intrauterine Growth Retardation Revisited Using Novel Algorithms Generating Semantic Maps and Prototypical Discriminating Variable Profiles

PubMed Central

Buscema, Massimo; Grossi, Enzo; Montanini, Luisa; Street, Maria E.

2015-01-01

Objectives Intra-uterine growth retardation is often of unknown origin, and is of great interest as a “Fetal Origin of Adult Disease” has been now well recognized. We built a benchmark based upon a previously analysed data set related to Intrauterine Growth Retardation with 46 subjects described by 14 variables, related with the insulin-like growth factor system and pro-inflammatory cytokines, namely interleukin -6 and tumor necrosis factor -α. Design and Methods We used new algorithms for optimal information sorting based on the combination of two neural network algorithms: Auto-contractive Map and Activation and Competition System. Auto-Contractive Map spatializes the relationships among variables or records by constructing a suitable embedding space where ‘closeness’ among variables or records reflects accurately their associations. The Activation and Competition System algorithm instead works as a dynamic non linear associative memory on the weight matrices of other algorithms, and is able to produce a prototypical variable profile of a given target. Results Classical statistical analysis, proved to be unable to distinguish intrauterine growth retardation from appropriate-for-gestational age (AGA) subjects due to the high non-linearity of underlying functions. Auto-contractive map succeeded in clustering and differentiating completely the conditions under study, while Activation and Competition System allowed to develop the profile of variables which discriminated the two conditions under study better than any other previous form of attempt. In particular, Activation and Competition System showed that ppropriateness for gestational age was explained by IGF-2 relative gene expression, and by IGFBP-2 and TNF-α placental contents. IUGR instead was explained by IGF-I, IGFBP-1, IGFBP-2 and IL-6 gene expression in placenta. Conclusion This further analysis provided further insight into the placental key-players of fetal growth within the insulin-like growth factor and cytokine systems. Our previous published analysis could identify only which variables were predictive of fetal growth in general, and identified only some relationships. PMID:26158499

Digital geologic map and Landsat image map of parts of Loralai, Sibi, Quetta, and Khuzar Divisions, Balochistan Province, west-central Pakistan

USGS Publications Warehouse

Maldonado, Florian; Menga, Jan Mohammad; Khan, Shabid Hasan; Thomas, Jean-Claude

2011-01-01

This generalized digital geologic map of west-central Pakistan is a product of the Balochistan Coal-Basin Synthesis Study, which was part of a cooperative program of the Geological Survey of Pakistan and the United States Geological Survey. The original nondigital map was published by Maldonado and others (1998). Funding was provided by the Government of Pakistan and the United States Agency for International Development. The sources of geologic map data are primarily 1:253,440-scale geologic maps obtained from Hunting Survey Corporation (1961) and the geologic map of the Muslim Bagh Ophiolite Complex and Bagh Complex area. The geology was modified based on reconnaissance field work and photo interpretation of 1:250,000-scale Landsat Thematic Mapper photo image. The descriptions and thicknesses of map units were based on published and unpublished reports and converted to U.S. Geological Survey format. In the nomenclature of the Geological Survey of Pakistan, there is both an Urak Group and an Urak Formation.

Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map.

PubMed

Larson, Wesley A; McKinney, Garrett J; Limborg, Morten T; Everett, Meredith V; Seeb, Lisa W; Seeb, James E

2016-03-01

Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Structural analysis of chromosomal rearrangements associated with the developmental mutations Ph, W19H, and Rw on mouse chromosome 5.

PubMed Central

Nagle, D L; Martin-DeLeon, P; Hough, R B; Bućan, M

1994-01-01

We are studying the chromosomal structure of three developmental mutations, dominant spotting (W), patch (Ph), and rump white (Rw) on mouse chromosome 5. These mutations are clustered in a region containing three genes encoding tyrosine kinase receptors (Kit, Pdgfra, and Flk1). Using probes for these genes and for a closely linked locus, D5Mn125, we established a high-resolution physical map covering approximately 2.8 Mb. The entire chromosomal segment mapped in this study is deleted in the W19H mutation. The map indicates the position of the Ph deletion, which encompasses not more than 400 kb around and including the Pdgfra gene. The map also places the distal breakpoint of the Rw inversion to a limited chromosomal segment between Kit and Pdgfra. In light of the structure of the Ph-W-Rw region, we interpret the previously published complementation analyses as indicating that the pigmentation defect in Rw/+ heterozygotes could be due to the disruption of Kit and/or Pdgfra regulatory sequences, whereas the gene(s) responsible for the recessive lethality of Rw/Rw embryos is not closely linked to the Ph and W loci and maps proximally to the W19H deletion. The structural analysis of chromosomal rearrangements associated with W19H, Ph, and Rw combined with the high-resolution physical mapping points the way toward the definition of these mutations in molecular terms and isolation of homologous genes on human chromosome 4. Images PMID:8041773

Monopole and dipole estimation for multi-frequency sky maps by linear regression

NASA Astrophysics Data System (ADS)

Wehus, I. K.; Fuskeland, U.; Eriksen, H. K.; Banday, A. J.; Dickinson, C.; Ghosh, T.; Górski, K. M.; Lawrence, C. R.; Leahy, J. P.; Maino, D.; Reich, P.; Reich, W.

2017-01-01

We describe a simple but efficient method for deriving a consistent set of monopole and dipole corrections for multi-frequency sky map data sets, allowing robust parametric component separation with the same data set. The computational core of this method is linear regression between pairs of frequency maps, often called T-T plots. Individual contributions from monopole and dipole terms are determined by performing the regression locally in patches on the sky, while the degeneracy between different frequencies is lifted whenever the dominant foreground component exhibits a significant spatial spectral index variation. Based on this method, we present two different, but each internally consistent, sets of monopole and dipole coefficients for the nine-year WMAP, Planck 2013, SFD 100 μm, Haslam 408 MHz and Reich & Reich 1420 MHz maps. The two sets have been derived with different analysis assumptions and data selection, and provide an estimate of residual systematic uncertainties. In general, our values are in good agreement with previously published results. Among the most notable results are a relative dipole between the WMAP and Planck experiments of 10-15μK (depending on frequency), an estimate of the 408 MHz map monopole of 8.9 ± 1.3 K, and a non-zero dipole in the 1420 MHz map of 0.15 ± 0.03 K pointing towards Galactic coordinates (l,b) = (308°,-36°) ± 14°. These values represent the sum of any instrumental and data processing offsets, as well as any Galactic or extra-Galactic component that is spectrally uniform over the full sky.

Regional Geologic Map of San Andreas and Related Faults in Carrizo Plain, Temblor, Caliente and La Panza Ranges and Vicinity, California; A Digital Database

USGS Publications Warehouse

Dibblee, T. W.; Digital database compiled by Graham, S. E.; Mahony, T.M.; Blissenbach, J.L.; Mariant, J.J.; Wentworth, C.M.

1999-01-01

This Open-File Report is a digital geologic map database. The report serves to introduce and describe the digital data. There is no paper map included in the Open-File Report. The report includes PostScript and PDF plot files that can be used to plot images of the geologic map sheet and explanation sheet. This digital map database is prepared from a previously published map by Dibblee (1973). The geologic map database delineates map units that are identified by general age, lithology, and clast size following the stratigraphic nomenclature of the U.S. Geological Survey. For descriptions of the units, their stratigraphic relations, and sources of geologic mapping, consult the explanation sheet (of99-14_4b.ps or of99-14_4d.pdf), or the original published paper map (Dibblee, 1973). The scale of the source map limits the spatial resolution (scale) of the database to 1:125,000 or smaller. For those interested in the geology of Carrizo Plain and vicinity who do not use an ARC/INFO compatible Geographic Information System (GIS), but would like to obtain a paper map and explanation, PDF and PostScript plot files containing map images of the data in the digital database, as well as PostScript and PDF plot files of the explanation sheet and explanatory text, have been included in the database package (please see the section 'Digital Plot Files', page 5). The PostScript plot files require a gzip utility to access them. For those without computer capability, we can provide users with the PostScript or PDF files on tape that can be taken to a vendor for plotting. Paper plots can also be ordered directly from the USGS (please see the section 'Obtaining Plots from USGS Open-File Services', page 5). The content and character of the database, methods of obtaining it, and processes of extracting the map database from the tar (tape archive) file are described herein. The map database itself, consisting of six ARC/INFO coverages, can be obtained over the Internet or by magnetic tape copy as described below. The database was compiled using ARC/INFO, a commercial Geographic Information System (Environmental Systems Research Institute, Redlands, California), with version 3.0 of the menu interface ALACARTE (Fitzgibbon and Wentworth, 1991, Fitzgibbon, 1991, Wentworth and Fitzgibbon, 1991). The ARC/INFO coverages are stored in uncompressed ARC export format (ARC/INFO version 7.x). All data files have been compressed, and may be uncompressed with gzip, which is available free of charge over the Internet via links from the USGS Public Domain Software page (http://edcwww.cr.usgs.gov/doc/edchome/ndcdb/public.html). ARC/INFO export files (files with the .e00 extension) can be converted into ARC/INFO coverages in ARC/INFO (see below) and can be read by some other Geographic Information Systems, such as MapInfo via ArcLink and ESRI's ArcView.

A radiation hybrid map of the proximal long arm of human chromosome 11 containing the multiple endocrine neoplasia type 1 (MEN-1) and bcl-1 disease loci.

PubMed Central

Richard, C W; Withers, D A; Meeker, T C; Maurer, S; Evans, G A; Myers, R M; Cox, D R

1991-01-01

We describe a high-resolution radiation hybrid map of the proximal long arm of human chromosome 11 containing the bcl-1 and multiple endocrine neoplasia type 1 (MEN-1) disease gene loci. We used X-ray irradiation and cell fusion to generate a panel of 102 hamster-human somatic cell hybrids containing fragments of human chromosome 11. Sixteen human loci in the 11q12-13 region were mapped by statistical analysis of the cosegregation of markers in these radiation hybrids. The most likely order for these loci is C1NH-OSBP-(CD5/CD20)-PGA-FTH1-COX8-PYGM -SEA-KRN1-(MTC/P11EH/HSTF1/INT2)-GST3- PPP1A. Our localization of the human protooncogene SEA between PYGM and INT2, two markers that flank MEN-1, suggests SEA as a potential candidate for the MEN-1 locus. We map two mitogenic fibroblast growth factor genes, HSTF1 and INT2, close to bcl-1, a mapping that is consistent with previously published data. Our map places the human leukocyte antigen genes CD5 and CD20 far from the bcl-1 locus, indicating that CD5 and CD20 expression is unlikely to be altered by bcl-1 rearrangements. PPP1A, which has been postulated as a MEN-1 candidate tumor suppressor gene, and GST3, a gene transcriptionally active in many human cancers, both map distal to the bcl-1 translocation cluster and the region containing MEN-1, and therefore are unlikely to be directly involved in bcl-1 or MEN-1. PMID:1684084

USGS National Seismic Hazard Maps

USGS Publications Warehouse

Frankel, A.D.; Mueller, C.S.; Barnhard, T.P.; Leyendecker, E.V.; Wesson, R.L.; Harmsen, S.C.; Klein, F.W.; Perkins, D.M.; Dickman, N.C.; Hanson, S.L.; Hopper, M.G.

2000-01-01

The U.S. Geological Survey (USGS) recently completed new probabilistic seismic hazard maps for the United States, including Alaska and Hawaii. These hazard maps form the basis of the probabilistic component of the design maps used in the 1997 edition of the NEHRP Recommended Provisions for Seismic Regulations for New Buildings and Other Structures, prepared by the Building Seismic Safety Council arid published by FEMA. The hazard maps depict peak horizontal ground acceleration and spectral response at 0.2, 0.3, and 1.0 sec periods, with 10%, 5%, and 2% probabilities of exceedance in 50 years, corresponding to return times of about 500, 1000, and 2500 years, respectively. In this paper we outline the methodology used to construct the hazard maps. There are three basic components to the maps. First, we use spatially smoothed historic seismicity as one portion of the hazard calculation. In this model, we apply the general observation that moderate and large earthquakes tend to occur near areas of previous small or moderate events, with some notable exceptions. Second, we consider large background source zones based on broad geologic criteria to quantify hazard in areas with little or no historic seismicity, but with the potential for generating large events. Third, we include the hazard from specific fault sources. We use about 450 faults in the western United States (WUS) and derive recurrence times from either geologic slip rates or the dating of pre-historic earthquakes from trenching of faults or other paleoseismic methods. Recurrence estimates for large earthquakes in New Madrid and Charleston, South Carolina, were taken from recent paleoliquefaction studies. We used logic trees to incorporate different seismicity models, fault recurrence models, Cascadia great earthquake scenarios, and ground-motion attenuation relations. We present disaggregation plots showing the contribution to hazard at four cities from potential earthquakes with various magnitudes and distances.

A radiation hybrid map of the proximal long arm of human chromosome 11 containing the multiple endocrine neoplasia type 1 (MEN-1) and bcl-1 disease loci.

PubMed

Richard, C W; Withers, D A; Meeker, T C; Maurer, S; Evans, G A; Myers, R M; Cox, D R

1991-12-01

We describe a high-resolution radiation hybrid map of the proximal long arm of human chromosome 11 containing the bcl-1 and multiple endocrine neoplasia type 1 (MEN-1) disease gene loci. We used X-ray irradiation and cell fusion to generate a panel of 102 hamster-human somatic cell hybrids containing fragments of human chromosome 11. Sixteen human loci in the 11q12-13 region were mapped by statistical analysis of the cosegregation of markers in these radiation hybrids. The most likely order for these loci is C1NH-OSBP-(CD5/CD20)-PGA-FTH1-COX8-PYGM -SEA-KRN1-(MTC/P11EH/HSTF1/INT2)-GST3- PPP1A. Our localization of the human protooncogene SEA between PYGM and INT2, two markers that flank MEN-1, suggests SEA as a potential candidate for the MEN-1 locus. We map two mitogenic fibroblast growth factor genes, HSTF1 and INT2, close to bcl-1, a mapping that is consistent with previously published data. Our map places the human leukocyte antigen genes CD5 and CD20 far from the bcl-1 locus, indicating that CD5 and CD20 expression is unlikely to be altered by bcl-1 rearrangements. PPP1A, which has been postulated as a MEN-1 candidate tumor suppressor gene, and GST3, a gene transcriptionally active in many human cancers, both map distal to the bcl-1 translocation cluster and the region containing MEN-1, and therefore are unlikely to be directly involved in bcl-1 or MEN-1.

Genetic dissection of fruiting body-related traits using quantitative trait loci mapping in Lentinula edodes.

PubMed

Gong, Wen-Bing; Li, Lei; Zhou, Yan; Bian, Yin-Bing; Kwan, Hoi-Shan; Cheung, Man-Kit; Xiao, Yang

2016-06-01

To provide a better understanding of the genetic architecture of fruiting body formation of Lentinula edodes, quantitative trait loci (QTLs) mapping was employed to uncover the loci underlying seven fruiting body-related traits (FBRTs). An improved L. edodes genetic linkage map, comprising 572 markers on 12 linkage groups with a total map length of 983.7 cM, was constructed by integrating 82 genomic sequence-based insertion-deletion (InDel) markers into a previously published map. We then detected a total of 62 QTLs for seven target traits across two segregating testcross populations, with individual QTLs contributing 5.5 %-30.2 % of the phenotypic variation. Fifty-three out of the 62 QTLs were clustered in six QTL hotspots, suggesting the existence of main genomic regions regulating the morphological characteristics of fruiting bodies in L. edodes. A stable QTL hotspot on MLG2, containing QTLs for all investigated traits, was identified in both testcross populations. QTLs for related traits were frequently co-located on the linkage groups, demonstrating the genetic basis for phenotypic correlation of traits. Meta-QTL (mQTL) analysis was performed and identified 16 mQTLs with refined positions and narrow confidence intervals (CIs). Nine genes, including those encoding MAP kinase, blue-light photoreceptor, riboflavin-aldehyde-forming enzyme and cyclopropane-fatty-acyl-phospholipid synthase, and cytochrome P450s, were likely to be candidate genes controlling the shape of fruiting bodies. The study has improved our understanding of the genetic architecture of fruiting body formation in L. edodes. To our knowledge, this is the first genome-wide QTL detection of FBRTs in L. edodes. The improved genetic map, InDel markers and QTL hotspot regions revealed here will assist considerably in the conduct of future genetic and breeding studies of L. edodes.

What is an evidence map? A systematic review of published evidence maps and their definitions, methods, and products.

PubMed

Miake-Lye, Isomi M; Hempel, Susanne; Shanman, Roberta; Shekelle, Paul G

2016-02-10

The need for systematic methods for reviewing evidence is continuously increasing. Evidence mapping is one emerging method. There are no authoritative recommendations for what constitutes an evidence map or what methods should be used, and anecdotal evidence suggests heterogeneity in both. Our objectives are to identify published evidence maps and to compare and contrast the presented definitions of evidence mapping, the domains used to classify data in evidence maps, and the form the evidence map takes. We conducted a systematic review of publications that presented results with a process termed "evidence mapping" or included a figure called an "evidence map." We identified publications from searches of ten databases through 8/21/2015, reference mining, and consulting topic experts. We abstracted the research question, the unit of analysis, the search methods and search period covered, and the country of origin. Data were narratively synthesized. Thirty-nine publications met inclusion criteria. Published evidence maps varied in their definition and the form of the evidence map. Of the 31 definitions provided, 67 % described the purpose as identification of gaps and 58 % referenced a stakeholder engagement process or user-friendly product. All evidence maps explicitly used a systematic approach to evidence synthesis. Twenty-six publications referred to a figure or table explicitly called an "evidence map," eight referred to an online database as the evidence map, and five stated they used a mapping methodology but did not present a visual depiction of the evidence. The principal conclusion of our evaluation of studies that call themselves "evidence maps" is that the implied definition of what constitutes an evidence map is a systematic search of a broad field to identify gaps in knowledge and/or future research needs that presents results in a user-friendly format, often a visual figure or graph, or a searchable database. Foundational work is needed to better standardize the methods and products of an evidence map so that researchers and policymakers will know what to expect of this new type of evidence review. Although an a priori protocol was developed, no registration was completed; this review did not fit the PROSPERO format.

A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius

PubMed Central

Fountain, Toby; Ravinet, Mark; Naylor, Richard; Reinhardt, Klaus; Butlin, Roger K.

2016-01-01

The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species. PMID:27733453

Application of decision tree model for the ground subsidence hazard mapping near abandoned underground coal mines.

PubMed

Lee, Saro; Park, Inhye

2013-09-30

Subsidence of ground caused by underground mines poses hazards to human life and property. This study analyzed the hazard to ground subsidence using factors that can affect ground subsidence and a decision tree approach in a geographic information system (GIS). The study area was Taebaek, Gangwon-do, Korea, where many abandoned underground coal mines exist. Spatial data, topography, geology, and various ground-engineering data for the subsidence area were collected and compiled in a database for mapping ground-subsidence hazard (GSH). The subsidence area was randomly split 50/50 for training and validation of the models. A data-mining classification technique was applied to the GSH mapping, and decision trees were constructed using the chi-squared automatic interaction detector (CHAID) and the quick, unbiased, and efficient statistical tree (QUEST) algorithms. The frequency ratio model was also applied to the GSH mapping for comparing with probabilistic model. The resulting GSH maps were validated using area-under-the-curve (AUC) analysis with the subsidence area data that had not been used for training the model. The highest accuracy was achieved by the decision tree model using CHAID algorithm (94.01%) comparing with QUEST algorithms (90.37%) and frequency ratio model (86.70%). These accuracies are higher than previously reported results for decision tree. Decision tree methods can therefore be used efficiently for GSH analysis and might be widely used for prediction of various spatial events. Copyright © 2013. Published by Elsevier Ltd.

Quantitative Susceptibility Mapping by Inversion of a Perturbation Field Model: Correlation with Brain Iron in Normal Aging

PubMed Central

Poynton, Clare; Jenkinson, Mark; Adalsteinsson, Elfar; Sullivan, Edith V.; Pfefferbaum, Adolf; Wells, William

2015-01-01

There is increasing evidence that iron deposition occurs in specific regions of the brain in normal aging and neurodegenerative disorders such as Parkinson's, Huntington's, and Alzheimer's disease. Iron deposition changes the magnetic susceptibility of tissue, which alters the MR signal phase, and allows estimation of susceptibility differences using quantitative susceptibility mapping (QSM). We present a method for quantifying susceptibility by inversion of a perturbation model, or ‘QSIP’. The perturbation model relates phase to susceptibility using a kernel calculated in the spatial domain, in contrast to previous Fourier-based techniques. A tissue/air susceptibility atlas is used to estimate B0 inhomogeneity. QSIP estimates in young and elderly subjects are compared to postmortem iron estimates, maps of the Field-Dependent Relaxation Rate Increase (FDRI), and the L1-QSM method. Results for both groups showed excellent agreement with published postmortem data and in-vivo FDRI: statistically significant Spearman correlations ranging from Rho = 0.905 to Rho = 1.00 were obtained. QSIP also showed improvement over FDRI and L1-QSM: reduced variance in susceptibility estimates and statistically significant group differences were detected in striatal and brainstem nuclei, consistent with age-dependent iron accumulation in these regions. PMID:25248179

Automated Feature Identification and Classification Using Automated Feature Weighted Self Organizing Map (FWSOM)

NASA Astrophysics Data System (ADS)

Starkey, Andrew; Usman Ahmad, Aliyu; Hamdoun, Hassan

2017-10-01

This paper investigates the application of a novel method for classification called Feature Weighted Self Organizing Map (FWSOM) that analyses the topology information of a converged standard Self Organizing Map (SOM) to automatically guide the selection of important inputs during training for improved classification of data with redundant inputs, examined against two traditional approaches namely neural networks and Support Vector Machines (SVM) for the classification of EEG data as presented in previous work. In particular, the novel method looks to identify the features that are important for classification automatically, and in this way the important features can be used to improve the diagnostic ability of any of the above methods. The paper presents the results and shows how the automated identification of the important features successfully identified the important features in the dataset and how this results in an improvement of the classification results for all methods apart from linear discriminatory methods which cannot separate the underlying nonlinear relationship in the data. The FWSOM in addition to achieving higher classification accuracy has given insights into what features are important in the classification of each class (left and right-hand movements), and these are corroborated by already published work in this area.

p53 regulates ERK1/2/CREB cascade via a novel SASH1/MAP2K2 crosstalk to induce hyperpigmentation.

PubMed

Zhou, Ding'an; Kuang, Zhongshu; Zeng, Xing; Wang, Ke; Ma, Jiangshu; Luo, Huangchao; Chen, Mei; Li, Yan; Zeng, Jiawei; Li, Shu; Luan, Fujun; He, Yong; Dai, Hongying; Liu, Beizhong; Li, Hui; He, Lin; Xing, Qinghe

2017-10-01

We previously reported that three point mutations in SASH1 and mutated SASH1 promote melanocyte migration in dyschromatosis universalis hereditaria (DUH) and a novel p53/POMC/Gαs/SASH1 autoregulatory positive feedback loop is regulated by SASH1 mutations to induce pathological hyperpigmentation phenotype. However, the underlying mechanism of molecular regulation to cause this hyperpigmentation disorder still remains unclear. In this study, we aimed to investigate the molecular mechanism undergirding hyperpigmentation in the dyschromatosis disorder. Our results revealed that SASH1 binds with MAP2K2 and is induced by p53-POMC-MC1R signal cascade to enhance the phosphorylation level of ERK1/2 and CREB. Moreover, increase in phosphorylated ERK1/2 and CREB levels and melanogenesis-specific molecules is induced by mutated SASH1 alleles. Together, our results suggest that a novel SASH1/MAP2K2 crosstalk connects ERK1/2/CREB cascade with p53-POMC-MC1R cascade to cause hyperpigmentation phenotype of DUH. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

An Annotated Bibliography of Concept Mapping

ERIC Educational Resources Information Center

Garcia, GNA

2008-01-01

A rich narrative-style bibliography of concept mapping (reviewing six articles published between 1992-2005). Articles reviewed include: (1) Cognitive mapping: A qualitative research method for social work (C. Bitoni); (2) Collaborative concept mapping: Provoking and supporting meaningful discourse (C. Boxtel, J. Linden, E. Roelofs, and G. Erkens);…

Evaluation of Allele-Specific Somatic Changes of Genome-Wide Association Study Susceptibility Alleles in Human Colorectal Cancers

PubMed Central

Gerber, Madelyn M.; Hampel, Heather; Schulz, Nathan P.; Fernandez, Soledad; Wei, Lai; Zhou, Xiao-Ping; de la Chapelle, Albert; Toland, Amanda Ewart

2012-01-01

Background Tumors frequently exhibit loss of tumor suppressor genes or allelic gains of activated oncogenes. A significant proportion of cancer susceptibility loci in the mouse show somatic losses or gains consistent with the presence of a tumor susceptibility or resistance allele. Thus, allele-specific somatic gains or losses at loci may demarcate the presence of resistance or susceptibility alleles. The goal of this study was to determine if previously mapped susceptibility loci for colorectal cancer show evidence of allele-specific somatic events in colon tumors. Methods We performed quantitative genotyping of 16 single nucleotide polymorphisms (SNPs) showing statistically significant association with colorectal cancer in published genome-wide association studies (GWAS). We genotyped 194 paired normal and colorectal tumor DNA samples and 296 paired validation samples to investigate these SNPs for allele-specific somatic gains and losses. We combined analysis of our data with published data for seven of these SNPs. Results No statistically significant evidence for allele-specific somatic selection was observed for the tested polymorphisms in the discovery set. The rs6983267 variant, which has shown preferential loss of the non-risk T allele and relative gain of the risk G allele in previous studies, favored relative gain of the G allele in the combined discovery and validation samples (corrected p-value = 0.03). When we combined our data with published allele-specific imbalance data for this SNP, the G allele of rs6983267 showed statistically significant evidence of relative retention (p-value = 2.06×10−4). Conclusions Our results suggest that the majority of variants identified as colon cancer susceptibility alleles through GWAS do not exhibit somatic allele-specific imbalance in colon tumors. Our data confirm previously published results showing allele-specific imbalance for rs6983267. These results indicate that allele-specific imbalance of cancer susceptibility alleles may not be a common phenomenon in colon cancer. PMID:22629442

A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome

PubMed Central

Moretzsohn, Márcio C; Barbosa, Andrea VG; Alves-Freitas, Dione MT; Teixeira, Cristiane; Leal-Bertioli, Soraya CM; Guimarães, Patrícia M; Pereira, Rinaldo W; Lopes, Catalina R; Cavallari, Marcelo M; Valls, José FM; Bertioli, David J; Gimenes, Marcos A

2009-01-01

Background Arachis hypogaea (peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for A. hypogaea is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability. Results In this work, we constructed a B-genome linkage map, which will complement the previously published map for the A-genome of Arachis, and produced an entire framework for the tetraploid genome. This map is based on an F2 population of 93 individuals obtained from the cross between the diploid A. ipaënsis (K30076) and the closely related A. magna (K30097), the former species being the most probable B genome donor to cultivated peanut. In spite of being classified as different species, the parents showed high crossability and relatively low polymorphism (22.3%), compared to other interspecific crosses. The map has 10 linkage groups, with 149 loci spanning a total map distance of 1,294 cM. The microsatellite markers utilized, developed for other Arachis species, showed high transferability (81.7%). Segregation distortion was 21.5%. This B-genome map was compared to the A-genome map using 51 common markers, revealing a high degree of synteny between both genomes. Conclusion The development of genetic maps for Arachis diploid wild species with A- and B-genomes effectively provides a genetic map for the tetraploid cultivated peanut in two separate diploid components and is a significant advance towards the construction of a transferable reference map for Arachis. Additionally, we were able to identify affinities of some Arachis linkage groups with Medicago truncatula, which will allow the transfer of information from the nearly-complete genome sequences of this model legume to the peanut crop. PMID:19351409

Geologic map of Chickasaw National Recreation Area, Murray County, Oklahoma

USGS Publications Warehouse

Blome, Charles D.; Lidke, David J.; Wahl, Ronald R.; Golab, James A.

2013-01-01

This 1:24,000-scale geologic map is a compilation of previous geologic maps and new geologic mapping of areas in and around Chickasaw National Recreation Area. The geologic map includes revisions of numerous unit contacts and faults and a number of previously “undifferentiated” rock units were subdivided in some areas. Numerous circular-shaped hills in and around Chickasaw National Recreation Area are probably the result of karst-related collapse and may represent the erosional remnants of large, exhumed sinkholes. Geospatial registration of existing, smaller scale (1:72,000- and 1:100,000-scale) geologic maps of the area and construction of an accurate Geographic Information System (GIS) database preceded 2 years of fieldwork wherein previously mapped geology (unit contacts and faults) was verified and new geologic mapping was carried out. The geologic map of Chickasaw National Recreation Area and this pamphlet include information pertaining to how the geologic units and structural features in the map area relate to the formation of the northern Arbuckle Mountains and its Arbuckle-Simpson aquifer. The development of an accurate geospatial GIS database and the use of a handheld computer in the field greatly increased both the accuracy and efficiency in producing the 1:24,000-scale geologic map.

Resource Needs and Pedagogical Value of Web Mapping for Spatial Thinking

ERIC Educational Resources Information Center

Manson, Steven; Shannon, Jerry; Eria, Sami; Kne, Len; Dyke, Kevin; Nelson, Sara; Batra, Lalit; Bonsal, Dudley; Kernik, Melinda; Immich, Jennifer; Matson, Laura

2014-01-01

Web mapping involves publishing and using maps via the Internet, and can range from presenting static maps to offering dynamic data querying and spatial analysis. Web mapping is seen as a promising way to support development of spatial thinking in the classroom but there are unanswered questions about how this promise plays out in reality. This…

Geologic map and structural analysis of the Victoria quadrangle (H2) of Mercury based on NASA MESSENGER images

NASA Astrophysics Data System (ADS)

Galluzzi, V.; Di Achille, G.; Ferranti, L.; Rothery, D. A.; Palumbo, P.

The first stratigraphic and geologic study of Mercury was released by Trask & Guest (1975) followed by Spudis & Guest (1988, and references therein), whose work was based on the images taken by Mariner 10 covering 42% of the total surface of Mercury. The planet has been officially divided into fifteen quadrangles: 2 polar, 5 equatorial and 8 at midlatitudes. Quadrangle H2 (= Hermes sheet n.2), named ``Victoria'' (20oN - 65oN Lon.; 270oE - 0o Lat.), was partially mapped by McGill & King (1983), though a wide area (˜64%) remained unmapped due to the lack of imagery. Following the terrain units recognized and described by the above authors, we have produced a geologic map of the entire quadrangle using MESSENGER (MErcury Surface, Space ENvironment, GEochemistry and Ranging) images. The images taken by the Mercury Dual Imaging System (MDIS) Wide Angle Camera (WAC) and Narrow Angle Camera (NAC) allowed us to map geologic and tectonic features in much greater detail than the previously published map (mapping scale range between 1:300k and 1:600k). We classified craters larger than 20 km using three relative age classes, which are a simplification of the past five degradation classes defined by McCauley et al. (1981). Victoria quadrangle is characterized by a localized N-S thrust array constituted by Victoria Rupes, Endeavour Rupes and Antoniadi Dorsum to the East and by a more diffuse system of NE-SW oriented fault arrays to the West: the two systems seem to be separated by a tectonic bulge. The Victoria-Endeavour-Antoniadi system has been interpreted as a fold-and-thrust belt by Byrne et al. (2014) and a previous study made on craters cross-cut by its thrusts reveals fault dips of 15-20o and a near dip slip motion (Galluzzi et al., 2015). This geologic map has the aim to build a regional model of its structural framework. Deciphering the geological setting of this quadrangle will bring important insights for understanding the tectonic evolution of the whole planet. Moreover, the results obtained with this study can help in the future targeting choices of the BepiColombo SIMBIOSYS instruments.

Impact of spatial inhomogeneities on stratospheric species vertical profiles from remote-sensing balloon-borne instruments

NASA Astrophysics Data System (ADS)

Berthet, Gwenael; Renard, Jean-Baptiste; Catoire, Valery; Huret, Nathalie; Lefevre, Franck; Hauchecorne, Alain; Chartier, Michel; Robert, Claude

Remote-sensing balloon observations have recurrently revealed high concentrations of polar stratospheric NO2 in particular in the lower stratosphere as can be seen in various published vertical profiles. A balloon campaign dedicated to the investigation of this problem through comparisons between remote-sensing (SALOMON) and in situ (SPIRALE) measurements of NO2 inside the polar vortex was conducted in January 2006. The published results show unexpected strong enhancements in the slant column densities of NO2 with respect to the elevation angle and displacement of the balloon. These fluctuations result from NO2 spatial inhomogeneities located above the balloon float altitude resulting from mid-latitude air intrusion as revealed by Potential Vorticity (PV) maps. The retrieval of the NO2 vertical profile is subsequently biased in the form of artificial excesses of NO2 concentrations. A direct implication is that the differences previously observed between measurements of NO2 and OClO and model results are probably mostly due to the improper inversion of NO2 in presence of either perturbed dynamical conditions or when mesospheric production events occur as recently highlighted from ENVISAT data. Through the occurrence of such events, we propose to re-examine formerly published high-latitude profiles from the remote-sensing instruments AMON and SALOMON using in parallel PV maps from the MIMOSA advection contour model and the REPROBUS CTM outputs. Mid-latitude profiles of NO2 will also be investigated since they are likely to be biased if presence of air from other latitudes was present at the time of the observations.

Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described. PMID:16420699

A geologic atlas of TIMS data

NASA Technical Reports Server (NTRS)

Abbott, Elsa

1986-01-01

In the three years since the first data were taken, it was well demonstrated that the Thermal Infrared Multispectral Scanner (TIMS), properly used, can be a most valuable tool for the geologist. Compilation of the TIMS data into a geological atlas was felt to be useful. Several data sets were extensively studied to establish TIMS as a geologic tool and to explore the optimum enhancement techniques. It was found that a decorrelation stretch of bands 1, 3, and 5 enhance the data to a form that is very useful and this enhancement will be used in the geologic atlas along with an accompanying geologic map and description. Many data sets are well published and familiar to TIMS users, but there are some sets that, for lack of time and funds, were not thoroughly studied or published. A short description of these least studied sets of data is presented. The images presented along with the many previously studied and published TIMS images constitute an enormously useful set of information for the geologist in the 8 to 10 micron range.

Alteration, slope-classified alteration, and potential lahar inundation maps of volcanoes for the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) Volcano Archive

USGS Publications Warehouse

Mars, John C.; Hubbard, Bernard E.; Pieri, David; Linick, Justin

2015-01-01

This study was undertaken during 2012–2013 in cooperation with the National Aeronautics and Space Administration (NASA). Since completion of this study, a new lahar modeling program (LAHAR_pz) has been released, which may produce slightly different modeling results from the LAHARZ model used in this study. The maps and data from this study should not be used in place of existing volcano hazard maps published by local authorities. For volcanoes without hazard maps and (or) published lahar-related hazard studies, this work will provide a starting point from which more accurate hazard maps can be produced. This is the first dataset to provide digital maps of altered volcanoes and adjacent watersheds that can be used for assessing volcanic hazards, hydrothermal alteration, and other volcanic processes in future studies.

Where do students struggle in the field? Computer-aided evaluation of mapping errors from an undergraduate Field Geology summer course

NASA Astrophysics Data System (ADS)

Lang, K. A.; Petrie, G.

2014-12-01

Extended field-based summer courses provide an invaluable field experience for undergraduate majors in the geosciences. These courses often utilize the construction of geological maps and structural cross sections as the primary pedagogical tool to teach basic map orientation, rock identification and structural interpretation. However, advances in the usability and ubiquity of Geographic Information Systems in these courses presents new opportunities to evaluate student work. In particular, computer-based quantification of systematic mapping errors elucidates the factors influencing student success in the field. We present a case example from a mapping exercise conducted in a summer Field Geology course at a popular field location near Dillon, Montana. We use a computer algorithm to automatically compare the placement and attribution of unit contacts with spatial variables including topographic slope, aspect, bedding attitude, ground cover and distance from starting location. We compliment analyses with anecdotal and survey data that suggest both physical factors (e.g. steep topographic slope) as well as structural nuance (e.g. low angle bedding) may dominate student frustration, particularly in courses with a high student to instructor ratio. We propose mechanisms to improve student experience by allowing students to practice skills with orientation games and broadening student background with tangential lessons (e.g. on colluvial transport processes). As well, we suggest low-cost ways to decrease the student to instructor ratio by supporting returning undergraduates from previous years or staging mapping over smaller areas. Future applications of this analysis might include a rapid and objective system for evaluation of student maps (including point-data, such as attitude measurements) and quantification of temporal trends in student work as class sizes, pedagogical approaches or environmental variables change. Long-term goals include understanding and characterizing stochasticity in geological mapping beyond the undergraduate classroom, and better quantifying uncertainty in published map products.

Assessment of the relative sensitivity of milk ELISA for detection of Mycobacterium avium ssp. paratuberculosis infectious dairy cows.

PubMed

Laurin, Emilie L; Sanchez, Javier; Chaffer, Marcelo; McKenna, Shawn L B; Keefe, Greg P

2017-01-01

Milk ELISA are commonly used for detection of Mycobacterium avium ssp. paratuberculosis (MAP) antibodies in dairy cows, due to low cost and quick processing for large numbers of samples. However, low sensitivity and variations from host and environmental factors can impede detection of MAP antibodies at early disease stages. The objectives of our study were to assess the sensitivity of milk ELISA in comparison with fecal tests and to evaluate how detectable antibody concentrations in milk vary with changes in fecal shedding of MAP, cow age, cow parity, days in milk, and time of year. To compare the sensitivity of a commercial milk ELISA with solid and broth fecal culture and with fecal real-time PCR, a longitudinal study was performed for the identification of MAP-infectious animals as determined by prior fecal testing for MAP shedding. In addition, associations between variation in milk MAP ELISA score and changes in fecal MAP shedding, host age, days in milk, and season were evaluated. Monthly milk and fecal samples were collected over 1 yr from 46 cows that were previously shedding MAP in their feces. Sensitivity of milk ELISA was 29.9% (95% CI: 24.8 to 35.1%), compared with 46.7% (40.7 to 52.7%) for fecal solid culture, 55.0% (49.3 to 60.7%) for fecal broth culture, and 78.4% (73.3 to 83.1%) for fecal direct real-time PCR. The effect of stage of lactation could not be separated from the effect of season, with increased milk ELISA scores at greater days in milk in winter. However, unpredictable monthly variations in results were observed among the 3 assays for individual cow testing, which highlights the importance of identifying patterns in pathogen and antibody detection over time in MAP-positive herds. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mapping a Nursing Terminology Subset to openEHR Archetypes. A Case Study of the International Classification for Nursing Practice.

PubMed

Nogueira, J R M; Cook, T W; Cavalini, L T

2015-01-01

Healthcare information technologies have the potential to transform nursing care. However, healthcare information systems based on conventional software architecture are not semantically interoperable and have high maintenance costs. Health informatics standards, such as controlled terminologies, have been proposed to improve healthcare information systems, but their implementation in conventional software has not been enough to overcome the current challenge. Such obstacles could be removed by adopting a multilevel model-driven approach, such as the openEHR specifications, in nursing information systems. To create an openEHR archetype model for the Functional Status concepts as published in Nursing Outcome Indicators Catalog of the International Classification for Nursing Practice (NOIC-ICNP). Four methodological steps were followed: 1) extraction of terms from the NOIC-ICNP terminology; 2) identification of previously published openEHR archetypes; 3) assessment of the adequacy of those openEHR archetypes to represent the terms; and 4) development of new openEHR archetypes when required. The "Barthel Index" archetype was retrieved and mapped to the 68 NOIC-ICNP Functional Status terms. There were 19 exact matches between a term and the correspondent archetype node and 23 archetype nodes that matched to one or more NOIC-INCP. No matches were found between the archetype and 14 of the NOIC-ICNP terms, and nine archetype nodes did not match any of the NOIC-ICNP terms. The openEHR model was sufficient to represent the semantics of the Functional Status concept according to the NOIC-ICNP, but there were differences in data granularity between the terminology and the archetype, thus producing a significantly complex mapping, which could be difficult to implement in real healthcare information systems. However, despite the technological complexity, the present study demonstrated the feasibility of mapping nursing terminologies to openEHR archetypes, which emphasizes the importance of adopting the multilevel model-driven approach for the achievement of semantic interoperability between healthcare information systems.

Rivers and flooded areas identified by medium-resolution remote sensing improve risk prediction of the highly pathogenic avian influenza H5N1 in Thailand

PubMed Central

Thanapongtharm, Weerapong; Van Boeckel, Thomas P.; Biradar, Chandrashekhar; Xiao, Xiangming; Gilbert, Marius

2016-01-01

Thailand experienced several epidemic waves of the highly pathogenic avian influenza (HPAI) H5N1 between 2004 and 2005. This study investigated the role of water in the landscape, which has not been previously assessed because of a lack of high-resolution information on the distribution of flooded land at the time of the epidemic. Nine Landsat 7-Enhanced Thematic Mapper Plus scenes covering 174,610 km2 were processed using k-means unsupervised classification to map the distribution of flooded areas as well as permanent lakes and reservoirs at the time of the main epidemic HPAI H5N1 wave of October 2004. These variables, together with other factors previously identified as significantly associated with risk, were entered into an autologistic regression model in order to quantify the gain in risk explanation over previously published models. We found that, in addition to other factors previously identified as associated with risk, the proportion of land covered by flooding along with expansion of rivers and streams, derived from an existing, sub-district level (administrative level no. 3) geographical information system database, was a highly significant risk factor in this 2004 HPAI epidemic. These results suggest that water-borne transmission could have partly contributed to the spread of HPAI H5N1 during the epidemic. Future work stemming from these results should involve studies where the actual distribution of small canals, rivers, ponds, rice paddy fields and farms are mapped and tested against farm-level data with respect to HPAI H5N1. PMID:24258895

Rivers and flooded areas identified by medium-resolution remote sensing improve risk prediction of the highly pathogenic avian influenza H5N1 in Thailand.

PubMed

Thanapongtharm, Weerapong; Van Boeckel, Thomas P; Biradar, Chandrashekhar; Xiao, Xiang-Ming; Gilbert, Marius

2013-11-01

Thailand experienced several epidemic waves of the highly pathogenic avian influenza (HPAI) H5N1 between 2004 and 2005. This study investigated the role of water in the landscape, which has not been previously assessed because of a lack of high-resolution information on the distribution of flooded land at the time of the epidemic. Nine Landsat 7 - Enhanced Thematic Mapper Plus scenes covering 174,610 km(2) were processed using k-means unsupervised classification to map the distribution of flooded areas as well as permanent lakes and reservoirs at the time of the main epidemic HPAI H5N1 wave of October 2004. These variables, together with other factors previously identified as significantly associated with risk, were entered into an autologistic regression model in order to quantify the gain in risk explanation over previously published models. We found that, in addition to other factors previously identified as associated with risk, the proportion of land covered by flooding along with expansion of rivers and streams, derived from an existing, sub-district level (administrative level no. 3) geographical information system database, was a highly significant risk factor in this 2004 HPAI epidemic. These results suggest that water-borne transmission could have partly contributed to the spread of HPAI H5N1 during the epidemic. Future work stemming from these results should involve studies where the actual distribution of small canals, rivers, ponds, rice paddy fields and farms are mapped and tested against farm-level data with respect to HPAI H5N1.

Global Simulation of Proton Precipitation Due to Field Line Curvature During Substorms

NASA Technical Reports Server (NTRS)

Gilson, M. L.; Raeder, J.; Donovan, E.; Ge, Y. S.; Kepko, L.

2012-01-01

The low latitude boundary of the proton aurora (known as the Isotropy Boundary or IB) marks an important boundary between empty and full downgoing loss cones. There is significant evidence that the IB maps to a region in the magnetosphere where the ion gyroradius becomes comparable to the local field line curvature. However, the location of the IB in the magnetosphere remains in question. In this paper, we show simulated proton precipitation derived from the Field Line Curvature (FLC) model of proton scattering and a global magnetohydrodynamic simulation during two substorms. The simulated proton precipitation drifts equatorward during the growth phase, intensifies at onset and reproduces the azimuthal splitting published in previous studies. In the simulation, the pre-onset IB maps to 7-8 RE for the substorms presented and the azimuthal splitting is caused by the development of the substorm current wedge. The simulation also demonstrates that the central plasma sheet temperature can significantly influence when and where the azimuthal splitting takes place.

A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.).

PubMed

Zong, Guo; Wang, Ahong; Wang, Lu; Liang, Guohua; Gu, Minghong; Sang, Tao; Han, Bin

2012-07-20

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding. Copyright © 2012. Published by Elsevier Ltd.

The 1982 control network of Mars

NASA Technical Reports Server (NTRS)

Davies, M. E.; Katayama, F. Y.

1983-01-01

Attention is given to a planet-wide control network of Mars that was computed in September 1982 using a large single-block analytical triangulation with 47,524 measurements of 6853 control points on 1054 Mariner 9 and 757 Viking pictures. In all, 19,139 normal equations were solved, with a resulting standard error of measurement of 18.06 microns. The control points identified by name and letter designation are given, as are the aerographic coordinates of the control points. In addition, the coordinates of the Viking I lander site are given: latitude, 22.480 deg; longitude, 47.962 deg (radius, 3389.32 km). This study expands and updates the previously published network (1978). It is noted that the computation differs in many respects from standard aerial mapping photogrammetric practice. In comparison with aerial mapping photography, the television formats are small and the focal lengths are long; stereo coverage is rare, the scale of the pictures varies greatly, and the residual camera distortions are large.

Self organizing map neural networks approach for lithologic interpretation of nuclear and electrical well logs in basaltic environment, Southern Syria.

PubMed

Asfahani, J; Ahmad, Z; Ghani, B Abdul

2018-07-01

An approach based on self organizing map (SOM) artificial neural networks is proposed herewith oriented towards interpreting nuclear and electrical well logging data. The well logging measurements of Kodana well in Southern Syria have been interpreted by applying the proposed approach. Lithological cross-section model of the basaltic environment has been derived and four different kinds of basalt have been consequently distinguished. The four basalts are hard massive basalt, hard basalt, pyroclastic basalt and the alteration basalt products- clay. The results obtained by SOM artificial neural networks are in a good agreement with the previous published results obtained by other different techniques. The SOM approach is practiced successfully in the case study of the Kodana well logging data, and can be therefore recommended as a suitable and effective approach for handling huge well logging data with higher number of variables required for lithological discrimination purposes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Geochemical landscapes of the conterminous United States; new map presentations for 22 elements

USGS Publications Warehouse

Gustavsson, N.; Bolviken, B.; Smith, D.B.; Severson, R.C.

2001-01-01

Geochemical maps of the conterminous United States have been prepared for seven major elements (Al, Ca, Fe, K, Mg, Na, and Ti) and 15 trace elements (As, Ba, Cr, Cu, Hg, Li, Mn, Ni, Pb, Se, Sr, V, Y, Zn, and Zr). The maps are based on an ultra low-density geochemical survey consisting of 1,323 samples of soils and other surficial materials collected from approximately 1960-1975. The data were published by Boerngen and Shacklette (1981) and black-and-white point-symbol geochemical maps were published by Shacklette and Boerngen (1984). The data have been reprocessed using weighted-median and Bootstrap procedures for interpolation and smoothing.

Mapping Inner Space: Learning and Teaching Visual Mapping. Second Edition.

ERIC Educational Resources Information Center

Margulies, Nancy

More than 10 years ago, when "Mapping Inner Space" was first published, a few teachers were using this creative technique and teaching it to their students. Today mapping is widely used in schools, universities, and the corporate world, as well. This second edition of the book explores a variety of mapping styles and also takes a fresh look at the…

Mars Global Geologic Mapping: Amazonian Results

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Dohm, J. M.; Irwin, R.; Kolb, E. J.; Skinner, J. A., Jr.; Hare, T. M.

2008-01-01

We are in the second year of a five-year effort to map the geology of Mars using mainly Mars Global Surveyor, Mars Express, and Mars Odyssey imaging and altimetry datasets. Previously, we have reported on details of project management, mapping datasets (local and regional), initial and anticipated mapping approaches, and tactics of map unit delineation and description [1-2]. For example, we have seen how the multiple types and huge quantity of image data as well as more accurate and detailed altimetry data now available allow for broader and deeper geologic perspectives, based largely on improved landform perception, characterization, and analysis. Here, we describe early mapping results, which include updating of previous northern plains mapping [3], including delineation of mainly Amazonian units and regional fault mapping, as well as other advances.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

PubMed

de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

2012-10-04

Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

PubMed Central

2012-01-01

Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest. PMID:23036012

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

PubMed Central

2011-01-01

Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Conclusions Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection). PMID:21797998

A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.).

PubMed

Diaz, Aurora; Fergany, Mohamed; Formisano, Gelsomina; Ziarsolo, Peio; Blanca, José; Fei, Zhanjun; Staub, Jack E; Zalapa, Juan E; Cuevas, Hugo E; Dace, Gayle; Oliver, Marc; Boissot, Nathalie; Dogimont, Catherine; Pitrat, Michel; Hofstede, René; van Koert, Paul; Harel-Beja, Rotem; Tzuri, Galil; Portnoy, Vitaly; Cohen, Shahar; Schaffer, Arthur; Katzir, Nurit; Xu, Yong; Zhang, Haiying; Fukino, Nobuko; Matsumoto, Satoru; Garcia-Mas, Jordi; Monforte, Antonio J

2011-07-28

A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).

Mycobacterium avium subsp paratuberculosis--incidences in milk and milk products, their isolation, enumeration, characterization, and role in human health.

PubMed

Patel, Ami; Shah, Nihir

2011-12-01

Mycobacterium avium subsp paratuberculosis (MAP), excreted in the feces and milk, is reported to be not easily inactivated by pasteurization and thermal treatments as other bacteria infecting humans and animals do. The D values of all MAP strains tested were considerably higher than those published for other pathogens. Culturing techniques for this organism are labor intensive. Although an increasing amount of scientific evidence suggests that this organism can be responsible for at least some cases of Crohn's disease (CD), there is controversy about MAP being a cause of CD in humans. In general, although some studies have described an association between the presence of MAP and CD, the role of Mycobacterium species and MAP in the etiology of this human disease remains unestablished. Although published reports indicate that it may not be completely inactivated by pasteurization of milk, the effectiveness of increasing the time or temperature in the pasteurization process has not been established and hence any potential benefit to human health cannot be determined. This article summarizes the incidences of MAP in milk and milk products with respect to human health and brief discussion of various serological as well as molecular techniques used for their isolation, enumeration, and characterization. Copyright © 2011. Published by Elsevier B.V.

Analyzing the Scientific Evolution of Social Work Using Science Mapping

ERIC Educational Resources Information Center

Martínez, Ma Angeles; Cobo, Manuel Jesús; Herrera, Manuel; Herrera-Viedma, Enrique

2015-01-01

Objectives: This article reports the first science mapping analysis of the social work field, which shows its conceptual structure and scientific evolution. Methods: Science Mapping Analysis Software Tool, a bibliometric science mapping tool based on co-word analysis and h-index, is applied using a sample of 18,794 research articles published from…

Preliminary geologic mapping of Cretaceous and Tertiary formations in the eastern part of the Little Snake River coal field, Carbon County, Wyoming

USGS Publications Warehouse

Haacke, Jon E.; Barclay, C. S. Venable; Hettinger, Robert D.

2016-09-30

In the 1970s and 1980s, C.S. Venable Barclay conducted geologic mapping of areas primarily underlain by Cretaceous coals in the eastern part of the Little Snake River coal field (LSR) in Carbon County, southwest Wyoming. With some exceptions, most of the mapping data were never published. Subsequently, after his retirement from the U.S. Geological Survey (USGS), his field maps and field notebooks were archived in the USGS Field Records. Due to a pending USGS coal assessment of the Little Snake River coal field area and planned geological mapping to be conducted by the Wyoming State Geological Survey, Barclay’s mapping data needed to be published to support these efforts. Subsequently, geologic maps were scanned and georeferenced into a geographic information system, and project and field notes were scanned into Portable Document Format (PDF) files. Data for seventeen 7½-minute quadrangles are presented in this report. This publication is solely intended to compile the mapping data as it was last worked on by Barclay and provides no interpretation or modification of his work.

Earthquakes in South Carolina and Vicinity 1698-2009

USGS Publications Warehouse

Dart, Richard L.; Talwani, Pradeep; Stevenson, Donald

2010-01-01

This map summarizes more than 300 years of South Carolina earthquake history. It is one in a series of three similar State earthquake history maps. The current map and the previous two for Virginia and Ohio are accessible at http://pubs.usgs.gov/of/2006/1017/ and http://pubs.usgs.gov/of/2008/1221/. All three State earthquake maps were collaborative efforts between the U.S. Geological Survey and respective State agencies. Work on the South Carolina map was done in collaboration with the Department of Geological Sciences, University of South Carolina. As with the two previous maps, the history of South Carolina earthquakes was derived from letters, journals, diaries, newspaper accounts, academic journal articles, and, beginning in the early 20th century, instrumental recordings (seismograms). All historical (preinstrumental) earthquakes that were large enough to be felt have been located based on felt reports. Some of these events caused damage to buildings and their contents. The more recent widespread use of seismographs has allowed many smaller earthquakes, previously undetected, to be recorded and accurately located. The seismicity map shows historically located and instrumentally recorded earthquakes in and near South Carolina

MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data.

PubMed

Murillo, Gabriel H; You, Na; Su, Xiaoquan; Cui, Wei; Reilly, Muredach P; Li, Mingyao; Ning, Kang; Cui, Xinping

2016-05-15

Single nucleotide variant (SNV) detection procedures are being utilized as never before to analyze the recent abundance of high-throughput DNA sequencing data, both on single and multiple sample datasets. Building on previously published work with the single sample SNV caller genotype model selection (GeMS), a multiple sample version of GeMS (MultiGeMS) is introduced. Unlike other popular multiple sample SNV callers, the MultiGeMS statistical model accounts for enzymatic substitution sequencing errors. It also addresses the multiple testing problem endemic to multiple sample SNV calling and utilizes high performance computing (HPC) techniques. A simulation study demonstrates that MultiGeMS ranks highest in precision among a selection of popular multiple sample SNV callers, while showing exceptional recall in calling common SNVs. Further, both simulation studies and real data analyses indicate that MultiGeMS is robust to low-quality data. We also demonstrate that accounting for enzymatic substitution sequencing errors not only improves SNV call precision at low mapping quality regions, but also improves recall at reference allele-dominated sites with high mapping quality. The MultiGeMS package can be downloaded from https://github.com/cui-lab/multigems xinping.cui@ucr.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Heat flow in Oklahoma

NASA Astrophysics Data System (ADS)

Cranganu, Constantin

Twenty new heat flow values are incorporated, along with 40 previously published data, into a heat flow map of Oklahoma. The new heat flow data were estimated using previous temperature measurements in boreholes made by American Petroleum Institute researchers and 1,498 thermal conductivity measurements on drill cuttings. The mean of 20 average thermal gradients is 30.50sp°C/km. In general, thermal gradients increase from SW (14.11sp°C/km) to NE (42.24sp°C/km). The range of 1,498 in situ thermal conductivity measurements (after corrections for anisotropy, in situ temperature, and porosity) is 0.90-6.1 W/m-K; the average is 1.68 W/m-K. Estimated near-surface heat flow (±20%) at 20 new sites in Oklahoma varies between 22 ± 4 mW/msp2 and 86 ± 17 mW/msp2; the average is 50 mW/msp2. Twenty-seven new heat-generation estimates, along with 22 previously published data, are used to create a heat generation map of Oklahoma. The range of heat production estimates is 1.1-3.5 muW/msp3, with an average of 2.5 muW/msp3. The heat flow regime in Oklahoma is primarily conductive in nature, except for a zone in northeast. Transient effects due to sedimentary processes and metamorphic/igneous activity, as well as past climatic changes, do not significantly influence the thermal state of the Oklahoma crust. Heat flow near the margins of the Arkoma and Anadarko Basins may be depressed or elevated by 5-13 mW/msp2 by refraction of heat from sedimentary rocks of relatively low thermal conductivity (1-2 W/m-K) into crystalline basement rocks of relatively high thermal conductivity (˜3-4 W/m-K). The heat generation-heat flow relationship shows a modest correlation. The relatively high heat flow (˜70-80 mW/msp2) in part of northeastern Oklahoma suggests that the thermal regime there may be perturbed by regional groundwater flow originating in the fractured outcrops of the Arbuckle-Simpson aquifer in the Arbuckle Mountains.

Cardiovascular and Metabolic Consequences of Testosterone Supplements in Young and Old Male Spontaneously Hypertensive Rats: Implications for Testosterone Supplements in Men.

PubMed

Dalmasso, Carolina; Patil, Chetan N; Yanes Cardozo, Licy L; Romero, Damian G; Maranon, Rodrigo O

2017-10-17

The safety of testosterone supplements in men remains unclear. In the present study, we tested the hypothesis that in young and old male spontaneously hypertensive rats (SHR), long-term testosterone supplements increase blood pressure and that the mechanism is mediated in part by activation of the renin-angiotensin system. In untreated males, serum testosterone exhibited a sustained decrease after 5 months of age, reaching a nadir by 18 to 22 months of age. The reductions in serum testosterone were accompanied by an increase in body weight until very old age (18 months). Testosterone supplements were given for 6 weeks to young (12 weeks-YMSHR) and old (21-22 months-OMSHR) male SHR that increased serum testosterone by 2-fold in young males and by 4-fold in old males. Testosterone supplements decreased body weight, fat mass, lean mass, and plasma leptin, and increased plasma estradiol in YMSHR but had no effect in OMSHR. Mean arterial pressure (MAP) was significantly higher in OMSHR than in YMSHR and testosterone supplements decreased MAP in OMSHR, but significantly increased MAP in YMSHR. Enalapril, the angiotensin-converting enzyme inhibitor, reduced MAP in both control and testosterone-supplemented YMSHR, but had a greater effect on MAP in testosterone-treated rats, suggesting the mechanism responsible for the increase in MAP in YMSHR is mediated at least in part by activation of the renin-angiotensin system. Taken together with previous studies, these data suggest that testosterone supplements may have differential effects on men depending on age, cardiovascular and metabolic status, and dose and whether given long-term or short-term. © 2017 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit) in red raspberry (Rubus idaeus L.) using AFLP and microsatellite markers

PubMed Central

Sargent, Daniel J; Fernández-Fernández, Felicidad; Rys, Alicja; Knight, Victoria H; Simpson, David W; Tobutt, Kenneth R

2007-01-01

Background Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus) F1 progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO), which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A1) and (dw) respectively. Results The progeny of 94 seedlings was scored for the segregation of 95 AFLP and 22 SSR markers and a linkage map was constructed that covers a total genetic distance of 505 cM over seven linkage groups. The average linkage group length was 72.2 cM and there was an average of 17 markers per linkage group, of which at least two were codominant SSRs, allowing comparisons with previously published maps of raspberry. The two phenotypic traits, A1 and dw, mapped to linkage groups 3 and 6 respectively. Conclusion The mapping of A1 will facilitate the discrimination of resistance genes from different sources and the pyramiding of aphid resistance genes in new raspberry cultivars; the mapping of dw will allow further investigations into the genetics of dwarfing habit in Rubus. PMID:17374159

A genetic linkage map for the apicomplexan protozoan parasite Eimeria maxima and comparison with Eimeria tenella.

PubMed

Blake, Damer P; Oakes, Richard; Smith, Adrian L

2011-02-01

Eimeria maxima is one of the seven Eimeria spp. that infect the chicken and cause the disease coccidiosis. The well characterised immunogenicity and genetic diversity associated with E. maxima promote its use in genetics-led studies on avian coccidiosis. The development of a genetic map for E. maxima, presented here based upon 647 amplified fragment length polymorphism markers typed from 22 clonal hybrid lines and assembled into 13 major linkage groups, is a major new resource for work with this parasite. Comparison with genetic maps produced for other coccidial parasites indicates relatively high levels of genetic recombination. Conversion of ∼14% of the markers representing the major linkage groups to sequence characterised amplified region markers can provide a scaffold for the assembly of future genomic sequences as well as providing a foundation for more detailed genetic maps. Comparison with the Eimeria tenella genetic map produced 10years ago has revealed a less biased marker distribution, with no more than nine markers mapped within any unresolved heritable unit. Nonetheless, preliminary bioinformatic characterisation of the three largest publicly available genomic E. maxima sequences suggest that the feature-poor/feature-rich structure which has previously been found to define the first sequenced E. tenella chromosome also defines the E. maxima genome. The significance of such a segmented genome and the apparent potential for variation in genetic recombination will be relevant to haplotype stability and the longevity of future anticoccidial strategies based upon multiple loci targeted by novel chemotherapeutic drugs or recombinant subunit vaccines. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Rapid simultaneous high-resolution mapping of myelin water fraction and relaxation times in human brain using BMC-mcDESPOT.

PubMed

Bouhrara, Mustapha; Spencer, Richard G

2017-02-15

A number of central nervous system (CNS) diseases exhibit changes in myelin content and magnetic resonance longitudinal, T 1 , and transverse, T 2 , relaxation times, which therefore represent important biomarkers of CNS pathology. Among the methods applied for measurement of myelin water fraction (MWF) and relaxation times, the multicomponent driven equilibrium single pulse observation of T 1 and T 2 (mcDESPOT) approach is of particular interest. mcDESPOT permits whole brain mapping of multicomponent T 1 and T 2 , with data acquisition accomplished within a clinically realistic acquisition time. Unfortunately, previous studies have indicated the limited performance of mcDESPOT in the setting of the modest signal-to-noise range of high-resolution mapping, required for the depiction of small structures and to reduce partial volume effects. Recently, we showed that a new Bayesian Monte Carlo (BMC) analysis substantially improved determination of MWF from mcDESPOT imaging data. However, our previous study was limited in that it did not discuss determination of relaxation times. Here, we extend the BMC analysis to the simultaneous determination of whole-brain MWF and relaxation times using the two-component mcDESPOT signal model. Simulation analyses and in-vivo human brain studies indicate the overall greater performance of this approach compared to the stochastic region contraction (SRC) algorithm, conventionally used to derive parameter estimates from mcDESPOT data. SRC estimates of the transverse relaxation time of the long T 2 fraction, T 2,l , and the longitudinal relaxation time of the short T 1 fraction, T 1,s , clustered towards the lower and upper parameter search space limits, respectively, indicating failure of the fitting procedure. We demonstrate that this effect is absent in the BMC analysis. Our results also showed improved parameter estimation for BMC as compared to SRC for high-resolution mapping. Overall we find that the combination of BMC analysis and mcDESPOT, BMC-mcDESPOT, shows excellent performance for accurate high-resolution whole-brain mapping of MWF and bi-component transverse and longitudinal relaxation times within a clinically realistic acquisition time. Published by Elsevier Inc.

Geologic map of the Cook Inlet region, Alaska, including parts of the Talkeetna, Talkeetna Mountains, Tyonek, Anchorage, Lake Clark, Kenai, Seward, Iliamna, Seldovia, Mount Katmai, and Afognak 1:250,000-scale quadrangles

USGS Publications Warehouse

Wilson, Frederic H.; Hults, Chad P.; Schmoll, Henry R.; Haeussler, Peter J.; Schmidt, Jeanine M.; Yehle, Lynn A.; Labay, Keith A.

2012-01-01

In 1976, L.B. Magoon, W.L. Adkinson, and R.M. Egbert published a major geologic map of the Cook Inlet region, which has served well as a compilation of existing information and a guide for future research and mapping. The map in this report updates Magoon and others (1976) and incorporates new and additional mapping and interpretation. This map is also a revision of areas of overlap with the geologic map completed for central Alaska (Wilson and others, 1998). Text from that compilation remains appropriate and is summarized here; many compromises have been made in strongly held beliefs to allow construction of this compilation. Yet our willingness to make interpretations and compromises does not allow resolution of all mapping conflicts. Nonetheless, we hope that geologists who have mapped in this region will recognize that, in incorporating their work, our regional correlations may have required some generalization or lumping of map units. Many sources were used to produce this geologic map and, in most cases, data from available maps were combined, without generalization, and new data were added where available. A preliminary version of this map was published as U.S. Geological Survey Open-File Report 2009–1108. The main differences between the versions concern revised mapping of surfical deposits in the northern and eastern parts of the map area. Minor error corrections have been made also.

Free-Air Gravity Map of the Moon

NASA Image and Video Library

2014-06-27

This still image features a free-air gravity map of the Moon's southern latitudes developed by S. Goossens et al. from data returned by the Gravity Recovery and Interior Laboratory (GRAIL) mission. If the Moon were a perfectly smooth sphere of uniform density, the gravity map would be a single, featureless color, indicating that the force of gravity at a given elevation was the same everywhere. But like other rocky bodies in the solar system, including Earth, the Moon has both a bumpy surface and a lumpy interior. Spacecraft in orbit around the Moon experience slight variations in gravity caused by both of these irregularities. The free-air gravity map shows deviations from the mean gravity that a cueball Moon would have. The deviations are measured in milliGals, a unit of acceleration. On the map, purple is at the low end of the range, at around -400 mGals, and red is at the high end near +400 mGals. Yellow denotes the mean. The map shown here extends from the south pole of the Moon up to 50°S and reveals the gravity for that region in even finer detail than the global gravity maps published previously. The image illustrates the very good correlation between the gravity map and topographic features such as peaks and craters, as well as the mass concentration lying beneath the large Schrödinger basin in the center of the frame. The terrain in the image is based on Lunar Reconnaissance Orbiter (LRO) altimeter and camera data. Credit: NASA's Scientific Visualization Studio NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Updated tops file for Cretaceous and lower Tertiary units, Piceance Basin, northwest Colorado

USGS Publications Warehouse

Johnson, Ronald C.; Dietrich, John D.; Mercier, Tracey J.

2015-08-04

Each entry for the base of the Long Point Bed was obtained at a location where the mapped Long Point Bed intersects a contour line on the published maps. Precision of each elevation is therefore dependent on the precision of the maps and the placement of the mapped contact by the authors.

Preliminary Bedrock Geologic Map of the Old Lyme Quadrangle, New London and Middlesex Counties, Connecticut

USGS Publications Warehouse

Walsh, Gregory J.; Scott, Robert B.; Aleinikoff, John N.; Armstrong, Thomas R.

2006-01-01

This report presents a preliminary map of the bedrock geology of the Old Lyme quadrangle, New London and Middlesex Counties, Connecticut. The map depicts contacts of bedrock geologic units, faults, outcrops, and structural geologic information. The map was published as part of a study of fractured bedrock aquifers and regional tectonics.

A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus

PubMed Central

Brondani, Rosana PV; Williams, Emlyn R; Brondani, Claudio; Grattapaglia, Dario

2006-01-01

Background Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs) in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. Results The consensus map covers ~90% of the recombining genome of Eucalyptus, involves 234 mapped EMBRA loci on 11 linkage groups, an observed length of 1,568 cM and a mean distance between markers of 8.4 cM. A compilation of all microsatellite linkage information published in Eucalyptus allowed us to establish the homology among linkage groups between this consensus map and other maps published for E. globulus. Comparative mapping analyses also resulted in the linkage group assignment of other 41 microsatellites derived from other Eucalyptus species as well as candidate genes and QTLs for wood and flowering traits published in the literature. This report significantly increases the availability of microsatellite markers and mapping information for species of Eucalyptus and corroborates the high conservation of microsatellite flanking sequences and locus ordering between species of the genus. Conclusion This work represents an important step forward for Eucalyptus comparative genomics, opening stimulating perspectives for evolutionary studies and molecular breeding applications. The generalized use of an increasingly larger set of interspecific transferable markers and consensus mapping information, will allow faster and more detailed investigations of QTL synteny among species, validation of expression-QTL across variable genetic backgrounds and positioning of a growing number of candidate genes co-localized with QTLs, to be tested in association mapping experiments. PMID:16995939

A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius.

PubMed

Fountain, Toby; Ravinet, Mark; Naylor, Richard; Reinhardt, Klaus; Butlin, Roger K

2016-12-07

The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F 2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species. Copyright © 2016 Fountain et al.

Naming the newly found landforms on Venus

NASA Technical Reports Server (NTRS)

Batson, R. M.; Russell, J. F.

1991-01-01

The mapping of Venus is unique in the history of cartigraphy; never has so much territory been discovered and mapped in so short a period of time. Therefore, in the interest of international scientific communication, there is a unique urgency to the development of a system of names for surface features on Venus. The process began with the naming of features seen on radar images taken from Earth and continued through mapping expeditions of the U.S. and U.S.S.R. However, the Magellan Mission resolves features twenty-five times smaller than those mapped previously, and its radar data will cover an area nearly equivalent to that of the continents and the sea-floors of the Earth combined. The International Astronomical Union (IAU) was charged with the formal endorsement of names of features on the planets. Proposed names are collected, approved, and applied through the IAU Working Group for Planetary System Nomenclature (WGPSN) and its task groups, prior to IAU approval by the IAU General Assembly. Names approved by the WGPSN and its task groups, prior to final approval may be used on published maps and articles, provided that their provisional nature is stipulated. The IAU has established themes for the names to be used on each of the planets; names of historical and mythological women are used on Venus. Names of political entities and those identified with active religions are not acceptable, and a person must have been deceased for three years or more to be considered. Any interested person may propose a name for consideration by the IAU.

Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

PubMed Central

Gong, L.; Stift, G.; Kofler, R.; Pachner, M.

2008-01-01

Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Ölkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety “Lady Godiva” (O5) and the Italian crookneck variety “Bianco Friulano” (CN), which are the parents of our previous F2 mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0750-2) contains supplementary material, which is available to authorized users. PMID:18379753

Constructivist developmental theory is needed in developmental neuroscience

NASA Astrophysics Data System (ADS)

Arsalidou, Marie; Pascual-Leone, Juan

2016-12-01

Neuroscience techniques provide an open window previously unavailable to the origin of thoughts and actions in children. Developmental cognitive neuroscience is booming, and knowledge from human brain mapping is finding its way into education and pediatric practice. Promises of application in developmental cognitive neuroscience rests however on better theory-guided data interpretation. Massive amounts of neuroimaging data from children are being processed, yet published studies often do not frame their work within developmental models—in detriment, we believe, to progress in this field. Here we describe some core challenges in interpreting the data from developmental cognitive neuroscience, and advocate the use of constructivist developmental theories of human cognition with a neuroscience interpretation.

Single-shot turbo spin echo acquisition for in vivo cardiac diffusion MRI.

PubMed

Edalati, Masoud; Lee, Gregory R; Hui Wang; Taylor, Michael D; Li, Yu Y

2016-08-01

Diffusion MRI offers the ability to noninvasively characterize the microstructure of myocardium tissue and detect disease related pathology in cardiovascular examination. This study investigates the feasibility of in vivo cardiac diffusion MRI under free-breathing condition. A high-speed imaging technique, correlation imaging, is used to enable single-shot turbo spin echo for free-breathing cardiac data acquisition. The obtained in vivo cardiac diffusion-weighted images illustrate robust image quality and minor geometry distortions. The resultant diffusion scalar maps show reliable quantitative values consistent with those previously published in the literature. It is demonstrated that this technique has the potential for in vivo free-breathing cardiac diffusion MRI.

Digital Bedrock Compilation: A Geodatabase Covering Forest Service Lands in California

NASA Astrophysics Data System (ADS)

Elder, D.; de La Fuente, J. A.; Reichert, M.

2010-12-01

This digital database contains bedrock geologic mapping for Forest Service lands within California. This compilation began in 2004 and the first version was completed in 2005. Second publication of this geodatabase was completed in 2010 and filled major gaps in the southern Sierra Nevada and Modoc/Medicine Lake/Warner Mountains areas. This digital map database was compiled from previously published and unpublished geologic mapping, with source mapping and review from California Geological Survey, the U.S. Geological Survey and others. Much of the source data was itself compilation mapping. This geodatabase is huge, containing ~107,000 polygons and ~ 280,000 arcs. Mapping was compiled from more than one thousand individual sources and covers over 41,000,000 acres (~166,000 km2). It was compiled from source maps at various scales - from ~ 1:4,000 to 1:250,000 and represents the best available geologic mapping at largest scale possible. An estimated 70-80% of the source information was digitized from geologic mapping at 1:62,500 scale or better. Forest Service ACT2 Enterprise Team compiled the bedrock mapping and developed a geodatabase to store this information. This geodatabase supports feature classes for polygons (e.g, map units), lines (e.g., contacts, boundaries, faults and structural lines) and points (e.g., orientation data, structural symbology). Lookup tables provide detailed information for feature class items. Lookup/type tables contain legal values and hierarchical groupings for geologic ages and lithologies. Type tables link coded values with descriptions for line and point attributes, such as line type, line location and point type. This digital mapping is at the core of many quantitative analyses and derivative map products. Queries of the database are used to produce maps and to quantify rock types of interest. These include the following: (1) ultramafic rocks - where hazards from naturally occurring asbestos are high, (2) granitic rocks - increased erosion hazards, (3) limestone, chert, sedimentary rocks - paleontological resources (Potential Fossil Yield Classification maps), (4) calcareous rocks (cave resources, water chemistry), and (5) lava flows - lava tubes (more caves). Map unit groupings (e.g., belts, terranes, tectonic & geomorphic provinces) can also be derived from the geodatabase. Digital geologic mapping was used in ground water modeling to predict effects of tunneling through the San Bernardino Mountains. Bedrock mapping is used in models that characterize watershed sediment regimes and quantify anthropogenic influences. When combined with digital geomorphology mapping, this geodatabase helps to assess landslide hazards.

Geologic map of the Caetano caldera, Lander and Eureka counties, Nevada

USGS Publications Warehouse

Colgan, Joseph P.; Henry, Christopher D.; John, David A.

2011-01-01

The Eocene (34 Ma) Caetano caldera in north-central Nevada offers an exceptional opportunity to study the physical and petrogenetic evolution of a large (20 km by 10–18 km pre-extensional dimensions) silicic magma chamber, from precursor magmatism to caldera collapse and intrusion of resurgent plutons. Caldera-related rocks shown on this map include two units of crystal-rich intracaldera tuff totaling over 4 km thickness, caldera collapse breccias, tuff dikes that fed the eruption, hydrothermally altered post-eruption rocks, and two generations of resurgent granitic intrusions (John et al., 2008). The map also depicts middle Miocene (about 16–12 Ma) normal faults and synextensional basins that accommodated >100 percent extension and tilted the caldera into a series of ~40° east-dipping blocks, producing exceptional 3-D exposures of the caldera interior (Colgan et al., 2008). This 1:75,000-scale map is a compilation of published maps and extensive new mapping by the authors (fig. 1), and supersedes a preliminary 1:100,000-scale map published by Colgan et al. (2008) and John et al. (2008). New mapping focused on the margins of the Caetano caldera, the distribution and lithology of rocks within the caldera, and on the Miocene normal faults and sedimentary basins that record Neogene extensional faulting. The definition of geologic units and their distribution within the caldera is based entirely on new mapping, except in the northern Toiyabe Range, where mapping by Gilluly and Gates (1965) was modified with new field observations. The distribution of pre-Cenozoic rocks outside the caldera was largely compiled from existing sources with minor modifications, with the exception of the northeastern caldera margin (west of the Cortez Hills Mine), which was remapped in the course of this work and published as a stand-alone 1:6000-scale map (Moore and Henry, 2010).

Empirical Model of Precipitating Ion Oval

NASA Astrophysics Data System (ADS)

Goldstein, Jerry

2017-10-01

In this brief technical report published maps of ion integral flux are used to constrain an empirical model of the precipitating ion oval. The ion oval is modeled as a Gaussian function of ionospheric latitude that depends on local time and the Kp geomagnetic index. The three parameters defining this function are the centroid latitude, width, and amplitude. The local time dependences of these three parameters are approximated by Fourier series expansions whose coefficients are constrained by the published ion maps. The Kp dependence of each coefficient is modeled by a linear fit. Optimization of the number of terms in the expansion is achieved via minimization of the global standard deviation between the model and the published ion map at each Kp. The empirical model is valid near the peak flux of the auroral oval; inside its centroid region the model reproduces the published ion maps with standard deviations of less than 5% of the peak integral flux. On the subglobal scale, average local errors (measured as a fraction of the point-to-point integral flux) are below 30% in the centroid region. Outside its centroid region the model deviates significantly from the H89 integral flux maps. The model's performance is assessed by comparing it with both local and global data from a 17 April 2002 substorm event. The model can reproduce important features of the macroscale auroral region but none of its subglobal structure, and not immediately following a substorm.

Mapping patient pathways and estimating resource use for point of care versus standard testing and treatment of chlamydia and gonorrhoea in genitourinary medicine clinics in the UK.

PubMed

Adams, Elisabeth J; Ehrlich, Alice; Turner, Katherine M E; Shah, Kunj; Macleod, John; Goldenberg, Simon; Meray, Robin K; Pearce, Vikki; Horner, Patrick

2014-07-23

We aimed to explore patient pathways using a chlamydia/gonorrhoea point-of-care (POC) nucleic acid amplification test (NAAT), and estimate and compare the costs of the proposed POC pathways with the current pathways using standard laboratory-based NAAT testing. Workshops were conducted with healthcare professionals at four sexual health clinics representing diverse models of care in the UK. They mapped out current pathways that used chlamydia/gonorrhoea tests, and constructed new pathways using a POC NAAT. Healthcare professionals' time was assessed in each pathway. The proposed POC pathways were then priced using a model built in Microsoft Excel, and compared to previously published costs for pathways using standard NAAT-based testing in an off-site laboratory. Pathways using a POC NAAT for asymptomatic and symptomatic patients and chlamydia/gonorrhoea-only tests were shorter and less expensive than most of the current pathways. Notably, we estimate that POC testing as part of a sexual health screen for symptomatic patients, or as stand-alone chlamydia/gonorrhoea testing, could reduce costs per patient by as much as £16 or £6, respectively. In both cases, healthcare professionals' time would be reduced by approximately 10 min per patient. POC testing for chlamydia/gonorrhoea in a clinical setting may reduce costs and clinician time, and may lead to more appropriate and quicker care for patients. Further study is warranted on how to best implement POC testing in clinics, and on the broader clinical and cost implications of this technology. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

PubMed

Strobel, Eric J; Watters, Kyle E; Nedialkov, Yuri; Artsimovitch, Irina; Lucks, Julius B

2017-07-07

RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

In preparation of the nationwide dissemination of the school-based obesity prevention program DOiT: stepwise development applying the intervention mapping protocol.

PubMed

van Nassau, Femke; Singh, Amika S; van Mechelen, Willem; Brug, Johannes; Chin A Paw, Mai J M

2014-08-01

The school-based Dutch Obesity Intervention in Teenagers (DOiT) program is an evidence-based obesity prevention program. In preparation for dissemination throughout the Netherlands, this study aimed to adapt the initial program and to develop an implementation strategy and materials. We revisited the Intervention Mapping (IM) protocol, using results of the previous process evaluation and additional focus groups and interviews with students, parents, teachers, and professionals. The adapted 2-year DOiT program consists of a classroom, an environmental and a parental component. The year 1 lessons aim to increase awareness and knowledge of healthy behaviors. The lessons in year 2 focus on the influence of the (obesogenic) environment. The stepwise development of the implementation strategy resulted in objectives that support teachers' implementation. We developed a 7-step implementation strategy and supporting materials by translating the objectives into essential elements and practical strategies. This study illustrates how revisiting the IM protocol resulted in an adapted program and tailored implementation strategy based on previous evaluations as well as input from different stakeholders. The stepwise development of DOiT can serve as an example for other evidence-based programs in preparation for wider dissemination. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Absolute color scale for improved diagnostics with wavefront error mapping.

PubMed

Smolek, Michael K; Klyce, Stephen D

2007-11-01

Wavefront data are expressed in micrometers and referenced to the pupil plane, but current methods to map wavefront error lack standardization. Many use normalized or floating scales that may confuse the user by generating ambiguous, noisy, or varying information. An absolute scale that combines consistent clinical information with statistical relevance is needed for wavefront error mapping. The color contours should correspond better to current corneal topography standards to improve clinical interpretation. Retrospective analysis of wavefront error data. Historic ophthalmic medical records. Topographic modeling system topographical examinations of 120 corneas across 12 categories were used. Corneal wavefront error data in micrometers from each topography map were extracted at 8 Zernike polynomial orders and for 3 pupil diameters expressed in millimeters (3, 5, and 7 mm). Both total aberrations (orders 2 through 8) and higher-order aberrations (orders 3 through 8) were expressed in the form of frequency histograms to determine the working range of the scale across all categories. The standard deviation of the mean error of normal corneas determined the map contour resolution. Map colors were based on corneal topography color standards and on the ability to distinguish adjacent color contours through contrast. Higher-order and total wavefront error contour maps for different corneal conditions. An absolute color scale was produced that encompassed a range of +/-6.5 microm and a contour interval of 0.5 microm. All aberrations in the categorical database were plotted with no loss of clinical information necessary for classification. In the few instances where mapped information was beyond the range of the scale, the type and severity of aberration remained legible. When wavefront data are expressed in micrometers, this absolute scale facilitates the determination of the severity of aberrations present compared with a floating scale, particularly for distinguishing normal from abnormal levels of wavefront error. The new color palette makes it easier to identify disorders. The corneal mapping method can be extended to mapping whole eye wavefront errors. When refraction data are expressed in diopters, the previously published corneal topography scale is suggested.

Geologic map of the northern plains of Mars

USGS Publications Warehouse

Tanaka, Kenneth L.; Skinner, James A.; Hare, Trent M.

2005-01-01

The northern plains of Mars cover nearly a third of the planet and constitute the planet's broadest region of lowlands. Apparently formed early in Mars' history, the northern lowlands served as a repository both for sediments shed from the adjacent ancient highlands and for volcanic flows and deposits from sources within and near the lowlands. Geomorphic evidence for extensive tectonic deformation and reworking of surface materials through release of volatiles occurs throughout the northern plains. In the polar region, Planum Boreum contains evidence for the accumulation of ice and dust, and surrounding dune fields suggest widespread aeolian transport and erosion. The most recent regional- and global-scale maps describing the geology of the northern plains are largely based on Viking Orbiter image data (Dial, 1984; Witbeck and Underwood, 1984; Scott and Tanaka, 1986; Greeley and Guest, 1987; Tanaka and Scott, 1987; Tanaka and others, 1992a; Rotto and Tanaka, 1995; Crumpler and others, 2001; McGill, 2002). These maps reveal highland, plains, volcanic, and polar units based on morphologic character, albedo, and relative ages using local stratigraphic relations and crater counts. This geologic map of the northern plains is the first published map that covers a significant part of Mars using topography and image data from both the Mars Global Surveyor and Mars Odyssey missions. The new data provide a fresh perspective on the geology of the region that reveals many previously unrecognizable units, features, and temporal relations. In addition, we adapted and instituted terrestrial mapping methods and stratigraphic conventions that we think result in a clearer and more objective map. We focus on mapping with the intent of reconstructing the history of geologic activity within the northern plains, including deposition, volcanism, erosion, tectonism, impact cratering, and other processes with the aid of comprehensive crater-density determinations. Mapped areas include all plains regions within the northern hemisphere of Mars, as well as an approximately 300-km-wide strip of cratered highland and volcanic regions, which border the plains. Note that not all of the contiguous northern plains are mapped, because some minor parts of Elysium and Amazonis Planitiae lie south of the equator.

An update on the "empirical turn" in bioethics: analysis of empirical research in nine bioethics journals.

PubMed

Wangmo, Tenzin; Hauri, Sirin; Gennet, Eloise; Anane-Sarpong, Evelyn; Provoost, Veerle; Elger, Bernice S

2018-02-07

A review of literature published a decade ago noted a significant increase in empirical papers across nine bioethics journals. This study provides an update on the presence of empirical papers in the same nine journals. It first evaluates whether the empirical trend is continuing as noted in the previous study, and second, how it is changing, that is, what are the characteristics of the empirical works published in these nine bioethics journals. A review of the same nine journals (Bioethics; Journal of Medical Ethics; Journal of Clinical Ethics; Nursing Ethics; Cambridge Quarterly of Healthcare Ethics; Hastings Center Report; Theoretical Medicine and Bioethics; Christian Bioethics; and Kennedy Institute of Ethics Journal) was conducted for a 12-year period from 2004 to 2015. Data obtained was analysed descriptively and using a non-parametric Chi-square test. Of the total number of original papers (N = 5567) published in the nine bioethics journals, 18.1% (n = 1007) collected and analysed empirical data. Journal of Medical Ethics and Nursing Ethics led the empirical publications, accounting for 89.4% of all empirical papers. The former published significantly more quantitative papers than qualitative, whereas the latter published more qualitative papers. Our analysis reveals no significant difference (χ2 = 2.857; p = 0.091) between the proportion of empirical papers published in 2004-2009 and 2010-2015. However, the increasing empirical trend has continued in these journals with the proportion of empirical papers increasing from 14.9% in 2004 to 17.8% in 2015. This study presents the current state of affairs regarding empirical research published nine bioethics journals. In the quarter century of data that is available about the nine bioethics journals studied in two reviews, the proportion of empirical publications continues to increase, signifying a trend towards empirical research in bioethics. The growing volume is mainly attributable to two journals: Journal of Medical Ethics and Nursing Ethics. This descriptive study further maps the still developing field of empirical research in bioethics. Additional studies are needed to completely map the nature and extent of empirical research in bioethics to inform the ongoing debate about the value of empirical research for bioethics.

Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico

NASA Astrophysics Data System (ADS)

Roberts, Jason J.; Best, Benjamin D.; Mannocci, Laura; Fujioka, Ei; Halpin, Patrick N.; Palka, Debra L.; Garrison, Lance P.; Mullin, Keith D.; Cole, Timothy V. N.; Khan, Christin B.; McLellan, William A.; Pabst, D. Ann; Lockhart, Gwen G.

2016-03-01

Cetaceans are protected worldwide but vulnerable to incidental harm from an expanding array of human activities at sea. Managing potential hazards to these highly-mobile populations increasingly requires a detailed understanding of their seasonal distributions and habitats. Pursuant to the urgent need for this knowledge for the U.S. Atlantic and Gulf of Mexico, we integrated 23 years of aerial and shipboard cetacean surveys, linked them to environmental covariates obtained from remote sensing and ocean models, and built habitat-based density models for 26 species and 3 multi-species guilds using distance sampling methodology. In the Atlantic, for 11 well-known species, model predictions resembled seasonal movement patterns previously suggested in the literature. For these we produced monthly mean density maps. For lesser-known taxa, and in the Gulf of Mexico, where seasonal movements were less well described, we produced year-round mean density maps. The results revealed high regional differences in small delphinoid densities, confirmed the importance of the continental slope to large delphinoids and of canyons and seamounts to beaked and sperm whales, and quantified seasonal shifts in the densities of migratory baleen whales. The density maps, freely available online, are the first for these regions to be published in the peer-reviewed literature.

An Embodiment Perspective on Number-Space Mapping in 3.5-Year-Old Dutch Children.

PubMed

van 't Noordende, Jaccoline E; Volman, M Chiel J M; Leseman, Paul P M; Kroesbergen, Evelyn H

2017-01-01

Previous research suggests that block adding, subtracting and counting direction are early forms of number-space mapping. In this study, an embodiment perspective on these skills was taken. Embodiment theory assumes that cognition emerges through sensory-motor interaction with the environment. In line with this assumption, it was investigated if counting and adding/subtracting direction in young children is related to the hand they use during task performance. Forty-eight 3.5-year-old children completed a block adding, subtracting and counting task. They had to add and remove a block from a row of three blocks and count a row of five blocks. Adding, subtracting and counting direction were related to the hand the children used for task performance. Most children who used their right hand added, removed and started counting the blocks at the right side of the row. Most children who used their left hand added, removed and started counting the blocks at the left side of the row. It can be concluded that number-space mapping, as measured by direction of adding, subtracting and counting blocks, in young children is embodied: It is not fixed, but is related to the situation. © 2016 The Authors Infant and Child Development Published by John Wiley & Sons, Ltd.

Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks.

PubMed

Deininger, Lisa; Patel, Ekta; Clench, Malcolm R; Sears, Vaughn; Sammon, Chris; Francese, Simona

2016-06-01

A bottom up in situ proteomic method has been developed enabling the mapping of multiple blood signatures on the intact ridges of blood fingermarks by Matrix Assisted Laser Desorption Mass Spectrometry Imaging (MALDI-MSI). This method, at a proof of concept stage, builds upon recently published work demonstrating the opportunity to profile and identify multiple blood signatures in bloodstains via a bottom up proteomic approach. The present protocol addresses the limitation of the previously developed profiling method with respect to destructivity; destructivity should be avoided for evidence such as blood fingermarks, where the ridge detail must be preserved in order to provide the associative link between the biometric information and the events of bloodshed. Using a blood mark reference model, trypsin concentration and spraying conditions have been optimised within the technical constraints of the depositor eventually employed; the application of MALDI-MSI and Ion Mobility MS have enabled the detection, confirmation and visualisation of blood signatures directly onto the ridge pattern. These results are to be considered a first insight into a method eventually informing investigations (and judicial debates) of violent crimes in which the reliable and non-destructive detection and mapping of blood in fingermarks is paramount to reconstruct the events of bloodshed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification

PubMed Central

Cain-Hom, Carol; Splinter, Erik; van Min, Max; Simonis, Marieke; van de Heijning, Monique; Martinez, Maria; Asghari, Vida

2017-01-01

Abstract Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events. PMID:28053125

Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico

PubMed Central

Roberts, Jason J.; Best, Benjamin D.; Mannocci, Laura; Fujioka, Ei; Halpin, Patrick N.; Palka, Debra L.; Garrison, Lance P.; Mullin, Keith D.; Cole, Timothy V. N.; Khan, Christin B.; McLellan, William A.; Pabst, D. Ann; Lockhart, Gwen G.

2016-01-01

Cetaceans are protected worldwide but vulnerable to incidental harm from an expanding array of human activities at sea. Managing potential hazards to these highly-mobile populations increasingly requires a detailed understanding of their seasonal distributions and habitats. Pursuant to the urgent need for this knowledge for the U.S. Atlantic and Gulf of Mexico, we integrated 23 years of aerial and shipboard cetacean surveys, linked them to environmental covariates obtained from remote sensing and ocean models, and built habitat-based density models for 26 species and 3 multi-species guilds using distance sampling methodology. In the Atlantic, for 11 well-known species, model predictions resembled seasonal movement patterns previously suggested in the literature. For these we produced monthly mean density maps. For lesser-known taxa, and in the Gulf of Mexico, where seasonal movements were less well described, we produced year-round mean density maps. The results revealed high regional differences in small delphinoid densities, confirmed the importance of the continental slope to large delphinoids and of canyons and seamounts to beaked and sperm whales, and quantified seasonal shifts in the densities of migratory baleen whales. The density maps, freely available online, are the first for these regions to be published in the peer-reviewed literature. PMID:26936335

Self-organizing feature maps for dynamic control of radio resources in CDMA microcellular networks

NASA Astrophysics Data System (ADS)

Hortos, William S.

1998-03-01

The application of artificial neural networks to the channel assignment problem for cellular code-division multiple access (CDMA) cellular networks has previously been investigated. CDMA takes advantage of voice activity and spatial isolation because its capacity is only interference limited, unlike time-division multiple access (TDMA) and frequency-division multiple access (FDMA) where capacities are bandwidth-limited. Any reduction in interference in CDMA translates linearly into increased capacity. To satisfy the high demands for new services and improved connectivity for mobile communications, microcellular and picocellular systems are being introduced. For these systems, there is a need to develop robust and efficient management procedures for the allocation of power and spectrum to maximize radio capacity. Topology-conserving mappings play an important role in the biological processing of sensory inputs. The same principles underlying Kohonen's self-organizing feature maps (SOFMs) are applied to the adaptive control of radio resources to minimize interference, hence, maximize capacity in direct-sequence (DS) CDMA networks. The approach based on SOFMs is applied to some published examples of both theoretical and empirical models of DS/CDMA microcellular networks in metropolitan areas. The results of the approach for these examples are informally compared to the performance of algorithms, based on Hopfield- Tank neural networks and on genetic algorithms, for the channel assignment problem.

Planetary maps

USGS Publications Warehouse

,

1992-01-01

An important goal of the USGS planetary mapping program is to systematically map the geology of the Moon, Mars, Venus, and Mercury, and the satellites of the outer planets. These geologic maps are published in the USGS Miscellaneous Investigations (I) Series. Planetary maps on sale at the USGS include shaded-relief maps, topographic maps, geologic maps, and controlled photomosaics. Controlled photomosaics are assembled from two or more photographs or images using a network of points of known latitude and longitude. The images used for most of these planetary maps are electronic images, obtained from orbiting television cameras, various optical-mechanical systems. Photographic film was only used to map Earth's Moon.

L-Mapping Solar Energetic Particles from LEO to High Altitudes at High Latitudes

NASA Astrophysics Data System (ADS)

Young, S. L.; Wilson, G.

2017-12-01

The current solar energetic particle (SEP) hazard specification is focused on geosynchronous orbit with some capability at LEO, but there is no specification for the large region between these orbital regimes. The L-mapping technique, which attempts to fill this capability gap, assumes that there is a simple relationship between magnetic L-shells and SEP penetration boundaries that can be exploited. A previous study compared POES observations that had been mapped to the Van Allen Probes with local observations. It found that more than 90% of the mapped and local fluxes were within a factor of four of each other; this is thought to be sucient for operational purposes. One concern with the previous study was the limited number of SEP events that have occurred during the Van Allen Probes mission. The current study examines the L-mapping method's accuracy at higher latitudes. Observations from a satellite that was launched into a HEO orbit with a 63° inclination before the peak of solar cycle 24 are compared to L-mapped POES observations. The larger number of events provides better statistics and the 63° orbit inclination allows us to examine the difference between mapping from POES to the magnetic equator, as in the previous study, and mapping from POES to higher latitudes.

[Learning from regional differences: online platform: http://www.versorgungsatlas.de].

PubMed

Mangiapane, S

2014-02-01

In 2011, the Central Research Institute of Ambulatory Health Care in Germany (ZI) published the website http://www.versorgungsatlas.de, a portal that presents research results from regional health services in Germany. The Web portal provides a publicly accessible source of information and a growing number of selected analyses focusing on regional variation in health care. Each topic is presented in terms of interactive maps, tables, and diagrams and is supplemented by a paper that examines the results in detail and provides an explanation of the findings. The portal has been designed to provide a forum on which health service researchers can publish their results derived from various data sources of different institutions in Germany and can comment on results already available on http://www.versorgungsatlas.de. For health policy actors, the discussion of regional differences offers a new, previously unavailable basis for determining the region-specific treatment needs and for providing health-care management with the goal of high-quality care for each resident.

Automation process for morphometric analysis of volumetric CT data from pulmonary vasculature in rats.

PubMed

Shingrani, Rahul; Krenz, Gary; Molthen, Robert

2010-01-01

With advances in medical imaging scanners, it has become commonplace to generate large multidimensional datasets. These datasets require tools for a rapid, thorough analysis. To address this need, we have developed an automated algorithm for morphometric analysis incorporating A Visualization Workshop computational and image processing libraries for three-dimensional segmentation, vascular tree generation and structural hierarchical ordering with a two-stage numeric optimization procedure for estimating vessel diameters. We combine this new technique with our mathematical models of pulmonary vascular morphology to quantify structural and functional attributes of lung arterial trees. Our physiological studies require repeated measurements of vascular structure to determine differences in vessel biomechanical properties between animal models of pulmonary disease. Automation provides many advantages including significantly improved speed and minimized operator interaction and biasing. The results are validated by comparison with previously published rat pulmonary arterial micro-CT data analysis techniques, in which vessels were manually mapped and measured using intense operator intervention. Published by Elsevier Ireland Ltd.

Perspectives on the strategic uses of concept mapping to address public health challenges.

PubMed

Anderson, Lynda A; Slonim, Amy

2017-02-01

We examine the adaptation of approaches used to plan and implement the steps of concept mapping to meet specialized needs and requirements in several public health projects. Seven published concept mapping projects are detailed to document how each of the phases were modified to meet the specific aims of each project. Concept mapping was found to be a useful tool to complement public health roles such as assessment, program development, and priority setting. The phases of concept mapping allow for a blending of diverse perspectives, which is critical to public health efforts. The adaptability of concept mapping permits the use of multiple modalities such as the addition of face-to-face brainstorming; use of qualitative methods, including structured interviews; and review and use of published literature and guidelines. Another positive aspect of concept mapping for public health practice is its ability to identify program elements, provide a visual map of generated ideas and their relationships to one another, and assist in identifying priorities. Our reflections on the adaptability should help inform another generation in designing concept mapping projects and related products that may benefit from unique adaptations and the rapidly expanding social media technology and platforms. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Netherlands in Fifty Maps: An Annotated Atlas.

ERIC Educational Resources Information Center

Tamsma, R.

1988-01-01

Statistical data relating to The Netherlands is presented in 50 maps that were originally published in the "Journal of Economic and Social Geography" between 1977 and 1986. Lengthy annotations accompanying each map provide important background information on the issues depicted. These elucidations were written with the foreign reader in…

Geochemical baseline studies of soil in Finland

NASA Astrophysics Data System (ADS)

Pihlaja, Jouni

2017-04-01

The soil element concentrations regionally vary a lot in Finland. Mostly this is caused by the different bedrock types, which are reflected in the soil qualities. Geological Survey of Finland (GTK) is carrying out geochemical baseline studies in Finland. In the previous phase, the research is focusing on urban areas and mine environments. The information can, for example, be used to determine the need for soil remediation, to assess environmental impacts or to measure the natural state of soil in industrial areas or mine districts. The field work is done by taking soil samples, typically at depth between 0-10 cm. Sampling sites are chosen to represent the most vulnerable areas when thinking of human impacts by possible toxic soil element contents: playgrounds, day-care centers, schools, parks and residential areas. In the mine districts the samples are taken from the areas locating outside the airborne dust effected areas. Element contents of the soil samples are then analyzed with ICP-AES and ICP-MS, Hg with CV-AAS. The results of the geochemical baseline studies are published in the Finnish national geochemical baseline database (TAPIR). The geochemical baseline map service is free for all users via internet browser. Through this map service it is possible to calculate regional soil baseline values using geochemical data stored in the map service database. Baseline data for 17 elements in total is provided in the map service and it can be viewed on the GTK's web pages (http://gtkdata.gtk.fi/Tapir/indexEN.html).

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps.

PubMed

Sood, Mariam R; Sereno, Martin I

2016-08-01

Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor-preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface-based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory-motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory-motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M-I. Hum Brain Mapp 37:2784-2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Mapping fire regimes from data you may already have: assessing LANDFIRE fire regime maps using local products

Treesearch

Melissa A. Thomas-Van Gundy

2014-01-01

LANDFIRE maps of fire regime groups are frequently used by land managers to help plan and execute prescribed burns for ecosystem restoration. Since LANDFIRE maps are generally applicable at coarse scales, questions often arise regarding their utility and accuracy. Here, the two recently published products from West Virginia, a rule-based and a witness tree-based model...

Delta-9-tetrahydrocannabinol (THC) affects forelimb motor map expression but has little effect on skilled and unskilled behavior.

PubMed

Scullion, K; Guy, A R; Singleton, A; Spanswick, S C; Hill, M N; Teskey, G C

2016-04-05

It has previously been shown in rats that acute administration of delta-9-tetrahydrocannabinol (THC) exerts a dose-dependent effect on simple locomotor activity, with low doses of THC causing hyper-locomotion and high doses causing hypo-locomotion. However the effect of acute THC administration on cortical movement representations (motor maps) and skilled learned movements is completely unknown. It is important to determine the effects of THC on motor maps and skilled learned behaviors because behaviors like driving place people at a heightened risk. Three doses of THC were used in the current study: 0.2mg/kg, 1.0mg/kg and 2.5mg/kg representing the approximate range of the low to high levels of available THC one would consume from recreational use of cannabis. Acute peripheral administration of THC to drug naïve rats resulted in dose-dependent alterations in motor map expression using high resolution short duration intracortical microstimulation (SD-ICMS). THC at 0.2mg/kg decreased movement thresholds and increased motor map size, while 1.0mg/kg had the opposite effect, and 2.5mg/kg had an even more dramatic effect. Deriving complex movement maps using long duration (LD)-ICMS at 1.0mg/kg resulted in fewer complex movements. Dosages of 1.0mg/kg and 2.5mg/kg THC reduced the number of reach attempts but did not affect percentage of success or the kinetics of reaching on the single pellet skilled reaching task. Rats that received 2.5mg/kg THC did show an increase in latency of forelimb removal on the bar task, while dose-dependent effects of THC on unskilled locomotor activity using the rotorod and horizontal ladder tasks were not observed. Rats may be employing compensatory strategies after receiving THC, which may account for the robust changes in motor map expression but moderate effects on behavior. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

Self Consistent Bathymetric Mapping Using Sub-maps: Survey Results From the TAG Hydrothermal Structure

NASA Astrophysics Data System (ADS)

Roman, C. N.; Reves-Sohn, R.; Singh, H.; Humphris, S.

2005-12-01

The spatial resolution of microbathymetry maps created using robotic vehicles such as ROVs, AUVs and manned submersibles in the deep ocean is currently limited by the accuracy of the vehicle navigation data. Errors in the vehicle position estimate commonly exceed the ranging errors of the acoustic mapping sensor itself, which creates inconsistency in the map making process and produces artifacts that lower resolution and distort map integrity. We present a methodology for producing self-consistent maps and improving vehicle position estimation by exploiting accurate local navigation and utilizing terrain relative measurements. The complete map is broken down into individual "sub-maps'', which are generated using short term Doppler based navigation. The sub-maps are pairwise registered to constrain the vehicle position estimates by matching terrain that has been imaged multiple times. This procedure is implemented using a delayed state Kalman filter to incorporate the sub-map registrations as relative position measurements between previously visited vehicle locations. Archiving of previous positions in a filter state vector allows for continual adjustment of the sub-map locations. The terrain registration is accomplished using a two dimensional correlation and a six degree of freedom point cloud alignment method tailored to bathymetric data. This registration procedure is applicable to fully 3 dimensional complex underwater environments. The complete bathymetric map is then created from the union of all sub-maps that have been aligned in a consistent manner. The method is applied to an SM2000 multibeam survey of the TAG hydrothermal structure on the Mid-Atlantic Ridge at 26(°)N using the Jason II ROV. The survey included numerous crossing tracklines designed to test this algorithm, and the final gridded bathymetry data is sub-meter accurate. The high-resolution map has allowed for the identification of previously unrecognized fracture patterns associated with flow focusing at TAG, as well as imaging of fine-scale features such as individual sulfide talus blocks and ODP re-entry cones.

Preliminary geologic map of the eastern Willapa Hills, Cowlitz, Lewis, and Wahkiakum Counties, Washington

USGS Publications Warehouse

Wells, Ray E.; Sawlan, Michael G.

2014-01-01

This digital map database and the PDF derived from the database were created from the analog geologic map: Wells, R.E. (1981), “Geologic map of the eastern Willapa Hills, Cowlitz, Lewis, and Wahkiakum Counties, Washington.” The geodatabase replicates the geologic mapping of the 1981 report with minor exceptions along water boundaries and also along the north and south map boundaries. Slight adjustments to contacts along water boundaries were made to correct differences between the topographic base map used in the 1981 compilation (analog USGS 15-minute series quadrangle maps at 1:62,500 scale) and the base map used for this digital compilation (scanned USGS 7.5-minute series quadrangle maps at 1:24,000 scale). These minor adjustments, however, did not materially alter the geologic map. No new field mapping was performed to create this digital map database, and no attempt was made to fit geologic contacts to the new 1:24,000 topographic base, except as noted above. We corrected typographical errors, formatting errors, and attribution errors (for example, the name change of Goble Volcanics to Grays River Volcanics following current State of Washington usage; Walsh and others, 1987). We also updated selected references, substituted published papers for abstracts, and cited published radiometric ages for the volcanic and plutonic rocks. The reader is referred to Magill and others (1982), Wells and Coe (1985), Walsh and others (1987), Moothart (1993), Payne (1998), Kleibacker (2001), McCutcheon (2003), Wells and others (2009), Chan and others (2012), and Wells and others (in press) for subsequent interpretations of the Willapa Hills geology.

Planetary Geologic Mapping Handbook - 2010. Appendix

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A., Jr.; Hare, T. M.

2010-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces. Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962. Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by the USGS now are primarily digital products using geographic information system (GIS) software and file formats. GIS mapping tools permit easy spatial comparison, generation, importation, manipulation, and analysis of multiple raster image, gridded, and vector data sets. GIS software has also permitted the development of projectspecific tools and the sharing of geospatial products among researchers. GIS approaches are now being used in planetary geologic mapping as well. Guidelines or handbooks on techniques in planetary geologic mapping have been developed periodically. As records of the heritage of mapping methods and data, these remain extremely useful guides. However, many of the fundamental aspects of earlier mapping handbooks have evolved significantly, and a comprehensive review of currently accepted mapping methodologies is now warranted. As documented in this handbook, such a review incorporates additional guidelines developed in recent years for planetary geologic mapping by the NASA Planetary Geology and Geophysics (PGG) Program's Planetary Cartography and Geologic Mapping Working Group's (PCGMWG) Geologic Mapping Subcommittee (GEMS) on the selection and use of map bases as well as map preparation, review, publication, and distribution. In light of the current boom in planetary exploration and the ongoing rapid evolution of available data for planetary mapping, this handbook is especially timely.

The Use of Maps in Turkish Newspapers

ERIC Educational Resources Information Center

Demirci, Ali; Suslu, Zeliha

2016-01-01

This study analyzes the use of maps in Turkish newspapers in order to evaluate their potential to contribute to the enhancement of geographic knowledge in society. This study reviewed the content of three Turkish newspapers published between January 2008 and August 2012. Only 835 maps were used in the newspapers during the study period, or an…

Scanning and georeferencing historical USGS quadrangles

USGS Publications Warehouse

Davis, Larry R.; Allord, G.J.

2011-01-01

The USGS Historical Quadrangle Scanning Project (HQSP) is scanning all scales and all editions of approximately 250,000 topographic maps published by the U.S. Geological Survey (USGS) since the inception of the topographic mapping program in 1884. This scanning will provide a comprehensive digital repository of USGS topographic maps, available to the public at no cost. This project serves the dual purpose of creating a master catalog and digital archive copies of the irreplaceable collection of topographic maps in the USGS Reston Map Library as well as making the maps available for viewing and downloading from the USGS Store and The National Map Viewer.

Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 2, Geology report. Revised final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1991-12-01

Detailed investigations of geologic, geomorphic, and seismic conditions at the Bodo Canyon disposal site were conducted. The purpose of these investigations was basic site characterization and identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies, such as analyses of hydrologic and liquefaction hazards, used the data developed in these studies. The geomorphic analysis was employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65 kilometer radius of the site, provided the basis for seismic design parameters. Themore » scope of work performed included the following: Compilation and analysis of previous published and unpublished geologic literature and maps; Review of historical and instrumental earthquake data; Review of site-specific subsurface geologic data, including lithologic and geophysical logs of exploratory boreholes advanced in the site area; Photogeologic interpretations of existing conventional aerial photographs; and, Ground reconnaissance and mapping of the site region.« less

A Compilation of Provisional Karst Geospatial Data for the Interior Low Plateaus Physiographic Region, Central United States

USGS Publications Warehouse

Taylor, Charles J.; Nelson, Hugh L.

2008-01-01

Geospatial data needed to visualize and evaluate the hydrogeologic framework and distribution of karst features in the Interior Low Plateaus physiographic region of the central United States were compiled during 2004-2007 as part of the Ground-Water Resources Program Karst Hydrology Initiative (KHI) project. Because of the potential usefulness to environmental and water-resources regulators, private consultants, academic researchers, and others, the geospatial data files created during the KHI project are being made available to the public as a provisional regional karst dataset. To enhance accessibility and visualization, the geospatial data files have been compiled as ESRI ArcReader data folders and user interactive Published Map Files (.pmf files), all of which are catalogued by the boundaries of surface watersheds using U.S. Geological Survey (USGS) eight-digit hydrologic unit codes (HUC-8s). Specific karst features included in the dataset include mapped sinkhole locations, sinking (or disappearing) streams, internally drained catchments, karst springs inventoried in the USGS National Water Information System (NWIS) database, relic stream valleys, and karst flow paths obtained from results of previously reported water-tracer tests.

Relations between some horizontal‐component ground‐motion intensity measures used in practice

USGS Publications Warehouse

Boore, David; Kishida, Tadahiro

2017-01-01

Various measures using the two horizontal components of recorded ground motions have been used in a number of studies that derive ground‐motion prediction equations and construct maps of shaking intensity. We update relations between a number of these measures, including those in Boore et al. (2006) and Boore (2010), using the large and carefully constructed global database of ground motions from crustal earthquakes in active tectonic regions developed as part of the Pacific Earthquake Engineering Research Center–Next Generation Attenuation‐West2 project. The ratios from the expanded datasets generally agree to within a few percent of the previously published ratios. We also provide some ratios that were not considered before, some of which will be useful in applications such as constructing ShakeMaps. Finally, we compare two important ratios with those from a large central and eastern North American database and from many records from subduction earthquakes in Japan and Taiwan. In general, the ratios from these regions are within several percent of those from crustal earthquakes in active tectonic regions.

Seasonal patterns of wind stress and wind stress curl over the Gulf of Mexico

NASA Astrophysics Data System (ADS)

de Velasco, Guillermo Gutiérrez; Winant, Clinton D.

1996-08-01

Meteorological observations from an array of stations deployed along the periphery of the Gulf of Mexico, between 1990 and 1993, are used to describe the seasonal fluctuations in patterns of atmospheric variables from a contemporary set of measurements. Seasonal maps of wind stress based on these measurements resemble wind stress maps based on ship observations, as published by Elliott [1979], rather than maps based on analyses of numerical weather forecasts, as published by Rhodes et al. [1989], particularly near the western boundary of the gulf. Seasonal maps of wind stress curl are characterized by positive curls over the western and southwestern gulf. The central result of this study is to document the important role of the mountain chain which extends along the southwestern section of the gulf in channeling the wind toward the Isthmus of Tehuantepec.

ResistoMap-online visualization of human gut microbiota antibiotic resistome.

PubMed

Yarygin, Konstantin S; Kovarsky, Boris A; Bibikova, Tatyana S; Melnikov, Damir S; Tyakht, Alexander V; Alexeev, Dmitry G

2017-07-15

We created ResistoMap—a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlates the gut resistome variations with the national clinical guidelines on antibiotics application. ResistoMap was implemented using AngularJS, CoffeeScript, D3.js and TopoJSON. The tool is publicly available at http://resistomap.rcpcm.org. yarygin@phystech.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Karst mapping in the United States: Past, present and future

USGS Publications Warehouse

Weary, David J.; Doctor, Daniel H.

2015-01-01

The earliest known comprehensive karst map of the entire USA was published by Stringfield and LeGrand (1969), based on compilations of William E. Davies of the U.S. Geological Survey (USGS). Various versions of essentially the same map have been published since. The USGS recently published new digital maps and databases depicting the extent of known karst, potential karst, and pseudokarst areas of the United States of America including Puerto Rico and the U.S. Virgin Islands (Weary and Doctor, 2014). These maps are based primarily on the extent of potentially karstic soluble rock types, and rocks with physical properties conducive to the formation of pseudokarst features. These data were compiled and refined from multiple sources at various spatial resolutions, mostly as digital data supplied by state geological surveys. The database includes polygons delineating areas with potential for karst and that are tagged with attributes intended to facilitate classification of karst regions. Approximately 18% of the surface of the fifty United States is underlain by significantly soluble bedrock. In the eastern United States the extent of outcrop of soluble rocks provides a good first-approximation of the distribution of karst and potential karst areas. In the arid western states, the extent of soluble rock outcrop tends to overestimate the extent of regions that might be considered as karst under current climatic conditions, but the new dataset encompasses those regions nonetheless. This database will be revised as needed, and the present map will be updated as new information is incorporated.

Latitudinal patterns of leaf N, P stoichiometry and nutrient resorption of Metasequoia glyptostroboides along the eastern coastline of China.

PubMed

Zhang, Hui; Guo, Weihong; Yu, Mukui; Wang, G Geoff; Wu, Tonggui

2018-03-15

Latitudinal patterns of leaf stoichiometry and nutrient resorption were not consistent among published studies, likely due to confounding effects from taxonomy (e.g., plant distribution and community composition), and environment, which is also influenced by altitude and longitude. Thus, the latitudinal patterns and environmental mechanism could be best revealed by testing a given species along a latitude gradient with similar altitude and longitude. We determined nitrogen (N) and phosphorus (P) concentrations of green (leaf) and senesced leaves (litter) from eight Metasequoia glyptostroboides forests along the eastern coastline of China, with similar altitude and longitude. Leaf N, P concentrations increased along latitude, mainly driven by mean annual temperature (MAT), mean annual precipitation (MAP), annual evaporation (AE), aridity index (AI), and annual total solar radiation (ATSR); While leaf N:P ratio was stable with no latitudinal pattern. Nitrogen resorption efficiency (NRE) increased along latitude, and was also mainly influenced by MAT, MAP, AE, and AI. Phosphorus resorption efficiency (PRE) first increased and then decreased with latitude, which was impacted by soil available P. These results indicated that only climate (such as heat, water, and light) controlled the shift in leaf stoichiometry and NRE, while soil nutrient was likely responsible for the shift in PRE along eastern China. Our findings also suggested that leaf N, P stoichiometry and NRE displayed similar latitudinal patterns at regional scale when studied for a given species (this study) or multi-species (previous studies). Copyright © 2017. Published by Elsevier B.V.

A Brief History of Soil Mapping and Classification in the USA

NASA Astrophysics Data System (ADS)

Brevik, Eric C.; Hartemink, Alfred E.

2014-05-01

Soil maps show the distribution of soils across an area but also depict soil science theory and ideas on soil formation and classification at the time the maps were created. The national soil mapping program in the USA was established in 1899. The first nation-wide soil map was published by M. Whitney in 1909 and showed soil provinces that were largely based on geology. In 1912, G.N. Coffey published the first country-wide map based on soil properties. The map showed 5 broad soil units that used parent material, color and drainage as diagnostic criteria. The 1913 national map was produced by C.F. Marbut, H.H. Bennett, J.E. Lapham, and M.H. Lapham and showed broad physiographic units that were further subdivided into soil series, soil classes and soil types. In 1935, Marbut drafted a series of maps based on soil properties, but these maps were replaced as official U.S. soil maps in 1938 with the work of M. Baldwin, C.E. Kellogg, and J. Thorp. A series of soil maps similar to modern USA maps appeared in the 1960s with the 7th Approximation followed by revisions with the 1975 and 1999 editions of Soil Taxonomy. This review has shown that soil maps in the United States produced since the early 1900s moved initially from a geologic-based concept to a pedologic concept of soils. Later changes were from property-based systems to process-based, and then back to property-based. The information in this presentation is based on Brevik and Hartemink (2013). Brevik, E.C., and A.E. Hartemink. 2013. Soil Maps of the United States of America. Soil Science Society of America Journal 77:1117-1132. doi:10.2136/sssaj2012.0390.

Effects of management practices on wetland birds: Yellow Rail

USGS Publications Warehouse

Goldade, Christopher M.; Dechant, Jill A.; Johnson, Douglas H.; Zimmerman, Amy L.; Jamison, Brent E.; Church, James O.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of wetland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on wetland birds: Virginia rail

USGS Publications Warehouse

Zimmerman, Amy L.; Dechant, Jill A.; Jamison, Brent E.; Johnson, Douglas H.; Goldade, Christopher M.; Church, James O.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of wetland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on wetland birds: Black tern

USGS Publications Warehouse

Zimmerman, Amy L.; Dechant, Jill A.; Johnson, Douglas A.; Goldade, Christopher M.; Jamison, Brent E.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on wetland birds: American Avocet

USGS Publications Warehouse

Dechant, Jill A.; Zimmerman, Amy L.; Johnson, Douglas H.; Goldade, Christopher M.; Jamison, Brent E.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of wetland birds and their responses to habitat management is posted at the Web site mentioned below.

OMG Earthquake! Can Twitter improve earthquake response?

NASA Astrophysics Data System (ADS)

Earle, P. S.; Guy, M.; Ostrum, C.; Horvath, S.; Buckmaster, R. A.

2009-12-01

The U.S. Geological Survey (USGS) is investigating how the social networking site Twitter, a popular service for sending and receiving short, public, text messages, can augment its earthquake response products and the delivery of hazard information. The goal is to gather near real-time, earthquake-related messages (tweets) and provide geo-located earthquake detections and rough maps of the corresponding felt areas. Twitter and other social Internet technologies are providing the general public with anecdotal earthquake hazard information before scientific information has been published from authoritative sources. People local to an event often publish information within seconds via these technologies. In contrast, depending on the location of the earthquake, scientific alerts take between 2 to 20 minutes. Examining the tweets following the March 30, 2009, M4.3 Morgan Hill earthquake shows it is possible (in some cases) to rapidly detect and map the felt area of an earthquake using Twitter responses. Within a minute of the earthquake, the frequency of “earthquake” tweets rose above the background level of less than 1 per hour to about 150 per minute. Using the tweets submitted in the first minute, a rough map of the felt area can be obtained by plotting the tweet locations. Mapping the tweets from the first six minutes shows observations extending from Monterey to Sacramento, similar to the perceived shaking region mapped by the USGS “Did You Feel It” system. The tweets submitted after the earthquake also provided (very) short first-impression narratives from people who experienced the shaking. Accurately assessing the potential and robustness of a Twitter-based system is difficult because only tweets spanning the previous seven days can be searched, making a historical study impossible. We have, however, been archiving tweets for several months, and it is clear that significant limitations do exist. The main drawback is the lack of quantitative information such as epicenter, magnitude, and strong-motion recordings. Without quantitative data, prioritization of response measures, including building and infrastructure inspection, are not possible. The main advantage of Twitter is speed, especially in sparsely instrumented areas. A Twitter based system potentially could provide a quick notification that there was a possible event and that seismographically derived information will follow. If you are interested in learning more, follow @USGSted on Twitter.

A global map of travel time to cities to assess inequalities in accessibility in 2015

NASA Astrophysics Data System (ADS)

Weiss, D. J.; Nelson, A.; Gibson, H. S.; Temperley, W.; Peedell, S.; Lieber, A.; Hancher, M.; Poyart, E.; Belchior, S.; Fullman, N.; Mappin, B.; Dalrymple, U.; Rozier, J.; Lucas, T. C. D.; Howes, R. E.; Tusting, L. S.; Kang, S. Y.; Cameron, E.; Bisanzio, D.; Battle, K. E.; Bhatt, S.; Gething, P. W.

2018-01-01

The economic and man-made resources that sustain human wellbeing are not distributed evenly across the world, but are instead heavily concentrated in cities. Poor access to opportunities and services offered by urban centres (a function of distance, transport infrastructure, and the spatial distribution of cities) is a major barrier to improved livelihoods and overall development. Advancing accessibility worldwide underpins the equity agenda of ‘leaving no one behind’ established by the Sustainable Development Goals of the United Nations. This has renewed international efforts to accurately measure accessibility and generate a metric that can inform the design and implementation of development policies. The only previous attempt to reliably map accessibility worldwide, which was published nearly a decade ago, predated the baseline for the Sustainable Development Goals and excluded the recent expansion in infrastructure networks, particularly in lower-resource settings. In parallel, new data sources provided by Open Street Map and Google now capture transportation networks with unprecedented detail and precision. Here we develop and validate a map that quantifies travel time to cities for 2015 at a spatial resolution of approximately one by one kilometre by integrating ten global-scale surfaces that characterize factors affecting human movement rates and 13,840 high-density urban centres within an established geospatial-modelling framework. Our results highlight disparities in accessibility relative to wealth as 50.9% of individuals living in low-income settings (concentrated in sub-Saharan Africa) reside within an hour of a city compared to 90.7% of individuals in high-income settings. By further triangulating this map against socioeconomic datasets, we demonstrate how access to urban centres stratifies the economic, educational, and health status of humanity.

Environmental variables across Pan troglodytes study sites correspond with the carbon, but not the nitrogen, stable isotope ratios of chimpanzee hair.

PubMed

Schoeninger, Margaret J; Most, Corinna A; Moore, Jim J; Somerville, Andrew D

2016-10-01

Diet influences the stable isotope ratios of carbon and nitrogen (δ(13) C and δ(15) N values) in animal tissue; but here we explore the influences of particular aspects of the local environment on those values in chimpanzees (Pan troglodytes). In this article we present new δ(13) C and δ(15) N values in Gombe chimpanzees using hairs collected from night nests in 1989. Then, we explore the influence of environmental factors by comparing our Gombe data to those from eight additional Pan study sites with previously published stable isotope data. We compare chimpanzee δ(13) Chair and δ(15) Nhar values to specific characteristics of local site ecology (biome and ecoregion) and to local Mean Annual Precipitation (MAP) to test hypotheses based on known effects of these variables on the δ(13) C and δ(15) N values in plant tissues. The comparison shows that hair from chimpanzees living in savanna sites with lower MAP have higher δ(13) Chair values than do chimpanzees living in woodland and forested sites with higher MAP. These results demonstrate the potential of using δ(13) C values in primate tissue to indicate aspects of their local ecology in cases where the ecology is uncertain, such as samples collected early in the last century and in fossil hominins. In contrast to expectations, however, chimpanzee δ(15) Nhair values from some savanna sites with lower MAP are lower, not higher, than those living in more forested areas with higher MAP. It is likely that diet selectivity by chimpanzees affects δ(15) Nhair values to a greater extent than does the influence of precipitation on plants. Am. J. Primatol. 78:1055-1069, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Laparoscopy Instructional Videos: The Effect of Preoperative Compared With Intraoperative Use on Learning Curves.

PubMed

Broekema, Theo H; Talsma, Aaldert K; Wevers, Kevin P; Pierie, Jean-Pierre E N

Previous studies have shown that the use of intraoperative instructional videos has a positive effect on learning laparoscopic procedures. This study investigated the effect of the timing of the instructional videos on learning curves in laparoscopic skills training. After completing a basic skills course on a virtual reality simulator, medical students and residents with less than 1 hour experience using laparoscopic instruments were randomized into 2 groups. Using an instructional video either preoperatively or intraoperatively, both groups then performed 4 repetitions of a standardized task on the TrEndo augmented reality. With the TrEndo, 9 motion analysis parameters (MAPs) were recorded for each session (4 MAPs for each hand and time). These were the primary outcome measurements for performance. The time spent watching the instructional video was also recorded. Improvement in performance was studied within and between groups. Medical Center Leeuwarden, a secondary care hospital located in Leeuwarden, The Netherlands. Right-hand dominant medical student and residents with more than 1 hour experience operating any kind of laparoscopic instruments were participated. A total of 23 persons entered the study, of which 21 completed the study course. In both groups, at least 5 of 9 MAPs showed significant improvements between repetition 1 and 4. When both groups were compared after completion of repetition 4, no significant differences in improvement were detected. The intraoperative group showed significant improvement in 3 MAPs of the left-nondominant-hand, compared with one MAP for the preoperative group. No significant differences in learning curves could be detected between the subjects who used intraoperative instructional videos and those who used preoperative instructional videos. Intraoperative video instruction may result in improved dexterity of the nondominant hand. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

A global map of travel time to cities to assess inequalities in accessibility in 2015.

PubMed

Weiss, D J; Nelson, A; Gibson, H S; Temperley, W; Peedell, S; Lieber, A; Hancher, M; Poyart, E; Belchior, S; Fullman, N; Mappin, B; Dalrymple, U; Rozier, J; Lucas, T C D; Howes, R E; Tusting, L S; Kang, S Y; Cameron, E; Bisanzio, D; Battle, K E; Bhatt, S; Gething, P W

2018-01-18

The economic and man-made resources that sustain human wellbeing are not distributed evenly across the world, but are instead heavily concentrated in cities. Poor access to opportunities and services offered by urban centres (a function of distance, transport infrastructure, and the spatial distribution of cities) is a major barrier to improved livelihoods and overall development. Advancing accessibility worldwide underpins the equity agenda of 'leaving no one behind' established by the Sustainable Development Goals of the United Nations. This has renewed international efforts to accurately measure accessibility and generate a metric that can inform the design and implementation of development policies. The only previous attempt to reliably map accessibility worldwide, which was published nearly a decade ago, predated the baseline for the Sustainable Development Goals and excluded the recent expansion in infrastructure networks, particularly in lower-resource settings. In parallel, new data sources provided by Open Street Map and Google now capture transportation networks with unprecedented detail and precision. Here we develop and validate a map that quantifies travel time to cities for 2015 at a spatial resolution of approximately one by one kilometre by integrating ten global-scale surfaces that characterize factors affecting human movement rates and 13,840 high-density urban centres within an established geospatial-modelling framework. Our results highlight disparities in accessibility relative to wealth as 50.9% of individuals living in low-income settings (concentrated in sub-Saharan Africa) reside within an hour of a city compared to 90.7% of individuals in high-income settings. By further triangulating this map against socioeconomic datasets, we demonstrate how access to urban centres stratifies the economic, educational, and health status of humanity.

Hazard map for volcanic ballistic impacts at El Chichón volcano (Mexico)

NASA Astrophysics Data System (ADS)

Alatorre-Ibarguengoitia, Miguel; Ramos-Hernández, Silvia; Jiménez-Aguilar, Julio

2014-05-01

The 1982 eruption of El Chichón Volcano in southeastern Mexico had a strong social and environmental impact. The eruption resulted in the worst volcanic disaster in the recorded history of Mexico, causing about 2,000 casualties, displacing thousands, and producing severe economic losses. Even when some villages were relocated after the 1982 eruption, many people still live and work in the vicinities of the volcano and may be affected in the case of a new eruption. The hazard map of El Chichón volcano (Macías et al., 2008) comprises pyroclastic flows, pyroclastic surges, lahars and ash fall but not ballistic projectiles, which represent an important threat to people, infrastructure and vegetation in the case of an eruption. In fact, the fatalities reported in the first stage of the 1982 eruption were caused by roof collapse induced by ashfall and lithic ballistic projectiles. In this study, a general methodology to delimit the hazard zones for volcanic ballistic projectiles during volcanic eruptions is applied to El Chichón volcano. Different scenarios are defined based on the past activity of the volcano and parameterized by considering the maximum kinetic energy associated with ballistic projectiles ejected during previous eruptions. A ballistic model is used to reconstruct the "launching" kinetic energy of the projectiles observed in the field. The maximum ranges expected for the ballistics in the different explosive scenarios defined for El Chichón volcano are presented in a ballistic hazard map which complements the published hazard map. These maps assist the responsible authorities to plan the definition and mitigation of restricted areas during volcanic crises.

Anatomical association between wrist extensor musculature and topographical pain sensitivity maps of the elbow area.

PubMed

Prados-Frutos, Juan Carlos; Ruiz-Ruiz, Beatriz; De-la-Llave-Rincón, Ana Isabel; Arendt-Nielsen, Lars; Madeleine, Pascal; Fernández-de-Las-Peñas, César

2012-06-01

High-density topographical sensitivity maps have been developed to visualize nonuniformity deep tissue pain sensitivity in, for example, lateral epicondylitis (LE). The aim of this cadaveric study was to determine the anatomical association between the topographical sensitivity maps over the elbow area and wrist extensor musculature. A topographical pressure sensitivity map consisting of 12 points forming a 3 × 4 matrix: 4 points in the superior part, 4 points in the middle, and 4 points in the lower part around the lateral epicondyle was marker on a 50-year embalmed cadaver. Color marker pins were inserted into each point. Pins were removed during the process of dissection, but the small holes created by their removal assured accurate relocation. Progressive dissection revealed that points 1 to 4 (superior line) were placed over the musculotendinous junction and belly of the extensor carpi radialis brevis (ECRB) muscle, points 6 to 8 (middle line) were placed over the musculotendinous junction and belly of the extensor digitorum communis muscle, and points 9 to 12 (inferior line) were located over the musculotendinous junction and belly of the extensor carpi ulnaris muscle. It was also observed that the superficial branch of the radial nerve runs between the belly of the ECRB and extensor digitorum communis muscles. This study confirmed that anatomical location previously assumed supporting the important wrist extensor muscles, particularly the ECRB, in patients with LE as depicted by pressure pain sensitivity maps. This study also suggests a potential role of the superficial branch of the radial nerve in LE. Copyright © 2012 National University of Health Sciences. Published by Mosby, Inc. All rights reserved.

Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance.

PubMed

Ogunola, Oluwaseun F; Hawkins, Leigh K; Mylroie, Erik; Kolomiets, Michael V; Borrego, Eli; Tang, Juliet D; Williams, W Paul; Warburton, Marilyn L

2017-01-01

Maize (Zea mays L.) is a globally important staple food crop prone to contamination by aflatoxin, a carcinogenic secondary metabolite produced by the fungus Aspergillus flavus. An efficient approach to reduce accumulation of aflatoxin is the development of germplasm resistant to colonization and toxin production by A. flavus. Lipoxygenases (LOXs) are a group of non-heme iron containing dioxygenase enzymes that catalyze oxygenation of polyunsaturated fatty acids (PUFAs). LOX derived oxylipins play critical roles in plant defense against pathogens including A. flavus. The objectives of this study were to summarize sequence diversity and expression patterns for all LOX genes in the maize genome, and map their effect on aflatoxin accumulation via linkage and association mapping. In total, 13 LOX genes were identified, characterized, and mapped. The sequence of one gene, ZmLOX10, is reported from 5 inbred lines. Genes ZmLOX1/2, 5, 8, 9, 10 and 12 (GRMZM2G156861, or V4 numbers ZM00001D042541 and Zm00001D042540, GRMZM2G102760, GRMZM2G104843, GRMZM2G017616, GRMZM2G015419, and GRMZM2G106748, respectively) fell under previously published QTL in one or more mapping populations and are linked to a measurable reduction of aflatoxin in maize grains. Association mapping results found 28 of the 726 SNPs tested were associated with reduced aflatoxin levels at p ≤ 9.71 x 10-4 according to association statistics. These fell within or near nine of the ZmLOX genes. This work confirms the importance of some lipoxygenases for resistance to aflatoxin accumulation and may be used to direct future genetic selection in maize.

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

DOE PAGES

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne; ...

2015-12-30

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, withmore » an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.« less

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, withmore » an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.« less

Genetic and environmental control of host-gut microbiota interactions.

PubMed

Org, Elin; Parks, Brian W; Joo, Jong Wha J; Emert, Benjamin; Schwartzman, William; Kang, Eun Yong; Mehrabian, Margarete; Pan, Calvin; Knight, Rob; Gunsalus, Robert; Drake, Thomas A; Eskin, Eleazar; Lusis, Aldons J

2015-10-01

Genetics provides a potentially powerful approach to dissect host-gut microbiota interactions. Toward this end, we profiled gut microbiota using 16s rRNA gene sequencing in a panel of 110 diverse inbred strains of mice. This panel has previously been studied for a wide range of metabolic traits and can be used for high-resolution association mapping. Using a SNP-based approach with a linear mixed model, we estimated the heritability of microbiota composition. We conclude that, in a controlled environment, the genetic background accounts for a substantial fraction of abundance of most common microbiota. The mice were previously studied for response to a high-fat, high-sucrose diet, and we hypothesized that the dietary response was determined in part by gut microbiota composition. We tested this using a cross-fostering strategy in which a strain showing a modest response, SWR, was seeded with microbiota from a strain showing a strong response, A×B19. Consistent with a role of microbiota in dietary response, the cross-fostered SWR pups exhibited a significantly increased response in weight gain. To examine specific microbiota contributing to the response, we identified various genera whose abundance correlated with dietary response. Among these, we chose Akkermansia muciniphila, a common anaerobe previously associated with metabolic effects. When administered to strain A×B19 by gavage, the dietary response was significantly blunted for obesity, plasma lipids, and insulin resistance. In an effort to further understand host-microbiota interactions, we mapped loci controlling microbiota composition and prioritized candidate genes. Our publicly available data provide a resource for future studies. © 2015 Org et al.; Published by Cold Spring Harbor Laboratory Press.

Gravity, aeromagnetic and rock-property data of the central California Coast Ranges

USGS Publications Warehouse

Langenheim, V.E.

2014-01-01

Gravity, aeromagnetic, and rock-property data were collected to support geologic-mapping, water-resource, and seismic-hazard studies for the central California Coast Ranges. These data are combined with existing data to provide gravity, aeromagnetic, and physical-property datasets for this region. The gravity dataset consists of approximately 18,000 measurements. The aeromagnetic dataset consists of total-field anomaly values from several detailed surveys that have been merged and gridded at an interval of 200 m. The physical property dataset consists of approximately 800 density measurements and 1,100 magnetic-susceptibility measurements from rock samples, in addition to previously published borehole gravity surveys from Santa Maria Basin, density logs from Salinas Valley, and intensities of natural remanent magnetization.

Public water supplies of North Carolina : a summary of water sources, use, treatment, and capacity of water-supply systems

USGS Publications Warehouse

Mann, L.T.

1978-01-01

Data were collected during 1970-76 on 224 public water supply systems in North Carolina with 500 or more customers. This report summarizes these data that were previously published in five separate regional reports. The data are presented in order to Council of Government region, county, and water system name and include population served, average and maximum daily use, industrial use, water source, allowable draft of surface-water supplies, raw water pumping capacity, raw and finished water storage, type of water treatment, treatment plant capacity, and a summary of the chemical quality of finished water. Tables and maps provide cross references for system names, counties, Council of Government regions and water source.

Tibetan Magmatism Database

NASA Astrophysics Data System (ADS)

Chapman, James B.; Kapp, Paul

2017-11-01

A database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan-Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web-based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high-flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

Physical and Genetic Mechanisms Guiding the Evolution and Development of Dendritic, Flapping Insect-Wings

DTIC Science & Technology

2010-04-12

computer graphics, to music . Map L systems [2, 6, 7] extend the parallel rewriting in L systems to planar graphs with cycles, called maps [8]. The maps...carbon. For easy of reading , in the results below the mass is represented by the percentage carbon laminate coverage. As explained previously, the...previously, that value can be read in the left vertical axis. There are nine designs in the Pareto front. Depending on design goals any of these individuals

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

PubMed

Li, Gang; Hillier, LaDeana W; Grahn, Robert A; Zimin, Aleksey V; David, Victor A; Menotti-Raymond, Marilyn; Middleton, Rondo; Hannah, Steven; Hendrickson, Sher; Makunin, Alex; O'Brien, Stephen J; Minx, Pat; Wilson, Richard K; Lyons, Leslie A; Warren, Wesley C; Murphy, William J

2016-06-01

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location. Copyright © 2016 Li et al.

GStream: Improving SNP and CNV Coverage on Genome-Wide Association Studies

PubMed Central

Alonso, Arnald; Marsal, Sara; Tortosa, Raül; Canela-Xandri, Oriol; Julià, Antonio

2013-01-01

We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method. PMID:23844243

Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.

PubMed

Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu; Scheuermann, Richard H

2016-01-01

Flow cytometry (FCM) is a fluorescence-based single-cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap-FR, a novel method for cell population mapping across FCM samples. FlowMap-FR is based on the Friedman-Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap-FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap-FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap-FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap-FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap-FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback-Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL-distance in distinguishing equivalent from nonequivalent cell populations. FlowMap-FR was also employed as a distance metric to match cell populations delineated by manual gating across 30 FCM samples from a benchmark FlowCAP data set. An F-measure of 0.88 was obtained, indicating high precision and recall of the FR-based population matching results. FlowMap-FR has been implemented as a standalone R/Bioconductor package so that it can be easily incorporated into current FCM data analytical workflows. © The Authors. Published by Wiley Periodicals, Inc. on behalf of ISAC.

The accuracy of selected land use and land cover maps at scales of 1:250,000 and 1:100,000

USGS Publications Warehouse

Fitzpatrick-Lins, Katherine

1980-01-01

Land use and land cover maps produced by the U.S. Geological Survey are found to meet or exceed the established standard of accuracy. When analyzed using a point sampling technique and binomial probability theory, several maps, illustrative of those produced for different parts of the country, were found to meet or exceed accuracies of 85 percent. Those maps tested were Tampa, Fla., Portland, Me., Charleston, W. Va., and Greeley, Colo., published at a scale of 1:250,000, and Atlanta, Ga., and Seattle and Tacoma, Wash., published at a scale of 1:100,000. For each map, the values were determined by calculating the ratio of the total number of points correctly interpreted to the total number of points sampled. Six of the seven maps tested have accuracies of 85 percent or better at the 95-percent lower confidence limit. When the sample data for predominant categories (those sampled with a significant number of points) were grouped together for all maps, accuracies of those predominant categories met the 85-percent accuracy criterion, with one exception. One category, Residential, had less than 85-percent accuracy at the 95-percent lower confidence limit. Nearly all residential land sampled was mapped correctly, but some areas of other land uses were mapped incorrectly as Residential.

An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers

USDA-ARS?s Scientific Manuscript database

Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a SNP-based genotyping platform was developed a...

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.)

PubMed Central

2013-01-01

Background Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. Results We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. Conclusions The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs. PMID:24160306

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).

PubMed

Yagi, Masafumi; Yamamoto, Toshiya; Isobe, Sachiko; Hirakawa, Hideki; Tabata, Satoshi; Tanase, Koji; Yamaguchi, Hiroyasu; Onozaki, Takashi

2013-10-26

Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.

The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence from Association Mapping

USDA-ARS?s Scientific Manuscript database

Our previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for ...

A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

PubMed Central

2010-01-01

Background The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank. Results Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome maps), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative. Conclusion A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement. PMID:20105299

Comparing Recent Organizing Templates for Test Content between ACS Exams in General Chemistry and AP Chemistry

ERIC Educational Resources Information Center

Holme, Thomas

2014-01-01

Two different versions of "big ideas" rooted content maps have recently been published for general chemistry. As embodied in the content outline from the College Board, one of these maps is designed to guide curriculum development and testing for advanced placement (AP) chemistry. The Anchoring Concepts Content Map for general chemistry…

Geologic map of the Gbanka Quadrangle, Liberia

USGS Publications Warehouse

Force, E.R.; Dunbar, J.D.N.

1974-01-01

As part of a program undertaken cooperatively by the Liberian Geological Survey (LGS) and the U. S. Geological Survey (USGS), under the sponsorship of the Government of Liberia and the Agency for International Development, U. S. Department of State, Liberia was mapped by geologic and geophysical methods during the period 1965 to 1972. The resulting geologic and geophysical maps are published in ten folios, each covering one quadrangle (see index map). 

MAP Estimators for Piecewise Continuous Inversion

DTIC Science & Technology

2016-08-08

MAP estimators for piecewise continuous inversion M M Dunlop1 and A M Stuart Mathematics Institute, University of Warwick, Coventry, CV4 7AL, UK E...Published 8 August 2016 Abstract We study the inverse problem of estimating a field ua from data comprising a finite set of nonlinear functionals of ua...then natural to study maximum a posterior (MAP) estimators. Recently (Dashti et al 2013 Inverse Problems 29 095017) it has been shown that MAP

Mapping patent classifications: portfolio and statistical analysis, and the comparison of strengths and weaknesses.

PubMed

Leydesdorff, Loet; Kogler, Dieter Franz; Yan, Bowen

2017-01-01

The Cooperative Patent Classifications (CPC) recently developed cooperatively by the European and US Patent Offices provide a new basis for mapping patents and portfolio analysis. CPC replaces International Patent Classifications (IPC) of the World Intellectual Property Organization. In this study, we update our routines previously based on IPC for CPC and use the occasion for rethinking various parameter choices. The new maps are significantly different from the previous ones, although this may not always be obvious on visual inspection. We provide nested maps online and a routine for generating portfolio overlays on the maps; a new tool is provided for "difference maps" between patent portfolios of organizations or firms. This is illustrated by comparing the portfolios of patents granted to two competing firms-Novartis and MSD-in 2016. Furthermore, the data is organized for the purpose of statistical analysis.

Draft Map of Human Proteome Published | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a recently published article in the journal Nature, researchers have developed a draft map of the human proteome.  Striving for the protein equivalent of the Human Genome Project, an international team of researchers has created an initial catalog of the human proteome. In total, using 30 different human tissues, the researchers identified proteins encoded by 17,294 genes, which is approximately 84 percent of all of the genes in the human genome predicted to encode proteins.

A fruit quality gene map of Prunus

PubMed Central

2009-01-01

Background Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance. Results A genetic linkage map of 211 markers was constructed for an intraspecific peach (Prunus persica) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the Prunus reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG. Conclusion The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the genetic architecture of fruit quality traits in Prunus crops. PMID:19995417

LANDSAT-1 data, its use in a soil survey program

NASA Technical Reports Server (NTRS)

Westin, F. C.; Frazee, C. J.

1975-01-01

The following applications of LANDSAT imagery were investigated: assistance in recognizing soil survey boundaries, low intensity soil surveys, and preparation of a base map for publishing thematic soils maps. The following characteristics of LANDSAT imagery were tested as they apply to the recognition of soil boundaries in South Dakota and western Minnesota: synoptic views due to the large areas covered, near-orthography and lack of distortion, flexibility of selecting the proper season, data recording in four parts of the spectrum, and the use of computer compatible tapes. A low intensity soil survey of Pennington County, South Dakota was completed in 1974. Low intensity inexpensive soil surveys can provide the data needed to evaluate agricultural land for the remaining counties until detailed soil surveys are completed. In using LANDSAT imagery as a base map for publishing thematic soil maps, the first step was to prepare a mosaic with 20 LANDSAT scenes from several late spring passes in 1973.

Visual Analysis Based on the Data of Chinese Surveying and Mapping Journals

NASA Astrophysics Data System (ADS)

Li, Jing; Liu, Haiyan; Guo, Wenyue; Yu, Anzhu

2016-06-01

Taking four influential Chinese surveying and mapping journals as the data source, 5863 papers published during the period of 2003-2013 were obtained. Using the method of bibliometrics and visual analysis, summarizing the surveying and mapping papers in the past ten years (2003-2013), research themes, authors, and geographical distribution were analyzed. In the study, the papers of geodesy, cartography and GIS are 59.9%, more than half of all the papers. We also determine that the core author group has 131 authors, mainly of whom are from big cities. 90% of top ten cities on the number of publishing papers are capital cities or municipalities directly under the central government.In conclusion, we found that the research focus was different every year, and the research content was richness, the content of geodesy, cartography and GIS were widely researched, and the development of surveying and mapping is imbalanced in China.

Map Database for Surficial Materials in the Conterminous United States

USGS Publications Warehouse

Soller, David R.; Reheis, Marith C.; Garrity, Christopher P.; Van Sistine, D. R.

2009-01-01

The Earth's bedrock is overlain in many places by a loosely compacted and mostly unconsolidated blanket of sediments in which soils commonly are developed. These sediments generally were eroded from underlying rock, and then were transported and deposited. In places, they exceed 1000 ft (330 m) in thickness. Where the sediment blanket is absent, bedrock is either exposed or has been weathered to produce a residual soil. For the conterminous United States, a map by Soller and Reheis (2004, scale 1:5,000,000; http://pubs.usgs.gov/of/2003/of03-275/) shows these sediments and the weathered, residual material; for ease of discussion, these are referred to as 'surficial materials'. That map was produced as a PDF file, from an Adobe Illustrator-formatted version of the provisional GIS database. The provisional GIS files were further processed without modifying the content of the published map, and are here published.

Mycobacterium avium Subspecies paratuberculosis: Human Exposure through Environmental and Domestic Aerosols

PubMed Central

Rhodes, Glenn; Richardson, Hollian; Hermon-Taylor, John; Weightman, Andrew; Higham, Andrew; Pickup, Roger

2014-01-01

Mycobacterium avium subspecies paratuberculosis (Map) causes Johne’s disease in animals and is significantly associated with Crohn’s disease (CD) in humans. Our previous studies have shown Map to be present in U.K. rivers due to land deposition from chronic livestock infection and runoff driven by rainfall. The epidemiology of CD in Cardiff showed a significant association with the River Taff, in which Map can be detected on a regular basis. We have previously hypothesized that aerosols from the river might influence the epidemiology of CD. In this preliminary study, we detected Map by quantitative PCR in one of five aerosol samples collected above the River Taff. In addition, we examined domestic showers from different regions in the U.K. and detected Map in three out of 30 independent samples. In detecting Map in river aerosols and those from domestic showers, this is the first study to provide evidence that aerosols are an exposure route for Map to humans and may play a role in the epidemiology of CD. PMID:25438013

Is the recall of verbal-spatial information from working memory affected by symptoms of ADHD?

PubMed

Caterino, Linda C; Verdi, Michael P

2012-10-01

OJECTIVE: The Kulhavy model for text learning using organized spatial displays proposes that learning will be increased when participants view visual images prior to related text. In contrast to previous studies, this study also included students who exhibited symptoms of ADHD. Participants were presented with either a map-text or text-map condition. The map-text condition led to a significantly higher performance than the text-map condition, overall. However, students who endorsed more symptoms of inattention and hyperactivity-impulsivity scored more poorly when asked to recall text facts, text features, and map features and were less able to correctly place map features on a reconstructed map than were students who endorsed fewer symptoms. The results of the study support the Kulhavy model for typical students; however, the benefit of viewing a display prior to text was not seen for students with ADHD symptoms, thus supporting previous studies that have demonstrated that ADHD appears to negatively affect operations that occur in working memory.

Water-Level and land-subsidence studies in the Mojave River and Morongo groundwater basins

USGS Publications Warehouse

Stamos, Christina L.; Glockhoff, Carolyn S.; McPherson, Kelly R.; Julich, Raymond J.

2007-01-01

What's New! Water-level data, contours, and meta data for spring 2008 are included in Version 2.0 of SIR 2007-5097 (http://ca.water.usgs.gov/mojave/wl_studies/wl2008.html). All the original data are still available on the web site. Introduction Since 1992, the U.S. Geological Survey (USGS), in cooperation with the Mojave Water Agency (MWA), has constructed a series of regional water-table maps for intermittent years in a continuing effort to monitor groundwater conditions in the Mojave River and Morongo groundwater basins. The previously published data, which were used to construct these maps, can be accessed on the interactive map. The associated reports describing the groundwater conditions for the Mojave River groundwater basin for 1992 (Stamos and Predmore, 1995), the Morongo groundwater basin for 1994 (Trayler and Koczot, 1995), and for both groundwater basins for 1996 (Mendez and Christensen, 1997); for 1998 (Smith and Pimentel, 2000), for 2000 (Smith, 2002), for 2002 (Smith and others, 2004), for 2004 (Stamos and others, 2004), and for 2006 (Stamos and others, 2007) can be accessed using this web site. Spatially detailed maps of interferometric synthetic aperture radar (InSAR) methods were used to characterize land subsidence associated with groundwater-level declines during various intervals of time between 1992 and 1999 in the Mojave River and Morongo groundwater basins (Sneed and others, 2003). Concerns related to the potential for new or renewed land subsidence in the basins resulted in a cooperative study between the MWA and the USGS in 2006. InSAR data were developed to determine the location, extent, and magnitude of vertical land-surface changes in the Mojave River and Morongo groundwater basins for time intervals ranging from about 35 days to 14 months between 1999 and 2000 and between 2003 and 2004. (interactive Google map) The results from many future land-subsidence studies, which are scheduled about every 10 years, will be available on this website. Mapping of water-level contours, water-level change and numerous InSAR images were combined in an interactive map. This interactive map may be customized to your needs and viewed at a scale that is appropriate for the data.

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.).

PubMed

Ma, Yu; Coyne, Clarice J; Grusak, Michael A; Mazourek, Michael; Cheng, Peng; Main, Dorrie; McGee, Rebecca J

2017-02-13

Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seeds requires the development of genome-wide tools. The objectives of this research were to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for levels of boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc in the seed, as well as for seed weight. In this study, 1609 high quality SNPs were found to be polymorphic between 'Kiflica' and 'Aragorn', two parents of an F 6 -derived recombinant inbred line (RIL) population. Mapping 1683 markers including 75 previously published markers and 1608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. Comparative mapping with other legumes demonstrated that the highest level of synteny was observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least one QTL for each of the mineral nutrient traits. In total, 46 seed mineral concentration QTLs, 37 seed mineral content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2.4% to 43.3% of the phenotypic variance. The genome-wide SNPs and the genetic linkage map developed in this study permitted QTL identification for pea seed mineral nutrients that will serve as important resources to enable marker-assisted selection (MAS) for nutritional quality traits in pea breeding programs.

The protein interaction map of bacteriophage lambda

PubMed Central

2011-01-01

Background Bacteriophage lambda is a model phage for most other dsDNA phages and has been studied for over 60 years. Although it is probably the best-characterized phage there are still about 20 poorly understood open reading frames in its 48-kb genome. For a complete understanding we need to know all interactions among its proteins. We have manually curated the lambda literature and compiled a total of 33 interactions that have been found among lambda proteins. We set out to find out how many protein-protein interactions remain to be found in this phage. Results In order to map lambda's interactions, we have cloned 68 out of 73 lambda open reading frames (the "ORFeome") into Gateway vectors and systematically tested all proteins for interactions using exhaustive array-based yeast two-hybrid screens. These screens identified 97 interactions. We found 16 out of 30 previously published interactions (53%). We have also found at least 18 new plausible interactions among functionally related proteins. All previously found and new interactions are combined into structural and network models of phage lambda. Conclusions Phage lambda serves as a benchmark for future studies of protein interactions among phage, viruses in general, or large protein assemblies. We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins. PMID:21943085

Preferred reporting items for studies mapping onto preference-based outcome measures: The MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-08-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. The primary audiences for the MAPS statement are researchers reporting mapping studies, the funders of the research, and peer reviewers and editors involved in assessing mapping studies for publication.A de novo list of 29 candidate reporting items and accompanying explanations was created by a working group comprised of six health economists and one Delphi methodologist. Following a two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, a final set of 23 items deemed essential for transparent reporting, and accompanying explanations, was developed. The items are contained in a user friendly 23 item checklist. They are presented numerically and categorised within six sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document.It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by eight health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in five years' time.This statement was published jointly in Applied Health Economics and Health Policy, Health and Quality of Life Outcomes, International Journal of Technology Assessment in Health Care, Journal of Medical Economics, Medical Decision Making, PharmacoEconomics, and Quality of Life Research.

A spatial database of bedding attitudes to accompany Geologic Map of Boulder-Fort Collins-Greeley Area, Colorado

USGS Publications Warehouse

Colton, Roger B.; Brandt, Theodore R.; Moore, David W.; Murray, Kyle E.

2003-01-01

This digital map shows bedding attitude data displayed over the geographic extent of rock stratigraphic units (formations) as compiled by Colton in 1976 (U.S.Geological Survey Map I-855-G) under the Front Range Urban Corridor Geology Program. Colton used his own mapping and published geologic maps having varied map unit schemes to compile one map with a uniform classification of geologic units. The resulting published color paper map was intended for planning for use of land in the Front Range Urban Corridor. In 1997-1999, under the USGS Front Range Infrastructure Resources Project, Colton's map was digitized to provide data at 1:100,000 scale to address urban growth issues(see cross-reference). In general, the west part of the map shows a variety of Precambrian igneous and metamorphic rocks, major faults and brecciated zones along an eastern strip (5-20 km wide) of the Front Range. The eastern and central part of the map (Colorado Piedmont) depicts a mantle of Quaternary unconsolidated deposits and interspersed Cretaceous or Tertiary-Cretaceous sedimentary rock outcrops. The Quaternary mantle is comprised of eolian deposits (quartz sand and silt), alluvium (gravel, sand, and silt of variable composition), colluvium, and few landslides. At the mountain front, north-trending, dipping Paleozoic and Mesozoic sandstone and shale formations (and sparse limestone) form hogbacks, intervening valleys, and in range-front folds, anticlines, and fault blocks. Localized dikes and sills of Tertiary rhyodacite and basalt intrude rocks near the range front, mostly in the Boulder area.

Planetary Geologic Mapping Handbook - 2009

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A.; Hare, T. M.

2009-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces (e.g., Varnes, 1974). Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962 (Hackman, 1962). Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by the USGS now are primarily digital products using geographic information system (GIS) software and file formats. GIS mapping tools permit easy spatial comparison, generation, importation, manipulation, and analysis of multiple raster image, gridded, and vector data sets. GIS software has also permitted the development of project-specific tools and the sharing of geospatial products among researchers. GIS approaches are now being used in planetary geologic mapping as well (e.g., Hare and others, 2009). Guidelines or handbooks on techniques in planetary geologic mapping have been developed periodically (e.g., Wilhelms, 1972, 1990; Tanaka and others, 1994). As records of the heritage of mapping methods and data, these remain extremely useful guides. However, many of the fundamental aspects of earlier mapping handbooks have evolved significantly, and a comprehensive review of currently accepted mapping methodologies is now warranted. As documented in this handbook, such a review incorporates additional guidelines developed in recent years for planetary geologic mapping by the NASA Planetary Geology and Geophysics (PGG) Program s Planetary Cartography and Geologic Mapping Working Group s (PCGMWG) Geologic Mapping Subcommittee (GEMS) on the selection and use of map bases as well as map preparation, review, publication, and distribution. In light of the current boom in planetary exploration and the ongoing rapid evolution of available data for planetary mapping, this handbook is especially timely.

Studies of Xenopus laevis mitochondrial DNA: D-loop mapping and characterization of DNA-binding proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cairns, S.S.

1987-01-01

In X. laevis oocytes, mitochondrial DNA accumulates to 10/sup 5/ times the somatic cell complement, and is characterized by a high frequency of a triple-stranded displacement hoop structure at the origin of replication. To map the termini of the single strands, it was necessary to correct the nucleotide sequence of the D-loop region. The revised sequence of 2458 nucleotides contains 54 discrepancies in comparison to a previously published sequence. Radiolabeling of the nascent strands of the D-loop structure either at the 5' end or at the 3' end identifies a major species with a length of 1670 nucleotides. Cleavage ofmore » the 5' labeled strands reveals two families of ends located near several matches to an element, designated CSB-1, that is conserved in this location in several vertebrate genomes. Cleavage of 3' labeled strands produced one fragment. The unique 3' end maps to about 15 nucleotides preceding the tRNA/sup Pro/ gene. A search for proteins which may bind to mtDNA in this region to regulate nucleic acid synthesis has identified three activities in lysates of X. laevis mitochondria. The DNA-binding proteins were assayed by monitoring their ability to retard the migration of labeled double- or single-stranded DNA fragments in polyacrylamide gels. The DNA binding preference was determined by competition with an excess of either ds- or ssDNA.« less

Locations of the ets subfamily members net, elk1, and sap1 (ELK3, ELK1, and ELK4) on three homologous regions of the mouse and human genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giovane, A.; Sobieszczuk, P.; Mignon, C.

1995-10-10

Net, Elk1, and Sap1 are related members of the Ets oncoprotein family. We show by in situ hybridization on banded chromosomes with specific cDNA probes that their map positions on mouse and human chromosomes (respectively) are net, 10C-D1 and 12q22-q23 (now called ELK3), sap1, 1E3-G and 1q32 (ELK4), and elk1, XA1-A3 and Xp11.2-p11.1 (ELK1), as well as a second locus 14q32 (ELK2) unique to the human genome. The results for the mouse net, sap1, and elk1 and human ELK3 genes are new. The human elk1 mapping confirms a previous study. The human ELK4 localization agrees with data published during themore » preparation of the manuscript. Human ELK3 colocalizes with sap2, and we confirm that they are identical. These results firmly establish for the first time that Net, Elk1, and Sap1 are distinct gene products with different chromosomal localizations in both the mouse and the human genomes. Net, Elk1, and Sap1 are conserved and map to homologous regions of the mouse and human chromosomes. 19 refs., 1 fig., 1 tab.« less

A new method for automated high-dimensional lesion segmentation evaluated in vascular injury and applied to the human occipital lobe.

PubMed

Mah, Yee-Haur; Jager, Rolf; Kennard, Christopher; Husain, Masud; Nachev, Parashkev

2014-07-01

Making robust inferences about the functional neuroanatomy of the brain is critically dependent on experimental techniques that examine the consequences of focal loss of brain function. Unfortunately, the use of the most comprehensive such technique-lesion-function mapping-is complicated by the need for time-consuming and subjective manual delineation of the lesions, greatly limiting the practicability of the approach. Here we exploit a recently-described general measure of statistical anomaly, zeta, to devise a fully-automated, high-dimensional algorithm for identifying the parameters of lesions within a brain image given a reference set of normal brain images. We proceed to evaluate such an algorithm in the context of diffusion-weighted imaging of the commonest type of lesion used in neuroanatomical research: ischaemic damage. Summary performance metrics exceed those previously published for diffusion-weighted imaging and approach the current gold standard-manual segmentation-sufficiently closely for fully-automated lesion-mapping studies to become a possibility. We apply the new method to 435 unselected images of patients with ischaemic stroke to derive a probabilistic map of the pattern of damage in lesions involving the occipital lobe, demonstrating the variation of anatomical resolvability of occipital areas so as to guide future lesion-function studies of the region. Copyright © 2012 Elsevier Ltd. All rights reserved.

High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

PubMed Central

Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

2013-01-01

Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

Improved Digitization of Lunar Mare Ridges with LROC Derived Products

NASA Astrophysics Data System (ADS)

Crowell, J. M.; Robinson, M. S.; Watters, T. R.; Bowman-Cisneros, E.; Enns, A. C.; Lawrence, S.

2011-12-01

Lunar wrinkle ridges (mare ridges) are positive-relief structures formed from compressional stress in basin-filling flood basalt deposits [1]. Previous workers have measured wrinkle ridge orientations and lengths to investigate their spatial distribution and infer basin-localized stress fields [2,3]. Although these plots include the most prominent mare ridges and their general trends, they may not have fully captured all of the ridges, particularly the smaller-scale ridges. Using Lunar Reconnaissance Orbiter Wide Angle Camera (WAC) global mosaics and derived topography (100m pixel scale) [4], we systematically remapped wrinkle ridges in Mare Serenitatis. By comparing two WAC mosaics with different lighting geometry, and shaded relief maps made from a WAC digital elevation model (DEM) [5], we observed that some ridge segments and some smaller ridges are not visible in previous structure maps [2,3]. In the past, mapping efforts were limited by a fixed Sun direction [6,7]. For systematic mapping we created three shaded relief maps from the WAC DEM with solar azimuth angles of 0°, 45°, and 90°, and a fourth map was created by combining the three shaded reliefs into one, using a simple averaging scheme. Along with the original WAC mosaic and the WAC DEM, these four datasets were imported into ArcGIS, and the mare ridges of Imbrium, Serenitatis, and Tranquillitatis were digitized from each of the six maps. Since the mare ridges are often divided into many ridge segments [8], each major component was digitized separately, as opposed to the ridge as a whole. This strategy enhanced our ability to analyze the lengths, orientations, and abundances of these ridges. After the initial mapping was completed, the six products were viewed together to identify and resolve discrepancies in order to produce a final wrinkle ridge map. Comparing this new mare ridge map with past lunar tectonic maps, we found that many mare ridges were not recorded in the previous works. It was noted in some cases, the lengths and orientations of previously digitized ridges were different than those of the ridges digitized in this study. This method of multi-map digitizing allows for a greater accuracy in spatial characterization of mare ridges than previous methods. We intend to map mare ridges on a global scale, creating a more comprehensive ridge map due to higher resolution. References Cited: [1] Schultz P.H. (1976) Moon Morphology, 308. [2] Wilhelms D.E. (1987) USGS Prof. Paper 1348, 5A-B. [3] Carr, M.H. (1966) USGS Geologic Atlas of the Moon, I-498. [4] Robinson M.S. (2010) Space Sci. Rev., 150:82. [5] Scholten F. et al. (2011) LPSC XLII, 2046. [6] Fielder G. and Kiang T. (1962) The Observatory: No. 926, 8. [7] Watters T.R. and Konopliv A.S. (2001) Planetary and Space Sci. 49. 743-748. [8] Aubele J.C. (1988) LPSC XIX, 19.

Magnetic field topology of τ Scorpii. The uniqueness problem of Stokes V ZDI inversions

NASA Astrophysics Data System (ADS)

Kochukhov, O.; Wade, G. A.

2016-02-01

Context. The early B-type star τ Sco exhibits an unusually complex, relatively weak surface magnetic field. Its topology was previously studied with the Zeeman Doppler imaging (ZDI) modelling of high-resolution circular polarisation (Stokes V) observations. Aims: Here we assess the robustness of the Stokes V ZDI reconstruction of the magnetic field geometry of τ Sco and explore the consequences of using different parameterisations of the surface magnetic maps. Methods: This analysis is based on the archival ESPaDOnS high-resolution Stokes V observations and employs an independent ZDI magnetic inversion code. Results: We succeeded in reproducing previously published magnetic field maps of τ Sco using both general harmonic expansion and a direct, pixel-based representation of the magnetic field. These maps suggest that the field topology of τ Sco is comprised of comparable contributions of the poloidal and toroidal magnetic components. At the same time, we also found that available Stokes V observations can be successfully fitted with restricted harmonic expansions, by either neglecting the toroidal field altogether, or linking the radial and horizontal components of the poloidal field as required by the widely used potential field extrapolation technique. These alternative modelling approaches lead to a stronger and topologically more complex surface field structure. The field distributions, which were recovered with different ZDI options, differ significantly and yield indistinguishable Stokes V profiles but different linear polarisation (Stokes Q and U) signatures. Conclusions: Our investigation underscores the well-known problem of non-uniqueness of the Stokes V ZDI inversions. For the magnetic stars with properties similar to τ Sco (relatively complex field, slow rotation) the outcome of magnetic reconstruction strongly depends on the adopted field parameterisation, rendering photospheric magnetic mapping and determination of the extended magnetospheric field topology ambiguous. Stokes Q and U spectropolarimetric observations represent the only way of breaking the degeneracy of surface magnetic field models. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

Mapping the pharmacological modulation of brain oxygen metabolism: The effects of caffeine on absolute CMRO2 measured using dual calibrated fMRI.

PubMed

Merola, Alberto; Germuska, Michael A; Warnert, Esther Ah; Richmond, Lewys; Helme, Daniel; Khot, Sharmila; Murphy, Kevin; Rogers, Peter J; Hall, Judith E; Wise, Richard G

2017-07-15

This study aims to map the acute effects of caffeine ingestion on grey matter oxygen metabolism and haemodynamics with a novel MRI method. Sixteen healthy caffeine consumers (8 males, age=24.7±5.1) were recruited to this randomised, double-blind, placebo-controlled study. Each participant was scanned on two days before and after the delivery of an oral caffeine (250mg) or placebo capsule. Our measurements were obtained with a newly proposed estimation approach applied to data from a dual calibration fMRI experiment that uses hypercapnia and hyperoxia to modulate brain blood flow and oxygenation. Estimates were based on a forward model that describes analytically the contributions of cerebral blood flow (CBF) and of the measured end-tidal partial pressures of CO 2 and O 2 to the acquired dual-echo GRE signal. The method allows the estimation of grey matter maps of: oxygen extraction fraction (OEF), CBF, CBF-related cerebrovascular reactivity (CVR) and cerebral metabolic rate of oxygen consumption (CMRO 2 ). Other estimates from a multi inversion time ASL acquisition (mTI-ASL), salivary samples of the caffeine concentration and behavioural measurements are also reported. We observed significant differences between caffeine and placebo on average across grey matter, with OEF showing an increase of 15.6% (SEM±4.9%, p<0.05) with caffeine, while CBF and CMRO 2 showed differences of -30.4% (SEM±1.6%, p<0.01) and -18.6% (SEM±2.9%, p<0.01) respectively with caffeine administration. The reduction in oxygen metabolism found is somehow unexpected, but consistent with a hypothesis of decreased energetic demand, supported by previous electrophysiological studies reporting reductions in spectral power with EEG. Moreover the maps of the physiological parameters estimated illustrate the spatial distribution of changes across grey matter enabling us to localise the effects of caffeine with voxel-wise resolution. CBF changes were widespread as reported by previous findings, while changes in OEF were found to be more restricted, leading to unprecedented mapping of significant CMRO 2 reductions mainly in frontal gyrus, parietal and occipital lobes. In conclusion, we propose the estimation framework based on our novel forward model with a dual calibrated fMRI experiment as a viable MRI method to map the effects of drugs on brain oxygen metabolism and haemodynamics with voxel-wise resolution. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Streamflow distribution maps for the Cannon River drainage basin, southeast Minnesota, and the St. Louis River drainage basin, northeast Minnesota

USGS Publications Warehouse

Smith, Erik A.; Sanocki, Chris A.; Lorenz, David L.; Jacobsen, Katrin E.

2017-12-27

Streamflow distribution maps for the Cannon River and St. Louis River drainage basins were developed by the U.S. Geological Survey, in cooperation with the Legislative-Citizen Commission on Minnesota Resources, to illustrate relative and cumulative streamflow distributions. The Cannon River was selected to provide baseline data to assess the effects of potential surficial sand mining, and the St. Louis River was selected to determine the effects of ongoing Mesabi Iron Range mining. Each drainage basin (Cannon, St. Louis) was subdivided into nested drainage basins: the Cannon River was subdivided into 152 nested drainage basins, and the St. Louis River was subdivided into 353 nested drainage basins. For each smaller drainage basin, the estimated volumes of groundwater discharge (as base flow) and surface runoff flowing into all surface-water features were displayed under the following conditions: (1) extreme low-flow conditions, comparable to an exceedance-probability quantile of 0.95; (2) low-flow conditions, comparable to an exceedance-probability quantile of 0.90; (3) a median condition, comparable to an exceedance-probability quantile of 0.50; and (4) a high-flow condition, comparable to an exceedance-probability quantile of 0.02.Streamflow distribution maps were developed using flow-duration curve exceedance-probability quantiles in conjunction with Soil-Water-Balance model outputs; both the flow-duration curve and Soil-Water-Balance models were built upon previously published U.S. Geological Survey reports. The selected streamflow distribution maps provide a proactive water management tool for State cooperators by illustrating flow rates during a range of hydraulic conditions. Furthermore, after the nested drainage basins are highlighted in terms of surface-water flows, the streamflows can be evaluated in the context of meeting specific ecological flows under different flow regimes and potentially assist with decisions regarding groundwater and surface-water appropriations. Presented streamflow distribution maps are foundational work intended to support the development of additional streamflow distribution maps that include statistical constraints on the selected flow conditions.

Paving the way for the use of the SDQ in economic evaluations of school-based population health interventions: an empirical analysis of the external validity of SDQ mapping algorithms to the CHU9D in an educational setting.

PubMed

Boyer, Nicole R S; Miller, Sarah; Connolly, Paul; McIntosh, Emma

2016-04-01

The Strengths and Difficulties Questionnaire (SDQ) is a behavioural screening tool for children. The SDQ is increasingly used as the primary outcome measure in population health interventions involving children, but it is not preference based; therefore, its role in allocative economic evaluation is limited. The Child Health Utility 9D (CHU9D) is a generic preference-based health-related quality of-life measure. This study investigates the applicability of the SDQ outcome measure for use in economic evaluations and examines its relationship with the CHU9D by testing previously published mapping algorithms. The aim of the paper is to explore the feasibility of using the SDQ within economic evaluations of school-based population health interventions. Data were available from children participating in a cluster randomised controlled trial of the school-based roots of empathy programme in Northern Ireland. Utility was calculated using the original and alternative CHU9D tariffs along with two SDQ mapping algorithms. t tests were performed for pairwise differences in utility values from the preference-based tariffs and mapping algorithms. Mean (standard deviation) SDQ total difficulties and prosocial scores were 12 (3.2) and 8.3 (2.1). Utility values obtained from the original tariff, alternative tariff, and mapping algorithms using five and three SDQ subscales were 0.84 (0.11), 0.80 (0.13), 0.84 (0.05), and 0.83 (0.04), respectively. Each method for calculating utility produced statistically significantly different values except the original tariff and five SDQ subscale algorithm. Initial evidence suggests the SDQ and CHU9D are related in some of their measurement properties. The mapping algorithm using five SDQ subscales was found to be optimal in predicting mean child health utility. Future research valuing changes in the SDQ scores would contribute to this research.

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

PubMed Central

2014-01-01

Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. Results The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. Conclusion The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps. PMID:24581289

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map.

PubMed

van Dijk, Thijs; Pagliarani, Giulia; Pikunova, Anna; Noordijk, Yolanda; Yilmaz-Temel, Hulya; Meulenbroek, Bert; Visser, Richard G F; van de Weg, Eric

2014-03-01

Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.

Perspectives on the methods of a large systematic mapping of maternal health interventions.

PubMed

Chersich, Matthew; Becerril-Montekio, Victor; Becerra-Posada, Francisco; Dumbaugh, Mari; Kavanagh, Josephine; Blaauw, Duane; Thwala, Siphiwe; Kern, Elinor; Penn-Kekana, Loveday; Vargas, Emily; Mlotshwa, Langelihle; Dhana, Ashar; Mannava, Priya; Portela, Anayda; Tristan, Mario; Rees, Helen; Bijlmakers, Leon

2016-08-25

Mapping studies describe a broad body of literature, and differ from classical systematic reviews, which assess more narrowly-defined questions and evaluate the quality of the studies included in the review. While the steps involved in mapping studies have been described previously, a detailed qualitative account of the methodology could inform the design of future mapping studies. Describe the perspectives of a large research team on the methods used and collaborative experiences in a study that mapped the literature published on maternal health interventions in low- and middle-income countries (2292 full text articles included, after screening 35,048 titles and abstracts in duplicate). Fifteen members of the mapping team, drawn from eight countries, provided their experiences and perspectives of the study in response to a list of questions and probes. The responses were collated and analysed thematically following a grounded theory approach. The objectives of the mapping evolved over time, posing difficulties in ensuring a uniform understanding of the purpose of the mapping among the team members. Ambiguity of some study variables and modifications in data extraction codes were the main threats to the quality of data extraction. The desire for obtaining detailed information on a few topics needed to be weighed against the benefits of collecting more superficial data on a wider range of topics. Team members acquired skills in systematic review methodology and software, and a broad knowledge of maternal health literature. Participation in analysis and dissemination was lower than during the screening of articles for eligibility and data coding. Though all respondents believed the workload involved was high, study outputs were viewed as novel and important contributions to evidence. Overall, most believed there was a favourable balance between the amount of work done and the project's outputs. A large mapping of literature is feasible with a committed team aiming to build their research capacity, and with a limited, simplified set of data extraction codes. In the team's view, the balance between the time spent on the review, and the outputs and skills acquired was favourable. Assessments of the value of a mapping need, however, to take into account the limitations inherent in such exercises, especially the exclusion of grey literature and of assessments of the quality of the studies identified.

Sharing our data—An overview of current (2016) USGS policies and practices for publishing data on ScienceBase and an example interactive mapping application

USGS Publications Warehouse

Chase, Katherine J.; Bock, Andrew R.; Sando, Roy

2017-01-05

This report provides an overview of current (2016) U.S. Geological Survey policies and practices related to publishing data on ScienceBase, and an example interactive mapping application to display those data. ScienceBase is an integrated data sharing platform managed by the U.S. Geological Survey. This report describes resources that U.S. Geological Survey Scientists can use for writing data management plans, formatting data, and creating metadata, as well as for data and metadata review, uploading data and metadata to ScienceBase, and sharing metadata through the U.S. Geological Survey Science Data Catalog. Because data publishing policies and practices are evolving, scientists should consult the resources cited in this paper for definitive policy information.An example is provided where, using the content of a published ScienceBase data release that is associated with an interpretive product, a simple user interface is constructed to demonstrate how the open source capabilities of the R programming language and environment can interact with the properties and objects of the ScienceBase item and be used to generate interactive maps.

Updated symbol catalogue for geologic and geomorphologic mapping in Planetary Scinces

NASA Astrophysics Data System (ADS)

Nass, Andrea; Fortezzo, Corey; Skinner, James, Jr.; Hunter, Marc; Hare, Trent

2017-04-01

Maps are one of the most powerful communication tools for spatial data. This is true for terrestrial data, as well as the many types of planetary data. Geologic and/or geomorphologic maps of planetary surfaces, in particular those of the Moon, Mars, and Venus, are standardized products and often prepared as a part of hypothesis-driven science investigations. The NASA-funded Planetary Geologic Mapping program, coordinated by the USGS Astrogeology Science Center (ASC), produces high-quality, standardized, and refereed geologic maps and digital databases of planetary bodies. In this context, 242 geologic, geomorphologic, and thematic map sheets and map series have been published since the 1962. However, outside of this program, numerous non-USGS published maps are created as result of scientific investigations and published, e.g. as figures or supplemental materials within a peer-reviewed journal article. Due to the complexity of planetary surfaces, diversity between different planet surfaces, and the varied resolution of the data, geomorphologic and geologic mapping is a challenging task. Because of these limiting conditions, the mapping process is a highly interpretative work and is mostly limited to remotely sensed satellite data - with a few expetions from rover data. Uniform and an unambiguous data are fundamental to make quality observations that lead to unbiased and supported interpretations, especially when there is no current groundtruthing. To allow for correlation between different map products (digital or analog), the most commonly used spatial objects are predefined cartographic symbols. The Federal Geographic Data Committee (FGDC) Digital Cartographic Standard for Geologic Map Symbolization (DCSGMS) defines the most commonly used symbols, colors, and hatch patterns in one comprehensive document. Chapter 25 of the DCSGMS defines the Planetary Geology Features based on the symbols defined in the Venus Mapper's Handbook. After reviewing the 242 planetary geological maps, we propose to 1) review standardized symbols for planetary maps, and 2) recommend an updated symbol collection for adoption by the planetary mapping community. Within these points, the focus is on the changing of symbology with respect to time and how it effects communication within and between the maps. Two key questions to address are 1) does chapter 25 provides enough variability within the subcategories (e.g., faults) to represent the data within the maps? 2) How recommendations to the mapping community and their steering committees could be delivered to enhance a map's communicability, and convey information succinctly but thoroughly. For determining the most representative symbol collection of existing maps to support future map results (within or outside of USGS mapping program) we defined a stepwise task list: 1) Statistical review of existing symbol sets and collections, 2) Establish a representative symbol set for planetary mapping, 3) Update cartographic symbols, 4) Implementation into GIS-based mapping software (this implementation will mimic the 2010 application of the planetary symbol set into ArcGIS (more information https://planetarymapping.wr.usgs.gov/Project). 6) Platform to provide the symbol set to the mapping community. This project was initiated within an ongoing cooperation work between the USGS ASC and the German Aerospace Center (DLR), Dept. of Planetary Geology.

Seismic hazard assessment of the cultural heritage sites: A case study in Cappadocia (Turkey)

NASA Astrophysics Data System (ADS)

Seyrek, Evren; Orhan, Ahmet; Dinçer, İsmail

2014-05-01

Turkey is one of the most seismically active regions in the world. Major earthquakes with the potential of threatening life and property occur frequently here. In the last decade, over 50,000 residents lost their lives, commonly as a result of building failures in seismic events. The Cappadocia region is one of the most important touristic sites in Turkey. At the same time, the region has been included to the Word Heritage List by UNESCO at 1985 due to its natural, historical and cultural values. The region is undesirably affected by several environmental conditions, which are subjected in many previous studies. But, there are limited studies about the seismic evaluation of the region. Some of the important historical and cultural heritage sites are: Goreme Open Air Museum, Uchisar Castle, Ortahisar Castle, Derinkuyu Underground City and Ihlara Valley. According to seismic hazard zonation map published by the Ministry of Reconstruction and Settlement these heritage sites fall in Zone III, Zone IV and Zone V. This map show peak ground acceleration or 10 percent probability of exceedance in 50 years for bedrock. In this connection, seismic hazard assessment of these heritage sites has to be evaluated. In this study, seismic hazard calculations are performed both deterministic and probabilistic approaches with local site conditions. A catalog of historical and instrumental earthquakes is prepared and used in this study. The seismic sources have been identified for seismic hazard assessment based on geological, seismological and geophysical information. Peak Ground Acceleration (PGA) at bed rock level is calculated for different seismic sources using available attenuation relationship formula applicable to Turkey. The result of the present study reveals that the seismic hazard at these sites is closely matching with the Seismic Zonation map published by the Ministry of Reconstruction and Settlement. Keywords: Seismic Hazard Assessment, Probabilistic Approach, Deterministic Approach, Historical Heritage, Cappadocia.

Database for the geologic map of upper Eocene to Holocene volcanic and related rocks in the Cascade Range, Washington

USGS Publications Warehouse

Barron, Andrew D.; Ramsey, David W.; Smith, James G.

2014-01-01

This digital database contains information used to produce the geologic map published as Sheet 1 in U.S. Geological Survey Miscellaneous Investigations Series Map I-2005. (Sheet 2 of Map I-2005 shows sources of geologic data used in the compilation and is available separately). Sheet 1 of Map I-2005 shows the distribution and relations of volcanic and related rock units in the Cascade Range of Washington at a scale of 1:500,000. This digital release is produced from stable materials originally compiled at 1:250,000 scale that were used to publish Sheet 1. The database therefore contains more detailed geologic information than is portrayed on Sheet 1. This is most noticeable in the database as expanded polygons of surficial units and the presence of additional strands of concealed faults. No stable compilation materials exist for Sheet 1 at 1:500,000 scale. The main component of this digital release is a spatial database prepared using geographic information systems (GIS) applications. This release also contains links to files to view or print the map sheet, main report text, and accompanying mapping reference sheet from Map I-2005. For more information on volcanoes in the Cascade Range in Washington, Oregon, or California, please refer to the U.S. Geological Survey Volcano Hazards Program website.

Database for the Geologic Map of Upper Eocene to Holocene Volcanic and Related Rocks of the Cascade Range, Oregon

USGS Publications Warehouse

Nimz, Kathryn; Ramsey, David W.; Sherrod, David R.; Smith, James G.

2008-01-01

Since 1979, Earth scientists of the Geothermal Research Program of the U.S. Geological Survey have carried out multidisciplinary research in the Cascade Range. The goal of this research is to understand the geology, tectonics, and hydrology of the Cascades in order to characterize and quantify geothermal resource potential. A major goal of the program is compilation of a comprehensive geologic map of the entire Cascade Range that incorporates modern field studies and that has a unified and internally consistent explanation. This map is one of three in a series that shows Cascade Range geology by fitting published and unpublished mapping into a province-wide scheme of rock units distinguished by composition and age; map sheets of the Cascade Range in Washington (Smith, 1993) and California will complete the series. The complete series forms a guide to exploration and evaluation of the geothermal resources of the Cascade Range and will be useful for studies of volcano hazards, volcanology, and tectonics. This digital release contains all the information used to produce the geologic map published as U.S. Geological Survey Geologic Investigations Series I-2569 (Sherrod and Smith, 2000). The main component of this digital release is a geologic map database prepared using ArcInfo GIS. This release also contains files to view or print the geologic map and accompanying descriptive pamphlet from I-2569.

An Enhanced Linkage Map of the Sheep Genome Comprising More Than 1000 Loci

PubMed Central

Maddox, Jillian F.; Davies, Kizanne P.; Crawford, Allan M.; Hulme, Dennis J.; Vaiman, Daniel; Cribiu, Edmond P.; Freking, Bradley A.; Beh, Ken J.; Cockett, Noelle E.; Kang, Nina; Riffkin, Christopher D.; Drinkwater, Roger; Moore, Stephen S.; Dodds, Ken G.; Lumsden, Joanne M.; van Stijn, Tracey C.; Phua, Sin H.; Adelson, David L.; Burkin, Heather R.; Broom, Judith E.; Buitkamp, Johannes; Cambridge, Lisa; Cushwa, William T.; Gerard, Emily; Galloway, Susan M.; Harrison, Blair; Hawken, Rachel J.; Hiendleder, Stefan; Henry, Hannah M.; Medrano, Juan F.; Paterson, Korena A.; Schibler, Laurent; Stone, Roger T.; van Hest, Beryl

2001-01-01

A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) ≥ 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of >20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of >1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community. PMID:11435411

Integrated terrain mapping with digital Landsat images in Queensland, Australia

USGS Publications Warehouse

Robinove, Charles Joseph

1979-01-01

Mapping with Landsat images usually is done by selecting single types of features, such as soils, vegetation, or rocks, and creating visually interpreted or digitally classified maps of each feature. Individual maps can then be overlaid on or combined with other maps to characterize the terrain. Integrated terrain mapping combines several terrain features into each map unit which, in many cases, is more directly related to uses of the land and to methods of land management than the single features alone. Terrain brightness, as measured by the multispectral scanners in Landsat 1 and 2, represents an integration of reflectance from the terrain features within the scanner's instantaneous field of view and is therefore more correlatable with integrated terrain units than with differentiated ones, such as rocks, soils, and vegetation. A test of the feasibilty of the technique of mapping integrated terrain units was conducted in a part of southwestern Queensland, Australia, in cooperation with scientists of the Queensland Department of Primary Industries. The primary purpose was to test the use of digital classification techniques to create a 'land systems map' usable for grazing land management. A recently published map of 'land systems' in the area (made by aerial photograph interpretation and ground surveys), which are integrated terrain units composed of vegetation, soil, topography, and geomorphic features, was used as a basis for comparison with digitally classified Landsat multispectral images. The land systems, in turn, each have a specific grazing capacity for cattle (expressed in beasts per km 2 ) which is estimated following analysis of both research results and property carrying capacities. Landsat images, in computer-compatible tape form, were first contrast-stretched to increase their visual interpretability, and digitally classified by the parallelepiped method into distinct spectral classes to determine their correspondence to the land systems classes and to areally smaller, but readily recognizable, 'land units.' Many land systems appeared as distinct spectral classes or as acceptably homogeneous combinations of several spectral classes. The digitally classified map corresponded to the general geographic patterns of many of the land systems. Statistical correlation of the digitally classified map and the published map was not possible because the published map showed only land systems whereas the digitally classified map showed some land units as well as systems. The general correspondence of spectral classes to the integrated terrain units means that the digital mapping of the units may precede fieldwork and act as a guide to field sampling and detailed terrain unit description as well as measuring of the location, area, and extent of each unit. Extension of the Landsat mapping and classification technique to other arid and semi-arid regions of the world may be feasible.

Changing Roles in Information Distribution. 1994 NFAIS Report Series, 1.

ERIC Educational Resources Information Center

Cunningham, Ann Marie, Ed.; Wicks, Wendy, Ed.

This report tracks the evolution of information through the eyes of the five traditional "players"--author, primary publisher, secondary publisher, distributor, and information consumer. It maps the trajectory of publishing through the media landscape--from print to online to CD-ROM to networks. Representatives from each constituency…

Analysis of improved government geological map information for mineral exploration: Incorporating efficiency, productivity, effectiveness, and risk considerations

USGS Publications Warehouse

Bernknopf, R.L.; Wein, A.M.; St-Onge, M. R.; Lucas, S.B.

2007-01-01

This bulletin/professional paper focuses on the value of geoscientific information and knowledge, as provided in published government bedrock geological maps, to the mineral exploration sector. An economic model is developed that uses an attribute- ranking approach to convert geological maps into domains of mineral favourability. Information about known deposits in these (or analogous) favourability domains allow the calculation of exploration search statistics that provide input into measures of exploration efficiency, productivity, effectiveness, risk, and cost stemming from the use of the published geological maps. Two case studies, the Flin Flon Belt (Manitoba and Saskatchewan) and the south Baffin Island area (Nunavut), demonstrate that updated, finer resolution maps can be used to identify more exploration campaign options, and campaigns thats are more efficient, more effective, and less risky than old, coarser resolution maps when used as a guide for mineral exploration. The Flin Flon Belt study illustrates that an updated, coarser resolution bedrock map enables improved mineral exploration efficiency, productivity, and effectiveness by locating 60% more targets and supporting an exploration campaign that is 44% more efficient. Refining the map resolution provides an additional 17% reduction in search effort across all favourable domains and a 55% reduction in search effort in the most favourable domain. The south Baffin Island case study projects a 40% increase in expected targets and a 27% reduction in search effort when the updated, finer resolution map is used in lieu of the old, coarser resolution map. On southern Baffin Island, the economic value of the up dated map ranges from CAN$2.28 million to CAN$15.21 million, which can be compared to the CAN$1.86 million that it cost to produce the map (a multiplier effect of up to eight).

Research notes : rainfall maps for the 21st century.

DOT National Transportation Integrated Search

2007-12-01

The report and included maps represent an update of the information contained in the precipitation-frequency atlas, published by the National Weather Service in 1973 (NOAA Atlas 2). Data collection for the National Weather Service (NWS) study ended i...

Lithological mapping of Kanjamalai hill using hyperspectral remote sensing tools in Salem district, Tamil Nadu, India

NASA Astrophysics Data System (ADS)

Arulbalaji, Palanisamy; Balasubramanian, Gurugnanam

2017-07-01

This study uses advanced spaceborne thermal emission and reflection radiometer (ASTER) hyperspectral remote sensing techniques to discriminate rock types composing Kanjamalai hill located in the Salem district of Tamil Nadu, India. Kanjamalai hill is of particular interest because it contains economically viable iron ore deposits. ASTER hyperspectral data were subjected to principal component analysis (PCA), independent component analysis (ICA), and minimum noise fraction (MNF) to improve identification of lithologies remotely and to compare these digital data results with published geologic maps. Hyperspectral remote sensing analysis indicates that PCA (R∶G∶B=2∶1∶3), MNF (R∶G∶B=3∶2∶1), and ICA (R∶G∶B=1∶3∶2) provide the best band combination for effective discrimination of lithological rock types composing Kanjamalai hill. The remote sensing-derived lithological map compares favorably with a published geological map from Geological Survey of India and has been verified with ground truth field investigations. Therefore, ASTER data-based lithological mapping provides fast, cost-effective, and accurate geologic data useful for lithological discrimination and identification of ore deposits.

Retrospective Conversion of Solar Data Printed in "Synoptic Maps of the Solar Chromosphere": A Scientific and Librarianship Project

NASA Astrophysics Data System (ADS)

Laurenceau, A.; Aboudarham, J.; Renié, C.

2015-04-01

Between 1928 and 2003, the Observatoire de Paris published solar activity maps and their corresponding data tables, first in the Annals of the Meudon Observatory, then in the Synoptic Maps of the Solar Chromosphere. These maps represent the main solar structures in a single view and spread out on a complete Carrington rotation as well as tables of associated data, containing various information on these structures such as positions, length, morphological characteristics, and behavior. Since 2003, these maps and data tables have not been released in print, as they are only published on the online BASS2000 database, the solar database maintained by LESIA (Laboratory for space studies and astrophysical instruments). In order to make the first 80 years of observations which were available only in paper accessible and usable, the LESIA and the Library of the Observatory have started a project to digitize the publications, enter the data with the assistance of a specialized company, and then migrate the files obtained in BASS2000 and in the Heliophysics Features Catalog created in the framework of the European project HELIO.

Hippocampal participation in navigational map learning in young homing pigeons is dependent on training experience.

PubMed

Ioalè, P; Gagliardo, A; Bingman, V P

2000-02-01

The homing pigeon navigational map is perhaps one of the most striking examples of a naturally occurring spatial representation of the environment used to guide navigation. In a previous study, it was found that hippocampal lesions thoroughly disrupt the ability of young homing pigeons held in an outdoor aviary to learn a navigational map. However, since that study an accumulation of anecdotal data has hinted that hippocampal-lesioned young pigeons allowed to fly during their first summer could learn a navigational map. In the present study, young control and hippocampal-lesioned homing pigeons were either held in an outdoor aviary or allowed to fly during the time of navigational map learning. At the end of their first summer, the birds were experimentally released to test for navigational map learning. Independent of training experience, control pigeons oriented homeward during the experimental releases demonstrating that they learned a navigational map. Surprisingly, while the aviary-held hippocampal-lesioned pigeons failed to learn a navigational map as reported previously, hippocampal-lesioned birds allowed flight experience learned a navigational map indistinguishable from the two control groups. A subsequent experiment revealed that the navigational map learned by the three groups was based on atmospheric odours. The results demonstrate that hippocampal participation in navigational map learning depends on the type of experience a young bird pigeon has, and presumably, the type of navigational map learned.

MAP18 regulates the direction of pollen tube growth in Arabidopsis by modulating F-actin organization.

PubMed

Zhu, Lei; Zhang, Yan; Kang, Erfang; Xu, Qiangyi; Wang, Miaoying; Rui, Yue; Liu, Baoquan; Yuan, Ming; Fu, Ying

2013-03-01

For fertilization to occur in plants, the pollen tube must be guided to enter the ovule via the micropyle. Previous reports have implicated actin filaments, actin binding proteins, and the tip-focused calcium gradient as key contributors to polar growth of pollen tubes; however, the regulation of directional pollen tube growth is largely unknown. We reported previously that Arabidopsis thaliana MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) contributes to directional cell growth and cortical microtubule organization. The preferential expression of MAP18 in pollen and in pollen tubes suggests that MAP18 also may function in pollen tube growth. In this study, we demonstrate that MAP18 functions in pollen tubes by influencing actin organization, rather than microtubule assembly. In vitro biochemical results indicate that MAP18 exhibits Ca(2+)-dependent filamentous (F)-actin-severing activity. Abnormal expression of MAP18 in map18 and MAP18 OX plants was associated with disorganization of the actin cytoskeleton in the tube apex, resulting in aberrant pollen tube growth patterns and morphologies, inaccurate micropyle targeting, and fewer fertilization events. Experiments with MAP18 mutants created by site-directed mutagenesis suggest that F-actin-severing activity is essential to the effects of MAP18 on pollen tube growth direction. Our study demonstrates that in Arabidopsis, MAP18 guides the direction of pollen tube growth by modulating actin filaments.

RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis.

PubMed

Glaab, Enrico; Schneider, Reinhard

2015-07-01

High-throughput omics datasets often contain technical replicates included to account for technical sources of noise in the measurement process. Although summarizing these replicate measurements by using robust averages may help to reduce the influence of noise on downstream data analysis, the information on the variance across the replicate measurements is lost in the averaging process and therefore typically disregarded in subsequent statistical analyses.We introduce RepExplore, a web-service dedicated to exploit the information captured in the technical replicate variance to provide more reliable and informative differential expression and abundance statistics for omics datasets. The software builds on previously published statistical methods, which have been applied successfully to biomedical omics data but are difficult to use without prior experience in programming or scripting. RepExplore facilitates the analysis by providing a fully automated data processing and interactive ranking tables, whisker plot, heat map and principal component analysis visualizations to interpret omics data and derived statistics. Freely available at http://www.repexplore.tk enrico.glaab@uni.lu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Geophysical evidence for the intersection of the St Paul, Cape Palmas and Grand Cess fracture zones with the continental margin of Liberia, West Africa

USGS Publications Warehouse

Behrendt, John C.; Schlee, J.; Robb, James M.

1974-01-01

PUBLISHED reconstructions of Gondwana continent1 (Fig. la) show a gap in fit near the junction of the Americas and Africa. To study this critical area, the Unitedgeo I made geophysical measurements and collected rock samples across the continental margin of Liberia (USGS-IDOE cruise leg 5) in November 1971. Figure Ib indicates the location of the 5,400 km of ship track on a generalised bathymetric map2. We shall discuss the data in detail elsewhere. Here we present the evidence for the existence of three fracture zones, two of which have not been reported previously, intersecting the continental margin at the north end of the South Atlantic, which remained closed probably until Cretaceous time. We suggest that Precambrian structures on the African continent controlled the location of these fracture zones. Figure Ic compares gravity and magnetic profiles and interpretations of the seismic profiles for three selected lines (27, 30 and 34) crossing the Grand Cess, Cape Palmas and St Paul fracture zones, respectively. ?? 1974 Nature Publishing Group.

Zero echo time MRI-only treatment planning for radiation therapy of brain tumors after resection.

PubMed

Boydev, C; Demol, B; Pasquier, D; Saint-Jalmes, H; Delpon, G; Reynaert, N

2017-10-01

Using magnetic resonance imaging (MRI) as the sole imaging modality for patient modeling in radiation therapy (RT) is a challenging task due to the need to derive electron density information from MRI and construct a so-called pseudo-computed tomography (pCT) image. We have previously published a new method to derive pCT images from head T1-weighted (T1-w) MR images using a single-atlas propagation scheme followed by a post hoc correction of the mapped CT numbers using local intensity information. The purpose of this study was to investigate the performance of our method with head zero echo time (ZTE) MR images. To evaluate results, the mean absolute error in bins of 20 HU was calculated with respect to the true planning CT scan of the patient. We demonstrated that applying our method using ZTE MR images instead of T1-w improved the correctness of the pCT in case of bone resection surgery prior to RT (that is, an example of large anatomical difference between the atlas and the patient). Copyright © 2017. Published by Elsevier Ltd.

A sequencing-based linkage map of cucumber

USDA-ARS?s Scientific Manuscript database

Genetic maps are important tools for molecular breeding, gene cloning, and study of meiotic recombination. In cucumber (Cucumis sativus L.), the marker density, resolution and genome coverage of previously developed genetic maps using PCR-based molecular markers are relatively low. In this study we ...

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

PubMed Central

2012-01-01

Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii. PMID:22967170

How to compare the faces of the Earth? Walachia in mid-19th century and nowadays

NASA Astrophysics Data System (ADS)

Bartos-Elekes, Zsombor; Magyari-Sáska, Zsolt; Timár, Gábor; Imecs, Zoltán

2014-05-01

In 1864 a detailed map was made about Walachia, its title is Charta României Meridionale (Map of Southern Romania), it has 112 map sheets, it is often called after his draughtsman: Szathmári's map. The map has an outstanding position in the history of Romanian cartography, because it indicates a turning-point. Before the map, foreigners (Austrians and Russians) had made topographic maps about this vassal principality of the Ottoman Empire. The Austrian topographic survey (1855-1859) - which served as a basis for this map - was the last one and the most detailed of these surveys. The map was made between the personal-union (1859) and independence (1878) of the Danubian Principalities. This map was the first (to a certain extent) own map of the forming country. In consequence of this survey and map, the Romanian mapping institute was founded, which one - based on this survey and map - began the topographic mapping of the country. In the Romanian scientific literature imperfect and contradictory information has been published about this map. Only a dozen copies of the map were kept in few map collections; the researchers could have reached them with difficulties. During our research we processed the circumstances of the survey and mapmaking discovering its documentation in the archives of Vienna, as well as using the Romanian, Hungarian and German scientific literature. We found the copies in map collections from Vienna to Bucharest. We digitized all the map sheets from different collections. We calculated the parameters of the used geodetic datum and map projection. We published on the web, such we made the map reachable for everybody. The map can be viewed in different zoom levels; can be downloaded; settlements can be found using the place name index; areas can be exported in modern projection, so the conditions of that time could be compared with today's reality. Our poster presents on the one hand the survey and the map realized in mid-19th century and our digital methods, on the other hand presents the faces of the Earth in Walachia -comparing details of the geo-referenced map from 19th century with maps of nowadays. This work was supported by a grant of the Romanian National Authority for Scientific Research, CNCS - UEFISCDI, project number PN-II-RU-TE-2011-3-0125.

Digital data for preliminary geologic map of the Mount Hood 30- by 60-minute quadrangle, northern Cascade Range, Oregon

USGS Publications Warehouse

Lina Ma,; Sherrod, David R.; Scott, William E.

2014-01-01

This geodatabase contains information derived from legacy mapping that was published in 1995 as U.S. Geological Survey Open-File Report 95-219. The main component of this publication is a geologic map database prepared using geographic information system (GIS) applications. Included are pdf files to view or print the map sheet, the accompanying pamphlet from Open-File Report 95-219, and links to the original publication, which is available as scanned files in pdf format.

The magnetic state of the Earth (according to the magnetic maps for 1880.0 published by the German Naval Office)

NASA Technical Reports Server (NTRS)

Icilius, G. V. Q.

1982-01-01

Publication of the magnetic maps in 1880 has made it possible to make the first continuation of the foundations for the Earth's magnetism established by Gauss in the general theory of Earth magnetism. A new calculation based on the maps valid for 1880, makes it possible to express the changes which have occurred over the last 50 years in numbers and only within the liability limits of the maps themselves.

Thermal Investigation in the Cappadocia Region, Central Anatolia-Turkey, Analyzing Curie Point Depth, Geothermal Gradient, and Heat-Flow Maps from the Aeromagnetic Data

NASA Astrophysics Data System (ADS)

Bilim, Funda; Kosaroglu, Sinan; Aydemir, Attila; Buyuksarac, Aydin

2017-12-01

In this study, curie point depth (CPD), heat flow, geothermal gradient, and radiogenic heat production maps of the Cappadocian region in central Anatolia are presented to reveal the thermal structure from the aeromagnetic data. The large, circular pattern in these maps matches with previously determined shallow (2 km in average) depression. Estimated CPDs in this depression filled with loose volcano-clastics and ignimbrite sheets of continental Neogene units vary from 7 to 12 km, while the geothermal gradient increases from 50 to 68 °C/km. Heat flows were calculated using two different conductivity coefficients of 2.3 and 2.7 Wm-1 K-1. The radiogenic heat production was also obtained between 0.45 and 0.70 μW m-3 in this area. Heat-flow maps were compared with the previous, regional heat-flow map of Turkey and significant differences were observed. In contrast to linear heat-flow increment through the northeast in the previous map in the literature, produced maps in this study include a large, caldera-like circular depression between Nevsehir, Aksaray, Nigde, and Yesilhisar cities indicating high geothermal gradient and higher heat-flow values. In addition, active deformation is evident with young magmatism in the Neogene and Quaternary times and a large volcanic cover on the surface. Boundaries of volcanic eruption centers and buried large intrusions are surrounded with the maxspots of the horizontal gradients of magnetic anomalies. Analytic signal (AS) map pointing-out exact locations of causative bodies is also presented in this study. Circular region in the combined map of AS and maxspots apparently indicates a possible caldera.

The tectonics of Venus: An overview

NASA Technical Reports Server (NTRS)

Solomon, Sean C.

1992-01-01

While the Pioneer Venus altimeter, Earth-based radar observatories, and the Venera 15-16 orbital imaging radars provided views of large-scale tectonic features on Venus at ever-increasing resolution, the radar images from Magellan constitute an improvement in resolution of at least an order of magnitude over the best previously available. A summary of early Magellan observations of tectonic features on Venus was published, but data available at that time were restricted to the first month of mapping and represented only about 15 percent of the surface of the planet. Magellan images and altimetry are now available for more than 95 percent of the Venus surface. Thus a more global perspective may be taken on the styles and distribution of lithospheric deformation on Venus and their implications for the tectonic history of the planet.

The new Landsat 8 potential for remote sensing of colored dissolved organic matter (CDOM).

PubMed

Slonecker, E Terrence; Jones, Daniel K; Pellerin, Brian A

2016-06-30

Due to a combination of factors, such as a new coastal/aerosol band and improved radiometric sensitivity of the Operational Land Imager aboard Landsat 8, the atmospherically-corrected Surface Reflectance product for Landsat data, and the growing availability of corrected fDOM data from U.S. Geological Survey gaging stations, moderate-resolution remote sensing of fDOM may now be achievable. This paper explores the background of previous efforts and shows preliminary examples of the remote sensing and data relationships between corrected fDOM and Landsat 8 reflectance values. Although preliminary results before and after Hurricane Sandy are encouraging, more research is needed to explore the full potential of Landsat 8 to continuously map fDOM in a number of water profiles. Published by Elsevier Ltd.

Bathymetry of the Republic of the Marshall Islands and vicinity

USGS Publications Warehouse

Hein, James R.; Wong, Florence L.; Mosier, Dan L.

1999-01-01

The bathymetric map of the Republic of the Marshall Islands and vicinity is bounded by a window of latitude 3 to 17 degrees North, longitude 153 to 175 degrees East. The map was compiled from surveys conducted by the USGS, Korean Ocean Research and Development Institute, and published gridded data. In addition to national jurisdictions, island and atoll coastlines are indicated on the map.

Countries of the World and International Organizations: Sources of Information

DTIC Science & Technology

2007-01-08

provides business addresses worldwide by geographical areas and by standard industrial classification (SIC) codes. Maps Map Catalog (New York, Tilden...Francisco. These offices are often excellent sources of free printed matter — brochures, maps, posters, etc. A directory of tourism offices worldwide is...Peterson’s Guides, Inc.). Published irregularly, these sources offer information by field of work (agriculture, business and industry , teaching English

2. Perspective Map of Buena Vista (In Buena Vista, VA, ...

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

2. Perspective Map of Buena Vista (In Buena Vista, VA, NY:South Publishing Co., 1891 n.p.) (copy on file at Virginia State Library, Richmond, VA) - North River Canal System, West side of Buena Vista, Buena Vista, Roanoke City, VA

Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map.

PubMed

Li, Ximei; Jin, Xin; Wang, Hantao; Zhang, Xianlong; Lin, Zhongxu

2016-06-01

A high-density linkage map was constructed using 1,885 newly obtained loci and 3,747 previously published loci, which included 5,152 loci with 4696.03 cM in total length and 0.91 cM in mean distance. Homology analysis in the cotton genome further confirmed the 13 expected homologous chromosome pairs and revealed an obvious inversion on Chr10 or Chr20 and repeated inversions on Chr07 or Chr16. In addition, two reciprocal translocations between Chr02 and Chr03 and between Chr04 and Chr05 were confirmed. Comparative genomics between the tetraploid cotton and the diploid cottons showed that no major structural changes exist between DT and D chromosomes but rather between AT and A chromosomes. Blast analysis between the tetraploid cotton genome and the mixed genome of two diploid cottons showed that most AD chromosomes, regardless of whether it is from the AT or DT genome, preferentially matched with the corresponding homologous chromosome in the diploid A genome, and then the corresponding homologous chromosome in the diploid D genome, indicating that the diploid D genome underwent converted evolution by the diploid A genome to form the DT genome during polyploidization. In addition, the results reflected that a series of chromosomal translocations occurred among Chr01/Chr15, Chr02/Chr14, Chr03/Chr17, Chr04/Chr22, and Chr05/Chr19. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.

PubMed

Franceschini, Nora; Fox, Ervin; Zhang, Zhaogong; Edwards, Todd L; Nalls, Michael A; Sung, Yun Ju; Tayo, Bamidele O; Sun, Yan V; Gottesman, Omri; Adeyemo, Adebawole; Johnson, Andrew D; Young, J Hunter; Rice, Ken; Duan, Qing; Chen, Fang; Li, Yun; Tang, Hua; Fornage, Myriam; Keene, Keith L; Andrews, Jeanette S; Smith, Jennifer A; Faul, Jessica D; Guangfa, Zhang; Guo, Wei; Liu, Yu; Murray, Sarah S; Musani, Solomon K; Srinivasan, Sathanur; Velez Edwards, Digna R; Wang, Heming; Becker, Lewis C; Bovet, Pascal; Bochud, Murielle; Broeckel, Ulrich; Burnier, Michel; Carty, Cara; Chasman, Daniel I; Ehret, Georg; Chen, Wei-Min; Chen, Guanjie; Chen, Wei; Ding, Jingzhong; Dreisbach, Albert W; Evans, Michele K; Guo, Xiuqing; Garcia, Melissa E; Jensen, Rich; Keller, Margaux F; Lettre, Guillaume; Lotay, Vaneet; Martin, Lisa W; Moore, Jason H; Morrison, Alanna C; Mosley, Thomas H; Ogunniyi, Adesola; Palmas, Walter; Papanicolaou, George; Penman, Alan; Polak, Joseph F; Ridker, Paul M; Salako, Babatunde; Singleton, Andrew B; Shriner, Daniel; Taylor, Kent D; Vasan, Ramachandran; Wiggins, Kerri; Williams, Scott M; Yanek, Lisa R; Zhao, Wei; Zonderman, Alan B; Becker, Diane M; Berenson, Gerald; Boerwinkle, Eric; Bottinger, Erwin; Cushman, Mary; Eaton, Charles; Nyberg, Fredrik; Heiss, Gerardo; Hirschhron, Joel N; Howard, Virginia J; Karczewsk, Konrad J; Lanktree, Matthew B; Liu, Kiang; Liu, Yongmei; Loos, Ruth; Margolis, Karen; Snyder, Michael; Psaty, Bruce M; Schork, Nicholas J; Weir, David R; Rotimi, Charles N; Sale, Michele M; Harris, Tamara; Kardia, Sharon L R; Hunt, Steven C; Arnett, Donna; Redline, Susan; Cooper, Richard S; Risch, Neil J; Rao, D C; Rotter, Jerome I; Chakravarti, Aravinda; Reiner, Alex P; Levy, Daniel; Keating, Brendan J; Zhu, Xiaofeng

2013-09-05

High blood pressure (BP) is more prevalent and contributes to more severe manifestations of cardiovascular disease (CVD) in African Americans than in any other United States ethnic group. Several small African-ancestry (AA) BP genome-wide association studies (GWASs) have been published, but their findings have failed to replicate to date. We report on a large AA BP GWAS meta-analysis that includes 29,378 individuals from 19 discovery cohorts and subsequent replication in additional samples of AA (n = 10,386), European ancestry (EA) (n = 69,395), and East Asian ancestry (n = 19,601). Five loci (EVX1-HOXA, ULK4, RSPO3, PLEKHG1, and SOX6) reached genome-wide significance (p < 1.0 × 10(-8)) for either systolic or diastolic BP in a transethnic meta-analysis after correction for multiple testing. Three of these BP loci (EVX1-HOXA, RSPO3, and PLEKHG1) lack previous associations with BP. We also identified one independent signal in a known BP locus (SOX6) and provide evidence for fine mapping in four additional validated BP loci. We also demonstrate that validated EA BP GWAS loci, considered jointly, show significant effects in AA samples. Consequently, these findings suggest that BP loci might have universal effects across studied populations, demonstrating that multiethnic samples are an essential component in identifying, fine mapping, and understanding their trait variability. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Geologic Map of Lassen Volcanic National Park and Vicinity, California

USGS Publications Warehouse

Clynne, Michael A.; Muffler, L.J. Patrick

2010-01-01

The geologic map of Lassen Volcanic National Park (LVNP) and vicinity encompasses 1,905 km2 at the south end of the Cascade Range in Shasta, Lassen, Tehama, and Plumas Counties, northeastern California (fig. 1, sheet 3). The park includes 430 km2 of scenic volcanic features, glacially sculpted terrain, and the most spectacular array of thermal features in the Cascade Range. Interest in preserving the scenic wonders of the Lassen area as a national park arose in the early 1900s to protect it from commercial development and led to the establishment in 1907 of two small national monuments centered on Lassen Peak and Cinder Cone. The eruptions of Lassen Peak in 1914-15 were the first in the Cascade Range since widespread settling of the West in the late 1800s. Through the printed media, the eruptions aroused considerable public interest and inspired renewed efforts, which had languished since 1907, to establish a national park. In 1916, Lassen Volcanic National Park was established by combining the areas of the previously established national monuments and adjacent lands. The southernmost Cascade Range is bounded on the west by the Sacramento Valley and the Klamath Mountains, on the south by the Sierra Nevada, and on the east by the Basin and Range geologic provinces. Most of the map area is underlain by middle to late Pleistocene volcanic rocks; Holocene, early Pleistocene, and late Pliocene volcanic rocks (<3.5 m.y.) are less common. Paleozoic and Mesozoic rocks are inferred to underlie the volcanic deposits (Jachens and Saltus, 1983), but the nearest exposures of pre-Tertiary rocks are 15 km to the south, 9 km to the southwest, and 12 km to the west. Diller (1895) recognized the young volcanic geology and produced the first geologic map of the Lassen area. The map (sheet 1) builds on and extends geologic mapping by Williams (1932), Macdonald (1963, 1964, 1965), and Wilson (1961). The Lassen Peak area mapped by Christiansen and others (2002) and published in greater detail (1:24,000) was modified for inclusion here. Figure 2 (sheet 3) shows the mapping credit for previous work; figure 3 (sheet 3) shows locations discussed throughout the text. A CD-ROM entitled Database for the Geologic Map of Lassen Volcanic National Park and Vicinity, California accompanies the printed map (Muffler and others, 2010). The CD-ROM contains ESRI compatible geographic information system data files used to create the 1:50,000-scale geologic map, both geologic and topographic data and their associated metadata files, and printable versions of the geologic map and pamphlet as PDF formatted files. The 1:50,000-scale geologic map was compiled from 1:24,000-scale geologic maps of individual quadrangles that are also included in the CD-ROM. It also contains ancillary data that support the map including locations of rock samples selected for chemical analysis (Clynne and others, 2008) and radiometric dating, photographs of geologic features, and links to related data or web sites. Data contained in the CD-ROM are also available on this Web site. The southernmost Cascade Range consists of a regional platform of basalt and basaltic andesite, with subordinate andesite and sparse dacite. Nested within these regional rocks are 'volcanic centers', defined as large, long-lived, composite, calc-alkaline edifices erupting the full range of compositions from basalt to rhyolite, but dominated by andesite and dacite. Volcanic centers are produced by the focusing of basaltic flux from the mantle and resultant enhanced interaction of mafic magma with the crust. Collectively, volcanic centers mark the axis of the southernmost Cascade Range. The map area includes the entire Lassen Volcanic Center, parts of three older volcanic centers (Maidu, Dittmar, and Latour), and the products of regional volcanism (fig. 4, sheet 3). Terminology used for subdivision of the Lassen Volcanic Center has been modified from Clynne (1984, 1990).

Exploiting the extraordinary genetic polymorphism of ciona for developmental genetics with whole genome sequencing.

PubMed

Abdul-Wajid, Sarah; Veeman, Michael T; Chiba, Shota; Turner, Thomas L; Smith, William C

2014-05-01

Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca(2+) channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.

Geologic map of the Seldovia quadrangle, south-central Alaska

USGS Publications Warehouse

Bradley, Dwight C.; Kusky, Timothy M.; Haeussler, Peter J.; Karl, Susan M.; Donley, D. Thomas

1999-01-01

This is a 1:250,000-scale map of the bedrock geology of the Seldovia quadrangle, south-central Alaska. The map area covers the southwestern end of the Kenai Peninsula, including the Kenai Lowlands and Kenai Mountains, on either side of Kachemak Bay. The waters of Cook Inlet cover roughly half of the map area, and a part of the Alaska Peninsula near Iliamna Volcano lies in the extreme northwest corner of the map. The bedrock geology is based on new reconnaissance field work by the U.S. Geological Survey during parts of the 1988-1993 field seasons, and on previous mapping from a number of sources. The new mapping focused on the previously little-known Chugach accretionary complex in the Kenai Mountains. Important new findings include the recognition of mappable subdivisions of the McHugh Complex (a subduction melange of mostly Mesozoic protoliths), more accurate placement of the thrust contact between the McHugh Complex and Valdez Group (Upper Cretaceous trench turbidites), and the recognition of several new near-trench plutons of early Tertiary age.

Mapping Malaria Risk in Low Transmission Settings: Challenges and Opportunities.

PubMed

Sturrock, Hugh J W; Bennett, Adam F; Midekisa, Alemayehu; Gosling, Roly D; Gething, Peter W; Greenhouse, Bryan

2016-08-01

As malaria transmission declines, it becomes increasingly focal and prone to outbreaks. Understanding and predicting patterns of transmission risk becomes an important component of an effective elimination campaign, allowing limited resources for control and elimination to be targeted cost-effectively. Malaria risk mapping in low transmission settings is associated with some unique challenges. This article reviews the main challenges and opportunities related to risk mapping in low transmission areas including recent advancements in risk mapping low transmission malaria, relevant metrics, and statistical approaches and risk mapping in post-elimination settings. Copyright © 2016. Published by Elsevier Ltd.

Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

DOE Office of Scientific and Technical Information (OSTI.GOV)

Escamilla, M.A.; Reus, V.I.; Smith, L.B.

1996-05-31

Linkage disequilibrium (LD) analysis provides a powerful means for screening the genome to map the location of disease genes, such as those for bipolar disorder (BP). As described in this paper, the population of the Central Valley of Costa Rica, which is descended from a small number of founders, should be suitable for LD mapping; this assertion is supported by reconstruction of extended haplotypes shared by distantly related individuals in this population suffering low-frequency hearing loss (LFHL1), which has previously been mapped by linkage analysis. A sampling strategy is described for applying LD methods to map genes for BP, andmore » clinical and demographic characteristics of an initially collected sample are discussed. This sample will provide a complement to a previously collected set of Costa Rican BP families which is under investigation using standard linkage analysis. 42 refs., 4 figs., 2 tabs.« less

An ultra-dense SNP linkage map for the octoploid, cultivated strawberry and its application in genetic research

USDA-ARS?s Scientific Manuscript database

We will present an ultra-dense genetic linkage map for the octoploid, cultivated strawberry (Fragaria x ananassa) consisting of over 13K Axiom® based SNP markers and 150 previously mapped reference SSR loci. The high quality of the map is demonstrated by the short sizes of each of the 28 linkage gro...

Special-Status Plant Species Surveys and Vegetation Mapping at Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, R E

This report presents the results of Jones & Stokes special-status plant surveys and vegetation mapping for the University of California, Lawrence Livermore National Laboratory (LLNL). Special-status plant surveys were conducted at Site 300 in April to May 1997 and in March to April 2002. Eight special-status plants were identified at Site 300: large-flowered fiddleneck, big tarplant, diamond-petaled poppy, round-leaved filaree, gypsum-loving larkspur, California androsace, stinkbells, and hogwallow starfish. Maps identifying the locations of these species, a discussion of the occurrence of these species at Site 300, and a checklist of the flora of Site 300 are presented. A reconnaissance surveymore » of the LLNL Livermore Site was conducted in June 2002. This survey concluded that no special-status plants occur at the Livermore Site. Vegetation mapping was conducted in 2001 at Site 300 to update a previous vegetation study done in 1986. The purpose of the vegetation mapping was to update and to delineate more precisely the boundaries between vegetation types and to map vegetation types that previously were not mapped. The vegetation map is presented with a discussion of the vegetation classification used.« less

An expanded map of vegetation communities at Big Muddy National Fish and Wildlife Refuge

USGS Publications Warehouse

Struckhoff, Matthew A.

2013-01-01

In 2012, a map of vegetation communities on Big Muddy National Fish and Wildlife Refuge was expanded based on interpretation of aerial photographs and field data. National Agricultural Imagery Program aerial photographs were used to identify distinct communities on previously unmapped refuge units and newly acquired parcels. Newly mapped polygons were then visited to adjust map boundaries, classify communities according to the National Vegetation Classification System, and quantify the abundance of dominant species and non-native, invasive species of concern to the refuge and other resource management agencies along the Missouri River. The expanded map now covers 6,136 hectares representing 33 community types, including 6 previously unmapped types. The full map includes 1,113 polygons, of which 627 are new, 21 are updated from the 2009 mapping effort, and 465 are unchanged from 2009. Mortality of primarily cottonwood stems, because of growing-season floods between 2008 and 2011, has reduced foliar cover of woody stems and created more open wooded communities. In herbaceous communities, dominance by herbaceous old fields has increased due to the inclusion of refuge units dominated by lands in recent agricultural production in the expanded map. Wetland community abundance has increased slightly due to recent flooding.

High-resolution maps of real and illusory tactile activation in primary somatosensory cortex in individual monkeys with functional magnetic resonance imaging and optical imaging.

PubMed

Chen, Li M; Turner, Gregory H; Friedman, Robert M; Zhang, Na; Gore, John C; Roe, Anna W; Avison, Malcolm J

2007-08-22

Although blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) has been widely used to explore human brain function, questions remain regarding the ultimate spatial resolution of positive BOLD fMRI, and indeed the extent to which functional maps revealed by positive BOLD correlate spatially with maps obtained with other high-spatial-resolution mapping techniques commonly used in animals, such as optical imaging of intrinsic signal (OIS) and single-unit electrophysiology. Here, we demonstrate that the positive BOLD signal at 9.4T can reveal the fine topography of individual fingerpads in single-condition activation maps in nonhuman primates. These digit maps are similar to maps obtained from the same animal using intrinsic optical imaging. Furthermore, BOLD fMRI reliably resolved submillimeter spatial shifts in activation in area 3b previously identified with OIS (Chen et al., 2003) as neural correlates of the "funneling illusion." These data demonstrate that at high field, high-spatial-resolution topographic maps can be achieved using the positive BOLD signal, weakening previous notions regarding the spatial specificity of the positive BOLD signal.

CRUST 5.1: A global crustal model at 5° x 5°

USGS Publications Warehouse

Mooney, Walter D.; Laske, Gabi; Masters, T. Guy

1998-01-01

We present a new global model for the Earth's crust based on seismic refraction data published in the period 1948–1995 and a detailed compilation of ice and sediment thickness. An extensive compilation of seismic refraction measurements has been used to determine the crustal structure on continents and their margins. Oceanic crust is modeled with both a standard model for normal oceanic crust, and variants for nonstandard regions, such as oceanic plateaus. Our model (CRUST 5.1) consists of 2592 5° × 5° tiles in which the crust and uppermost mantle are described by eight layers: (1) ice, (2) water, (3) soft sediments, (4) hard sediments, (5) crystalline upper, (6) middle, (7) lower crust, and (8) uppermost mantle. Topography and bathymetry are adopted from a standard database (ETOPO-5). Compressional wave velocity in each layer is based on field measurements, and shear wave velocity and density are estimated using recently published empirical Vp- Vs and Vp-density relationships. The crustal model differs from previous models in that (1) the thickness and seismic/density structure of sedimentary basins is accounted for more completely, (2) the velocity structure of unmeasured regions is estimated using statistical averages that are based on a significantly larger database of crustal structure, (3) the compressional wave, shear wave, and density structure have been explicitly specified using newly available constraints from field and laboratory studies. Thus this global crustal model is based on substantially more data than previous models and differs from them in many important respects. A new map of the thickness of the Earth's crust is presented, and we illustrate the application of this model by using it to provide the crustal correction for surface wave phase velocity maps. Love waves at 40 s are dominantly sensitive to crustal structure, and there is a very close correspondence between observed phase velocities at this period and those predicted by CRUST 5.1. We find that the application of crustal corrections to long-period (167 s) Rayleigh waves significantly increases the variance in the phase velocity maps and strengthens the upper mantle velocity anomalies beneath stable continental regions. A simple calculation of crustal isostacy indicates significant lateral variations in upper mantle density. The model CRUST 5.1 provides a complete description of the physical properties of the Earth's crust at a scale of 5° × 5° and can be used for a wide range of seismological and nonseismological problems.

A Review of the Match Technique as Applied to AASE-2/EASOE and SOLVE/THESEO 2000

NASA Technical Reports Server (NTRS)

Morris, Gary A.; Bojkov, Bojan R.; Lait, Leslie R.; Schoeberl, Mark R.; Rex, Markus

2004-01-01

We apply the GSFC trajectory model with a series of ozonesondes to derive ozone loss rates in the lower stratosphere for the AASE-2/EASOE mission (January - March 1992) and for the SOLVE/THESEO 2000 mission (January - March 2000) in an approach similar to Match. Ozone loss rates are computed by comparing the ozone concentrations provided by ozonesondes launched at the beginning and end of the trajectories connecting the launches. We investigate the sensitivity of the Match results on the various parameters used to reject potential matches in the original Match technique and conclude that only a filter based on potential vorticity changes along the calculated back trajectory seems necessary. Our study also demonstrates that calculated ozone loss rates can vary by up to a factor of two depending upon the precise trajectory paths calculated for each trajectory. As a result an additional systematic error might need to be added to the statistical uncertainties published with previous Match results. The sensitivity to the trajectory path is particularly pronounced in the month of January, the month during which the largest ozone loss rate discrepancies between photochemical models and Match are found. For most of the two study periods, our ozone loss rates agree with those previously published. Notable exceptions are found for January 1992 at 475 K and late February/early March 2000 at 450 K, both periods during which we find less loss than the previous studies. Integrated ozone loss rates in both years compare well with those found in numerous other studies and in a potential vorticity/potential temperature approach shown previously and in this paper. Finally, we suggest an alternate approach to Match using trajectory mapping that appears to more accurately reflect the true uncertainties associated with Match and reduces the dependence upon filters that may bias the results of Match through the rejection of greater than or equal to 80% of the matched sonde pairs and >99% of matched observations.

Digital data set that describe aquifer characteristics of the Antlers aquifer in southeastern Oklahoma

USGS Publications Warehouse

Abbott, Marvin M.; Runkle, D.L.; Rea, Alan

1997-01-01

ARC/INFO export and nonproprietary format file This diskette contains digitized aquifer boundaries and maps of hydraulic conductivity, recharge, and ground-water level elevation contours for the Antlers aquifer in southeastern Oklahoma. The Early Cretaceous-age Antlers Sandstone is an important source of water in an area that underlies about 4,400-square miles of all or part of Atoka, Bryan, Carter, Choctaw, Johnston, Love, Marshall, McCurtain, and Pushmataha Counties. The Antlers aquifer consists of sand, clay, conglomerate, and limestone in the outcrop area. The upper part of the Antlers aquifer consists of beds of sand, poorly cemented sandstone, sandy shale, silt, and clay. The Antlers aquifer is unconfined where it outcrops in about an 1,800-square-mile area. The recharge, hydraulic conductivity, and aquifer boundaries data sets include the outcrop area of the Antlers Sandstone in Oklahoma and areas where the Antlers is overlain by alluvial and terrace deposits and a few small thin outcrops of the Goodland Limestone. Most of the lines in these data sets were extracted from published digital geology data sets. Some of the lines were interpolated in areas where the Antlers aquifer is overlain by alluvial and terrace deposits near streams and rivers. The interpolated lines are very similar to the aquifer boundaries published in a ground-water modeling report for the Antlers aquifer. The maps from which this data set was derived were scanned or digitized from maps published at a scale of 1:250,000. The water-level elevation contours were digitized from a map at a scale of 1:250,000 that was used to prepare the final map published in a ground-water flow model report. Hydraulic conductivity and recharge values also are published in the ground-water model report for the Antlers aquifer. Ground-water flow models are numerical representations that simplify and aggregate natural systems. Models are not unique; different combinations of aquifer characteristics may produce similar results. Therefore, values of hydraulic conductivity and recharge used in the model and presented in this data set are not precise, but are within a reasonable range when compared to independently collected data.

Linear Mapping of Numbers onto Space Requires Attention

ERIC Educational Resources Information Center

Anobile, Giovanni; Cicchini, Guido Marco; Burr, David C.

2012-01-01

Mapping of number onto space is fundamental to mathematics and measurement. Previous research suggests that while typical adults with mathematical schooling map numbers veridically onto a linear scale, pre-school children and adults without formal mathematics training, as well as individuals with dyscalculia, show strong compressive,…

The National Atlas of the United States now on the Web and in print

USGS Publications Warehouse

Hutchinson, John A.

2004-01-01

The National Atlas of the United States of America® was published in 1970 as a book, with more than 400 pages and 765 maps. Since then, many people have called for a new edition, and many maps have been published as single sheets using the classic National Atlas 1:7,500,000-scale format. Work began in 1997 on a new, web-based edition of the National Atlas of the United States®. Accessible at http://nationalatlas.gov, the new atlas features an interactive mapmaker with more than 1,000 data layers. Developed as a coordinated package of dynamic webbased map products and services, and printed and printable maps for selected themes, the National Atlas of the United States of America® has grown beyond a book. Yet, the cartographer’s fundamental job remains the same as it was in 1970—to translate national-level geographic data into an understandable view of the nation.

Mapping the literature of transcultural nursing*

PubMed Central

Murphy, Sharon C.

2006-01-01

Overview: No bibliometric studies of the literature of the field of transcultural nursing have been published. This paper describes a citation analysis as part of the project undertaken by the Nursing and Allied Health Resources Section of the Medical Library Association to map the literature of nursing. Objective: The purpose of this study was to identify the core literature and determine which databases provided the most complete access to the transcultural nursing literature. Methods: Cited references from essential source journals were analyzed for a three-year period. Eight major databases were compared for indexing coverage of the identified core list of journals. Results: This study identifies 138 core journals. Transcultural nursing relies on journal literature from associated health sciences fields in addition to nursing. Books provide an important format. Nearly all cited references were from the previous 18 years. In comparing indexing coverage among 8 major databases, 3 databases rose to the top. Conclusions: No single database can claim comprehensive indexing coverage for this broad field. It is essential to search multiple databases. Based on this study, PubMed/MEDLINE, Social Sciences Citation Index, and CINAHL provide the best coverage. Collections supporting transcultural nursing require robust access to literature beyond nursing publications. PMID:16710461

Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia

PubMed Central

Addepalli, Balasubrahmanym; Lesner, Nicholas P.; Limbach, Patrick A.

2015-01-01

A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNATyr I. Analysis of MC1 digestion products by ion-pairing reverse phase liquid-chromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5′-termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated. PMID:26221047

Mesoscale brain explorer, a flexible python-based image analysis and visualization tool.

PubMed

Haupt, Dirk; Vanni, Matthieu P; Bolanos, Federico; Mitelut, Catalin; LeDue, Jeffrey M; Murphy, Tim H

2017-07-01

Imaging of mesoscale brain activity is used to map interactions between brain regions. This work has benefited from the pioneering studies of Grinvald et al., who employed optical methods to image brain function by exploiting the properties of intrinsic optical signals and small molecule voltage-sensitive dyes. Mesoscale interareal brain imaging techniques have been advanced by cell targeted and selective recombinant indicators of neuronal activity. Spontaneous resting state activity is often collected during mesoscale imaging to provide the basis for mapping of connectivity relationships using correlation. However, the information content of mesoscale datasets is vast and is only superficially presented in manuscripts given the need to constrain measurements to a fixed set of frequencies, regions of interest, and other parameters. We describe a new open source tool written in python, termed mesoscale brain explorer (MBE), which provides an interface to process and explore these large datasets. The platform supports automated image processing pipelines with the ability to assess multiple trials and combine data from different animals. The tool provides functions for temporal filtering, averaging, and visualization of functional connectivity relations using time-dependent correlation. Here, we describe the tool and show applications, where previously published datasets were reanalyzed using MBE.

Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens

PubMed Central

Stedtfeld, Robert D.; Williams, Maggie R.; Fakher, Umama; Johnson, Timothy A.; Stedtfeld, Tiffany M.; Wang, Fang; Khalife, Walid T.; Hughes, Mary; Etchebarne, Brett E.; Tiedje, James M.; Hashsham, Syed A.

2016-01-01

An antibiotic resistance (AR) Dashboard application is being developed regarding the occurrence of antibiotic resistance genes (ARG) and bacteria (ARB) in environmental and clinical settings. The application gathers and geospatially maps AR studies, reported occurrence and antibiograms, which can be downloaded for offline analysis. With the integration of multiple data sets, the database can be used on a regional or global scale to identify hot spots for ARGs and ARB; track and link spread and transmission, quantify environmental or human factors influencing presence and persistence of ARG harboring organisms; differentiate natural ARGs from those distributed via human or animal activity; cluster and compare ARGs connections in different environments and hosts; and identify genes that can be used as proxies to routinely monitor anthropogenic pollution. To initially populate and develop the AR Dashboard, a qPCR ARG array was tested with 30 surface waters, primary influent from three waste water treatment facilities, ten clinical isolates from a regional hospital and data from previously published studies including river, park soil and swine farm samples. Interested users are invited to download a beta version (available on iOS or Android), submit AR information using the application, and provide feedback on current and prospective functionalities. PMID:26850162

Examining Neural Correlates of Psychopathology Using a Lesion-Based Approach.

PubMed

Calamia, Matthew; Markon, Kristian E; Sutterer, Matthew J; Tranel, Daniel

2018-06-22

Studies of individuals with focal brain damage have long been used to expand understanding of the neural basis of psychopathology. However, most previous studies were conducted using small sample sizes and relatively coarse methods for measuring psychopathology or mapping brain-behavior relationships. Here, we examined the factor structure and neural correlates of psychopathology in 232 individuals with focal brain damage, using their responses to the Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF). Factor analysis and voxel-based lesion symptom mapping were used to examine the structure and neural correlates of psychopathology in this sample. Consistent with existing MMPI-2-RF literature, separate internalizing, externalizing, and psychotic symptom dimensions were found. In addition, a somatic dimension likely reflecting neurological symptoms was identified. Damage to the medial temporal lobe, including the hippocampus, was associated with scales related to both internalizing problems and psychoticism. Damage to the medial temporal lobe and orbitofrontal cortex was associated with both a general distrust of others and beliefs that one is being personally targeted by others. These findings provide evidence for the critical role of dysfunction in specific frontal and temporal regions in the development of psychopathology. Copyright © 2018. Published by Elsevier Ltd.

MSX Colors of Radio-Selected HII Regions in the Milky Way

NASA Astrophysics Data System (ADS)

Giveon, U.; Becker, R. H.; Helfand, D. J.; White, R. L.

2003-12-01

Investigation of the color-space properties of mid-infrared sources in the MSX Galactic plane catalog reveals two distinct populations - a blue population composed mainly of evolved stars, masers and molecular clouds, and a red population comprising sources of a nebular nature - HII regions, planetary nebulae, and unclassified radio sources. We compare the MSX catalog to 5 GHz VLA maps of the first quadrant of the Galactic plane. A catalog extracted from these maps was published first by Becker et al., but we have re-reduced the data with significantly improved calibration and mosaicing procedures, resulting in an increase of ˜ 60% in the number of detected sources. Comparison of the radio and infrared catalogs resulted in a sample of 491 matches, out of which we estimate 38 to be false counterparts, all of them from the MSX red population. The radio sources with infrared counterparts are found to have extremely small scale height (FWHM of 14' or ˜ 35 pc), and have thermal radio spectrum. These properties suggest that the sample is dominated by HII regions, most of them are previously uncataloged. This research is supported be the National Science Foundation.

Genetic mapping of the rice resistance-breaking gene of the brown planthopper Nilaparvata lugens.

PubMed

Kobayashi, Tetsuya; Yamamoto, Kimiko; Suetsugu, Yoshitaka; Kuwazaki, Seigo; Hattori, Makoto; Jairin, Jirapong; Sanada-Morimura, Sachiyo; Matsumura, Masaya

2014-07-22

Host plant resistance has been widely used for controlling the major rice pest brown planthopper (BPH, Nilaparvata lugens). However, adaptation of the wild BPH population to resistance limits the effective use of resistant rice varieties. Quantitative trait locus (QTL) analysis was conducted to identify resistance-breaking genes against the anti-feeding mechanism mediated by the rice resistance gene Bph1. QTL analysis in iso-female BPH lines with single-nucleotide polymorphism (SNP) markers detected a single region on the 10th linkage group responsible for the virulence. The QTL explained from 57 to 84% of the total phenotypic variation. Bulked segregant analysis with next-generation sequencing in F2 progenies identified five SNPs genetically linked to the virulence. These analyses showed that virulence to Bph1 was controlled by a single recessive gene. In contrast to previous studies, the gene-for-gene relationship between the major resistance gene Bph1 and virulence gene of BPH was confirmed. Identified markers are available for map-based cloning of the major gene controlling BPH virulence to rice resistance. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Lithology and aggregate quality attributes for the digital geologic map of Colorado

USGS Publications Warehouse

Knepper, Daniel H.; Green, Gregory N.; Langer, William H.

1999-01-01

This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map.

Symbolic, Nonsymbolic and Conceptual: An Across-Notation Study on the Space Mapping of Numerals.

PubMed

Zhang, Yu; You, Xuqun; Zhu, Rongjuan

2016-07-01

Previous studies suggested that there are interconnections between two numeral modalities of symbolic notation and nonsymbolic notation (array of dots), differences and similarities of the processing, and representation of the two modalities have both been found in previous research. However, whether there are differences between the spatial representation and numeral-space mapping of the two numeral modalities of symbolic notation and nonsymbolic notation is still uninvestigated. The present study aims to examine whether there are differences between the spatial representation and numeral-space mapping of the two numeral modalities of symbolic notation and nonsymbolic notation; especially how zero, as both a symbolic magnitude numeral and a nonsymbolic conceptual numeral, mapping onto space; and if the mapping happens automatically at an early stage of the numeral information processing. Results of the two experiments demonstrate that the low-level processing of symbolic numerals including zero and nonsymbolic numerals except zero can mapping onto space, whereas the low-level processing of nonsymbolic zero as a semantic conceptual numeral cannot mapping onto space, which indicating the specialty of zero in the numeral domain. The present study indicates that the processing of non-semantic numerals can mapping onto space, whereas semantic conceptual numerals cannot mapping onto space. © The Author(s) 2016.

RECENT DEVELOPMENTS IN THE U. S. GEOLOGICAL SURVEY'S LANDSAT IMAGE MAPPING PROGRAM.

USGS Publications Warehouse

Brownworth, Frederick S.; Rohde, Wayne G.

1986-01-01

At the 1984 ASPRS-ACSM Convention in Washington, D. C. a paper on 'The Emerging U. S. Geological Survey Image Mapping Program' was presented that discussed recent satellite image mapping advancements and published products. Since then Landsat image mapping has become an integral part of the National Mapping Program. The Survey currently produces about 20 Landsat multispectral scanner (MSS) and Thematic Mapper (TM) image map products annually at 1:250,000 and 1:100,000 scales, respectively. These Landsat image maps provide users with a regional or synoptic view of an area. The resultant geographical presentation of the terrain and cultural features will help planners and managers make better decisions regarding the use of our national resources.

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.

PubMed

Meyers, Robin M; Bryan, Jordan G; McFarland, James M; Weir, Barbara A; Sizemore, Ann E; Xu, Han; Dharia, Neekesh V; Montgomery, Phillip G; Cowley, Glenn S; Pantel, Sasha; Goodale, Amy; Lee, Yenarae; Ali, Levi D; Jiang, Guozhi; Lubonja, Rakela; Harrington, William F; Strickland, Matthew; Wu, Ting; Hawes, Derek C; Zhivich, Victor A; Wyatt, Meghan R; Kalani, Zohra; Chang, Jaime J; Okamoto, Michael; Stegmaier, Kimberly; Golub, Todd R; Boehm, Jesse S; Vazquez, Francisca; Root, David E; Hahn, William C; Tsherniak, Aviad

2017-12-01

The CRISPR-Cas9 system has revolutionized gene editing both at single genes and in multiplexed loss-of-function screens, thus enabling precise genome-scale identification of genes essential for proliferation and survival of cancer cells. However, previous studies have reported that a gene-independent antiproliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, thereby leading to false-positive results in copy number-amplified regions. We developed CERES, a computational method to estimate gene-dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy number-specific effect. In our efforts to define a cancer dependency map, we performed genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this data set. We found that CERES decreased false-positive results and estimated sgRNA activity for both this data set and previously published screens performed with different sgRNA libraries. We further demonstrate the utility of this collection of screens, after CERES correction, for identifying cancer-type-specific vulnerabilities.

Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells

PubMed Central

Meyers, Robin M.; Bryan, Jordan G.; McFarland, James M.; Weir, Barbara A.; Sizemore, Ann E.; Xu, Han; Dharia, Neekesh V.; Montgomery, Phillip G.; Cowley, Glenn S.; Pantel, Sasha; Goodale, Amy; Lee, Yenarae; Ali, Levi D.; Jiang, Guozhi; Lubonja, Rakela; Harrington, William F.; Strickland, Matthew; Wu, Ting; Hawes, Derek C.; Zhivich, Victor A.; Wyatt, Meghan R.; Kalani, Zohra; Chang, Jaime J.; Okamoto, Michael; Stegmaier, Kimberly; Golub, Todd R.; Boehm, Jesse S.; Vazquez, Francisca; Root, David E.; Hahn, William C.; Tsherniak, Aviad

2017-01-01

The CRISPR-Cas9 system has revolutionized gene editing both on single genes and in multiplexed loss-of-function screens, enabling precise genome-scale identification of genes essential to proliferation and survival of cancer cells1,2. However, previous studies reported that a gene-independent anti-proliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, leading to false positive results in copy number amplified regions3,4. We developed CERES, a computational method to estimate gene dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy-number-specific effect. As part of our efforts to define a cancer dependency map, we performed genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this dataset. We found that CERES reduced false positive results and estimated sgRNA activity for both this dataset and previously published screens performed with different sgRNA libraries. Here, we demonstrate the utility of this collection of screens, upon CERES correction, in revealing cancer-type-specific vulnerabilities. PMID:29083409

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy.

PubMed

Coulthart, Michael B; Posada, David; Crandall, Keith A; Dekaban, Gregory A

2006-03-01

Recently, the putative finding of ancient human T cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) DNA sequences in association with a 1500-year-old Chilean mummy has stirred vigorous debate. The debate is based partly on the inherent uncertainties associated with phylogenetic reconstruction when only short sequences of closely related genotypes are available. However, a full analysis of what phylogenetic information is present in the mummy data has not previously been published, leaving open the question of what precisely is the range of admissible interpretation. To fulfill this need, we re-analyzed the mummy data in a new way. We first performed phylogenetic analysis of 188 published LTR DNA sequences from extant strains belonging to the HTLV-1 Cosmopolitan clade, using the method of statistical parsimony which is designed both to optimize phylogenetic resolution among sequences with little evolutionary divergence, and to permit precise mapping of individual sequence mutations onto branches of a divergence network. We then deduced possible phylogenetic positions for the two main categories of published Chilean mummy sequences, based on their published 157-nucleotide LTR sequences. The possible phylogenetic placements for one of the mummy sequence categories are consistent with a modern origin. However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade.

Paleobathymetric Reconstruction of Ross Sea: seismic data processing and regional reflectors mapping

NASA Astrophysics Data System (ADS)

Olivo, Elisabetta; De Santis, Laura; Wardell, Nigel; Geletti, Riccardo; Busetti, Martina; Sauli, Chiara; Bergamasco, Andrea; Colleoni, Florence; Vanzella, Walter; Sorlien, Christopher; Wilson, Doug; De Conto, Robert; Powell, Ross; Bart, Phil; Luyendyk, Bruce

2017-04-01

PURPOSE: New maps of some major unconformities of the Ross Sea have been reconstructed, by using seismic data grids, combined with the acoustic velocities from previous works, from new and reprocessed seismic profiles. This work is carried out with the support of PNRA and in the frame of the bilateral Italy-USA project GLAISS (Global Sea Level Rise & Antarctic Ice Sheet Stability predictions), funded by the Ministry of Foreign Affairs. Paleobathymetric maps of 30, 14 and 4 million years ago, three 'key moments' for the glacial history of the Antarctic Ice Sheet, coinciding with global climatic changes. The paleobathymetric maps will then be used for numeric simulations focused on the width and thickness of the Ross Sea Ice Sheet. PRELIMINARY RESULTS: The first step was to create TWT maps of three main unconformity (RSU6, RSU4, and RSU2) of Ross Sea, revisiting and updating the ANTOSTRAT maps, through the interpretation of sedimentary bodies and erosional features, used to infer active or old processes along the slope, we identified the main seismic unconformities. We used the HIS Kingdom academic license. The different groups contribution was on the analysis of the Eastern Ross Sea continental slope and rise (OGS), of the Central Basin (KOPRI) of the western and central Ross Sea (Univ. of Santa Barbara and OGS), where new drill sites and seismic profiles were collected after the publication of the ANTOSTRAT maps. Than we joined our interpretation with previous interpretations. We examined previous processing of several seismic lines and all the old acoustic velocity analysis. In addiction we reprocessed some lines in order to have a higher data coverage. Then, combining the TWT maps of the unconformity with the old and new speed data we created new depth maps of the study area. The new depth maps will then be used for reconstructing the paleobathymetry of the Ross Sea by applying backstripping technique.

Seismic Tomography of the Sacramento -- San Joaquin River Delta: Joint P-wave/Gravity and Ambient Noise Methods

NASA Astrophysics Data System (ADS)

Teel, Alexander C.

The Sacramento -- San Joaquin River Delta (SSJRD) is an area that has been identified as having high seismic hazard but has resolution gaps in the seismic velocity models of the area due to a scarcity of local seismic stations and earthquakes. I present new three-dimensional (3D) P-wave velocity (Vp) and S-wave velocity (Vs) models for the SSJRD which fill in the sampling gaps of previous studies. I have created a new 3D seismic velocity model for the SSJRD, addressing an identified need for higher resolution velocity models in the region, using a new joint gravity/body-wave tomography algorithm. I am able to fit gravity and arrival-time residuals jointly using an empirical density-velocity relationship to take advantage of existing gravity data in the region to help fill in the resolution gaps of previous velocity models in the area. I find that the method enhances the ability to resolve the relief of basin structure relative to seismic-only tomography at this location. I find the depth to the basement to be the greatest in the northwest portion of the SSJRD and that there is a plateau in the basement structure beneath the southeast portion of the SSJRD. From my findings I infer that the SSJRD may be prone to focusing effects and basin amplification of ground motion. A 3D, Vs model for the SSJRD and surrounding area was created using ambient noise tomography. The empirical Green's functions are in good agreement with published cross-correlations and match earthquake waveforms sharing similar paths. The group velocity and shear velocity maps are in good agreement with published regional scale models. The new model maps velocity values on a local scale and successfully recovers the basin structure beneath the Delta. From this Vs model I find the maximum depth of the basin to reach approximately 15 km with the Great Valley Ophiolite body rising to a depth of 10 km east of the SSJRD. We consider our basement-depth estimates from the Vp model to be more robust than from the Vs model.

Mars Polar Thermal Inertia and Albedo Properties Using TES Data

NASA Astrophysics Data System (ADS)

Scherbenski, J. M.; Paige, D. A.

2002-12-01

We present north and south polar thermal inertia and albedo maps derived from MGS TES observations. The maps were derived using the same robust approach developed to make polar thermal and inertia and albedo maps using IRTM observationsby Paige, Bachman, and Keegan (1994) and Paige and Keegan (1994). The data processing approach involved reading TES reduced data records in PDS format using the Vanilla software tool, and sending the data down a processing pipeline that constrains and bins the data, and compares it to the results of a diurnal and seasonal thermal model to obtain the best fit thermal inertia and apparent albedo. To facilitate comparison, the TES maps were created at the same Ls ranges as the published IRTM maps using TES spectral surface temperature results. The north polar maps used TES nadir observations obtained during a 50-day period from Ls 98.39 to Ls 121.25. The south polar maps used TES nadir observations obtained during a 30-day period from Ls 321.58 to 338.07. The creation of these maps employ a basic thermal model that does not include the effects of the atmosphere, as well as a one-dimensional radiative-convective model that does include the effects of the atmosphere. The spatial resolution of the north polar maps is 0.1 degrees of latitude and 1.0 degrees of longitude. The spatial resolution of the south polar maps is 2 degrees of latitude and 2 degrees of longitude. The TES north polar maps show the residual cap area in significantly greater detail than has been available previously. The IRTM maps showed that the north polar sand sea that surrounds the cap has unusually low thermal inertia. The TES maps confirm this conclusion, but also show that the dark renetrant features in chama boreal and elsewhere on the cap also have low thermal inertias. This strongly supports the proposal that these dark rentrants are the sources of the dune material. The TES maps also show that the darker layered deposits which are found at the periphery of the cap have high thermal inertias, just like the brighter water ice deposits elsewhere on the cap. This strongly supports the conclusion that even the darker north polar layered deposits are mostly ice. The TES south polar maps show similar features to those observed by IRTM, including the presence of a low thermal inertia region centered on the south pole, and a region of anomalously high apparent albedo southward of 78 degrees latitude. References: Paige, D. A., J. E. Bachman and K. D. Keegan, Thermal and albedo mapping of the polar regions of Mars using Viking thermal mapper observations: 1. North polar region, J. Geophys. Res. 99, 24,959-25,991, 1994. Paige, D. A. and K. D. Keegan, Thermal and albedo mapping of the polar regions of Mars using Viking thermal mapper observations: 1. South polar region, J. Geophys. Res. 99, 24,993-26,013, 1994.

Geologic and geophysical maps of the Las Vegas 30' x 60' quadrangle, Clark and Nye counties, Nevada, and Inyo County, California

USGS Publications Warehouse

Page, William R.; Lundstrom, Scott C.; Harris, Anita G.; Langenheim, V.E.; Workman, Jeremiah B.; Mahan, Shannon; Paces, James B.; Dixon, Gary L.; Rowley, Peter D.; Burchfiel, B.C.; Bell, John W.; Smith, Eugene I.

2005-01-01

Las Vegas and Pahrump are two of the fastest growing cities in the US, and the shortage of water looms as among the greatest future problems for these cities. These new maps of the Las Vegas 30 x 60-minute quadrangle provide a geologic and geophysical framework and fundamental earth science database needed to address societal issues such as ground water supply and contamination, surface flood, landslide, and seismic hazards, and soil properties and their changing impact by and on urbanization. The mountain ranges surrounding Las Vegas and Pahrump consist of Mesozoic, Paleozoic and Proterozoic rocks. A majority of these rocks are Paleozoic carbonate rocks that are part of Nevada's carbonate rock aquifer province. The Spring Mountains represent a major recharge site in the province, where maximum altitude is 3,632 m (Charleston Peak) above sea level. Rocks in the Sheep and Las Vegas Ranges and Spring Mountains contain correlative, northeast-striking, southeast-verging thrust faults that are part of the Cretaceous, Sevier orogenic belt. These thrusts were offset during the Miocene by the Las Vegas Valley shear system (LVVSZ). We conducted new mapping in the Blue Diamond area, highlighting refined work on the Bird Spring thrust, newly studied ancient landslides, and gravity-slide blocks. We conducted new mapping in the Las Vegas Range and mapped previously unrecognized structures such as the Valley thrust and fold belt; recognition of these structures has led to a refined correlation of Mesozoic thrust faults across the LVVSZ. New contributions in the quadrangle also include a greatly refined stratigraphy of Paleozoic bedrock units based on conodont biostragraphy. We collected over 200 conodont samples in the quadrangle and established stratigraphic reference sections used to correlate units across the major Mesozoic thrust faults. Quaternary deposits cover about half of the map area and underlie most of the present urbanized area. Deposits consist of large coalescing alluvial fans that grade downslope to extensive areas of fine-grained sediment indicative of groundwater-discharge during the Pleistocene. In the central areas of Las Vegas and Pahrump valleys, Quaternary fault scarps associated with past ground-water discharge deposits suggest a genetic relationship. In collaboration with NBMG and University of Nevada, a variety of ages of gravelly alluvium are newly mapped using surficial characteristics and soil development, along with reassessment of previously published mapping during compilation. Reconnaissance geochronology (thermoluminescence and U-series) of eolian and authigenic components of surficial and buried soils and spring deposits is applied to test hypotheses of geomorphic and hydrologic response to climate change over the past 100 k.y.). The major structure in the Las Vegas quadrangle is the LVVSZ. Because the LVVSZ is concealed by thick basin-fill deposits of Quaternary and Tertiary age, it was characterized primarily based on geophysics. Likewise, the newly described State line fault system in Pahrump Valley has also been characterized by geophysics, where geophysically inferred structures correlate remarkably with surface structures defined by our new geologic mapping in the Mound Spring and Hidden Hills Ranch 7.5-minute quadrangles.

A population 'consensus', partial linkage map of Picea abies Karst. based on RAPD markers

Treesearch

G. Bucci; Thomas L. Kubisiak; W.L. Nance; P. Menozzi

1997-01-01

The authors built a "consensus" partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight...

Black-backed woodpecker habitat suitability mapping using conifer snag basal area estimated from airborne laser scanning

NASA Astrophysics Data System (ADS)

Casas Planes, Á.; Garcia, M.; Siegel, R.; Koltunov, A.; Ramirez, C.; Ustin, S.

2015-12-01

Occupancy and habitat suitability models for snag-dependent wildlife species are commonly defined as a function of snag basal area. Although critical for predicting or assessing habitat suitability, spatially distributed estimates of snag basal area are not generally available across landscapes at spatial scales relevant for conservation planning. This study evaluates the use of airborne laser scanning (ALS) to 1) identify individual conifer snags and map their basal area across a recently burned forest, and 2) map habitat suitability for a wildlife species known to be dependent on snag basal area, specifically the black-backed woodpecker (Picoides arcticus). This study focuses on the Rim Fire, a megafire that took place in 2013 in the Sierra Nevada Mountains of California, creating large patches of medium- and high-severity burned forest. We use forest inventory plots, single-tree ALS-derived metrics and Gaussian processes classification and regression to identify conifer snags and estimate their stem diameter and basal area. Then, we use the results to map habitat suitability for the black-backed woodpecker using thresholds for conifer basal area from a previously published habitat suitability model. Local maxima detection and watershed segmentation algorithms resulted in 75% detection of trees with stem diameter larger than 30 cm. Snags are identified with an overall accuracy of 91.8 % and conifer snags are identified with an overall accuracy of 84.8 %. Finally, Gaussian process regression reliably estimated stem diameter (R2 = 0.8) using height and crown area. This work provides a fast and efficient methodology to characterize the extent of a burned forest at the tree level and a critical tool for early wildlife assessment in post-fire forest management and biodiversity conservation.

Toward uniform probabilistic seismic hazard assessments for Southeast Asia

NASA Astrophysics Data System (ADS)

Chan, C. H.; Wang, Y.; Shi, X.; Ornthammarath, T.; Warnitchai, P.; Kosuwan, S.; Thant, M.; Nguyen, P. H.; Nguyen, L. M.; Solidum, R., Jr.; Irsyam, M.; Hidayati, S.; Sieh, K.

2017-12-01

Although most Southeast Asian countries have seismic hazard maps, various methodologies and quality result in appreciable mismatches at national boundaries. We aim to conduct a uniform assessment across the region by through standardized earthquake and fault databases, ground-shaking scenarios, and regional hazard maps. Our earthquake database contains earthquake parameters obtained from global and national seismic networks, harmonized by removal of duplicate events and the use of moment magnitude. Our active-fault database includes fault parameters from previous studies and from the databases implemented for national seismic hazard maps. Another crucial input for seismic hazard assessment is proper evaluation of ground-shaking attenuation. Since few ground-motion prediction equations (GMPEs) have used local observations from this region, we evaluated attenuation by comparison of instrumental observations and felt intensities for recent earthquakes with predicted ground shaking from published GMPEs. We then utilize the best-fitting GMPEs and site conditions into our seismic hazard assessments. Based on the database and proper GMPEs, we have constructed regional probabilistic seismic hazard maps. The assessment shows highest seismic hazard levels near those faults with high slip rates, including the Sagaing Fault in central Myanmar, the Sumatran Fault in Sumatra, the Palu-Koro, Matano and Lawanopo Faults in Sulawesi, and the Philippine Fault across several islands of the Philippines. In addition, our assessment demonstrates the important fact that regions with low earthquake probability may well have a higher aggregate probability of future earthquakes, since they encompass much larger areas than the areas of high probability. The significant irony then is that in areas of low to moderate probability, where building codes are usually to provide less seismic resilience, seismic risk is likely to be greater. Infrastructural damage in East Malaysia during the 2015 Sabah earthquake offers a case in point.

Adaptation of a Fast Optimal Interpolation Algorithm to the Mapping of Oceangraphic Data

NASA Technical Reports Server (NTRS)

Menemenlis, Dimitris; Fieguth, Paul; Wunsch, Carl; Willsky, Alan

1997-01-01

A fast, recently developed, multiscale optimal interpolation algorithm has been adapted to the mapping of hydrographic and other oceanographic data. This algorithm produces solution and error estimates which are consistent with those obtained from exact least squares methods, but at a small fraction of the computational cost. Problems whose solution would be completely impractical using exact least squares, that is, problems with tens or hundreds of thousands of measurements and estimation grid points, can easily be solved on a small workstation using the multiscale algorithm. In contrast to methods previously proposed for solving large least squares problems, our approach provides estimation error statistics while permitting long-range correlations, using all measurements, and permitting arbitrary measurement locations. The multiscale algorithm itself, published elsewhere, is not the focus of this paper. However, the algorithm requires statistical models having a very particular multiscale structure; it is the development of a class of multiscale statistical models, appropriate for oceanographic mapping problems, with which we concern ourselves in this paper. The approach is illustrated by mapping temperature in the northeastern Pacific. The number of hydrographic stations is kept deliberately small to show that multiscale and exact least squares results are comparable. A portion of the data were not used in the analysis; these data serve to test the multiscale estimates. A major advantage of the present approach is the ability to repeat the estimation procedure a large number of times for sensitivity studies, parameter estimation, and model testing. We have made available by anonymous Ftp a set of MATLAB-callable routines which implement the multiscale algorithm and the statistical models developed in this paper.

Analysis of the rdd locus in chicken: a model for human retinitis pigmentosa.

PubMed

Burt, David W; Morrice, David R; Lester, Douglas H; Robertson, Graeme W; Mohamed, Moin D; Simmons, Ian; Downey, Louise M; Thaung, Caroline; Bridges, Leslie R; Paton, Ian R; Gentle, Mike; Smith, Jacqueline; Hocking, Paul M; Inglehearn, Chris F

2003-04-30

To identify the locus responsible for the blind mutation rdd (retinal dysplasia and degeneration) in chickens and to further characterise the rdd phenotype. The eyes of blind and sighted birds were subjected to ophthalmic, morphometric and histopathological examination to confirm and extend published observations. Electroretinography was used to determine age of onset. Birds were crossed to create pedigrees suitable for genetic mapping. DNA samples were obtained and subjected to a linkage search. Measurement of IOP, axial length, corneal diameter, and eye weight revealed no gross morphological changes in the rdd eye. However, on ophthalmic examination, rdd homozygotes have a sluggish pupillary response, atrophic pecten, and widespread pigmentary disturbance that becomes more pronounced with age. Older birds also have posterior subcapsular cataracts. At three weeks of age, homozygotes have a flat ERG indicating severe loss of visual function. Pathological examination shows thinning of the RPE, ONL, photoreceptors and INL, and attenuation of the ganglion cell layer. From 77 classified backcross progeny, 39 birds were blind and 38 sighted. The rdd mutation was shown to be sex-linked and not autosomal as previously described. Linkage analysis mapped the rdd locus to a small region of the chicken Z chromosome with homologies to human chromosomes 5q and 9p. Ophthalmic, histopathologic, and electrophysiological observations suggest rdd is similar to human recessive retinitis pigmentosa. Linkage mapping places rdd in a region homologous to human chromosomes 9p and 5q. Candidate disease genes or loci include PDE6A, WGN1, and USH2C. This is the first use of genetic mapping in a chicken model of human disease.

HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics.

PubMed

Zheng, Jie; Rodriguez, Santiago; Laurin, Charles; Baird, Denis; Trela-Larsen, Lea; Erzurumluoglu, Mesut A; Zheng, Yi; White, Jon; Giambartolomei, Claudia; Zabaneh, Delilah; Morris, Richard; Kumari, Meena; Casas, Juan P; Hingorani, Aroon D; Evans, David M; Gaunt, Tom R; Day, Ian N M

2017-01-01

Fine mapping is a widely used approach for identifying the causal variant(s) at disease-associated loci. Standard methods (e.g. multiple regression) require individual level genotypes. Recent fine mapping methods using summary-level data require the pairwise correlation coefficients ([Formula: see text]) of the variants. However, haplotypes rather than pairwise [Formula: see text], are the true biological representation of linkage disequilibrium (LD) among multiple loci. In this article, we present an empirical iterative method, HAPlotype Regional Association analysis Program (HAPRAP), that enables fine mapping using summary statistics and haplotype information from an individual-level reference panel. Simulations with individual-level genotypes show that the results of HAPRAP and multiple regression are highly consistent. In simulation with summary-level data, we demonstrate that HAPRAP is less sensitive to poor LD estimates. In a parametric simulation using Genetic Investigation of ANthropometric Traits height data, HAPRAP performs well with a small training sample size (N < 2000) while other methods become suboptimal. Moreover, HAPRAP's performance is not affected substantially by single nucleotide polymorphisms (SNPs) with low minor allele frequencies. We applied the method to existing quantitative trait and binary outcome meta-analyses (human height, QTc interval and gallbladder disease); all previous reported association signals were replicated and two additional variants were independently associated with human height. Due to the growing availability of summary level data, the value of HAPRAP is likely to increase markedly for future analyses (e.g. functional prediction and identification of instruments for Mendelian randomization). The HAPRAP package and documentation are available at http://apps.biocompute.org.uk/haprap/ CONTACT: : jie.zheng@bristol.ac.uk or tom.gaunt@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Mars Global Geologic Mapping Progress and Suggested Geographic-Based Hierarchal Systems for Unit Grouping and Naming

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Dohm, J. M.; Irwin, R.; Kolb, E. J.; Skinner, J. A., Jr.; Hare, T. M.

2010-01-01

We are in the fourth year of a fiveyear effort to map the global geology of Mars at 1:20M scale using mainly Mars Global Surveyor, Mars Express, and Mars Odyssey image and altimetry datasets. Previously, we reported on details of project management, mapping datasets (local and regional), initial and anticipated mapping approaches, and tactics of map unit delineation and description [1-2]. Last year, we described mapping and unit delineation results thus far, a new unit identified in the northern plains, and remaining steps to complete the map [3].

Advances in 6d diffraction contrast tomography

NASA Astrophysics Data System (ADS)

Viganò, N.; Ludwig, W.

2018-04-01

The ability to measure 3D orientation fields and to determine grain boundary character plays a key role in understanding many material science processes, including: crack formation and propagation, grain coarsening, and corrosion processes. X-ray diffraction imaging techniques offer the ability to retrieve such information in a non-destructive manner. Among them, Diffraction Contrast Tomography (DCT) is a monochromatic beam, near-field technique, that uses an extended beam and offers fast mapping of 3D sample volumes. It was previously shown that the six-dimensional extension of DCT can be applied to moderately deformed samples (<= 5% total strain), made from materials that exhibit low levels of elastic deformation of the unit cell (<= 1%). In this article, we improved over the previously proposed 6D-DCT reconstruction method, through the introduction of both a more advanced forward model and reconstruction algorithm. The results obtained with the proposed improvements are compared against the reconstructions previously published in [1], using Electron Backscatter Diffraction (EBSD) measurements as a reference. The result was a noticeably higher quality reconstruction of the grain boundary positions and local orientation fields. The achieved reconstruction quality, together with the low acquisition times, render DCT a valuable tool for the stop-motion study of polycrystalline microstructures, evolving as a function of applied strain or thermal annealing treatments, for selected materials.

Pair-correlated stereodynamics for diatom-diatom rotational energy transfer: NO(A2Σ+) + N2

NASA Astrophysics Data System (ADS)

Luxford, Thomas F. M.; Sharples, Thomas R.; McKendrick, Kenneth G.; Costen, Matthew. L.

2017-07-01

We have performed a crossed molecular beam velocity-map ion imaging study of state-to-state rotational energy transfer of NO(A2Σ+, v = 0, N = 0, j = 0.5) in collisions with N2 and have measured rotational angular momentum polarization dependent images of product NO(A) rotational levels N' = 3 and 5-11 for collisions at an average energy of 797 cm-1. We present an extension of our previously published [T. F. M. Luxford et al., J. Chem. Phys. 145, 174 304 (2016)] image analysis which includes the effect of rotational excitation of the unobserved collision partner and critically evaluate this methodology. We report differential cross sections and angle-resolved angular momentum alignment moments for NO(A) levels N' = 3 and 5-11 as a function of the rotational excitation of the coincident N2 partner. The scattering dynamics of NO(A) + N2 share similarities with those previously reported for NO(A) + Ne and Ar, although with detailed differences. We use comparison of the measurements reported here to the scattering of NO(A) with Ne, and the known NO(A)-Ne potential energy surface, to draw conclusions about the previously unknown NO(A)-N2 potential.

Navigating moral distress using the moral distress map.

PubMed

Dudzinski, Denise Marie

2016-05-01

The plethora of literature on moral distress has substantiated and refined the concept, provided data about clinicians' (especially nurses') experiences, and offered advice for coping. Fewer scholars have explored what makes moral distress moral If we acknowledge that patient care can be distressing in the best of ethical circumstances, then differentiating distress and moral distress may refine the array of actions that are likely to ameliorate it. This article builds upon scholarship exploring the normative and conceptual dimensions of moral distress and introduces a new tool to map moral distress from emotional source to corrective actions. The Moral Distress Map has proven useful in clinical teaching and ethics-related debriefings. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

The Application of an Emerging Technique for Protein–Protein Interaction Interface Mapping: The Combination of Photo-Initiated Cross-Linking Protein Nanoprobes with Mass Spectrometry

PubMed Central

Ptáčková, Renata; Ječmen, Tomáš; Novák, Petr; Hudeček, Jiří; Stiborová, Marie; Šulc, Miroslav

2014-01-01

Protein–protein interaction was investigated using a protein nanoprobe capable of photo-initiated cross-linking in combination with high-resolution and tandem mass spectrometry. This emerging experimental approach introduces photo-analogs of amino acids within a protein sequence during its recombinant expression, preserves native protein structure and is suitable for mapping the contact between two proteins. The contact surface regions involved in the well-characterized interaction between two molecules of human 14-3-3ζ regulatory protein were used as a model. The employed photo-initiated cross-linking techniques extend the number of residues shown to be within interaction distance in the contact surface of the 14-3-3ζ dimer (Gln8–Met78). The results of this study are in agreement with our previously published data from molecular dynamic calculations based on high-resolution chemical cross-linking data and Hydrogen/Deuterium exchange mass spectrometry. The observed contact is also in accord with the 14-3-3ζ X-ray crystal structure (PDB 3dhr). The results of the present work are relevant to the structural biology of transient interaction in the 14-3-3ζ protein, and demonstrate the ability of the chosen methodology (the combination of photo-initiated cross-linking protein nanoprobes and mass spectrometry analysis) to map the protein-protein interface or regions with a flexible structure. PMID:24865487

Evidence of demyelination in mild cognitive impairment and dementia using a direct and specific magnetic resonance imaging measure of myelin content.

PubMed

Bouhrara, Mustapha; Reiter, David A; Bergeron, Christopher M; Zukley, Linda M; Ferrucci, Luigi; Resnick, Susan M; Spencer, Richard G

2018-04-18

We investigated brain demyelination in aging, mild cognitive impairment (MCI), and dementia using magnetic resonance imaging of myelin. Brains of young and old controls and old subjects with MCI, Alzheimer's disease, or vascular dementia were scanned using our recently developed myelin water fraction (MWF) mapping technique, which provides greatly improved accuracy over previous comparable methods. Maps of MWF, a direct and specific myelin measure, and relaxation times and magnetization transfer ratio, indirect and nonspecific measures, were constructed. MCI subjects showed decreased MWF compared with old controls. Demyelination was greater in Alzheimer's disease or vascular dementia. As expected, decreased MWF was accompanied by decreased magnetization transfer ratio and increased relaxation times. The young subjects showed greater myelin content than the old subjects. We believe this to be the first demonstration of myelin loss in MCI, Alzheimer's disease, and vascular dementia using a method that provides a quantitative magnetic resonance imaging-based measure of myelin. Our findings add to the emerging evidence that myelination may represent an important biomarker for the pathology of MCI and dementia. This study supports the investigation of the role of myelination in MCI and dementia through use of this quantitative magnetic resonance imaging approach in clinical studies of disease progression, relationship of functional status to myelination status, and therapeutics. Furthermore, mapping MWF may permit myelin to serve as a therapeutic target in clinical trials. Copyright © 2018. Published by Elsevier Inc.

Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps.

PubMed

Swanson, Larry W

2018-04-15

The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to "Google Maps" for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3-D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. © 2018 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Two novel translocation breakpoints upstream of SOX9 define borders of the proximal and distal breakpoint cluster region in campomelic dysplasia.

PubMed

Leipoldt, M; Erdel, M; Bien-Willner, G A; Smyk, M; Theurl, M; Yatsenko, S A; Lupski, J R; Lane, A H; Shanske, A L; Stankiewicz, P; Scherer, G

2007-01-01

The semilethal skeletal malformation syndrome campomelic dysplasia (CD) with or without XY sex reversal is caused by mutations within the SOX9 gene on 17q24.3 or by chromosomal aberrations (translocations, inversions or deletions) with breakpoints outside the SOX9 coding region. The previously published CD translocation breakpoints upstream of SOX9 fall into two clusters: a proximal cluster with breakpoints between 50-300 kb and a distal cluster with breakpoints between 899-932 kb. Here, we present clinical, cytogenetic and molecular data from two novel CD translocation cases. Case 1 with karyotype 46,XY,t(1;17)(q42.1;q24.3) has characteristic symptoms of CD, including mild tibial bowing, cryptorchidism and hypospadias. By standard fluorescence in situ hybridization (FISH) and by high-resolution fiber FISH, the 17q breakpoint was mapped 375 kb from SOX9, defining the centromeric border of the proximal breakpoint cluster region. Case 2 with karyotype 46,X,t(Y;17)(q11.2;q24.3) has the acampomelic form of CD and complete XY sex reversal. By FISH and somatic cell hybrid analysis, the 17q breakpoint was mapped 789 kb from SOX9, defining the telomeric border of the distal breakpoint cluster region. We discuss the structure of the 1 Mb cis-control region upstream of SOX9 and the correlation between the position of the 14 mapped translocation breakpoints with respect to disease severity and XY sex reversal.

Magnetic Doppler imaging considering atmospheric structure modifications due to local abundances: a luxury or a necessity?

NASA Astrophysics Data System (ADS)

Kochukhov, O.; Wade, G. A.; Shulyak, D.

2012-04-01

Magnetic Doppler imaging is currently the most powerful method of interpreting high-resolution spectropolarimetric observations of stars. This technique has provided the very first maps of stellar magnetic field topologies reconstructed from time series of full Stokes vector spectra, revealing the presence of small-scale magnetic fields on the surfaces of Ap stars. These studies were recently criticised by Stift et al., who claimed that magnetic inversions are not robust and are seriously undermined by neglecting a feedback on the Stokes line profiles from the local atmospheric structure in the regions of enhanced metal abundance. We show that Stift et al. misinterpreted published magnetic Doppler imaging results and consistently neglected some of the most fundamental principles behind magnetic mapping. Using state-of-the-art opacity sampling model atmosphere and polarized radiative transfer codes, we demonstrate that the variation of atmospheric structure across the surface of a star with chemical spots affects the local continuum intensity but is negligible for the normalized local Stokes profiles except for the rare situation of a very strong line in an extremely Fe-rich atmosphere. For the disc-integrated spectra of an Ap star with extreme abundance variations, we find that the assumption of a mean model atmosphere leads to moderate errors in Stokes I but is negligible for the circular and linear polarization spectra. Employing a new magnetic inversion code, which incorporates the horizontal variation of atmospheric structure induced by chemical spots, we reconstructed new maps of magnetic field and Fe abundance for the bright Ap star α2 CVn. The resulting distribution of chemical spots changes insignificantly compared to the previous modelling based on a single model atmosphere, while the magnetic field geometry does not change at all. This shows that the assertions by Stift et al. are exaggerated as a consequence of unreasonable assumptions and extrapolations, as well as methodological flaws and inconsistencies of their analysis. Our discussion proves that published magnetic inversions based on a mean stellar atmosphere are highly robust and reliable, and that the presence of small-scale magnetic field structures on the surfaces of Ap stars is indeed real. Incorporating horizontal variations of atmospheric structure in Doppler imaging can marginally improve reconstruction of abundance distributions for stars showing very large iron overabundances. But this costly technique is unnecessary for magnetic mapping with high-resolution polarization spectra.

Geology, structure, and statistics of multi-ring basins on Mars

NASA Technical Reports Server (NTRS)

Schultz, Richard A.; Frey, Herbert V.

1990-01-01

Available data on Martian multi-ring basins were compiled and evaluated using the new 1:15 million scale geologic maps of Mars and global topography was revised as base maps. Published center coordinates and ring diameters of Martian basins were plotted by computer and superimposed onto the base maps. In many cases basin centers or ring diameters or both had to be adjusted to achieve a better fit to the revised maps. It was also found that additional basins can explain subcircular topographic lows as well as map patterns of old Noachian materials, volcanic plains units, and channels in the Tharsis region.

Applied regional monitoring of the vernal advancement and retrogradation (Green wave effect) of natural vegetation in the Great Plains corridor. [Texas and Oklahoma

NASA Technical Reports Server (NTRS)

Rouse, J. W., Jr. (Principal Investigator)

1976-01-01

The author has identified the following significant results. A TV16 isoline map at the 6.25 million hectare extended test site area in north central Texas and southern Oklahoma was produced. The map was compared to a published USDA Statistical Reporting Service map, which shows pasture and range feed conditions, as reported by rancher respondents. Both maps show similar areas of drought stress and good to excellent forage conditions, but preliminary indications are that the LANDSAT-derived map more accurately depicts the areal extent of each condition class.

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

PubMed Central

2013-01-01

Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species. PMID:23324311

JournalMap: Discovering location-relevant knowledge from published studies for sustainable land use, preventing degradation, and restoring landscapes

USDA-ARS?s Scientific Manuscript database

Finding relevant knowledge and information to prevent land degradation and support restoration has historically involved researchers working from their own knowledge, querying people they know, and tediously searching topical literature reviews.To address this need we created JournalMap (http://www....

Staff - Kenneth R. Papp | Alaska Division of Geological & Geophysical

Science.gov Websites

Alaska MAPTEACH Tsunami Inundation Mapping Energy Resources Gas Hydrates STATEMAP Program information Alaska Energy Authority, and the Curator of the Geologic Materials Center (2009-2015). Position: Division survey-wide interface for geologists to publish digital map data (DGGS) Established the Alaska Energy

77 FR 2054 - Proposed Agency Information Collection

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-13

... Consumption Data Access and Control Questionnaire; (3) Type of Request: New; (4) Purpose: The U.S. Department of Energy (DOE) will generate a ``crowd-sourced map'' that discloses consumer access to personal... questionnaire device that captures and publishes the necessary information as a series of web-based maps upon...

Wilderness quality mapping - the Australian experiences

Treesearch

Nick Sawyer

2015-01-01

By 1995 wilderness quality maps developed under the Australian Government's National Wilderness Inventory (NWI) program had been published for most of Australia, but few traces of the NWI now remain and the word "wilderness" has become almost unmentionable in government and professional land management circles. Yet its popular appeal is demonstrated by...

Air Navigation. Aerospace Education II.

ERIC Educational Resources Information Center

Cox, Rodney V., Jr.

This revised textbook, published for the Air Force ROTC program, contains a discussion of basic and essential understandings about air navigation. The first part of the book describes maps, air navigation charts, flight planning, and pilotage preflight. Basic differences between ground maps and air charts are described and the methods of…

Geologic Communications | Alaska Division of Geological & Geophysical

Science.gov Websites

improves a database for the Division's digital and map-based geological, geophysical, and geochemical data interfaces DGGS metadata and digital data distribution - Geospatial datasets published by DGGS are designed to be compatible with a broad variety of digital mapping software, to present DGGS's geospatial data

MAPS of Cancer

NASA Technical Reports Server (NTRS)

Gray, Lincoln

1998-01-01

Our goal was to produce an interactive visualization from a mathematical model that successfully predicts metastases from head and neck cancer. We met this goal early in the project. The visualization is available for the public to view. Our work appears to fill a need for more information about this deadly disease. The idea of this project was to make an easily interpretable visualization based on what we call "functional maps" of disease. A functional map is a graphic summary of medical data, where distances between parts of the body are determined by the probability of disease, not by anatomical distances. Functional maps often beat little resemblance to anatomical maps, but they can be used to predict the spread of disease. The idea of modeling the spread of disease in an abstract multidimensional space is difficult for many people. Our goal was to make the important predictions easy to see. NASA must face this problem frequently: how to help laypersons and professionals see important trends in abstract, complex data. We took advantage of concepts perfected in NASA's graphics libraries. As an analogy, consider a functional map of early America. Suppose we choose travel times, rather than miles, as our measures of inter-city distances. For Abraham Lincoln, travel times would have been the more meaningful measure of separation between cities. In such a map New Orleans would be close to Memphis because of the Mississippi River. St. Louis would be close to Portland because of the Oregon Trail. Oklahoma City would be far from Little Rock because of the Cheyenne. Such a map would look puzzling to those of us who have always seen physical maps, but the functional map would be more useful in predicting the probabilities of inter-site transit. Continuing the analogy, we could predict the spread of social diseases such as gambling along the rivers and cattle rustling along the trails. We could simply print the functional map of America, but it would be more interesting to show meaningful patterns of dispersal. We had previously published the functional map of the head and neck, but it was difficult to explain to either patients or surgeons because that view of our body did not resemble anatomy. This discrepancy between functional and physical maps is just a mathematical restatement of the well-known fact that some diseases, such as head and neck cancer, spread in complex patterns, not always to the next nearest site. We had discovered that a computer could re-arrange anatomy so that this particular disease spreads to the next nearest site. The functional map explains over 95% of the metastases in 1400 patients. In a sense, we had graphed what our body "looks like" to a tumor. The tumor readily travels between adjacent areas in the functional map. The functional map is a succinct visual display of trends that are not easily appreciated in tables of probabilities.

A topographic feature taxonomy for a U.S. national topographic mapping ontology

USGS Publications Warehouse

Varanka, Dalia E.

2013-01-01

Using legacy feature lists from the U.S. National Topographic Mapping Program of the twentieth century, a taxonomy of features is presented for purposes of developing a national topographic feature ontology for geographic mapping and analysis. After reviewing published taxonomic classifications, six basic classes are suggested; terrain, surface water, ecological regimes, built-up areas, divisions, and events. Aspects of ontology development are suggested as the taxonomy is described.

An Overview and Parametric Evaluation of the CGS ShakeMap Automated System in CISN

NASA Astrophysics Data System (ADS)

Hagos, L. Z.; Haddadi, H. R.; Shakal, A. F.

2014-12-01

In the recent years, ShakeMap has been extensively used in California for earthquake rapid response. Serving as a backup to the Northern and Southern seismic regions of the California Integrated Seismic Network (CISN), the California Geological Survey (CGS) is running a ShakeMap system configured such that it effectively produces ShakeMaps for earthquakes occurring in both regions. In achieving this goal, CGS has worked to improve the robustness of its ShakeMap system and the quality of its products. Peak ground motion amplitude data are exchanged between the CISN data centers to provide robust generation of ShakeMap. Most exchanged ground motion packets come associated with an earthquake by the authoritative network. However, for ground motion packets that come unassociated, CGS employs an event association scheme to associate them with the corresponding earthquake. The generated ShakeMap products are published to the CGS server which can also be accessed through the CISN website. The backup function is designed to publish ShakeMap products to the USGS NEIC server without collision with the regional networks, only acting in cases where the authoritative region encounters a system failure. Depending on the size, location and significance of the earthquake, review of ShakeMap products by a seismologist may involve changes to ShakeMap parameters from the default. We present an overview of the CGS ShakeMap system and highlight some of the parameters a seismologist may adjust including parameters related to basin effects, directivity effects when finite fault models are available, site corrections, etc. We also analyze the sensitivity and dependence of the ShakeMap intensity and ground motion maps on the number of observed data included in the computation. In light of the available strong motion amplitude data, we attempt to address the question of what constitutes an adequate quality ShakeMap in the tradeoff between rapidity and completeness. We also present a brief comparative study of the available Ground Motion to Intensity Conversion Equations (GMICE) by studying selected earthquakes in California region. Results of these studies can be used as a tool in ShakeMap generation for California earthquakes when the use of non-default parameters is required.