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Sample records for integrated physical mapping

  1. Integrating the USMARC genetic map for the pig with the pig physical map

    USDA-ARS?s Scientific Manuscript database

    A comprehensive genetic linkage map containing 3418 markers and spanning 2,326 cM of the autosomal genome was generated and integrated with the available physical maps for the pig. Marker types consisted of 1531 microsatellites and 1887 markers based on single feature polymorphisms, insertion/delet...

  2. A physical map of the papaya genome with integrated genetic map and genome sequence

    PubMed Central

    2009-01-01

    Background Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly. Results The physical map consists of 963 contigs, representing 9.4× genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes. Conclusion A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly

  3. A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

    PubMed

    Kobayashi, Fuminori; Wu, Jianzhong; Kanamori, Hiroyuki; Tanaka, Tsuyoshi; Katagiri, Satoshi; Karasawa, Wataru; Kaneko, Satoko; Watanabe, Shota; Sakaguchi, Toyotaka; Hanawa, Yumiko; Fujisawa, Hiroko; Kurita, Kanako; Abe, Chikako; Iehisa, Julio C M; Ohno, Ryoko; Šafář, Jan; Šimková, Hana; Mukai, Yoshiyuki; Hamada, Masao; Saito, Mika; Ishikawa, Goro; Katayose, Yuichi; Endo, Takashi R; Takumi, Shigeo; Nakamura, Toshiki; Sato, Kazuhiro; Ogihara, Yasunari; Hayakawa, Katsuyuki; Doležel, Jaroslav; Nasuda, Shuhei; Matsumoto, Takashi; Handa, Hirokazu

    2015-08-12

    A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91% of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87% of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B.

  4. Progress towards integrated physical and genetic maps of chromosome 22

    SciTech Connect

    Bell, C.J.; Barnoski, B.; Budarf, M.L.

    1994-09-01

    Our immediate objective is to identify and characterize a set of overlapping YAC clones spanning the long arm of chromosome 22 by STS content mapping of the CEPH YAC libraries. STSs are assigned to bins defined by a 25 interval hybrid mapping panel and the YAC libraries are screened by amplification of hierarchical pools of yeast DNAs. Thus far, 382 probes and STSs have been assigned to bins and 251 probes and STSs have been used to identify a total 659 YACs, which is nearly 5X coverage of the chromosome. We have assembled more than twenty putative contigs using simulated annealing, split and merge, and backtracking optimization algorithms. The largest contig contains 82 STSs linked with 250 YACs, connects bin 12 to 15, and contains approximately one third of the long arm. The proximal region also contains two large contigs in bins 1-2 and bin 9, between them containing 26 STSs and 62 YACs. The DiGeorge (DGCR) region, encompassing bins 3-5, is currently 80% covered in a contig of cosmids. The distal portion (bins 17-22) is the least represented in YACs, due to a paucity of markers and a lower hit-rate of YACs per STS. We are targeting this region with new STSs from inter-Alu PCR plasmid libraries derived from radiation hybrid cell lines that retain relevant portions of the chromosome. A concurrent objective of the center is to construct a robust multi-point linkage map of the chromosome. STRPs (simple tandem repeat polymorphisms) were assembled into a 20-point skeletal map and a 29-point framework map; 15 of the markers in the skeletal map have been unequivocally assigned to single intervals in the hybrid panel with identical linkage and bin orders. This genetic map, combined with markers ordered by pulsed field gel maps covering large portions of the chromosome, provides a robust framework for ordering YACs within contigs and ordering contigs along the chromosome.

  5. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes.

    PubMed

    Soto, Johana Carolina; Ortiz, Juan Felipe; Perlaza-Jiménez, Laura; Vásquez, Andrea Ximena; Lopez-Lavalle, Luis Augusto Becerra; Mathew, Boby; Léon, Jens; Bernal, Adriana Jimena; Ballvora, Agim; López, Camilo Ernesto

    2015-03-16

    Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a

  6. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map

    SciTech Connect

    Kelleher, Colin; CHIU, Dr. R.; Shin, Dr. H.; Krywinski, Martin; Fjell, Chris; Wilkin, Jennifer; Yin, Tongming; Difazio, Stephen P.

    2007-01-01

    As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 {+-} 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

  7. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.

    PubMed

    Krzywinski, Martin; Wallis, John; Gösele, Claudia; Bosdet, Ian; Chiu, Readman; Graves, Tina; Hummel, Oliver; Layman, Dan; Mathewson, Carrie; Wye, Natasja; Zhu, Baoli; Albracht, Derek; Asano, Jennifer; Barber, Sarah; Brown-John, Mabel; Chan, Susanna; Chand, Steve; Cloutier, Alison; Davito, Jonathon; Fjell, Chris; Gaige, Tony; Ganten, Detlev; Girn, Noreen; Guggenheimer, Kurtis; Himmelbauer, Heinz; Kreitler, Thomas; Leach, Stephen; Lee, Darlene; Lehrach, Hans; Mayo, Michael; Mead, Kelly; Olson, Teika; Pandoh, Pawan; Prabhu, Anna-Liisa; Shin, Heesun; Tänzer, Simone; Thompson, Jason; Tsai, Miranda; Walker, Jason; Yang, George; Sekhon, Mandeep; Hillier, LaDeana; Zimdahl, Heike; Marziali, Andre; Osoegawa, Kazutoyo; Zhao, Shaying; Siddiqui, Asim; de Jong, Pieter J; Warren, Wes; Mardis, Elaine; McPherson, John D; Wilson, Richard; Hübner, Norbert; Jones, Steven; Marra, Marco; Schein, Jacqueline

    2004-04-01

    As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

  8. Twenty-one polymorphic markers from human chromosome 12 for integration of genetic and physical maps

    SciTech Connect

    LeBlanc-Straceski, J.M.; Kissel, H.; Murtaugh, L.; Kucherlapati, R.; Montogmery, K.T.; Krauter, K.S. ); Tsai, P.; Ward, D.C. )

    1994-01-15

    Twenty-one physically mapped, polymorphic markers have been developed from a chromosome 12-specific cosmid library. The markers consist of CA repeat-containing sequence-tagged sites (STSs) derived from cosmid clones mapped by fluorescence in situ hybridization (FISH). Three methods for determining the sequence flanking CA microsatellites were used, including one using degenerate primer sets for direct sequence analysis. Oligonucleotide primer pairs suitable for use in polymerase chain reaction (PCR) were selected from the sequences flanking the CA microsatellite and were tested for their ability to generate unique PCR products. The informativeness of these STSs as genetic markers was determined by typing 10 unrelated individuals who are part of the Centre d'Etude du Polymorphisme Humaine (EPH) pedigrees. Eleven of the 21 FISH-mapped, polymorphic STSs are heterozygous in 7 or more of the individuals tested. Since these markers are derived from physically mapped cosmids, genetic linkage analysis with them will facilitate the integration of the developing physical and genetic maps of chromosome 12. 29 refs., 4 figs., 2 tabs.

  9. Automated integration of genomic physical mapping data via parallel simulated annealing

    SciTech Connect

    Slezak, T.

    1994-06-01

    The Human Genome Center at the Lawrence Livermore National Laboratory (LLNL) is nearing closure on a high-resolution physical map of human chromosome 19. We have build automated tools to assemble 15,000 fingerprinted cosmid clones into 800 contigs with minimal spanning paths identified. These islands are being ordered, oriented, and spanned by a variety of other techniques including: Fluorescence Insitu Hybridization (FISH) at 3 levels of resolution, ECO restriction fragment mapping across all contigs, and a multitude of different hybridization and PCR techniques to link cosmid, YAC, AC, PAC, and Pl clones. The FISH data provide us with partial order and distance data as well as orientation. We made the observation that map builders need a much rougher presentation of data than do map readers; the former wish to see raw data since these can expose errors or interesting biology. We further noted that by ignoring our length and distance data we could simplify our problem into one that could be readily attacked with optimization techniques. The data integration problem could then be seen as an M x N ordering of our N cosmid clones which ``intersect`` M larger objects by defining ``intersection`` to mean either contig/map membership or hybridization results. Clearly, the goal of making an integrated map is now to rearrange the N cosmid clone ``columns`` such that the number of gaps on the object ``rows`` are minimized. Our FISH partially-ordered cosmid clones provide us with a set of constraints that cannot be violated by the rearrangement process. We solved the optimization problem via simulated annealing performed on a network of 40+ Unix machines in parallel, using a server/client model built on explicit socket calls. For current maps we can create a map in about 4 hours on the parallel net versus 4+ days on a single workstation. Our biologists are now using this software on a daily basis to guide their efforts toward final closure.

  10. A database system for constructing, integrating, and displaying physical maps of chromosome 19

    SciTech Connect

    Slezak, T.; Wagner, M.; Yeh, Mimi; Ashworth, L.; Nelson, D.; Ow, D.; Branscomb, E.; Carrano, A.

    1994-06-01

    Efforts are underway at numerous sites around the world to construct physical maps of all human chromosomes. These maps will enable researchers to locate, characterize, and eventually understand the genes that control human structure and function. Accomplishing this goal will require a staggering amount of innovation and advancement of biological technology. The volume and complexity of the data already generated requires a sophisticated array of computational support to collect, store, analyze, integrate, and display it in biologically meaningful ways. The Human Genome Center at Livermore has spent the last 6 years constructing a database system to support its physical mapping efforts on human chromosome 19. Our computational support team is composed of experienced computer professionals who share a common pragmatic primary goal of rapidly supplying tools that meet the ever-changing needs of the biologists. Most papers describing computational support of genome research concentrate on mathematical details of key algorithms. However, in this paper we would like to concentrate on the design issues, tradeoffs, and consequences from the point of view of building a complex database system to support leading-edge genomic research. We introduce the topic of physical mapping, discuss the key design issues involved in our databases, and discuss the use of this data by our major tools (DNA fingerprint analysis and overlap computation, contig assembly, map integration, and database browsing.) Given the advantage of hindsight, we discuss what worked, what didn`t, and how we will evolve from here. As early pioneers in this field we hope that our experience may prove useful to others who are now beginning to design and construct similar systems.

  11. Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).

    PubMed

    Varshney, Rajeev K; Mir, Reyazul Rouf; Bhatia, Sabhyata; Thudi, Mahendar; Hu, Yuqin; Azam, Sarwar; Zhang, Yong; Jaganathan, Deepa; You, Frank M; Gao, Jinliang; Riera-Lizarazu, Oscar; Luo, Ming-Cheng

    2014-03-01

    Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.

  12. A first generation integrated physical and genetic map of the rainbow trout genome

    USDA-ARS?s Scientific Manuscript database

    The rainbow trout physical map was previously constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of ...

  13. Integration of the Aedes aegypti mosquito genetic linkage and physical maps.

    PubMed Central

    Brown, S E; Severson, D W; Smith, L A; Knudson, D L

    2001-01-01

    Two approaches were used to correlate the Aedes aegypti genetic linkage map to the physical map. STS markers were developed for previously mapped RFLP-based genetic markers so that large genomic clones from cosmid libraries could be found and placed to the metaphase chromosome physical maps using standard FISH methods. Eight cosmids were identified that contained eight RFLP marker sequences, and these cosmids were located on the metaphase chromosomes. Twenty-one cDNAs were mapped directly to metaphase chromosomes using a FISH amplification procedure. The chromosome numbering schemes of the genetic linkage and physical maps corresponded directly and the orientations of the genetic linkage maps for chromosomes 2 and 3 were inverted relative to the physical maps. While the chromosome 2 linkage map represented essentially 100% of chromosome 2, approximately 65% of the chromosome 1 linkage map mapped to only 36% of the short p-arm and 83% of the chromosome 3 physical map contained the complete genetic linkage map. Since the genetic linkage map is a RFLP cDNA-based map, these data also provide a minimal estimate for the size of the euchromatic regions. The implications of these findings on positional cloning in A. aegypti are discussed. PMID:11238414

  14. Integration of the Aedes aegypti mosquito genetic linkage and physical maps.

    PubMed

    Brown, S E; Severson, D W; Smith, L A; Knudson, D L

    2001-03-01

    Two approaches were used to correlate the Aedes aegypti genetic linkage map to the physical map. STS markers were developed for previously mapped RFLP-based genetic markers so that large genomic clones from cosmid libraries could be found and placed to the metaphase chromosome physical maps using standard FISH methods. Eight cosmids were identified that contained eight RFLP marker sequences, and these cosmids were located on the metaphase chromosomes. Twenty-one cDNAs were mapped directly to metaphase chromosomes using a FISH amplification procedure. The chromosome numbering schemes of the genetic linkage and physical maps corresponded directly and the orientations of the genetic linkage maps for chromosomes 2 and 3 were inverted relative to the physical maps. While the chromosome 2 linkage map represented essentially 100% of chromosome 2, approximately 65% of the chromosome 1 linkage map mapped to only 36% of the short p-arm and 83% of the chromosome 3 physical map contained the complete genetic linkage map. Since the genetic linkage map is a RFLP cDNA-based map, these data also provide a minimal estimate for the size of the euchromatic regions. The implications of these findings on positional cloning in A. aegypti are discussed.

  15. The Effects of Integrating Computer-Based Concept Mapping for Physics Learning in Junior High School

    ERIC Educational Resources Information Center

    Chang, Cheng-Chieh; Yeh, Ting-Kuang; Shih, Chang-Ming

    2016-01-01

    It generally is accepted that concept mapping has a noticeable impact on learning. But literatures show the use of concept mapping is not benefit all learners. The present study explored the effects of incorporating computer-based concept mapping in physics instruction. A total of 61 9th-grade students participated in this study. By using a…

  16. The Effects of Integrating Computer-Based Concept Mapping for Physics Learning in Junior High School

    ERIC Educational Resources Information Center

    Chang, Cheng-Chieh; Yeh, Ting-Kuang; Shih, Chang-Ming

    2016-01-01

    It generally is accepted that concept mapping has a noticeable impact on learning. But literatures show the use of concept mapping is not benefit all learners. The present study explored the effects of incorporating computer-based concept mapping in physics instruction. A total of 61 9th-grade students participated in this study. By using a…

  17. Fundamentals of Physical Mapping

    USDA-ARS?s Scientific Manuscript database

    This book chapter provides an overview of physical mapping in plants and its use for map-based gene cloning. A brief overview of cytogenetics-based physical mapping strategies, and physical mapping approaches currently used and the lessons learnt from the success stories were furnished. The statisti...

  18. An Integrated Physical Map for the Short Arm of Human Chromosome 5

    PubMed Central

    Peterson, Ellen T.; Sutherland, Robert; Robinson, Donna L.; Chasteen, Leslie; Gersh, Meryl; Overhauser, Joan; Deaven, Larry L.; Moyzis, Robert K.; Grady, Deborah L.

    1999-01-01

    The short arm of human chromosome 5 contains ∼48 Mb of DNA and comprises 1.5% of the genome. We have constructed a mega-YAC/ STS map of this region that includes 436 YACs anchored by 216 STSs. By combining and integrating our map with the 5p maps of other groups using the same recombinant DNA library, a comprehensive map was constructed that includes 552 YACs and 504 markers. The YAC map covers >94% of 5p in four YAC contigs, bridges the centromere, and includes an additional 5 Mb of 5q DNA. The average marker density is 95 kb. This integrated 5p map will serve as a resource for the continuing localization of genes on the short arm of human chromosome 5 and as a framework for both generating and aligning the DNA sequence of this region. PMID:10613848

  19. ODS2: a multiplatform software application for creating integrated physical and genetic maps.

    PubMed

    Hall, D; Bhandarkar, S M; Wang, J

    2001-03-01

    A contig map is a physical map that shows the native order of a library of overlapping genomic clones. One common method for creating such maps involves using hybridization to detect clone overlaps. False- positive and false-negative hybridization errors, the presence of chimeric clones, and gaps in library coverage lead to ambiguity and error in the clone order. Genomes with good genetic maps, such as Neurospora crassa, provide a means for reducing ambiguities and errors when constructing contig maps if clones can be anchored with genetic markers to the genetic map. A software application called ODS2 for creating contig maps based on clone-clone hybridization data is presented. This application is also designed to exploit partial ordering information provided by anchorage of clones to a genetic map. This information, along with clone-clone hybridization data, is used by a clone ordering algorithm and is represented graphically, allowing users to interactively align physical and genetic maps. ODS2 has a graphical user interface and is implemented entirely in Java, so it runs on multiple platforms. Other features include the flexibility of storing data in a local file or relational database and the ability to create full or minimum tiling contig maps.

  20. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

    SciTech Connect

    Kelleher, Colin; Chiu, Readman; Shin, Heesun; Bosdet, Ian; Krywinski, Martin; Fjell, Chris; Wilkin, Jennifer; Yin, Tongming; DiFazio, Stephen P; Ali, Johar; Asano, Jennifer; Chan, Susanna; Cloutier, Alison; Girn, Noreen; Leach, Stephen; Lee, Darlene; Mathewson, Carrie; Olson, Teika; O'Connor, Katie; Prabhu, Anna-Liisa; Smailus, Duane; Stott, Jeffery; Tsai, Miranda; Wye, Natasaja; Yang, George; Zhuang, Jun; Holt, Robert A.; Putnam, Nicholas; Vrebalov, Julia; Giovannoni, James; Grimwood, Jane; Schmutz, Jeremy; Rokhsar, Daniel; Jones, Steven; Marra, Marco; Tuskan, Gerald A; Bohlmann, J.; Ellis, Brian; Ritland, Kermit; Douglas, Carl; Schein, Jacqueline

    2007-01-01

    As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the first maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2,802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the 485+10 Mb Populus genome, as estimated from the genome sequence assembly. BAC ends were sequenced to aid in long-range assembly of whole genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat (SSR)-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. 2,411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa v1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

  1. Integrating the genetic and physical maps of Arabidopsis thaliana: identification of mapped alleles of cloned essential (EMB) genes.

    PubMed

    Meinke, David; Sweeney, Colleen; Muralla, Rosanna

    2009-10-08

    The classical genetic map of Arabidopsis includes more than 130 genes with an embryo-defective (emb) mutant phenotype. Many of these essential genes remain to be cloned. Hundreds of additional EMB genes have been cloned and catalogued (www.seedgenes.org) but not mapped. To facilitate EMB gene identification and assess the current level of saturation, we updated the classical map, compared the physical and genetic locations of mapped loci, and performed allelism tests between mapped (but not cloned) and cloned (but not mapped) emb mutants with similar chromosome locations. Two hundred pairwise combinations of genes located on chromosomes 1 and 5 were tested and more than 1100 total crosses were screened. Sixteen of 51 mapped emb mutants examined were found to be disrupted in a known EMB gene. Alleles of a wide range of published EMB genes (YDA, GLA1, TIL1, AtASP38, AtDEK1, EMB506, DG1, OEP80) were discovered. Two EMS mutants isolated 30 years ago, T-DNA mutants with complex insertion sites, and a mutant with an atypical, embryo-specific phenotype were resolved. The frequency of allelism encountered was consistent with past estimates of 500 to 1000 EMB loci. New EMB genes identified among mapped T-DNA insertion mutants included CHC1, which is required for chromatin remodeling, and SHS1/AtBT1, which encodes a plastidial nucleotide transporter similar to the maize Brittle1 protein required for normal endosperm development. Two classical genetic markers (PY, ALB1) were identified based on similar map locations of known genes required for thiamine (THIC) and chlorophyll (PDE166) biosynthesis. The alignment of genetic and physical maps presented here should facilitate the continued analysis of essential genes in Arabidopsis and further characterization of a broad spectrum of mutant phenotypes in a model plant.

  2. Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant.

    PubMed

    Wu, Pingzhi; Zhou, Changpin; Cheng, Shifeng; Wu, Zhenying; Lu, Wenjia; Han, Jinli; Chen, Yanbo; Chen, Yan; Ni, Peixiang; Wang, Ying; Xu, Xun; Huang, Ying; Song, Chi; Wang, Zhiwen; Shi, Nan; Zhang, Xudong; Fang, Xiaohua; Yang, Qing; Jiang, Huawu; Chen, Yaping; Li, Meiru; Wang, Ying; Chen, Fan; Wang, Jun; Wu, Guojiang

    2015-03-01

    The family Euphorbiaceae includes some of the most efficient biomass accumulators. Whole genome sequencing and the development of genetic maps of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27,172 putative protein-coding genes. We established a linkage map containing 1208 markers and anchored the genome assembly (81.7%) to this map to produce 11 pseudochromosomes. After gene family clustering, 15,268 families were identified, of which 13,887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome-inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.

  3. Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

    PubMed

    Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan; Sønderkær, Mads; Amoros, Walter; Carboni, Martin Federico; D'Ambrosio, Juan Martín; de la Cruz, German; Di Genova, Alex; Douches, David S; Eguiluz, Maria; Guo, Xiao; Guzman, Frank; Hackett, Christine A; Hamilton, John P; Li, Guangcun; Li, Ying; Lozano, Roberto; Maass, Alejandro; Marshall, David; Martinez, Diana; McLean, Karen; Mejía, Nilo; Milne, Linda; Munive, Susan; Nagy, Istvan; Ponce, Olga; Ramirez, Manuel; Simon, Reinhard; Thomson, Susan J; Torres, Yerisf; Waugh, Robbie; Zhang, Zhonghua; Huang, Sanwen; Visser, Richard G F; Bachem, Christian W B; Sagredo, Boris; Feingold, Sergio E; Orjeda, Gisella; Veilleux, Richard E; Bonierbale, Merideth; Jacobs, Jeanne M E; Milbourne, Dan; Martin, David Michael Alan; Bryan, Glenn J

    2013-11-06

    The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

  4. Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

    PubMed Central

    Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan; Sønderkær, Mads; Amoros, Walter; Carboni, Martin Federico; D’Ambrosio, Juan Martín; de la Cruz, German; Di Genova, Alex; Douches, David S.; Eguiluz, Maria; Guo, Xiao; Guzman, Frank; Hackett, Christine A.; Hamilton, John P.; Li, Guangcun; Li, Ying; Lozano, Roberto; Maass, Alejandro; Marshall, David; Martinez, Diana; McLean, Karen; Mejía, Nilo; Milne, Linda; Munive, Susan; Nagy, Istvan; Ponce, Olga; Ramirez, Manuel; Simon, Reinhard; Thomson, Susan J.; Torres, Yerisf; Waugh, Robbie; Zhang, Zhonghua; Huang, Sanwen; Visser, Richard G. F.; Bachem, Christian W. B.; Sagredo, Boris; Feingold, Sergio E.; Orjeda, Gisella; Veilleux, Richard E.; Bonierbale, Merideth; Jacobs, Jeanne M. E.; Milbourne, Dan; Martin, David Michael Alan; Bryan, Glenn J.

    2013-01-01

    The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”. PMID:24062527

  5. An Integrated Genetic and Physical Map for the Malaria Vector Anopheles funestus

    PubMed Central

    Wondji, Charles S.; Hunt, Richard H.; Pignatelli, Patricia; Steen, Keith; Coetzee, Maureen; Besansky, Nora; Lobo, Neil; Collins, Frank H.; Hemingway, Janet; Ranson, Hilary

    2005-01-01

    We have constructed a genetic map of the major African malaria vector, Anopheles funestus, using genetic markers segregating in F2 progeny from crosses between two strains colonized from different field sites. Genotyping was performed on 174 progeny from three families using 33 microsatellite markers, a single RFLP, and 15 single nucleotide polymorphism (SNP) loci. Four linkage groups were resolved and these were anchored to chromosomes X and 2 and chromosomal arms 3R and 3L by comparison with a physical map of this species. Five markers were linked to the X chromosome, 16 markers to chromosome 2, and 10 and 11 markers to chromosomal arms 3R and 3L, respectively. This significantly increases the number of chromosomally defined genetic markers for this species and will facilitate the identification of genes controlling epidemiologically important traits such as resistance to insecticides or vector competence. PMID:16143619

  6. The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps

    USDA-ARS?s Scientific Manuscript database

    Methods to automatically integrate sequence information with physical and genetic maps are scarce. The Locus Lookup Tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are reported. Using the Locus Look...

  7. Map of physics

    NASA Astrophysics Data System (ADS)

    2008-10-01

    Based on bibliometric data from information-services provider Thomson Reuters, this map reveals "core areas" of physics, shown as coloured circular nodes, and the relationship between these subdisciplines, shown as lines.

  8. Integrating Physical and Topographic Information Into a Fuzzy Scheme to Map Flooded Area by SAR

    PubMed Central

    Pierdicca, Nazzareno; Chini, Marco; Pulvirenti, Luca; Macina, Flavia

    2008-01-01

    A flood mapping procedure based on a fuzzy sets theory has been developed. The method is based on the integration of Synthetic Aperture Radar (SAR) measurements with additional data on the inundated area, such as a land cover map and a digital elevation model (DEM). The information on land cover has allowed us to account for both specular reflection, typical of open water, and double bounce backscattering, typical of forested and urban areas. DEM has been exploited to include simple hydraulic considerations on the dependence of inundation probability on surface characteristics. Contextual information has been taken into account too. The proposed algorithm has been tested on a flood occurred in Italy on November 1994. A pair of ERS-1 images, collected before and after (three days later) the flood, has been used. The results have been compared with the data provided by a ground survey carried out when the flood reached its maximum extension. Despite the temporal mismatch between the survey and the post-inundation SAR image, the comparison has yielded encouraging results, with the 87% of the pixels correctly classified as inundated. PMID:27879928

  9. Integrating maps requires integrated data

    SciTech Connect

    Weissenbach, J.; Bentolila, S.

    1996-06-01

    The molecular genetics movement has proceeded admirably thanks to new technologies such as polymerase chain reaction (PCR) sequencing. However, the integration of mapping data has not yet been achieved. This article discussing several problem areas and serves as a reminder of the urgency of such concerns.

  10. Assessment and mapping of debris flow hazard through integrated physically based models and GIS assisted methods.

    NASA Astrophysics Data System (ADS)

    Aronica, Giuseppe T.; Cascone, Ernesto; Randazzo, Giovanni; Biondi, Giovanni; Lanza, Stefania; Fraccarollo, Luigi; Brigandi, Giuseppina

    2010-05-01

    Catastrophic events periodically occur in the area of Messina (Sicily, Italy). Both in October 2007 and in October 2009 debris/mud flows triggered by heavy rainfall affected various towns and villages located along the jonian coast of the town, highlighting the destructive potential of these events. The two events gave rise to severe property damage and in the latter more than 40 people were killed. Objective of this study is to present an integrated modelling approach based on three different models, namely an hydrological model, a slope stability model and an hydraulic model, to identify potential debris flow hazard areas. A continuous semi-distributed form of the well known hydrological model IHACRES has been used to derive soil moisture conditions by simulating the infiltration process in Hortonian form. As matter of fact, the soil is conceptually schematized with a catchment storage parameter which represents catchment wetness/soil moisture. The slope stability model allows identifying potential debris-flow sources and is based on the model SHALSTAB that permits to detect those parts of the catchment whose stability conditions are strongly affected by pore water pressure build-up due to local rainfall and soil conductivity and those parts of the basin that, conversely, are unconditionally stable under static loading conditions. Assuming that the solids and the interstitial fluid move downstream with the same velocity, debris flow propagation is described using a two dimensional depth averaged model. Based on extensive sediment sampling and morphological observations, the rheological characterization of the flowing mixture, along with erosion/deposition mechanisms, will be carefully considered in the model. Differential equations are integrated with an implicit Galerkin finite element scheme or, alternatively, finite volume methods. To illustrate this approach, the proposed methodology is applied to a debris flow occurred in the Mastroguglielmo catchment in

  11. Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization.

    PubMed

    Li, Jinhong; Webster, Margaret A; Wright, Jonathan; Cocker, Jonathan M; Smith, Matthew C; Badakshi, Farah; Heslop-Harrison, Pat; Gilmartin, Philip M

    2015-10-01

    Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location. We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization. We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair. These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus.

  12. A High-throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map

    PubMed Central

    Klein, Patricia E.; Klein, Robert R.; Cartinhour, Samuel W.; Ulanch, Paul E.; Dong, Jianmin; Obert, Jacque A.; Morishige, Daryl T.; Schlueter, Shannon D.; Childs, Kevin L.; Ale, Melissa; Mullet, John E.

    2000-01-01

    Sorghum is an important target for plant genomic mapping because of its adaptation to harsh environments, diverse germplasm collection, and value for comparing the genomes of grass species such as corn and rice. The construction of an integrated genetic and physical map of the sorghum genome (750 Mbp) is a primary goal of our sorghum genome project. To help accomplish this task, we have developed a new high-throughput PCR-based method for building BAC contigs and locating BAC clones on the sorghum genetic map. This task involved pooling 24,576 sorghum BAC clones (∼4× genome equivalents) in six different matrices to create 184 pools of BAC DNA. DNA fragments from each pool were amplified using amplified fragment length polymorphism (AFLP) technology, resolved on a LI-COR dual-dye DNA sequencing system, and analyzed using Bionumerics software. On average, each set of AFLP primers amplified 28 single-copy DNA markers that were useful for identifying overlapping BAC clones. Data from 32 different AFLP primer combinations identified ∼2400 BACs and ordered ∼700 BAC contigs. Analysis of a sorghum RIL mapping population using the same primer pairs located ∼200 of the BAC contigs on the sorghum genetic map. Restriction endonuclease fingerprinting of the entire collection of sorghum BAC clones was applied to test and extend the contigs constructed using this PCR-based methodology. Analysis of the fingerprint data allowed for the identification of 3366 contigs each containing an average of 5 BACs. BACs in ∼65% of the contigs aligned by AFLP analysis had sufficient overlap to be confirmed by DNA fingerprint analysis. In addition, 30% of the overlapping BACs aligned by AFLP analysis provided information for merging contigs and singletons that could not be joined using fingerprint data alone. Thus, the combination of fingerprinting and AFLP-based contig assembly and mapping provides a reliable, high-throughput method for building an integrated genetic and physical map

  13. Nonlinear Dynamics: Maps, Integrators and Solitons

    SciTech Connect

    Parsa, Z.

    1998-10-01

    For many physical systems of interest in various disciplines, the solution to nonlinear differential equations describing the physical systems can be generated using maps, symplectic integrators and solitons. We discuss these methods and apply them for various examples.

  14. Physical Parameter Eclipse Mapping

    NASA Astrophysics Data System (ADS)

    Vrielmann, S.

    The tomographic method Physical Parameter Eclipse Mapping is a tool to reconstruct spatial distributions of physical parameters (like temperatures and surface densities) in accretion discs of cataclysmic variables. After summarizing the method, we apply it to multi-colour eclipse light curves of various dwarf novae and nova-likes like VZ Scl, IP Peg in outburst, UU Aqr, V2051 Oph and HT Cas in order to derive the temperatures (and surface densities) in the disc, the white dwarf temperature, the disc size, the effective temperatures and the viscosities. The results allows us to establish or refine a physical model for the accretion disc. Our maps of HT Cas and V 2051Oph, for example, indicate that the (quiescent) disc must be structured into a cool, optically thick inner disc sandwiched by hot, optically thin chromospheres. In addition, the disc of HT Cas must be patchy with a covering factor of about 40% caused by magnetic activity in the disc.

  15. An integrated genetic and physical map of the autosomal recessive polycystic kidney disease region

    SciTech Connect

    Lens, X.M.; Onuchic, L.F.; Daoust, M.

    1997-05-01

    Autosomal recessive polycystic kidney disease is one of the most common hereditary renal cystic diseases in children. Genetic studies have recently assigned the only known locus for this disorder, PKHD1, to chromosome 6p21-p12. We have generated a YAC contig that spans {approximately}5 cM of this region, defined by the markers D6S1253-D6S295, and have mapped 43 sequence-tagged sites (STS) within this interval. This set includes 20 novel STSs, which define 12 unique positions in the region, and three ESTs. A minimal set of two YACs spans the segment D6S465-D6S466, which contains PKHD1, and estimates of their sizes based on information in public databases suggest that the size of the critical region is <3.1 Mb. Twenty-eight STSs map to this interval, giving an average STS density of <1/150 kb. These resources will be useful for establishing a complete trancription map of the PKHD1 region. 10 refs., 1 fig., 1 tab.

  16. Genetic and physical map correlation

    USDA-ARS?s Scientific Manuscript database

    Genetic and physical maps illustrate the arrangement of genes and DNA markers on a chromosome. The relative distances between positions on a genetic map are calculated using recombination frequencies while a physical map is based on the actual number of nucleotide pairs between loci. These maps ar...

  17. An integrated cytogenetic and physical map reveals unevenly distributed recombination spots along the papaya sex chromosomes.

    PubMed

    Wai, Ching Man; Moore, Paul H; Paull, Robert E; Ming, Ray; Yu, Qingyi

    2012-08-01

    Papaya is a model system for the study of sex chromosome evolution in plants. However, the cytological structures of the papaya chromosomes remain largely unknown and chromosomal features have not been linked with any genetic or genomic data. We constructed a cytogenetic map of the papaya sex chromosome (chromosome 1) by hybridizing 16 microsatellite markers and 2 cytological feature-associated markers on pachytene chromosomes using fluorescence in situ hybridization (FISH). Except for three markers, the order of the markers was concordant to that of marker loci along the linkage map. This discrepancy was likely caused by skewed segregation in the highly heterochromatic or centromeric regions. The papaya sex chromosome is largely euchromatic, its heterochromatin spans about 15 % of the Y chromosome and is mostly restricted to the centromeric and pericentromeric regions. Analysis of the recombination frequency along the papaya sex chromosome revealed a complete suppression of recombination in the centromere and pericentromere region and 60 % higher recombination rate in the long arm than in the short arm. The uneven distribution of recombination events might be caused by differences in sequence composition. Sequence analysis of 18 scaffolds in total length of 15 Mb revealed higher gene density towards the telomeres and lower gene density towards the centromere, and a relatively higher gene density in the long arm than in the short arm. In an opposite trend, the centromeric and pericentromeric region contained the highest repetitive sequences and the long arm showed the lowest repetitive sequences. This cytogenetic map provides essential information for evolutionary study of sex chromosomes in Caricaceae and will facilitate the analysis of papaya sex chromosomes.

  18. A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps

    PubMed Central

    Yim, Young-Sun; Moak, Patricia; Sanchez-Villeda, Hector; Musket, Theresa A; Close, Pamela; Klein, Patricia E; Mullet, John E; McMullen, Michael D; Fang, Zheiwei; Schaeffer, Mary L; Gardiner, Jack M; Coe, Edward H; Davis, Georgia L

    2007-01-01

    Background Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps. Results A total of 110,592 maize BAC clones (~ 6x haploid genome equivalents) were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI) and the Arizona Genomics Computational Laboratory (AGCoL) to assemble the BAC contigs using the FingerPrinted Contigs (FPC) software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5%) anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize [1,2]. Conclusion This BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information. PMID:17291341

  19. Statistical methods in physical mapping

    SciTech Connect

    Nelson, David O.

    1995-05-01

    One of the great success stories of modern molecular genetics has been the ability of biologists to isolate and characterize the genes responsible for serious inherited diseases like fragile X syndrome, cystic fibrosis and myotonic muscular dystrophy. This dissertation concentrates on constructing high-resolution physical maps. It demonstrates how probabilistic modeling and statistical analysis can aid molecular geneticists in the tasks of planning, execution, and evaluation of physical maps of chromosomes and large chromosomal regions. The dissertation is divided into six chapters. Chapter 1 provides an introduction to the field of physical mapping, describing the role of physical mapping in gene isolation and ill past efforts at mapping chromosomal regions. The next two chapters review and extend known results on predicting progress in large mapping projects. Such predictions help project planners decide between various approaches and tactics for mapping large regions of the human genome. Chapter 2 shows how probability models have been used in the past to predict progress in mapping projects. Chapter 3 presents new results, based on stationary point process theory, for progress measures for mapping projects based on directed mapping strategies. Chapter 4 describes in detail the construction of all initial high-resolution physical map for human chromosome 19. This chapter introduces the probability and statistical models involved in map construction in the context of a large, ongoing physical mapping project. Chapter 5 concentrates on one such model, the trinomial model. This chapter contains new results on the large-sample behavior of this model, including distributional results, asymptotic moments, and detection error rates. In addition, it contains an optimality result concerning experimental procedures based on the trinomial model. The last chapter explores unsolved problems and describes future work.

  20. Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.).

    PubMed

    Ha, Jungmin; Abernathy, Brian; Nelson, William; Grant, David; Wu, Xiaolei; Nguyen, Henry T; Stacey, Gary; Yu, Yeisoo; Wing, Rod A; Shoemaker, Randy C; Jackson, Scott A

    2012-03-01

    Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547 Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.

  1. The Integration of Recombination and Physical Maps in a Large-Genome Monocot Using Haploid Genome Analysis in a Trihybrid Allium Population

    PubMed Central

    Khrustaleva, L. I.; de Melo, P. E.; van Heusden, A. W.; Kik, C.

    2005-01-01

    Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa × (A. roylei × A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions. PMID:15654085

  2. The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population.

    PubMed

    Khrustaleva, L I; de Melo, P E; van Heusden, A W; Kik, C

    2005-03-01

    Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa x (A. roylei x A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.

  3. Integrating maps of chromosome 21.

    PubMed

    Patterson, D

    1992-06-01

    The past year has seen major progress in the construction of various types of maps of human chromosome 21. Perhaps more significantly, the chromosome 21 research community is making very significant progress on integration of these maps through the use of common resources and increased collaboration and communication.

  4. Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber.

    PubMed

    Lou, Qunfeng; He, Yuhua; Cheng, Chunyan; Zhang, Zhonghua; Li, Ji; Huang, Sanwen; Chen, Jinfeng

    2013-01-01

    Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH). Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics in cucumber.

  5. Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

    PubMed Central

    Hass-Jacobus, Barbara L; Futrell-Griggs, Montona; Abernathy, Brian; Westerman, Rick; Goicoechea, Jose-Luis; Stein, Joshua; Klein, Patricia; Hurwitz, Bonnie; Zhou, Bin; Rakhshan, Fariborz; Sanyal, Abhijit; Gill, Navdeep; Lin, Jer-Young; Walling, Jason G; Luo, Mei Zhong; Ammiraju, Jetty Siva S; Kudrna, Dave; Kim, Hye Ran; Ware, Doreen; Wing, Rod A; Miguel, Phillip San; Jackson, Scott A

    2006-01-01

    Background With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8–10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40–50 million years ago. Results Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa. Conclusion The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which

  6. A 1.7-Mb YAC contig around the human BDNF gene (11p13): integration of the physical, genetic, and cytogenetic maps in relation to WAGR syndrome

    SciTech Connect

    Rosier, M.F.; Martin, A.; Houlgatte, R.

    1994-11-01

    WAGR (Wilms tumor, aniridia, genito-urinary abnormalities, mental retardation) syndrome in humans is associated with deletions of the 11p13 region. The brain-derived neurotrophic factor (BDNF) gene maps to this region, and its deletion seems to contribute to the severity of the patient`s mental retardation. Yeast artificial chromosomes (YACs) carrying the BDNF gene have been isolated and characterized. Localization of two known exons of this gene leads to a minimal estimation of its size of about 40 kb. Chimerism of the BDNF YACs has been investigated by fluorescence in situ hybridization and chromosome assignment on somatic cell hybrids. Using the BDNF gene, YAC end sequence tagged sites (STS), and Genethon microsatellite markers, the authors constructed a 1.7-Mb contig and refined the cytogenetic map at 11p13. The resulting integrated physical, genetic, and cytogenetic map constitutes a resource for the characterization of genes that may be involved in the WAGR syndrome. 42 refs., 2 figs., 3 tabs.

  7. Map of the Physical Sciences

    SciTech Connect

    Boyack, Kevin W.

    1999-07-02

    Various efforts to map the structure of science have been undertaken over the years. Using a new tool, VxInsight{trademark}, we have mapped and displayed 3000 journals in the physical sciences. This map is navigable and interactively reveals the structure of science at many different levels. Science mapping studies are typically focused at either the macro-or micro-level. At a macro-level such studies seek to determine the basic structural units of science and their interrelationships. The majority of studies are performed at the discipline or specialty level, and seek to inform science policy and technical decision makers. Studies at both levels probe the dynamic nature of science, and the implications of the changes. A variety of databases and methods have been used for these studies. Primary among databases are the citation indices (SCI and SSCI) from the Institute for Scientific Information, which have gained widespread acceptance for bibliometric studies. Maps are most often based on computed similarities between journal articles (co-citation), keywords or topics (co-occurrence or co-classification), or journals (journal-journal citation counts). Once the similarity matrix is defined, algorithms are used to cluster the data.

  8. Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

    USDA-ARS?s Scientific Manuscript database

    Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the pre...

  9. Individual chromosome identification, chromosomal collinearity and genetic-physical integrated map in Gossypium darwinii and four D genome cotton species revealed by BAC-FISH.

    PubMed

    Gan, Yimei; Liu, Fang; Peng, Renhai; Wang, Chunying; Li, Shaohui; Zhang, Xiangdi; Wang, Yuhong; Wang, Kunbo

    2012-01-01

    The study was conducted on the individual chromosome identification in Gossypium darwinii (A(d)D(d)), G. klotzschianum (D(3k)), G. davidsonii (D(3d)), G. armourianum (D(2-1)) and G. aridum (D(4)) using a multi-probe fluorescence of in situ hybridization (FISH) system. Comparative analysis on their genetic maps with that of physical maps was made as well. The FISH probes used contained two sets of bacterial artificial chromosome (BAC) clones [one is specific to 26 individual chromosomes from A and D subgenomes of G. hirsutum (A(h) and D(h)) while the other is a D genome centromere-specific BAC clone 150D24], 45S and 5S rDNA clones. The results showed that all A(d) chromosomes were marked with the 13 A(h) chromosome-specific BAC clones, whilst all D(d), D(3k), D(3d), D(2-1) and D(4) chromosomes and chromosomal arms were identified with the 13 D(h) chromosome-specific BAC clones and the D genome centromere-specific BAC. According to the homology within D subgenomes which are between A (D) genome and A (D) subgenome, the systematic nomenclature for individual chromosome in the five species was established. The chromosomes of A (D) subgenomes in G. darwinii were named as A(d)01-A(d)13 (D(d)01-D(d)13). The chromosomes in D(3k), D(3d), D(2-1) and D(4) were named as D(3k)01-D(3k)13, D(3d)01-D(3d)13, D(2-1)01-D(2-1)13 and D(4)01-D(4)13, respectively. Based on the successful identification for individual chromosomes, 45S and 5S rDNA were located to the special chromosomes and chromosomal arms for all five species. And there appeared chromosomal collinearity from the BAC clones among different species by comparing BACs positions, which suggested that the majority of chromosome segment homology may exist between D genomes and D subgenome. Moreover, as the genetic map and physical map were integrated, the orientations of genetic maps for D(d) and D genomes of diploid cotton were established. The orientations of some of chromosomes in genetic maps (D(d)03, D(d)04, D(d)06, D(d)09

  10. Physical mapping of complex genomes

    DOEpatents

    Evans, Glen A.

    1993-01-01

    Method for simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts int he pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert int he common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed. In other preferred

  11. Physical mapping of complex genomes

    DOEpatents

    Evans, G.A.

    1993-06-15

    A method for the simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts in the pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert in the common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed.

  12. Sex-Integrated Physical Education

    ERIC Educational Resources Information Center

    Kneer, Marian E.

    1978-01-01

    Title IX requires that the practice of segregating physical education classes on the basis of sex must cease. This article offers suggestions on how to ease the transition to sex-integrated physical education programs. (Author/DS)

  13. Integrating Physical Education, Math, and Physics

    ERIC Educational Resources Information Center

    Hatch, Greg M.; Smith, Darla R.

    2004-01-01

    The primary goal of education is to help students gain the knowledge and skills necessary to solve the problems that occur in real-life situations. One of the most touted methods for achieving this goal is through curriculum integration. Physical education students can benefit from an integrated curriculum. NASPE's (National Association tar Sport…

  14. A physical map of the human genome

    SciTech Connect

    McPherson, J.D.; Marra, M.; Hillier, L.; Waterston, R.H.; Chinwalla, A.; Wallis, J.; Sekhon, M.; Wylie, K.; Mardis, E.R.; Wilson, R.K.; Fulton, R.; Kucaba, T.A.; Wagner-McPherson, C.; Barbazuk, W.B.; Gregory, S.G.; Humphray, S.J.; French, L.; Evans, R.S.; Bethel, G.; Whittaker, A.; Holden, J.L.; McCann, O.T.; Dunham, A.; Soderlund, C.; Scott, C.E.; Bentley, D.R.; Schuler, G.; Chen, H.-C.; Jang, W.; Green, E.D.; Idol, J.R.; Maduro, V.V. Braden; Montgomery, K.T.; Lee, E.; Miller, A.; Emerling, S.; Kucherlapati; Gibbs, R.; Scherer, S.; Gorrell, J.H.; Sodergren, E.; Clerc-Blankenburg, K.; Tabor, P.; Naylor, S.; Garcia, D.; de Jong, P.J.; Catanese, J.J.; Nowak, N.; Osoegawa, K.; Qin, S.; Rowen, L.; Madan, A.; Dors, M.; Hood, L.; Trask, B.; Friedman, C.; Massa, H.; Cheung, V.G.; Kirsch, I.R.; Reid, T.; Yonescu, R.; Weissenbach, J.; Bruls, T.; Heilig, R.; Branscomb, E.; Olsen, A.; Doggett, N.; Cheng, J.F.; Hawkins, T.; Myers, R.M.; Shang, J.; Ramirez, L.; Schmutz, J.; Velasquez, O.; Dixon, K.; Stone, N.E.; Cox, D.R.; Haussler, D.; Kent, W.J.; Furey, T.; Rogic, S.; Kennedy, S.; Jones, S.; Rosenthal, A.; Wen, G.; Schilhabel, M.; Gloeckner, G.; Nyakatura, G.; Siebert, R.; Schlegelberger, B.; Korenberg, J.; Chen, X.N.; Fujiyama, A.; Hattori, M.; Toyoda, A.; Yada, T.; Park, H.S.; Sakaki, Y.; Shimizu, N.; Asakawa, S.; Kawasaki, K.; Sasaki, T.; Shintani, A.; Shimizu, A.; Shibuya, K.; Kudoh, J.; Minoshima, S.; Ramser, J.; Seranski, P.; Hoff, C.; Poustka, A.; Reinhardt, R.; Lehrach, H.

    2001-01-01

    The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

  15. Recent developments in MAP - MODULAR APPROACH to PHYSICS

    NASA Astrophysics Data System (ADS)

    Rae, Jennifer; Austen, Dave; Brouwer, Wytze

    2002-05-01

    We present recent developments in MAP - MODULAR APPROACH to PHYSICS - JAVA enhanced modules to be used as aids in teaching the first 3 terms of university physics. The MAP project is very comprehensive and consists of a modular approach to physics that utilizes JAVA applets, FLASH animations and HTML based tutorials. The overall instructional philosophy of MAP is constructivist and the project emphasizes active learner participation. In this talk we will provide a quick overview of the project and the results of recent pilot testing at several Canadian universities. It will also include a discussion of the VIDEO LAB aspect of MAP. This is a component that is integrated into MAP and permits students to capture and evaluate otherwise difficult to study phenomena on video.

  16. Integrating Physically Handicapped Pupils.

    ERIC Educational Resources Information Center

    Hodgson, Ann

    1984-01-01

    Intended for regular class teachers working with mainstreamed physically handicapped pupils, the article offers guidelines regarding school organization, conditions directly affecting the pupil, and classroom considerations. A brief review of the major conditions (such as allergies, cerebral palsy, and muscular dystrophy) is presented. (CL)

  17. Integrating Physically Handicapped Pupils.

    ERIC Educational Resources Information Center

    Hodgson, Ann

    1984-01-01

    Intended for regular class teachers working with mainstreamed physically handicapped pupils, the article offers guidelines regarding school organization, conditions directly affecting the pupil, and classroom considerations. A brief review of the major conditions (such as allergies, cerebral palsy, and muscular dystrophy) is presented. (CL)

  18. Integrable mappings via rational elliptic surfaces

    NASA Astrophysics Data System (ADS)

    Tsuda, Teruhisa

    2004-02-01

    We present a geometric description of the QRT map (which is an integrable mapping introduced by Quispel, Roberts and Thompson) in terms of the addition formula of a rational elliptic surface. By this formulation, we classify all the cases when the QRT map is periodic; and show that its period is 2, 3, 4, 5 or 6. A generalization of the QRT map which acts birationally on a pencil of K3 surfaces, or Calabi-Yau manifolds, is also presented.

  19. Non-integrability vs. integrability in pentagram maps

    NASA Astrophysics Data System (ADS)

    Khesin, Boris; Soloviev, Fedor

    2015-01-01

    We revisit recent results on integrable cases for higher-dimensional generalizations of the 2D pentagram map: short-diagonal, dented, deep-dented, and corrugated versions, and define a universal class of pentagram maps, which are proved to possess projective duality. We show that in many cases the pentagram map cannot be included into integrable flows as a time-one map, and discuss how the corresponding notion of discrete integrability can be extended to include jumps between invariant tori. We also present a numerical evidence that certain generalizations of the integrable 2D pentagram map are non-integrable and present a conjecture for a necessary condition of their discrete integrability.

  20. A physical map of the bovine genome

    PubMed Central

    Snelling, Warren M; Chiu, Readman; Schein, Jacqueline E; Hobbs, Matthew; Abbey, Colette A; Adelson, David L; Aerts, Jan; Bennett, Gary L; Bosdet, Ian E; Boussaha, Mekki; Brauning, Rudiger; Caetano, Alexandre R; Costa, Marcos M; Crawford, Allan M; Dalrymple, Brian P; Eggen, André; Everts-van der Wind, Annelie; Floriot, Sandrine; Gautier, Mathieu; Gill, Clare A; Green, Ronnie D; Holt, Robert; Jann, Oliver; Jones, Steven JM; Kappes, Steven M; Keele, John W; de Jong, Pieter J; Larkin, Denis M; Lewin, Harris A; McEwan, John C; McKay, Stephanie; Marra, Marco A; Mathewson, Carrie A; Matukumalli, Lakshmi K; Moore, Stephen S; Murdoch, Brenda; Nicholas, Frank W; Osoegawa, Kazutoyo; Roy, Alice; Salih, Hanni; Schibler, Laurent; Schnabel, Robert D; Silveri, Licia; Skow, Loren C; Smith, Timothy PL; Sonstegard, Tad S; Taylor, Jeremy F; Tellam, Ross; Van Tassell, Curtis P; Williams, John L; Womack, James E; Wye, Natasja H; Yang, George; Zhao, Shaying

    2007-01-01

    Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans. PMID:17697342

  1. Physics Integration KErnels (PIKE)

    SciTech Connect

    Pawlowski, Roger

    2014-07-31

    Pike is a software library for coupling and solving multiphysics applications. It provides basic interfaces and utilities for performing code-to-code coupling. It provides simple “black-box” Picard iteration methods for solving the coupled system of equations including Jacobi and Gauss-Seidel solvers. Pike was developed originally to couple neutronics and thermal fluids codes to simulate a light water nuclear reactor for the Consortium for Simulation of Light-water Reactors (CASL) DOE Energy Innovation Hub. The Pike library contains no physics and just provides interfaces and utilities for coupling codes. It will be released open source under a BSD license as part of the Trilinos solver framework (trilinos.org) which is also BSD. This code provides capabilities similar to other open source multiphysics coupling libraries such as LIME, AMP, and MOOSE.

  2. A physical map of the mouse genome.

    PubMed

    Gregory, Simon G; Sekhon, Mandeep; Schein, Jacqueline; Zhao, Shaying; Osoegawa, Kazutoyo; Scott, Carol E; Evans, Richard S; Burridge, Paul W; Cox, Tony V; Fox, Christopher A; Hutton, Richard D; Mullenger, Ian R; Phillips, Kimbly J; Smith, James; Stalker, Jim; Threadgold, Glen J; Birney, Ewan; Wylie, Kristine; Chinwalla, Asif; Wallis, John; Hillier, LaDeana; Carter, Jason; Gaige, Tony; Jaeger, Sara; Kremitzki, Colin; Layman, Dan; Maas, Jason; McGrane, Rebecca; Mead, Kelly; Walker, Rebecca; Jones, Steven; Smith, Michael; Asano, Jennifer; Bosdet, Ian; Chan, Susanna; Chittaranjan, Suganthi; Chiu, Readman; Fjell, Chris; Fuhrmann, Dan; Girn, Noreen; Gray, Catharine; Guin, Ran; Hsiao, Letticia; Krzywinski, Martin; Kutsche, Reta; Lee, Soo Sen; Mathewson, Carrie; McLeavy, Candice; Messervier, Steve; Ness, Steven; Pandoh, Pawan; Prabhu, Anna-Liisa; Saeedi, Parvaneh; Smailus, Duane; Spence, Lorraine; Stott, Jeff; Taylor, Sheryl; Terpstra, Wesley; Tsai, Miranda; Vardy, Jill; Wye, Natasja; Yang, George; Shatsman, Sofiya; Ayodeji, Bola; Geer, Keita; Tsegaye, Getahun; Shvartsbeyn, Alla; Gebregeorgis, Elizabeth; Krol, Margaret; Russell, Daniel; Overton, Larry; Malek, Joel A; Holmes, Mike; Heaney, Michael; Shetty, Jyoti; Feldblyum, Tamara; Nierman, William C; Catanese, Joseph J; Hubbard, Tim; Waterston, Robert H; Rogers, Jane; de Jong, Pieter J; Fraser, Claire M; Marra, Marco; McPherson, John D; Bentley, David R

    2002-08-15

    A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.

  3. A first generation integrated map of the rainbow trout genome.

    PubMed

    Palti, Yniv; Genet, Carine; Luo, Ming-Cheng; Charlet, Aurélie; Gao, Guangtu; Hu, Yuqin; Castaño-Sánchez, Cecilia; Tabet-Canale, Kamila; Krieg, Francine; Yao, Jianbo; Vallejo, Roger L; Rexroad, Caird E

    2011-04-07

    Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. An integrated physical and genetic map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) programs for improving rainbow trout aquaculture production. The first generation integrated map of the rainbow trout genome is composed of 238 BAC contigs anchored to chromosomes of the genetic map. It covers more than 10% of the genome across segments from all 29 chromosomes. Anchoring of 203 contigs to chromosomes of the National Center for Cool and Cold Water Aquaculture (NCCCWA) genetic map was achieved through mapping of 288 genetic markers derived from BAC end sequences (BES), screening of the BAC library with previously mapped markers and matching of SNPs with BES reads. In addition, 35 contigs were anchored to linkage groups of the INRA (French National Institute of Agricultural Research) genetic map through markers that were not informative for linkage analysis in the NCCCWA mapping panel. The ratio of physical to genetic linkage distances varied substantially among chromosomes and BAC contigs with an average of 3,033 Kb/cM. The integrated map described here provides a framework for a robust composite genome map for rainbow trout. This resource is needed for genomic analyses in this research model and economically important species and will facilitate comparative genome mapping with other salmonids and with model fish species. This resource will also facilitate efforts to assemble a whole

  4. A first generation integrated map of the rainbow trout genome

    PubMed Central

    2011-01-01

    Background Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. An integrated physical and genetic map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) programs for improving rainbow trout aquaculture production. Results The first generation integrated map of the rainbow trout genome is composed of 238 BAC contigs anchored to chromosomes of the genetic map. It covers more than 10% of the genome across segments from all 29 chromosomes. Anchoring of 203 contigs to chromosomes of the National Center for Cool and Cold Water Aquaculture (NCCCWA) genetic map was achieved through mapping of 288 genetic markers derived from BAC end sequences (BES), screening of the BAC library with previously mapped markers and matching of SNPs with BES reads. In addition, 35 contigs were anchored to linkage groups of the INRA (French National Institute of Agricultural Research) genetic map through markers that were not informative for linkage analysis in the NCCCWA mapping panel. The ratio of physical to genetic linkage distances varied substantially among chromosomes and BAC contigs with an average of 3,033 Kb/cM. Conclusions The integrated map described here provides a framework for a robust composite genome map for rainbow trout. This resource is needed for genomic analyses in this research model and economically important species and will facilitate comparative genome mapping with other salmonids and with model fish species. This resource will also facilitate efforts to

  5. The Pentagram Map: A Discrete Integrable System

    NASA Astrophysics Data System (ADS)

    Ovsienko, Valentin; Schwartz, Richard; Tabachnikov, Serge

    2010-10-01

    The pentagram map is a projectively natural transformation defined on (twisted) polygons. A twisted polygon is a map from {mathbb Z} into {{mathbb{RP}}^2} that is periodic modulo a projective transformation called the monodromy. We find a Poisson structure on the space of twisted polygons and show that the pentagram map relative to this Poisson structure is completely integrable. For certain families of twisted polygons, such as those we call universally convex, we translate the integrability into a statement about the quasi-periodic motion for the dynamics of the pentagram map. We also explain how the pentagram map, in the continuous limit, corresponds to the classical Boussinesq equation. The Poisson structure we attach to the pentagram map is a discrete version of the first Poisson structure associated with the Boussinesq equation. A research announcement of this work appeared in [16].

  6. Physical and genetic maps for chromosome 10

    SciTech Connect

    Lichter, J.B.; Difilippantonio, M.J.; Pakstis, A.J.; Ward, D.C.; Kidd, K.K.; Goodfellow, P.J.

    1993-05-01

    A fluorescence in situ hybridization (FISH) physical map of 14 polymorphic loci on chromosome 10 covers over 62% of the fractional length of chromosome 10. The positions of three previously mapped loci are confirmed, nine more are refined, and two new loci are cytogenetically mapped. The order of loci determined by FISH agrees with that obtained by genetic linkage studies. When the distance estimates for the physical map are compared to the distance estimates of the existing linkage map, the sex average ratio of the fractional length (FL) per centimorgan (cM) for this portion of chromosome 10 is 0.004 (or 0.4% FL/cM). However, the average ratios for male- and female-specific genetic distances are quite different, in agreement with an overall higher rate of recombination in females (0.008 FL/cM and 0.003 FL/cM, respectively). Moreover, the ratio across the centromere is larger for both the male (0.031 FL/cM) and the female (0.009 FL/cM) than the ratio encompassing the q arm (0.006 FL/cM for males and 0.002 FL/cM for females), suggesting that there is reduced recombination at the centromere in both the male and the female maps when compared to the physical distance generated from FISH on metaphase chromosomes. 15 refs., 3 figs., 1 tab.

  7. Statistical and computational challenges in physical mapping

    SciTech Connect

    Nelson, D.O.; Speed, T.P.

    1994-06-01

    One of the great success stories of modern molecular genetics has been the ability of biologists to isolate and characterize the genes responsible for serious inherited diseases like Huntington`s disease, cystic fibrosis, and myotonic dystrophy. Instrumental in these efforts has been the construction of so-called {open_quotes}physical maps{close_quotes} of large regions of human chromosomes. Constructing a physical map of a chromosome presents a number of interesting challenges to the computational statistician. In addition to the general ill-posedness of the problem, complications include the size of the data sets, computational complexity, and the pervasiveness of experimental error. The nature of the problem and the presence of many levels of experimental uncertainty make statistical approaches to map construction appealing. Simultaneously, however, the size and combinatorial complexity of the problem make such approaches computationally demanding. In this paper we discuss what physical maps are and describe three different kinds of physical maps, outlining issues which arise in constructing them. In addition, we describe our experience with powerful, interactive statistical computing environments. We found that the ability to create high-level specifications of proposed algorithms which could then be directly executed provided a flexible rapid prototyping facility for developing new statistical models and methods. The ability to check the implementation of an algorithm by comparing its results to that of an executable specification enabled us to rapidly debug both specification and implementation in an environment of changing needs.

  8. IntegratedMap: a Web interface for integrating genetic map data.

    PubMed

    Yang, Hongyu; Wang, Hongyu; Gingle, Alan R

    2005-05-01

    IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources. IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp

  9. Outcome mapping for health system integration

    PubMed Central

    Tsasis, Peter; Evans, Jenna M; Forrest, David; Jones, Richard Keith

    2013-01-01

    Health systems around the world are implementing integrated care strategies to improve quality, reduce or maintain costs, and improve the patient experience. Yet few practical tools exist to aid leaders and managers in building the prerequisites to integrated care, namely a shared vision, clear roles and responsibilities, and a common understanding of how the vision will be realized. Outcome mapping may facilitate stakeholder alignment on the vision, roles, and processes of integrated care delivery via participative and focused dialogue among diverse stakeholders on desired outcomes and enabling actions. In this paper, we describe an outcome-mapping exercise we conducted at a Local Health Integration Network in Ontario, Canada, using consensus development conferences. Our preliminary findings suggest that outcome mapping may help stakeholders make sense of a complex system and foster collaborative capital, a resource that can support information sharing, trust, and coordinated change toward integration across organizational and professional boundaries. Drawing from the theoretical perspectives of complex adaptive systems and collaborative capital, we also outline recommendations for future outcome-mapping exercises. In particular, we emphasize the potential for outcome mapping to be used as a tool not only for identifying and linking strategic outcomes and actions, but also for studying the boundaries, gaps, and ties that characterize social networks across the continuum of care. PMID:23526058

  10. Outcome mapping for health system integration.

    PubMed

    Tsasis, Peter; Evans, Jenna M; Forrest, David; Jones, Richard Keith

    2013-01-01

    Health systems around the world are implementing integrated care strategies to improve quality, reduce or maintain costs, and improve the patient experience. Yet few practical tools exist to aid leaders and managers in building the prerequisites to integrated care, namely a shared vision, clear roles and responsibilities, and a common understanding of how the vision will be realized. Outcome mapping may facilitate stakeholder alignment on the vision, roles, and processes of integrated care delivery via participative and focused dialogue among diverse stakeholders on desired outcomes and enabling actions. In this paper, we describe an outcome-mapping exercise we conducted at a Local Health Integration Network in Ontario, Canada, using consensus development conferences. Our preliminary findings suggest that outcome mapping may help stakeholders make sense of a complex system and foster collaborative capital, a resource that can support information sharing, trust, and coordinated change toward integration across organizational and professional boundaries. Drawing from the theoretical perspectives of complex adaptive systems and collaborative capital, we also outline recommendations for future outcome-mapping exercises. In particular, we emphasize the potential for outcome mapping to be used as a tool not only for identifying and linking strategic outcomes and actions, but also for studying the boundaries, gaps, and ties that characterize social networks across the continuum of care.

  11. Boolean differentiation and integration using Karnaugh maps

    NASA Technical Reports Server (NTRS)

    Tucker, J. H.; Tapia, M. A.; Bennett, A. W.

    1977-01-01

    Algorithms are presented for differentiation and integration of Boolean functions by means of Karnaugh maps. The algorithms are considered simple when the number of variables is six or less; in this case Boolean differentiation and integration is said to be as easy as the Karnaugh map method of simplifying switching functions. It is suggested that the algorithms would be useful in the analysis of faults in combinational systems and in the synthesis of asynchronous sequential systems which utilize edge-sensitive flip-flops.

  12. A Fine Physical Map of the Rice Chromosome 4

    PubMed Central

    Zhao, Qiang; Zhang, Yu; Cheng, Zhukuan; Chen, Mingsheng; Wang, Shengyue; Feng, Qi; Huang, Yucheng; Li, Ying; Tang, Yesheng; Zhou, Bo; Chen, Zhehua; Yu, Shuliang; Zhu, Jingjie; Hu, Xin; Mu, Jie; Ying, Kai; Hao, Pei; Zhang, Lei; Lu, Yiqi; Zhang, Lei S.; Liu, Yilei; Yu, Zhen; Fan, Danlin; Weng, Qijun; Chen, Ling; Lu, Tingting; Liu, Xiaohui; Jia, Peixin; Sun, Tongguo; Wu, Yongrui; Zhang, Yujun; Lu, Ying; Li, Can; Wang, Rong; Lei, Haiyan; Li, Tao; Hu, Hao; Wu, Mei; Zhang, Runquan; Guan, Jianping; Zhu, Jia; Fu, Gang; Gu, Minghong; Hong, Guofan; Xue, Yongbiao; Wing, Rod; Jiang, Jiming; Han, Bin

    2002-01-01

    As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies. [The following individuals and institutions kindly provided reagents, samples, or unpublished information as indicated in the paper: S. McCouch, T. Sasaki, and Monsanto.] PMID:11997348

  13. Technologies for large-scale physical mapping of human chromosomes

    SciTech Connect

    Beugelsdijk, T.J.

    1994-12-01

    Since its inception 6 years ago, the Human Genome Project has made rapid progress towards its ultimate goal of developing the complete sequence of all human chromosomes. This progress has been made possible through the development of automated devices by laboratories throughout the world that aid the molecular biologist in various phases of the project. The initial phase involves the generation of physical and genetic maps of each chromosome. This task is nearing completion at a low resolution level with several instances of very high detailed maps being developed for isolated chromosomes. In support of the initial mapping thrust of this program, the robotics and automation effort at Los Alamos National Laboratory has developed DNA gridding technologies along with associated database and user interface systems. This paper will discuss these systems in detail and focus on the formalism developed for subsystems which allow for facile system integration.

  14. Discrete mappings with an explicit discrete Lyapunov function related to integrable mappings

    NASA Astrophysics Data System (ADS)

    Inoue, Hironori; Takahashi, Daisuke; Matsukidaira, Junta

    2006-05-01

    We propose discrete mappings of second order that have a discrete analogue of Lyapunov function. The mappings are extensions of the integrable Quispel-Roberts-Thompson (QRT) mapping, and a discrete Lyapunov function of the mappings is identical to an explicit conserved quantity of the QRT mapping. Moreover we can obtain a differential and an ultradiscrete limit of the mappings preserving the existence of Lyapunov function. We also give applications of a mapping with an adjusted parameter, a probabilistic mapping and coupled mappings.

  15. Integrating Databases with Maps: The Delivery of Cultural Data through TimeMap.

    ERIC Educational Resources Information Center

    Johnson, Ian

    TimeMap is a unique integration of database management, metadata and interactive maps, designed to contextualise and deliver cultural data through maps. TimeMap extends conventional maps with the time dimension, creating and animating maps "on-the-fly"; delivers them as a kiosk application or embedded in Web pages; links flexibly to…

  16. Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to 14q13.3-q21.1

    PubMed Central

    Gough, Sheryl M; McDonald, Margaret; Chen, Xiao-Ning; Korenberg, Julie R; Neri, Antonino; Kahn, Tomas; Eccles, Michael R; Morris, Christine M

    2003-01-01

    Background Chromosome band 10q24 is a gene-rich domain and host to a number of cancer, developmental, and neurological genes. Recurring translocations, deletions and mutations involving this chromosome band have been observed in different human cancers and other disease conditions, but the precise identification of breakpoint sites, and detailed characterization of the genetic basis and mechanisms which underlie many of these rearrangements has yet to be resolved. Towards this end it is vital to establish a definitive genetic map of this region, which to date has shown considerable volatility through time in published works of scientific journals, within different builds of the same international genomic database, and across the differently constructed databases. Results Using a combination of chromosome and interphase fluorescent in situ hybridization (FISH), BAC end-sequencing and genomic database analysis we present a physical map showing that the order and chromosomal orientation of selected genes within 10q24 is CEN-CYP2C9-PAX2-HOX11-NFKB2-TEL. Our analysis has resolved the orientation of an otherwise dynamically evolving assembly of larger contigs upstream of this region, and in so doing verifies the order and orientation of a further 9 cancer-related genes and GOT1. This study further shows that the previously reported human papillomavirus type 6a DNA integration site HPV6AI1 does not map to 10q24, but that it maps at the interface of chromosome bands 14q13.3-q21.1. Conclusions This revised map will allow more precise localization of chromosome rearrangements involving chromosome band 10q24, and will serve as a useful baseline to better understand the molecular aetiology of chromosomal instability in this region. In particular, the relocation of HPV6AI1 is important to report because this HPV6a integration site, originally isolated from a tonsillar carcinoma, was shown to be rearranged in other HPV6a-related malignancies, including 2 of 25 genital condylomas

  17. Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.)

    USDA-ARS?s Scientific Manuscript database

    Soybean is a model for the legume research community due to its importance as a crop, a well populated genetic map, and the availability of a genome sequence. Even though a whole genome shotgun sequence and Bacterial Artificial Chromosome (BAC) libraries are available, a high-resolution chromosome-b...

  18. Physical mapping of human chromosome 16. Annual progress report

    SciTech Connect

    Sutherland, G.R.

    1993-08-01

    We aim to isolate cDNAs mapping to human chromosome 16 and localise such cDNAs on the high resolution physical map. In collaboration with LANL, PCR primers will be synthesised from cDNA sequences mapped to chromosome 16 and used as ESTs in the generation of mega-YAC contigs for this chromosome. Probing of high density cosmid grids will enable integration of the ESTs into cosmid contigs and location of the cosmid contigs on the YAC contig. A hn-cDNA library has been constructed from the hybrid CY18 which contains chromosome 16 as the only human chromosome. A modified screening protocol has been successfully developed and 15 hn-cDNA clones have been sequenced and localised on the hybrid map. Sequence analysis of four of these revealed that they were known cDNAs, which are now mapped to chromosome 16. Development of techniques to allow the isolation of longer cDNAs from the identified exons is in progress. This will depend on PCR amplification of cDNAs from a total human CDNA library.

  19. Physics as an Integrative Theme in Oceanography.

    ERIC Educational Resources Information Center

    Myers, Richard L.

    1990-01-01

    The teaching of physics as an integral part of an undergraduate oceanography course is described. A general outline of oceanography and the corresponding physics topics is given. The objectives, organization, and difficulties of such a course are discussed. (CW)

  20. Nomenclature for physical mapping of complex genomes

    SciTech Connect

    Not Available

    1989-08-01

    Among these issues, that of establishing nomenclature conventions, was seen to be fundamental to the development of useful data management systems and essential for the orderly and efficient development of such systems. Therefore, the present workshop was convened, as the first in the recommended series, to identify the issues involved in establishing nomenclature standards and to develop a set of recommendations for such standards. This report summarizes the proceedings of the workshop and lays out specific proposals for naming DNA entities for physical mapping. The scientific community should discuss and develop these proposals so that naming conventions can be established. The proposals apply specifically to human DNA entities; however, the relevance to nomenclature in other systems should be part of the broader discussion. 13 refs.

  1. Big data integration for regional hydrostratigraphic mapping

    NASA Astrophysics Data System (ADS)

    Friedel, M. J.

    2013-12-01

    Numerical models provide a way to evaluate groundwater systems, but determining the hydrostratigraphic units (HSUs) used in devising these models remains subjective, nonunique, and uncertain. A novel geophysical-hydrogeologic data integration scheme is proposed to constrain the estimation of continuous HSUs. First, machine-learning and multivariate statistical techniques are used to simultaneously integrate borehole hydrogeologic (lithology, hydraulic conductivity, aqueous field parameters, dissolved constituents) and geophysical (gamma, spontaneous potential, and resistivity) measurements. Second, airborne electromagnetic measurements are numerically inverted to obtain subsurface resistivity structure at randomly selected locations. Third, the machine-learning algorithm is trained using the borehole hydrostratigraphic units and inverted airborne resistivity profiles. The trained machine-learning algorithm is then used to estimate HSUs at independent resistivity profile locations. We demonstrate efficacy of the proposed approach to map the hydrostratigraphy of a heterogeneous surficial aquifer in northwestern Nebraska.

  2. A first generation BAC-based physical map of the rainbow trout genome.

    PubMed

    Palti, Yniv; Luo, Ming-Cheng; Hu, Yuqin; Genet, Carine; You, Frank M; Vallejo, Roger L; Thorgaard, Gary H; Wheeler, Paul A; Rexroad, Caird E

    2009-10-08

    Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map. The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning

  3. Building a cognitive map by assembling multiple path integration systems.

    PubMed

    Wang, Ranxiao Frances

    2016-06-01

    Path integration and cognitive mapping are two of the most important mechanisms for navigation. Path integration is a primitive navigation system which computes a homing vector based on an animal's self-motion estimation, while cognitive map is an advanced spatial representation containing richer spatial information about the environment that is persistent and can be used to guide flexible navigation to multiple locations. Most theories of navigation conceptualize them as two distinctive, independent mechanisms, although the path integration system may provide useful information for the integration of cognitive maps. This paper demonstrates a fundamentally different scenario, where a cognitive map is constructed in three simple steps by assembling multiple path integrators and extending their basic features. The fact that a collection of path integration systems can be turned into a cognitive map suggests the possibility that cognitive maps may have evolved directly from the path integration system.

  4. Generating a physical map of chromosome 11

    SciTech Connect

    Nowak, N.; Oin, S.; Sait, S.

    1994-09-01

    A four-hit chromosome-specific YAC library is being used to construct an overlapping YAC clone physical map of human chromosome 11. Each of the 1824 YAC clones have been sized by pulsed-field gel analysis with a resulting average insert size of 350 kb. Three hundred of the clones have been localized to a chromosome band by fluorescence in situ hybridization (FISH). We are using two complementary approaches to assemble YAC contigs: hybridization-based screening with Alu-PCR products and STS-based screening. Both screening approaches use pooling strategies to uniquely address each of the well locations with a minimum number of DNA pools. Since our main source of YAC clones is a chromosome specific library, the pool complexity is an order of magnitude smaller in comparison to total genomic libraries. Alu products with three different Alu primers were generated from both the monochromosomal J1 hybrid and individual YAC clones. YAC clones were chosen to generate probes using a sample without replacement strategy. Greater than 1700 YAC clones have been assembled into contigs. These initial contigs are estimated to be on average 1 Mb in size. Each of the contigs have been binned into a chromosomal band by virture of it containing YACs localized by FISH or YACs positive for one or more mapped STSs. Confirmation of the contigs is being achieved with Line I fingerprinting. The initial contigs are currently being joined using probes derived from the YAC clone ends defining the outermost points in the contigs for hybridization of colony filters. Remaining gaps in the contigs will be joined using alternative large insert libraries.

  5. FUNdamental Integrative Training (FIT) for Physical Education

    ERIC Educational Resources Information Center

    Bukowsky, Michael; Faigenbaum, Avery D.; Myer, Gregory D.

    2014-01-01

    There is a growing need for physical education teachers to integrate different types of fitness activities into their lessons in order to provide opportunities for all students to learn and practice a variety of movement skills that will enhance their physical fitness and support free-time physical activity. An increased focus on age-appropriate…

  6. FUNdamental Integrative Training (FIT) for Physical Education

    ERIC Educational Resources Information Center

    Bukowsky, Michael; Faigenbaum, Avery D.; Myer, Gregory D.

    2014-01-01

    There is a growing need for physical education teachers to integrate different types of fitness activities into their lessons in order to provide opportunities for all students to learn and practice a variety of movement skills that will enhance their physical fitness and support free-time physical activity. An increased focus on age-appropriate…

  7. Integration of the feline radiation hybrid and linkage maps.

    PubMed

    Sun, S; Murphy, W J; Menotti-Raymond, M; O'Brien, S J

    2001-06-01

    The recent development of genome mapping resources for the domestic cat provides a unique opportunity to study comparative medicine in this companion animal which can inform and benefit both veterinary and human biomedical concerns. We describe here the integration and order comparison of the feline radiation hybrid (RH) map with the feline interspecies backcross (ISB) genetic linkage map, constructed by a backcross of F1 hybrids between domestic cat (Felis catus) and the Asian leopard cat (Prionailurus bengalensis). Of 253 microsatellite loci mapped in the ISB, 176 equivalently spaced markers were ordered among a framework of 424 Type I coding markers in the RH map. The integration of the RH and ISB maps resolves the orientation of multiple linkage groups and singleton loci from the ISB genetic map. This integrated map provides the foundation for gene mapping assessments in the domestic cat and in related species of the Felidae family.

  8. Conflation and integration of archived geologic maps and associated uncertainties

    USGS Publications Warehouse

    Shoberg, Thomas G.

    2016-01-01

    Old, archived geologic maps are often available with little or no associated metadata. This creates special problems in terms of extracting their data to use with a modern database. This research focuses on some problems and uncertainties associated with conflating older geologic maps in regions where modern geologic maps are, as yet, non-existent as well as vertically integrating the conflated maps with layers of modern GIS data (in this case, The National Map of the U.S. Geological Survey). Ste. Genevieve County, Missouri was chosen as the test area. It is covered by six archived geologic maps constructed in the years between 1928 and 1994. Conflating these maps results in a map that is internally consistent with these six maps, is digitally integrated with hydrography, elevation and orthoimagery data, and has a 95% confidence interval useful for further data set integration.

  9. Integrated Genomic Map from Uropathogenic Escherichia coli J96

    PubMed Central

    Melkerson-Watson, Lyla J.; Rode, Christopher K.; Zhang, Lixin; Foxman, Betsy; Bloch, Craig A.

    2000-01-01

    Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratory E. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain K-12. We report an integrated physical and genetic map of the 5,120-kb J96 genome. The chromosome contains 26 NotI, 13 BlnI, and 7 I-CeuI macrorestriction sites. Macrorestriction mapping was rapidly accomplished by a novel transposon-based procedure: analysis of modified minitransposon insertions served to align the overlapping macrorestriction fragments generated by three different enzymes (each sharing a common cleavage site within the insert), thus integrating the three different digestion patterns and ordering the fragments. The resulting map, generated from a total of 54 mini-Tn10 insertions, was supplemented with auxanography and Southern analysis to indicate the positions of insertionally disrupted aminosynthetic genes and cloned virulence genes, respectively. Thus, it contains not only physical, macrorestriction landmarks but also the loci for eight housekeeping genes shared with strain K-12 and eight acknowledged urovirulence genes; the latter confirmed clustering of virulence genes at the large unique accessory chromosomal segments. The 115-kb J96 plasmid was resolved by pulsed-field gel electrophoresis in NotI digests. However, because the plasmid lacks restriction sites for the enzymes BlnI and I-CeuI, it was visualized in BlnI and I-CeuI digests only of derivatives carrying plasmid inserts artificially introducing these sites. Owing to an I-SceI site on the transposon, the plasmid could also be visualized and sized from plasmid insertion mutants after digestion with this enzyme. The insertional strains generated in construction of

  10. Physically Important Integrals Without Calculus

    ERIC Educational Resources Information Center

    Reif, F.; Larkin, Jill H.

    1976-01-01

    Develops a geometric solution to be used with spatial integrals needed for finding electric and magnetic fields. The method is used in the calculation of the electric fields due to a uniformly charged plane, line and sphere. (CP)

  11. Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources

    USDA-ARS?s Scientific Manuscript database

    Recent efforts in Gossypium SNP development have produced thousands of putative SNPs for G. barbadense, G. mustelinum, and G. tomentosum relative to G. hirsutum. Here we report on current efforts to localize putative SNPs using physical mapping resources. Recent advances in physical mapping resour...

  12. Physical mapping of genetic markers on the short arm of chromosome 5

    SciTech Connect

    Gersh, M.; Goodart, S.A.; Overhauser, J.

    1994-12-01

    The deletion of the short arm of chromosome 5 is associated with the cri-du-chat syndrome. In addition, loss of this portion of a chromosome is a common cytogenetic marker in a number of malignancies. However, to date, no genes associated with these disorders have been identified. Physical maps are the first step in isolating causative genes, and genes involved in autosomal recessive disorders are now routinely mapped through the identification of linked markers. Extensive genetic maps based upon polymorphic short tandem repeats (STRs) have provided researchers with a large number of markers to which such disorders can be genetically mapped. However, the physical locations of many of these STRs have not been determined. Toward the goal of integrating the human genetic maps with the physical maps, a 5p somatic cell hybrid deletion mapping panel that was derived from patients with 5p deletions or translocations was used to physically map 47 STRs that have been used to construct genetic maps of 5p. These data will be useful in the localization of disease genes that map to 5p and may be involved in the etiology of the cri-du-chat syndrome. 26 refs., 1 fig.

  13. High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa.

    PubMed

    Kirov, Ilya V; Van Laere, Katrijn; Khrustaleva, Ludmila I

    2015-07-02

    Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae.

  14. Meeting the Demands of Professional Education: A Study of Mind Mapping in a Professional Doctoral Physical Therapy Education Program

    ERIC Educational Resources Information Center

    Pollard, Elicia L.

    2010-01-01

    The purposes of this study are to investigate whether the quiz scores of physical therapy students who integrated mind mapping in their learning strategies are significantly different than the quiz scores of students who did not use mind mapping to learn in a lecture-based research course and examine the students' perceptions of mind mapping as a…

  15. Meeting the Demands of Professional Education: A Study of Mind Mapping in a Professional Doctoral Physical Therapy Education Program

    ERIC Educational Resources Information Center

    Pollard, Elicia L.

    2010-01-01

    The purposes of this study are to investigate whether the quiz scores of physical therapy students who integrated mind mapping in their learning strategies are significantly different than the quiz scores of students who did not use mind mapping to learn in a lecture-based research course and examine the students' perceptions of mind mapping as a…

  16. A physical map of the bovine genome

    USDA-ARS?s Scientific Manuscript database

    Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential geneti...

  17. Integrated Learning with Physical Education and Music

    ERIC Educational Resources Information Center

    Humphries, Charlotte A.; Bidner, Sara; Edwards, Cheryl

    2011-01-01

    Integrated learning is well established in education, primarily in the classroom subjects. This article describes settings and ways for extending integrated instruction to physical education and music. Benefits of these connections include reinforcing content and better meeting the needs of students whose intelligences include the bodily…

  18. Integrated Learning with Physical Education and Music

    ERIC Educational Resources Information Center

    Humphries, Charlotte A.; Bidner, Sara; Edwards, Cheryl

    2011-01-01

    Integrated learning is well established in education, primarily in the classroom subjects. This article describes settings and ways for extending integrated instruction to physical education and music. Benefits of these connections include reinforcing content and better meeting the needs of students whose intelligences include the bodily…

  19. 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

  20. Physics Research Integrated Development Environment (PRIDE)

    SciTech Connect

    Burton, J.; Cormell, L.

    1993-12-01

    Past efforts to implement a Software Engineering approach to High Energy Physics computing have been met with significant resistance and have been, in many cases, only marginally successful. At least a portion of the problem has been the Lick of an integrated development environment, tailored to High Energy Physics and incorporating a suite of Computer Aided Software Engineering tools. The Superconducting Super Collider Physics Research Division Computing Department is implementing pilot projects to develop just such an environment.

  1. Semantic integration for mapping the underworld

    NASA Astrophysics Data System (ADS)

    Fu, Gaihua; Cohn, Anthony G.

    2008-10-01

    Utility infrastructure is vital to the daily life of modern society. As the vast majority of urban utility assets are buried underneath public roads, the need to install/repair utility assets often requires opening ground with busy traffic. Unfortunately, at present most excavation works are carried out without knowing exactly what is where, which causes far more street breakings than necessary. This research studies how maximum benefit can be gained from the existing knowledge of buried assets. The key challenge here is that utility data is heterogeneous, which arises due to different domain perceptions and varying data modelling practices. This research investigates factors which prevent utility knowledge from being fully exploited and suggests that integration techniques can be applied for reconciling semantic heterogeneity within the utility domain. In this paper we discuss the feasibility of a common utility ontology to describe underground assets, and present techniques for constructing a basic utility ontology in the form of a thesaurus. The paper also demonstrates how the utility thesaurus developed is employed as a shared ontology for mapping utility data. Experiments have been performed to evaluate the techniques proposed, and feedback from industrial partners is encouraging and shows that techniques work effectively with real world utility data.

  2. Integrable mappings of the plane preserving biquadratic invariant curves

    NASA Astrophysics Data System (ADS)

    Iatrou, Apostolos; Roberts, John A. G.

    2001-08-01

    We provide a general framework to construct integrable mappings of the plane that preserve a one-parameter family B(x,y,K) of biquadratic invariant curves where parametrization by K is very general. These mappings are reversible by construction (i.e. they are the composition of two involutions) and can be shown to be measure preserving. They generalize integrable maps previously given by McMillan and Quispel, Roberts and Thompson. By considering a transformation of the case of the symmetric biquadratic to a canonical form, we provide a normal form for the symmetric integrable map acting on each invariant curve. We give a Lax pair for a large subclass of our symmetric integrable maps, including at least a 10-parameter subfamily of the 12-parameter symmetric Quispel-Roberts-Thompson maps.

  3. Construction of genome-wide physical BAC contigs using mapped cDNA as probes: Toward an integrated BAC library resource for genome sequencing and analysis. Annual report, July 1995--January 1997

    SciTech Connect

    Mitchell, S.C.; Bocskai, D.; Cao, Y.

    1997-12-31

    The goal of human genome project is to characterize and sequence entire genomes of human and several model organisms, thus providing complete sets of information on the entire structure of transcribed, regulatory and other functional regions for these organisms. In the past years, a number of useful genetic and physical markers on human and mouse genomes have been made available along with the advent of BAC library resources for these organisms. The advances in technology and resource development made it feasible to efficiently construct genome-wide physical BAC contigs for human and other genomes. Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes are available for human genome mapping. ESTs and cDNAs are excellent resources for building contig maps for two reasons. Firstly, they exist in two alternative forms--as both sequence information for PCR primer pairs, and cDoreen genomic libraries efficiently for large number of DNA probes by combining over 100 cDNA probes in each hybridization. Second, the linkage and order of genes are rather conserved among human, mouse and other model organisms. Therefore, gene markers have advantages over random anonymous STSs in building maps for comparative genomic studies.

  4. An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

    PubMed Central

    2011-01-01

    Background Integration of molecular, genetic and cytological maps is still a challenge for most plant species. Recent progress in molecular and cytogenetic studies created a basis for developing integrated maps in cucumber (Cucumis sativus L.). Results In this study, eleven fosmid clones and three plasmids containing 45S rDNA, the centromeric satellite repeat Type III and the pericentriomeric repeat CsRP1 sequences respectively were hybridized to cucumber metaphase chromosomes to assign their cytological location on chromosome 2. Moreover, an integrated molecular cytogenetic map of cucumber chromosomes 2 was constructed by fluorescence in situ hybridization (FISH) mapping of 11 fosmid clones together with the cucumber centromere-specific Type III sequence on meiotic pachytene chromosomes. The cytogenetic map was fully integrated with genetic linkage map since each fosmid clone was anchored by a genetically mapped simple sequence repeat marker (SSR). The relationship between the genetic and physical distances along chromosome was analyzed. Conclusions Recombination was not evenly distributed along the physical length of chromosome 2. Suppression of recombination was found in centromeric and pericentromeric regions. Our results also indicated that the molecular markers composing the linkage map for chromosome 2 provided excellent coverage of the chromosome. PMID:21272311

  5. Cyber/Physical Security Vulnerability Assessment Integration

    SciTech Connect

    MacDonald, Douglas G.; Clements, Samuel L.; Patrick, Scott W.; Perkins, Casey J.; Muller, George; Lancaster, Mary J.; Hutton, William J.

    2013-02-28

    Securing high value and critical assets is one of the biggest challenges facing this nation and others around the world. In modern integrated systems, there are four potential modes of attack available to an adversary: • physical only attack, • cyber only attack, • physical-enabled cyber attack, • cyber-enabled physical attack. Blended attacks involve an adversary working in one domain to reduce system effectiveness in another domain. This enables the attacker to penetrate further into the overall layered defenses. Existing vulnerability assessment (VA) processes and software tools which predict facility vulnerabilities typically evaluate the physical and cyber domains separately. Vulnerabilities which result from the integration of cyber-physical control systems are not well characterized and are often overlooked by existing assessment approaches. In this paper, we modified modification of the timely detection methodology, used for decades in physical security VAs, to include cyber components. The Physical and Cyber Risk Analysis Tool (PACRAT) prototype illustrates an integrated vulnerability assessment that includes cyber-physical interdependencies. Information about facility layout, network topology, and emplaced safeguards is used to evaluate how well suited a facility is to detect, delay, and respond to attacks, to identify the pathways most vulnerable to attack, and to evaluate how often safeguards are compromised for a given threat or adversary type. We have tested the PACRAT prototype on critical infrastructure facilities and the results are promising. Future work includes extending the model to prescribe the recommended security improvements via an automated cost-benefit analysis.

  6. An integration of integrated information theory with fundamental physics

    PubMed Central

    Barrett, Adam B.

    2014-01-01

    To truly eliminate Cartesian ghosts from the science of consciousness, we must describe consciousness as an aspect of the physical. Integrated Information Theory states that consciousness arises from intrinsic information generated by dynamical systems; however existing formulations of this theory are not applicable to standard models of fundamental physical entities. Modern physics has shown that fields are fundamental entities, and in particular that the electromagnetic field is fundamental. Here I hypothesize that consciousness arises from information intrinsic to fundamental fields. This hypothesis unites fundamental physics with what we know empirically about the neuroscience underlying consciousness, and it bypasses the need to consider quantum effects. PMID:24550877

  7. An integration of integrated information theory with fundamental physics.

    PubMed

    Barrett, Adam B

    2014-01-01

    To truly eliminate Cartesian ghosts from the science of consciousness, we must describe consciousness as an aspect of the physical. Integrated Information Theory states that consciousness arises from intrinsic information generated by dynamical systems; however existing formulations of this theory are not applicable to standard models of fundamental physical entities. Modern physics has shown that fields are fundamental entities, and in particular that the electromagnetic field is fundamental. Here I hypothesize that consciousness arises from information intrinsic to fundamental fields. This hypothesis unites fundamental physics with what we know empirically about the neuroscience underlying consciousness, and it bypasses the need to consider quantum effects.

  8. A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of synteny with model fish genomes

    USDA-ARS?s Scientific Manuscript database

    In this paper we generated DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is compose...

  9. Correlation of physical and genetic maps of human chromosome 16

    SciTech Connect

    Sutherland, G.R.

    1991-01-01

    This project aimed to divide chromosome 16 into approximately 50 intervals of {approximately}2Mb in size by constructing a series of mouse/human somatic cell hybrids each containing a rearranged chromosome 16. Using these hybrids, DNA probes would be regionally mapped by Southern blot or PCR analysis. Preference would be given to mapping probes which demonstrated polymorphisms for which the CEPH panel of families had been typed. This would allow a correlation of the physical and linkage maps of this chromosome. The aims have been substantially achieved. 49 somatic cell hybrids have been constructed which have allowed definition of 46, and potentially 57, different physical intervals on the chromosome. 164 loci have been fully mapped into these intervals. A correlation of the physical and genetic maps of the chromosome is in an advanced stage of preparation. The somatic cell hybrids constructed have been widely distributed to groups working on chromosome 16 and other genome projects.

  10. Singular Function Integration in Computational Physics

    NASA Astrophysics Data System (ADS)

    Hasbun, Javier

    2009-03-01

    In teaching computational methods in the undergraduate physics curriculum, standard integration approaches taught include the rectangular, trapezoidal, Simpson, Romberg, and others. Over time, these techniques have proven to be invaluable and students are encouraged to employ the most efficient method that is expected to perform best when applied to a given problem. However, some physics research applications require techniques that can handle singularities. While decreasing the step size in traditional approaches is an alternative, this may not always work and repetitive processes make this route even more inefficient. Here, I present two existing integration rules designed to handle singular integrals. I compare them to traditional rules as well as to the exact analytic results. I suggest that it is perhaps time to include such approaches in the undergraduate computational physics course.

  11. A first generation BAC-based physical map of the channel catfish genome

    PubMed Central

    Quiniou, Sylvie M-A; Waldbieser, Geoffrey C; Duke, Mary V

    2007-01-01

    Background Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes. Results A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing. Conclusion This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits. PMID:17284319

  12. Multiscale mapping: Physical concepts and mathematical techniques

    USDA-ARS?s Scientific Manuscript database

    This is an introductory summary for papers either invited or a part of a symposium at the 18th World Congress of Soil Science, July 2006 in Philadelphia. The symposium, titled "Multiscale Mapping of Soil Properties for Environmental Studies, Agriculture, and Decision Making," focused on techniques u...

  13. ArkMAP: integrating genomic maps across species and data sources.

    PubMed

    Paterson, Trevor; Law, Andy

    2013-08-13

    The visualisation of genetic and genomic maps aligned within and between species and across data sources can be used to inform studies of genome evolution, assist genome assembly projects and aid gene discovery and identification. Whilst annotation, integration and exploration of assembled genome sequences is well supported, there are fewer tools available which can display genetic maps for less well-characterized species, and integrate these maps with annotated reference genomes to support cross species comparisons. We have developed a desktop application to draw and align genetic and genomic maps, retrieved from remote data sources or loaded as local files. Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes). By using the JEnsembl API, maps can be drawn for any release version of any of the thousands of species present in Ensembl data sources, allowing not only inter-specific comparisons, but also comparisons between different versions/revisions of assembled genomes. Maps can be aligned by relating identical or synonymous markers across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compara databases, allowing ready visualization of regions of conserved synteny between species. The map drawing canvas is highly configurable, supports interactive exploration of maps, markers and relationships and allows export of publication quality graphics. ArkMAP allows users to draw and interactively explore gene and variation maps for any version of any annotated genome curated in the Ensembl data sources, and to integrate local mapping data. The maps and inter-map relationships drawn are highly configurable and ArkMAP may be used to produce publication quality graphics. ArkMAP is freely available as an auto-updating Java 'Web Start' application, or as a standalone archived application.

  14. Methods of geometrical integration in accelerator physics

    NASA Astrophysics Data System (ADS)

    Andrianov, S. N.

    2016-12-01

    In the paper we consider a method of geometric integration for a long evolution of the particle beam in cyclic accelerators, based on the matrix representation of the operator of particles evolution. This method allows us to calculate the corresponding beam evolution in terms of two-dimensional matrices including for nonlinear effects. The ideology of the geometric integration introduces in appropriate computational algorithms amendments which are necessary for preserving the qualitative properties of maps presented in the form of the truncated series generated by the operator of evolution. This formalism extends both on polarized and intense beams. Examples of practical applications are described.

  15. A physical genome map of Pseudomonas aeruginosa PAO.

    PubMed Central

    Römling, U; Grothues, D; Bautsch, W; Tümmler, B

    1989-01-01

    A complete macrorestriction map of the 5.9 Mb genome of Pseudomonas aeruginosa PAO (DSM 1707) was constructed by the combination of various one- and two-dimensional pulsed field gel electrophoresis techniques. A total of 51 restriction sites (36 SpeI sites, 15 DpnI sites) were placed on the physical map yielding an average resolution of 110 kb. Several genes encoding virulence factors and enzymes of metabolic pathways were located on the anonymous map by Southern hybridization. Distances between the gene loci were similar on the genetic and physical maps, suggesting an even distribution of genome mobility throughout the bacterial chromosome. The four rRNA operons were organized in pairs of inverted repeats. The two-dimensional macro-restriction techniques described herein are generally applicable for the genome mapping of any prokaryote and lower eukaryote which yields resolvable fragment patterns on two-dimensional pulsed field gels. Images PMID:2512121

  16. Physical limits for scaling of integrated circuits

    NASA Astrophysics Data System (ADS)

    Nawrocki, Waldemar

    2010-11-01

    In this paper we discuss some physical limits for scaling of devices and conducting paths inside of semiconductor integrated circuits (ICs). Since 40 years only a semiconductor technology, mostly the CMOS and the TTL technologies, are used for fabrication of integrated circuits in the industrial scale. Miniaturization of electronic devices in integrated circuits has technological limits and physical limits as well. In 2010 best parameters of commercial ICs shown the dual-core Intel Core i5-670 processor manufactured in the technology of 32 nm. Its clock frequency in turbo mode is 3.73 GHz. A forecast of the development of the semiconductor industry (ITRS 2009) predicts that sizes of electronic devices in ICs circuits will be smaller than 10 nm in the next 10 years. The physical gate length in a MOSFET will even amount 7 nm in the year 2024. At least 5 physical effects should be taken into account if we discuss limits of scaling of integrated circuits.

  17. 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

  18. Cortical cartography reveals political and physical maps.

    PubMed

    Loring, David W; Gaillard, William Davis; Bookheimer, Susan Y; Meador, Kimford J; Ojemann, Jeffrey G

    2014-05-01

    Advances in functional imaging have provided noninvasive techniques to probe brain organization of multiple constructs including language and memory. Because of high overall rates of agreements with older techniques, including Wada testing and cortical stimulation mapping (CSM), some have proposed that those approaches should be largely abandoned because of their invasiveness, and replaced with noninvasive functional imaging methods. High overall agreement, however, is based largely on concordant language lateralization in series dominated by cases of typical cerebral dominance. Advocating a universal switch from Wada testing and cortical stimulation mapping to functional magnetic resonance imaging (fMRI) or magnetoencephalography (MEG) ignores the differences in specific expertise across epilepsy centers, many of which often have greater skill with one approach rather than the other, and that Wada, CSM, fMRI, and MEG protocols vary across institutions resulting in different outcomes and reliability. Specific patient characteristics also affect whether Wada or CSM might influence surgical management, making it difficult to accept broad recommendations against currently useful clinical tools. Although the development of noninvasive techniques has diminished the frequency of more invasive approaches, advocating their use to replace Wada testing and CSM across all epilepsy surgery programs without consideration of the different skills, protocols, and expertise at any given center site is ill-advised. Wiley Periodicals, Inc. © 2014 International League Against Epilepsy.

  19. Integrating Vegetation Classification, Mapping, and Strategic Inventory for Forest Management

    Treesearch

    C. K. Brewer; R. Bush; D. Berglund; J. A. Barber; S. R. Brown

    2006-01-01

    Many of the analyses needed to address multiple resource issues are focused on vegetation pattern and process relationships and most rely on the data models produced from vegetation classification, mapping, and/or inventory. The Northern Region Vegetation Mapping Project (R1-VMP) data models are based on these three integrally related, yet separate processes. This...

  20. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

    PubMed Central

    Moroldo, Marco; Paillard, Sophie; Marconi, Raffaella; Fabrice, Legeai; Canaguier, Aurelie; Cruaud, Corinne; De Berardinis, Veronique; Guichard, Cecile; Brunaud, Veronique; Le Clainche, Isabelle; Scalabrin, Simone; Testolin, Raffaele; Di Gaspero, Gabriele; Morgante, Michele; Adam-Blondon, Anne-Francoise

    2008-01-01

    Background Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. Results The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. Conclusion Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in

  1. A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map

    PubMed Central

    2011-01-01

    Background The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map. Results We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au. Conclusions The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map. PMID:21854555

  2. What Do Pre-Service Physics Teachers Know and Think about Concept Mapping?

    ERIC Educational Resources Information Center

    Didis, Nilüfer; Özcan, Özgür; Azar, Ali

    2014-01-01

    In order to use concept maps in physics classes effectively, teachers' knowledge and ideas about concept mapping are as important as the physics knowledge used in mapping. For this reason, we aimed to examine pre-service physics teachers' knowledge on concept mapping, their ideas about the implementation of concept mapping in physics…

  3. What Do Pre-Service Physics Teachers Know and Think about Concept Mapping?

    ERIC Educational Resources Information Center

    Didis, Nilüfer; Özcan, Özgür; Azar, Ali

    2014-01-01

    In order to use concept maps in physics classes effectively, teachers' knowledge and ideas about concept mapping are as important as the physics knowledge used in mapping. For this reason, we aimed to examine pre-service physics teachers' knowledge on concept mapping, their ideas about the implementation of concept mapping in physics…

  4. Creation of a global land cover and a probability map through a new map integration method

    NASA Astrophysics Data System (ADS)

    Kinoshita, Tsuguki; Iwao, Koki; Yamagata, Yoshiki

    2014-05-01

    Global land cover maps are widely used for assessment and in research of various kinds, and in recent years have also come to be used for socio-economic forecasting. However, existing maps are not very accurate, and differences between maps also contribute to their unreliability. Improving the accuracy of global land cover maps would benefit a number of research fields. In this paper, we propose a methodology for using ground truth data to integrate existing global land cover maps. We checked the accuracy of a map created using this methodology and found that the accuracy of the new map is 74.6%, which is 3% higher than for existing maps. We then created a 0.5-min latitude by 0.5-min longitude probability map. This map indicates the probability of agreement between the category class of the new map and truth data. Using the map, we found that the probabilities of cropland and grassland are relatively low compared with other land cover types. This appears to be because the definitions of cropland differ between maps, so the accuracy may be improved by including pasture and idle plot categories.

  5. Non-integrability of measure preserving maps via Lie symmetries

    NASA Astrophysics Data System (ADS)

    Cima, Anna; Gasull, Armengol; Mañosa, Víctor

    2015-11-01

    We consider the problem of characterizing, for certain natural number m, the local Cm-non-integrability near elliptic fixed points of smooth planar measure preserving maps. Our criterion relates this non-integrability with the existence of some Lie Symmetries associated to the maps, together with the study of the finiteness of its periodic points. One of the steps in the proof uses the regularity of the period function on the whole period annulus for non-degenerate centers, question that we believe that is interesting by itself. The obtained criterion can be applied to prove the local non-integrability of the Cohen map and of several rational maps coming from second order difference equations.

  6. A physical map of 30,000 human genes.

    PubMed

    Deloukas, P; Schuler, G D; Gyapay, G; Beasley, E M; Soderlund, C; Rodriguez-Tomé, P; Hui, L; Matise, T C; McKusick, K B; Beckmann, J S; Bentolila, S; Bihoreau, M; Birren, B B; Browne, J; Butler, A; Castle, A B; Chiannilkulchai, N; Clee, C; Day, P J; Dehejia, A; Dibling, T; Drouot, N; Duprat, S; Fizames, C; Fox, S; Gelling, S; Green, L; Harrison, P; Hocking, R; Holloway, E; Hunt, S; Keil, S; Lijnzaad, P; Louis-Dit-Sully, C; Ma, J; Mendis, A; Miller, J; Morissette, J; Muselet, D; Nusbaum, H C; Peck, A; Rozen, S; Simon, D; Slonim, D K; Staples, R; Stein, L D; Stewart, E A; Suchard, M A; Thangarajah, T; Vega-Czarny, N; Webber, C; Wu, X; Hudson, J; Auffray, C; Nomura, N; Sikela, J M; Polymeropoulos, M H; James, M R; Lander, E S; Hudson, T J; Myers, R M; Cox, D R; Weissenbach, J; Boguski, M S; Bentley, D R

    1998-10-23

    A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.

  7. Integrating Radar Image Data with Google Maps

    NASA Technical Reports Server (NTRS)

    Chapman, Bruce D.; Gibas, Sarah

    2010-01-01

    A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

  8. Memory integration constructs maps of space, time, and concepts.

    PubMed

    Morton, Neal W; Sherrill, Katherine R; Preston, Alison R

    2017-10-01

    Recent evidence demonstrates that new events are learned in the context of their relationships to existing memories. Within the hippocampus and medial prefrontal cortex, related memories are represented by integrated codes that connect events experienced at different times and places. Integrated codes form the basis of spatial, temporal, and conceptual maps of experience. These maps represent information that goes beyond direct experience and support generalization behaviors that require knowledge be used in new ways. The degree to which an individual memory is integrated into a coherent map is determined by its spatial, temporal, and conceptual proximity to existing knowledge. Integration is observed over a wide range of scales, suggesting that memories contain information about both broad and fine-grained contexts.

  9. HuGeMap: a distributed and integrated Human Genome Map database.

    PubMed Central

    Barillot, E; Guyon, F; Cussat-Blanc, C; Viara, E; Vaysseix, G

    1998-01-01

    The HuGeMap database stores the major genetic and physical maps of the human genome. It is also interconnected with the gene radiation hybrid mapping database RHdb. HuGeMap is accessible through a Web server for interactive browsing at URL http://www.infobiogen. fr/services/Hugemap , as well as through a CORBA server for effective programming. HuGeMap is intended as an attempt to build open, interconnected databases, that is databases that distribute their objects worldwide in compliance with a recognized standard of distribution. Maps can be displayed and compared with a java applet (http://babbage.infobiogen.fr:15000/Mappet/Show. html ) that queries the HuGeMap ORB server as well as the RHdb ORB server at the EBI. PMID:9399811

  10. Examining the Conceptual Organization of Students in an Integrated Algebra and Physical Science Class.

    ERIC Educational Resources Information Center

    Westbrook, Susan L.

    1998-01-01

    Compares the conceptual organization of students in an integrated algebra and physical science class (SAM 9) with that of students in a discipline-specific physical science class (PSO). Analysis of students' concept maps indicates that the SAM9 students used a greater number of procedural linkages to connect mathematics and science concepts than…

  11. DNA fiber mapping techniques for the assembly of high-resolution physical maps.

    PubMed

    Weier, H U

    2001-08-01

    High-resolution physical maps are indispensable for directed sequencing projects or the finishing stages of shotgun sequencing projects. These maps are also critical for the positional cloning of disease genes and genetic elements that regulate gene expression. Typically, physical maps are based on ordered sets of large insert DNA clones from cosmid, P1/PAC/BAC, or yeast artificial chromosome (YAC) libraries. Recent technical developments provide detailed information about overlaps or gaps between clones and precisely locate the position of sequence tagged sites or expressed sequences, and thus support efforts to determine the complete sequence of the human genome and model organisms. Assembly of physical maps is greatly facilitated by hybridization of non-isotopically labeled DNA probes onto DNA molecules that were released from interphase cell nuclei or recombinant DNA clones, stretched to some extent and then immobilized on a solid support. The bound DNA, collectively called "DNA fibers," may consist of single DNA molecules in some experiments or bundles of chromatin fibers in others. Once released from the interphase nuclei, the DNA fibers become more accessible to probes and detection reagents. Hybridization efficiency is therefore increased, allowing the detection of DNA targets as small as a few hundred base pairs. This review summarizes different approaches to DNA fiber mapping and discusses the detection sensitivity and mapping accuracy as well as recent achievements in mapping expressed sequence tags and DNA replication sites.

  12. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

    PubMed Central

    Wu, Xiaolei; Zhong, Guohua; Findley, Seth D; Cregan, Perry; Stacey, Gary; Nguyen, Henry T

    2008-01-01

    Background Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. Results A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1× genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. Conclusion We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and

  13. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map.

    PubMed

    Wu, Xiaolei; Zhong, Guohua; Findley, Seth D; Cregan, Perry; Stacey, Gary; Nguyen, Henry T

    2008-01-22

    Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (approximately 1x genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and duplicated regions

  14. Successful Curriculum Mapping: Fostering Smooth Technology Integration

    ERIC Educational Resources Information Center

    Morehead, Pamela; LaBeau, Barbara

    2005-01-01

    Four years ago, the staff at our school (Marie C. Graham Elementary School in Harrison Township, Michigan) agreed to take an evaluative look at the use of technology in the classroom. Through a self-study process and a district technology initiative called Project 2000, teachers had the opportunity for change relative to technology integration.…

  15. Physical and Comparative Mapping of Distal Mouse Chromosome 16

    PubMed Central

    Cabin, Deborah E.; McKee-Johnson, Jennifer W.; Matesic, Lydia E.; Wiltshire, Tim; Rue, Elizabeth E.; Mjaatvedt, Anne E.; Huo, Yong Kang; Korenberg, Julie R.; Reeves, Roger H.

    1998-01-01

    Distal mouse Chromosome 16 (Chr. 16) includes a region of conserved linkage with human Chromosome 21 (Chr. 21). Mouse models of Down syndrome based on trisomy of distal Chr. 16 have several phenotypes similar to those seen in human patients and have proven useful for correlating dosage imbalance of specific genes with specific developmental anomalies. The degree to which such findings can be related to Down syndrome depends on how well the conserved synteny is maintained. Twenty-four genes have been mapped in both species and there are no discordancies, but the region could carry hundreds of genes. Comparative sequence represents the ultimate comparative map and will aid in identification of genes and their regulatory sequences. A physical map of the distal 4.5 Mb of Chr. 16 has been assembled as an essential step toward a map of sequence-ready templates. The map consists of 51 YACs and 15 BACs and includes 18 transcripts, 9 of which are mapped for the first time in mouse, and 3 of which are, for the first time, described in either species. YAC fragmentation was used to precisely localize the 49 markers on the map. Comparison of this physical map with that of the corresponding region on Chr. 21 shows conservation not only of gene order but of size in the 3 Mb from Cbr1 to Ets2; distal to Ets2, the human map is expanded. [The sequence data described in this paper have been submitted to GenBank. See Tables 1 and 2 for accession nos.] PMID:9750193

  16. CYBER/PHYSICAL SECURITY VULNERABILITY ASSESSMENT INTEGRATION

    SciTech Connect

    MacDonald, Douglas G.; Key, Brad; Clements, Samuel L.; Hutton, William J.; Craig, Philip A.; Patrick, Scott W.; Crawford, Cary E.

    2011-07-17

    This internally funded Laboratory-Directed R&D project by the Pacific Northwest National Laboratory, in conjunction with QinetiQ North America, is intended to identify and properly assess areas of overlap (and interaction) in the vulnerability assessment process between cyber security and physical protection. Existing vulnerability analysis (VA) processes and software tools exist, and these are heavily utilized in the determination of predicted vulnerability within the physical and cyber security domains. These determinations are normally performed independently of one another, and only interact on a superficial level. Both physical and cyber security subject matter experts have come to realize that though the various interactive elements exist, they are not currently quantified in most periodic security assessments. This endeavor aims to evaluate both physical and cyber VA techniques and provide a strategic approach to integrate the interdependent relationships of each into a single VA capability. This effort will also transform the existing suite of software currently utilized in the physical protection world to more accurately quantify the risk associated with a blended attack scenario. Performance databases will be created to support the characterization of the cyber security elements, and roll them into prototype software tools. This new methodology and software capability will enable analysts to better identify and assess the overall risk during a vulnerability analysis.

  17. A cytological-physical map of 22q11

    SciTech Connect

    Lindsay, E.A.; Rizzu, P.; Gaddini, L.

    1994-09-01

    Our laboratory is involved in the construction of a cytological-physical map of 22q11 and isolation of expressed sequences from the region involved in DiGeorge syndrome (DGS) and Velo-Cardio-Facial syndrome (VCFS). One of the goals of the mapping is an understanding of the molecular mechanisms which generate the 22q11 microdeletions observed with high frequency in DGS and VCFS. Our of over 60 deleted patients studied in our laboratory, all but one were deleted for two loci approximately 1-2 Mb apart. There is evidence from patients with balanced and unbalanced translocations that deletion of the whole region is not necessary for determination of the clinical phenotype. Therefore, it is possible that deletion breakpoints occur as a consequence of structural characteristics of the DNA that predispose to rearrangements. A striking characteristic of the 22q11 region is the abundance of low copy repeat sequences. It is reasonable to think that recombination between these repeats may lead to microdeletions. However, a direct demonstration of such mechanism is not available yet. The presence of repeats makes standard physical mapping techniques based on hybridization or STS mapping often difficult to interpret. For example, we have found clones positive for the same STS that are located in different positions within 22q11. For this reason we have used high resolution cytological mapping as a supporting technique for map validation. We present the current status map which includes known polymorphic and non-polymorphic loci, newly isolated clones and chromosomal deletion breakpoints. The map extends from the loci D22S9/D22S24 to TOP1P2. Extended chromatin hybridization experiments visually demonstrate the presence of at least two repeat islands flanking (or at) the region where chromosomal breakpoints of the commonly deleted region occur.

  18. Integrating physical stress, growth, and development.

    PubMed

    Uyttewaal, Magalie; Traas, Jan; Hamant, Olivier

    2010-02-01

    Linking the gene regulatory network to morphogenesis is a central question in developmental biology. Shape relies on the combined actions of biochemistry and biophysics, two parameters that are under local genetic control. The blooming of molecular biology since the 1970s has promoted a biochemical view of development, leaving behind the contribution of physical forces. Recently, the development of new techniques, such as live imaging, micromechanical approaches, and computer modeling, has revitalized the biomechanics field. In this review, we use shoot apical meristem development to illustrate how biochemistry and biomechanics cooperate to integrate the local cellular gene input into global growth patterns. Copyright 2009 Elsevier Ltd. All rights reserved.

  19. A standard cytogenetic map of Culex quinquefasciatus polytene chromosomes in application for fine-scale physical mapping.

    PubMed

    Unger, Maria F; Sharakhova, Maria V; Harshbarger, Adam J; Glass, Patrick; Collins, Frank H

    2015-06-06

    Southern house mosquito Culex quinquefasciatus belongs to the C. pipiens cryptic species complex, with global distribution and unclear taxonomy. Mosquitoes of the complex can transmit human and animal pathogens, such as filarial worm, West Nile virus and avian malarial Plasmodium. Physical gene mapping is crucial to understanding genome organization, function, and systematic relationships of cryptic species, and is a basis for developing new vector control strategies. However, physical mapping was not established previously for Culex due to the lack of well-structured polytene chromosomes. Inbreeding was used to diminish inversion polymorphism and asynapsis of chromosomal homologs. Identification of larvae of the same developmental stage using the shape of imaginal discs allowed achievement of uniformity in chromosomal banding pattern. This together with high-resolution phase-contrast photography enabled the development of a cytogenetic map. Fluorescent in situ hybridization was used for gene mapping. A detailed cytogenetic map of C. quinquefasciatus polytene chromosomes was produced. Landmarks for chromosome recognition and cytological boundaries for two inversions were identified. Locations of 23 genes belonging to 16 genomic supercontigs, and 2 cDNA were established. Six supercontigs were oriented and one was found putatively misassembled. The cytogenetic map was linked to the previously developed genetic linkage groups by corresponding positions of 2 genetic markers and 10 supercontigs carrying genetic markers. Polytene chromosomes were numbered according to the genetic linkage groups. This study developed a new standard cytogenetic photomap of the polytene chromosomes for C. quinquefasciatus and was applied for the fine-scale physical mapping. It allowed us to infer chromosomal position of 1333 of annotated genes belonging to 16 genomic supercontigs and find orientation of 6 of these supercontigs; the new cytogenetic and previously developed genetic linkage

  20. Numerical and physical magnitudes are mapped into time.

    PubMed

    Ben-Meir, Shachar; Ganor-Stern, Dana; Tzelgov, Joseph

    2012-01-01

    In two experiments we investigated mapping of numerical and physical magnitudes with temporal order. Pairs of digits were presented sequentially for a size comparison task. An advantage for numbers presented in ascending order was found when participants were comparing the numbers' physical and numerical magnitudes. The effect was more robust for comparisons of physical size, as it was found using both select larger and select smaller instructions, while for numerical comparisons it was found only for select larger instructions. Varying both the digits' numerical and physical sizes resulted in a size congruity effect, indicating automatic processing of the irrelevant magnitude dimension. Temporal order and the congruency between numerical and physical magnitudes affected comparisons in an additive manner, thus suggesting that they affect different stages of the comparison process.

  1. Cognitive Mapping of Advanced Level Physics Students' Conceptions of Quantum Physics.

    ERIC Educational Resources Information Center

    Mashhadi, Azam; Woolnough, Brian

    This paper presents findings from a study that investigated students' understanding of quantum phenomena and focused on how students incorporate the ideas of quantum physics into their overall cognitive framework. The heuristic metaphor of the map is used to construct graphic representations of students' understanding of quantum physics. The…

  2. A draft physical map of a D-genome cotton species (Gossypium raimondii)

    PubMed Central

    2010-01-01

    Background Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. Results A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. Conclusion Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence. PMID:20569427

  3. Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage.

    PubMed

    Jamil, Hasan M

    2015-01-01

    Traditionally, biological objects such as genes, proteins, and pathways are represented by a convenient identifier, or ID, which is then used to cross reference, link and describe objects in biological databases. Relationships among the objects are often established using non-trivial and computationally complex ID mapping systems or converters, and are stored in authoritative databases such as UniGene, GeneCards, PIR and BioMart. Despite best efforts, such mappings are largely incomplete and riddled with false negatives. Consequently, data integration using record linkage that relies on these mappings produces poor quality of data, inadvertently leading to erroneous conclusions. In this paper, we discuss this largely ignored dimension of data integration, examine how the ubiquitous use of identifiers in biological databases is a significant barrier to knowledge fusion using distributed computational pipelines, and propose two algorithms for ad hoc and restriction free ID mapping of arbitrary types using online resources. We also propose two declarative statements for ID conversion and data integration based on ID mapping on-the-fly.

  4. Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation.

    PubMed

    Figueroa, Debbie M; Bass, Hank W

    2012-05-01

    Integrated cytogenetic pachytene fluorescence in situ hybridization (FISH) maps were developed for chromosomes 1, 3, 4, 5, 6, and 8 of maize using restriction fragment length polymorphism marker-selected Sorghum propinquum bacterial artificial chromosomes (BACs) for 19 core bin markers and 4 additional genetic framework loci. Using transgenomic BAC FISH mapping on maize chromosome addition lines of oats, we found that the relative locus position along the pachytene chromosome did not change as a function of total arm length, indicative of uniform axial contraction along the fibers during mid-prophase for tested loci on chromosomes 4 and 5. Additionally, we cytogenetically FISH mapped six loci from chromosome 9 onto their duplicated syntenic regions on chromosomes 1 and 6, which have varying amounts of sequence divergence, using sorghum BACs homologous to the chromosome 9 loci. We found that successful FISH mapping was possible even when the chromosome 9 selective marker had no counterpart in the syntenic block. In total, these 29 FISH-mapped loci were used to create the most extensive pachytene FISH maps to date for these six maize chromosomes. The FISH-mapped loci were then merged into one composite karyotype for direct comparative analysis with the recombination nodule-predicted cytogenetic, genetic linkage, and genomic physical maps using the relative marker positions of the loci on all the maps. Marker colinearity was observed between all pair-wise map comparisons, although marker distribution patterns varied widely in some cases. As expected, we found that the recombination nodule-based predictions most closely resembled the cytogenetic map positions overall. Cytogenetic and linkage map comparisons agreed with previous studies showing a decrease in marker spacing in the peri-centromeric heterochromatin region on the genetic linkage maps. In fact, there was a general trend with most loci mapping closer towards the telomere on the linkage maps than on the

  5. Integrating Terrain Maps Into a Reactive Navigation Strategy

    NASA Technical Reports Server (NTRS)

    Howard, Ayanna; Werger, Barry; Seraji, Homayoun

    2006-01-01

    An improved method of processing information for autonomous navigation of a robotic vehicle across rough terrain involves the integration of terrain maps into a reactive navigation strategy. Somewhat more precisely, the method involves the incorporation, into navigation logic, of data equivalent to regional traversability maps. The terrain characteristic is mapped using a fuzzy-logic representation of the difficulty of traversing the terrain. The method is robust in that it integrates a global path-planning strategy with sensor-based regional and local navigation strategies to ensure a high probability of success in reaching a destination and avoiding obstacles along the way. The sensor-based strategies use cameras aboard the vehicle to observe the regional terrain, defined as the area of the terrain that covers the immediate vicinity near the vehicle to a specified distance a few meters away.

  6. A high utility integrated map of the pig genome

    USDA-ARS?s Scientific Manuscript database

    Background: The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genome...

  7. A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos).

    PubMed

    Avila, Felipe; Baily, Malorie P; Perelman, Polina; Das, Pranab J; Pontius, Joan; Chowdhary, Renuka; Owens, Elaine; Johnson, Warren E; Merriwether, David A; Raudsepp, Terje

    2014-01-01

    Genome analysis of the alpaca (Lama pacos, LPA) has progressed slowly compared to other domestic species. Here, we report the development of the first comprehensive whole-genome integrated cytogenetic map for the alpaca using fluorescence in situ hybridization (FISH) and CHORI-246 BAC library clones. The map is comprised of 230 linearly ordered markers distributed among all 36 alpaca autosomes and the sex chromosomes. For the first time, markers were assigned to LPA14, 21, 22, 28, and 36. Additionally, 86 genes from 15 alpaca chromosomes were mapped in the dromedary camel (Camelus dromedarius, CDR), demonstrating exceptional synteny and linkage conservation between the 2 camelid genomes. Cytogenetic mapping of 191 protein-coding genes improved and refined the known Zoo-FISH homologies between camelids and humans: we discovered new homologous synteny blocks (HSBs) corresponding to HSA1-LPA/CDR11, HSA4-LPA/CDR31 and HSA7-LPA/CDR36, and revised the location of breakpoints for others. Overall, gene mapping was in good agreement with the Zoo-FISH and revealed remarkable evolutionary conservation of gene order within many human-camelid HSBs. Most importantly, 91 FISH-mapped markers effectively integrated the alpaca whole-genome sequence and the radiation hybrid maps with physical chromosomes, thus facilitating the improvement of the sequence assembly and the discovery of genes of biological importance.

  8. Discrete Integrable Systems and Poisson Algebras From Cluster Maps

    NASA Astrophysics Data System (ADS)

    Fordy, Allan P.; Hone, Andrew

    2014-01-01

    We consider nonlinear recurrences generated from cluster mutations applied to quivers that have the property of being cluster mutation-periodic with period 1. Such quivers were completely classified by Fordy and Marsh, who characterised them in terms of the skew-symmetric matrix that defines the quiver. The associated nonlinear recurrences are equivalent to birational maps, and we explain how these maps can be endowed with an invariant Poisson bracket and/or presymplectic structure. Upon applying the algebraic entropy test, we are led to a series of conjectures which imply that the entropy of the cluster maps can be determined from their tropical analogues, which leads to a sharp classification result. Only four special families of these maps should have zero entropy. These families are examined in detail, with many explicit examples given, and we show how they lead to discrete dynamics that is integrable in the Liouville-Arnold sense.

  9. Research on Integrated Mapping——A Case Study of Integrated Land Use with Swamp Mapping

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Yan, F.; Chang, L.

    2015-12-01

    Unified real estate registration system shows the attention, determination and effort to of CPC Central Committee and State Council on real estate registration in China. However, under current situation, China's real estate registration work made less progress. One of the reasons is that it's hard to express the property right of real estate on one map under the multi-sector management system. Under current multi-sector management system in China, different departments usually just survey and mapping the land type under its jurisdiction. For example, wetland investigation only mapping all kinds of wetland resources but not mapping other resource types. As a result, it cause he problem of coincidence or leak in integration of different results from different departments. As resources of the earth's surface, the total area of forest, grassland, wetland and so on should be equal to the total area of the earth's surface area. However, under the current system, the area of all kinds of resources is not equal to the sum of the earth's surface. Therefore, it is of great importance to express all the resources on one map. On one hand, this is conducive to find out the real area and distribution of resources and avoid the problem of coincidence or leak in integration; On the other hand, it is helpful to study the dynamic change of different resources. Therefore, we first proposed the "integrated mapping" as a solution, and take integrated land use with swamp mapping in Northeast China as an example to investigate the feasibility and difficulty. Study showed that: integrated land use with swamp mapping can be achieved through combining land use survey standards with swamps survey standards and "second mapping" program. Based on the experience of integrated land use with swamp mapping, we point out its reference function on integrated mapping and unified real estate registration system. We concluded that: (1) Comprehending and integrating different survey standard of

  10. Integrating genetic linkage maps with pachytene chromosome structure in maize.

    PubMed

    Anderson, Lorinda K; Salameh, Naser; Bass, Hank W; Harper, Lisa C; Cande, W Z; Weber, Gerd; Stack, Stephen M

    2004-04-01

    Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1). all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2). each RN corresponds to one crossover, and (3). the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r(2) = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

  11. An integrated radiation physics computer code system.

    NASA Technical Reports Server (NTRS)

    Steyn, J. J.; Harris, D. W.

    1972-01-01

    An integrated computer code system for the semi-automatic and rapid analysis of experimental and analytic problems in gamma photon and fast neutron radiation physics is presented. Such problems as the design of optimum radiation shields and radioisotope power source configurations may be studied. The system codes allow for the unfolding of complex neutron and gamma photon experimental spectra. Monte Carlo and analytic techniques are used for the theoretical prediction of radiation transport. The system includes a multichannel pulse-height analyzer scintillation and semiconductor spectrometer coupled to an on-line digital computer with appropriate peripheral equipment. The system is geometry generalized as well as self-contained with respect to material nuclear cross sections and the determination of the spectrometer response functions. Input data may be either analytic or experimental.

  12. An integrated radiation physics computer code system.

    NASA Technical Reports Server (NTRS)

    Steyn, J. J.; Harris, D. W.

    1972-01-01

    An integrated computer code system for the semi-automatic and rapid analysis of experimental and analytic problems in gamma photon and fast neutron radiation physics is presented. Such problems as the design of optimum radiation shields and radioisotope power source configurations may be studied. The system codes allow for the unfolding of complex neutron and gamma photon experimental spectra. Monte Carlo and analytic techniques are used for the theoretical prediction of radiation transport. The system includes a multichannel pulse-height analyzer scintillation and semiconductor spectrometer coupled to an on-line digital computer with appropriate peripheral equipment. The system is geometry generalized as well as self-contained with respect to material nuclear cross sections and the determination of the spectrometer response functions. Input data may be either analytic or experimental.

  13. An integrated map with cosmid/PAC contigs of a 4-Mb down syndrome critical region

    SciTech Connect

    Osoegawa, Kazutoyo; Susukida, Rie; Okano, Saishi

    1996-03-05

    The major phenotypic features of Down syndrome have been correlated with partial trisomies of chromosome 21, allowing us to define the candidate gene region to a 4-Mb segment on the 21q22.2 band. We present here a high resolution physical map with megabase-sized cosmid/PAC contigs. This ordered clone library has provided unique material for the integration of a variety of mappable objects, including exons, cDNAs, restriction sites etc. Furthermore, our results have emplified a strategy for the completion of the chromosome 21 map to sequencing. 42 refs., 5 figs.

  14. Integrability and vesture for harmonic maps into symmetric spaces

    NASA Astrophysics Data System (ADS)

    Beheshti, Shabnam; Tahvildar-Zadeh, Shadi

    2016-05-01

    After formulating the notion of integrability for axially symmetric harmonic maps from ℝ3 into symmetric spaces, we give a complete and rigorous proof that, subject to some mild restrictions on the target, all such maps are integrable. Furthermore, we prove that a variant of the inverse scattering method, called vesture (dressing) can always be used to generate new solutions for the harmonic map equations starting from any given solution. In particular, we show that the problem of finding N-solitonic harmonic maps into a non-compact Grassmann manifold SU(p,q)/S(U(p) × U(q)) is completely reducible via the vesture (dressing) method to a problem in linear algebra which we prove is solvable in general. We illustrate this method, and establish its agreement with previously known special cases, by explicitly computing a 1-solitonic harmonic map for the two cases (p = 1,q = 1) and (p = 2,q = 1) and showing that the family of solutions obtained in each case contains respectively the Kerr family of solutions to the Einstein vacuum equations, and the Kerr-Newman family of solutions to the Einstein-Maxwell equations in the hyperextreme sector of the corresponding parameters.

  15. Comparing the performance of various digital soil mapping approaches to map physical soil properties

    NASA Astrophysics Data System (ADS)

    Laborczi, Annamária; Takács, Katalin; Pásztor, László

    2015-04-01

    Spatial information on physical soil properties is intensely expected, in order to support environmental related and land use management decisions. One of the most widely used properties to characterize soils physically is particle size distribution (PSD), which determines soil water management and cultivability. According to their size, different particles can be categorized as clay, silt, or sand. The size intervals are defined by national or international textural classification systems. The relative percentage of sand, silt, and clay in the soil constitutes textural classes, which are also specified miscellaneously in various national and/or specialty systems. The most commonly used is the classification system of the United States Department of Agriculture (USDA). Soil texture information is essential input data in meteorological, hydrological and agricultural prediction modelling. Although Hungary has a great deal of legacy soil maps and other relevant soil information, it often occurs, that maps do not exist on a certain characteristic with the required thematic and/or spatial representation. The recent developments in digital soil mapping (DSM), however, provide wide opportunities for the elaboration of object specific soil maps (OSSM) with predefined parameters (resolution, accuracy, reliability etc.). Due to the simultaneous richness of available Hungarian legacy soil data, spatial inference methods and auxiliary environmental information, there is a high versatility of possible approaches for the compilation of a given soil map. This suggests the opportunity of optimization. For the creation of an OSSM one might intend to identify the optimum set of soil data, method and auxiliary co-variables optimized for the resources (data costs, computation requirements etc.). We started comprehensive analysis of the effects of the various DSM components on the accuracy of the output maps on pilot areas. The aim of this study is to compare and evaluate different

  16. An integrated restriction fragment length polymorphism--amplified fragment length polymorphism linkage map for cultivated sunflower.

    PubMed

    Gedil, M A; Wye, C; Berry, S; Segers, B; Peleman, J; Jones, R; Leon, A; Slabaugh, M B; Knapp, S J

    2001-04-01

    Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2 population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 x HA372 F2 progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 x HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 x HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.

  17. A microsatellite-based, physically anchored linkage map for the gray, short-tailed opossum (Monodelphis domestica).

    PubMed

    Samollow, Paul B; Gouin, Nicolas; Miethke, Pat; Mahaney, Susan M; Kenney, Margaret; VandeBerg, John L; Graves, Jennifer A Marshall; Kammerer, Candace M

    2007-01-01

    The genome of the gray, short-tailed opossum, Monodelphis domestica, will be the first of any marsupial to be fully sequenced. The utility of this sequence will be greatly enhanced by construction and integration of detailed genetic and physical maps. Therefore, it is important to verify the unusual recombinational characteristics that were suggested by the 'first-generation' M. domestica linkage map; specifically, very low levels of recombination and severely reduced female recombination, both of which are contrary to patterns in other vertebrates. We constructed a new linkage map based on a different genetic cross, using a new and much larger set of map markers, and physically anchored and oriented the linkage groups onto chromosomes via fluorescence in-situ hybridization mapping. This map includes 150 loci in eight autosomal linkage groups corresponding to the eight autosome pairs, and spans 86-89% of the autosomal genome. The sex-averaged autosomal map covers 715 cM, with a full-length estimate of 866 cM; the shortest full-length linkage map reported for any vertebrate. The sex-specific maps confirmed severely reduced female recombination in all linkage groups, and an overall F/M map ratio = 0.54. These results greatly extend earlier findings, and provide an improved microsatellite-based linkage map for this species.

  18. Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa

    PubMed Central

    2011-01-01

    Background The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available. Results We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa. Conclusions Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research. PMID:21306613

  19. Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

    PubMed

    Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling

    2016-05-01

    Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. The genetic map and comparative analysis with the physical map of Trypanosoma brucei.

    PubMed

    MacLeod, Annette; Tweedie, Alison; McLellan, Sarah; Taylor, Sonya; Hall, Neil; Berriman, Matthew; El-Sayed, Najib M; Hope, Michelle; Turner, C Michael R; Tait, Andy

    2005-01-01

    Trypanosoma brucei is the causative agent of African sleeping sickness in humans and contributes to the debilitating disease 'Nagana' in cattle. To date we know little about the genes that determine drug resistance, host specificity, pathogenesis and virulence in these parasites. The availability of the complete genome sequence and the ability of the parasite to undergo genetic exchange have allowed genetic investigations into this parasite and here we report the first genetic map of T.brucei for the genome reference stock TREU 927, comprising of 182 markers and 11 major linkage groups, that correspond to the 11 previously identified chromosomes. The genetic map provides 90% probability of a marker being 11 cM from any given locus. Its comparison to the available physical map has revealed the average physical size of a recombination unit to be 15.6 Kb/cM. The genetic map coupled with the genome sequence and the ability to undertake crosses presents a new approach to identifying genes relevant to the disease and its prevention in this important pathogen through forward genetic analysis and positional cloning.

  1. Integrated Modeling, Mapping, and Simulation (IMMS) framework for planning exercises.

    SciTech Connect

    Friedman-Hill, Ernest J.; Plantenga, Todd D.

    2010-06-01

    The Integrated Modeling, Mapping, and Simulation (IMMS) program is designing and prototyping a simulation and collaboration environment for linking together existing and future modeling and simulation tools to enable analysts, emergency planners, and incident managers to more effectively, economically, and rapidly prepare, analyze, train, and respond to real or potential incidents. When complete, the IMMS program will demonstrate an integrated modeling and simulation capability that supports emergency managers and responders with (1) conducting 'what-if' analyses and exercises to address preparedness, analysis, training, operations, and lessons learned, and (2) effectively, economically, and rapidly verifying response tactics, plans and procedures.

  2. Mapping of topological quantum circuits to physical hardware.

    PubMed

    Paler, Alexandru; Devitt, Simon J; Nemoto, Kae; Polian, Ilia

    2014-04-11

    Topological quantum computation is a promising technique to achieve large-scale, error-corrected computation. Quantum hardware is used to create a large, 3-dimensional lattice of entangled qubits while performing computation requires strategic measurement in accordance with a topological circuit specification. The specification is a geometric structure that defines encoded information and fault-tolerant operations. The compilation of a topological circuit is one important aspect of programming a quantum computer, another is the mapping of the topological circuit into the operations performed by the hardware. Each qubit has to be controlled, and measurement results are needed to propagate encoded quantum information from input to output. In this work, we introduce an algorithm for mapping an topological circuit to the operations needed by the physical hardware. We determine the control commands for each qubit in the computer and the relevant measurements that are needed to track information as it moves through the circuit.

  3. Physically based feature mapping concepts in bond interface evaluation

    NASA Astrophysics Data System (ADS)

    Jiao, D.; Rose, J.; Hodiwalla, N.

    Feature mapping in bond interface evaluation is explored to produce a number of physically based images of the interface state, drawing upon a number of different features in both time and frequency domain extracted from experimentally obtained bulk and guided wave test data. Gaussian filters are applied to the obtained RF signals, and F-maps of interface echoes are obtained to show the image variations as a function of frequency. Experiments on two specimens are conducted to inspect the bonding qualities by transverse wave oblique incidence, longitudinal wave normal incidence, as well as leaky Lamb wave techniques. Other features, such as skewness and kurtosis, can also provide information on the influence of the frequency and the interface properties of the interface layer.

  4. The new integrable symplectic map and the symmetry of integrable nonlinear lattice equation

    NASA Astrophysics Data System (ADS)

    Dong, Huanhe; Zhang, Yong; Zhang, Xiaoen

    2016-07-01

    A discrete matrix spectral problem is presented and the hierarchy of discrete integrable systems is derived. Their Hamiltonian structures are established. As to the discrete integrable system, nonlinearization of the spatial parts of the Lax pairs and the adjoint Lax pairs generate a new integrable symplectic map. Based on the theory, a new integrable symplectic map and a family of finite-dimension completely integrable systems are given. Especially, two explicit equations are obtained under the Bargmann constraint. Finally, the symmetry of the discrete equation is provided according to the recursion operator and the seed symmetry. Although the solutions of the discrete equations have been gained by many methods, there are few articles that solving the discrete equation via the symmetry. So the solution of the discrete lattice equation is obtained through the symmetry theory.

  5. TOWARD EFFICIENT RIPARIAN RESTORATION: INTEGRATING ECONOMIC, PHYSICAL, AND BIOLOGICAL MODELS

    EPA Science Inventory

    This paper integrates economic, biological, and physical models to determine the efficient combination and spatial allocation of conservation efforts for water quality protection and salmonid habitat enhancement in the Grande Ronde basin, Oregon. The integrated modeling system co...

  6. TOWARD EFFICIENT RIPARIAN RESTORATION: INTEGRATING ECONOMIC, PHYSICAL, AND BIOLOGICAL MODELS

    EPA Science Inventory

    This paper integrates economic, biological, and physical models to determine the efficient combination and spatial allocation of conservation efforts for water quality protection and salmonid habitat enhancement in the Grande Ronde basin, Oregon. The integrated modeling system co...

  7. Movement and Learning: Integrating Physical Activity into the Classroom

    ERIC Educational Resources Information Center

    Reeves, Emily; Miller, Stacia; Chavez, Crystal

    2016-01-01

    We know the benefits of physical activity, and yet recess and physical education classes are being cut or scaled back to make room for meeting academic standards. Is cutting recess and physical education really benefiting academics? A look at some recent studies suggests that it is not. Integrating physical activity into the classroom may increase…

  8. Movement and Learning: Integrating Physical Activity into the Classroom

    ERIC Educational Resources Information Center

    Reeves, Emily; Miller, Stacia; Chavez, Crystal

    2016-01-01

    We know the benefits of physical activity, and yet recess and physical education classes are being cut or scaled back to make room for meeting academic standards. Is cutting recess and physical education really benefiting academics? A look at some recent studies suggests that it is not. Integrating physical activity into the classroom may increase…

  9. Dogs, Cats, and Kids: Integrating Yoga into Elementary Physical Education

    ERIC Educational Resources Information Center

    Toscano, Lisa; Clemente, Fran

    2008-01-01

    This article describes the benefits of integrating yoga into elementary physical education classes. Taught as warm-up exercises or as an entire class, yoga offers children of any age and physical ability the opportunity to experience success in physical activity. Children need to experience joy while participating in physical activity in order to…

  10. Dogs, Cats, and Kids: Integrating Yoga into Elementary Physical Education

    ERIC Educational Resources Information Center

    Toscano, Lisa; Clemente, Fran

    2008-01-01

    This article describes the benefits of integrating yoga into elementary physical education classes. Taught as warm-up exercises or as an entire class, yoga offers children of any age and physical ability the opportunity to experience success in physical activity. Children need to experience joy while participating in physical activity in order to…

  11. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps

    USDA-ARS?s Scientific Manuscript database

    Physical maps can be an invaluable resource for improving and assessing the quality of a whole-genome sequence assembly. Here we report the identification and screening of 3,290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the physical map of the cultivar Williams 8...

  12. Fast Mapping Rapidly Integrates Information into Existing Memory Networks

    PubMed Central

    Coutanche, Marc N.; Thompson-Schill, Sharon L.

    2014-01-01

    Successful learning involves integrating new material into existing memory networks. A learning procedure known as fast mapping (FM), thought to simulate the word-learning environment of children, has recently been linked to distinct neuroanatomical substrates in adults. This idea has suggested the (never-before tested) hypothesis that FM may promote rapid incorporation into cortical memory networks. We test this hypothesis here in two experiments. In our first experiment, we introduced fifty participants to sixteen unfamiliar animals and names through FM or explicit encoding (EE), and tested subjects on the training day, and again after sleep. Learning through EE produced strong declarative memories, without immediate lexical competition, as expected from slow-consolidation models. Learning through FM, however, led to almost immediate lexical competition, which continued to the next day. Additionally, the learned words began to prime related concepts on the day following FM (but not EE) training. In a second experiment, we replicated the lexical integration results, and determined that presenting an already-known item during learning was crucial for rapid integration through FM. The findings presented here indicate that learned items can be integrated into cortical memory networks at an accelerated rate through fast mapping. The retrieval of a known related concept, in order to infer the target of the FM question, is critical for this effect. PMID:25222265

  13. The Circumpolar Arctic Vegetation Map: AVHRR-derived base maps, environmental controls, and integrated mapping procedures

    Treesearch

    D. A. WALKER; W. A. GOULD; MAIERH. A.; M. K. RAYNOLDS

    2002-01-01

    A new false-colour-infrared image derived from biweekly 1993 and 1995 Advanced Very High Resolution Radiometer (AVHRR) data provides a snow-free and cloud-free base image for the interpretation of vegetation as part of a 1:7.5M-scale Circumpolar Arctic Vegetation Map (CAVM). A maximum-NDVI (Normalized DiVerence Vegetation Index) image prepared from the same data...

  14. MapGene2Chrom, a tool to draw gene physical map based on Perl and SVG languages.

    PubMed

    Jiangtao, Chao; Yingzhen, Kong; Qian, Wang; Yuhe, Sun; Daping, Gong; Jing, Lv; Guanshan, Liu

    2015-01-01

    Genetic linkage map is helpful for analysis on heredity of some gene families and map-based gene cloning because of its simple and elegant manifestation. One software is in need to draw a gene physical map, which shows a manner similar to the genetic linkage map, based on the relative physical distance between genes. Although some tools like GBrowse and MapViewer etc. are available to draw gene physical map, there are obvious limitations for them: (1) the data need to be decorated in advance; (2) users can't modify results. Therefore, we developed a bio-assisted mapping software--MapGene2Chrom with PC and web versions, which is based on Perl and SVG languages. The software can be used to draw the corresponding physical map quickly in SVG format based on the input data. It will become a useful tool for drawing gene physical map with the advantages of simple input data format, easily modified output and very good portability.

  15. IEMIS (Integrated Emergency Management Information System) Floodplain Mapping Based on a Lidar Derived Data Set.

    DTIC Science & Technology

    1988-02-05

    0-A193 971 IEMIS (INTEGRATED EMERGENCY MANAGEMENT INFORMATION SYSTEM ) FLOODPLRIN MAP.. (U) ARMY ENGINEER WATERWAYS EXPERIMENT STATION VICKSBURG HS J...illustrate the application of the automated mapping capabilities of the Integrated Emergency Management Information System (IEMIS) to FISs. Unclassified...mapping capabilities of the Integrated Emergency Management Information System (IEMIS) to FISs. II. BACKGROUND The concept of mounting laser ranging

  16. A physical genome map of the Burkholderia cepacia type strain.

    PubMed

    Rodley, P D; Römling, U; Tümmler, B

    1995-07-01

    Burkholderia cepacia (basonym Pseudomonas cepacia), the type species of the new genus Burkholderia, is of interest, not only because of its broad catabolic capacity and its ability to antagonize soil-borne plant pathogens, but also because of its causative role in infections in man, which are particularly evident in patients with cystic fibrosis. A physical map of the 8.1 Mb genome of the B. cepacia type-strain ATCC 25416 was constructed by applying two-dimensional pulsed-field gel electrophoresis techniques. Placed onto the macrorestriction map were 38 SpeI, 11 SwaI, 11 PacI, 11 PmeI and six I-CeuI sites, resulting in an average resolution of 105 kbp. Random single-hit linearization by irradiation and restriction mapping uncovered the presence of four circular replicons of 3.65 Mb, 3.17 Mb, 1.07 Mb and 200 kbp in size. The largest replicon harbours four rrn operons while the other two Megabase-size replicons each contain a single rrn operon, suggesting that the genome has three chromosomes and a large plasmid. Within the beta subdivision of proteobacteria, the existence of multiple replicons is not confined to B. cepacia. The phylogenetically related species Burkholderia glumae, Burkholderia pickettii, Burkholderia solanacearum, Alcaligenes eutrophus and the so far unassigned Pseudomonas glathei were also found to harbour more than one Megabase-size replicon.

  17. Physical and transcriptional map in the CMT 1A region

    SciTech Connect

    Chevillard, C.; Passage, E.; Cudrey, C.

    1994-09-01

    The Charcot-Marie-Tooth disease type 1A (CMT1A) has been mapped to the proximal short arm of chromosome 17. CMT1A is the most frequent of the motor and sensory peripheral neuropathies and is associated with a duplication of a 1.5 Mb fragment in proximal 17p12. Several groups have proposed that the gene coding for peripheral myelin protein-22 (PMP-22) as the candidate gene for CMT1A. We have recently published a {open_quote}MegaYAC{close_quote} contig of 6 Mb which covers the CMT1A critical region. In order to isolate new genes localized in this region, we used a {open_quote}physical trapping {close_quote} strategy derived from the direct cDNA selection technique developed by Parimoo et al. This approach has allowed us to construct cDNA {open_quotes}minilibraries{close_quotes} using YAC DNA from the CMT1A region. One of the clones in these minilibraries has been mapped back to the CMT1A duplication. Other potentially interesting clones are in the process of further characterization. Furthermore, we have mapped several Genethon microsatellites in the 6 Mb YAC contig and some are located in the CMT1A duplicated region. These highly polymorphic markers should prove useful for diagnostic testing in CMT1A.

  18. Integration of common bean ( Phaseolus vulgaris L.) linkage and chromosomal maps.

    PubMed

    Pedrosa, A; Vallejos, C E; Bachmair, A; Schweizer, D

    2003-01-01

    Fluorescent in situ hybridisation of pooled, closely linked RFLP markers was used to integrate the genetic linkage map and the mitotic chromosome map of the common bean. Pooled RFLP probes showed clear and reproducible signals and allowed the assignment of all linkage groups to the chromosomes of two Phaseolus vulgaris cultivars, Saxa and Calima. Low extension values for signals originating from clustered RFLPs suggest that these clones are physically close to each other and that clusters in the genetic map are not a result of suppression of recombination due to the occurrence of chromosome rearrangements. For linkage group K, clustering of markers could be associated with proximity to centromeres. High variation in the number of 45S rDNA loci was observed among cultivars, suggesting that these terminal sites are highly recombinogenic in common bean.

  19. Integrating Recent Land Cover Mapping Efforts to Update the National Gap Analysis Program's Species Habitat Map

    NASA Astrophysics Data System (ADS)

    McKerrow, A. J.; Davidson, A.; Earnhardt, T. S.; Benson, A. L.

    2014-11-01

    Over the past decade, great progress has been made to develop national extent land cover mapping products to address natural resource issues. One of the core products of the GAP Program is range-wide species distribution models for nearly 2000 terrestrial vertebrate species in the U.S. We rely on deductive modeling of habitat affinities using these products to create models of habitat availability. That approach requires that we have a thematically rich and ecologically meaningful map legend to support the modeling effort. In this work, we tested the integration of the Multi-Resolution Landscape Characterization Consortium's National Land Cover Database 2011 and LANDFIRE's Disturbance Products to update the 2001 National GAP Vegetation Dataset to reflect 2011 conditions. The revised product can then be used to update the species models. We tested the update approach in three geographic areas (Northeast, Southeast, and Interior Northwest). We used the NLCD product to identify areas where the cover type mapped in 2011 was different from what was in the 2001 land cover map. We used Google Earth and ArcGIS base maps as reference imagery in order to label areas identified as "changed" to the appropriate class from our map legend. Areas mapped as urban or water in the 2011 NLCD map that were mapped differently in the 2001 GAP map were accepted without further validation and recoded to the corresponding GAP class. We used LANDFIRE's Disturbance products to identify changes that are the result of recent disturbance and to inform the reassignment of areas to their updated thematic label. We ran species habitat models for three species including Lewis's Woodpecker (Melanerpes lewis) and the White-tailed Jack Rabbit (Lepus townsendii) and Brown Headed nuthatch (Sitta pusilla). For each of three vertebrate species we found important differences in the amount and location of suitable habitat between the 2001 and 2011 habitat maps. Specifically, Brown headed nuthatch habitat in

  20. An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae.

    PubMed Central

    Philipp, W J; Poulet, S; Eiglmeier, K; Pascopella, L; Balasubramanian, V; Heym, B; Bergh, S; Bloom, B R; Jacobs, W R; Cole, S T

    1996-01-01

    An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis, was constructed by using a twin-pronged approach. Pulsed-field gel electrophoretic analysis enabled cleavage sites for Asn I and Dra I to be positioned on the 4.4-Mb circular chromosome, while, in parallel, clones from two cosmid libraries were ordered into contigs by means of fingerprinting and hybridization mapping. The resultant contig map was readily correlated with the physical map of the genome via the landmarked restriction sites. Over 165 genes and markers were localized on the integrated map, thus enabling comparisons with the leprosy bacillus, Mycobacterium leprae, to be undertaken. Mycobacterial genomes appear to have evolved as mosaic structures since extended segments with conserved gene order and organization are interspersed with different flanking regions. Repetitive sequences and insertion elements are highly abundant in M. tuberculosis, but the distribution of IS6110 is apparently nonrandom. Images Fig. 1 Fig. 2 PMID:8610181

  1. An Integrated Rapid Mapping System for Disaster Management

    NASA Astrophysics Data System (ADS)

    Hein, D.; Bayer, S.; Berger, R.; Kraft, T.; Lesmeister, D.

    2017-05-01

    Natural disasters as well as major man made incidents are an increasingly serious threat for civil society. Effective, fast and coordinated disaster management crucially depends on the availability of a real-time situation picture of the affected area. However, in situ situation assessment from the ground is usually time-consuming and of limited effect, especially when dealing with large or inaccessible areas. A rapid mapping system based on aerial images can enable fast and effective assessment and analysis of medium to large scale disaster situations. This paper presents an integrated rapid mapping system that is particularly designed for real-time applications, where comparatively large areas have to be recorded in short time. The system includes a lightweight camera system suitable for UAV applications and a software tool for generating aerial maps from recorded sensor data within minutes after landing. The paper describes in particular which sensors are applied and how they are operated. Furthermore it outlines the procedure, how the aerial map is generated from image and additional gathered sensor data.

  2. Reconstructing the integrated Sachs-Wolfe map with galaxy surveys

    NASA Astrophysics Data System (ADS)

    Muir, Jessica; Huterer, Dragan

    2016-08-01

    The integrated Sachs-Wolfe (ISW) effect is a large-angle modulation of the cosmic microwave background (CMB), generated when CMB photons traverse evolving potential wells associated with large scale structure (LSS). Recent efforts have been made to reconstruct maps of the ISW signal using information from surveys of galaxies and other LSS tracers, but investigation into how survey systematics affect their reliability has so far been limited. Using simulated ISW and LSS maps, we study the impact of galaxy survey properties and systematic errors on the accuracy of a reconstructed ISW signal. We find that systematics that affect the observed distribution of galaxies along the line of sight, such as photo-z and bias-evolution related errors, have a relatively minor impact on reconstruction quality. In contrast, however, we find that direction-dependent calibration errors can be very harmful. Specifically, we find that, in order to avoid significant degradation of our reconstruction quality statistics, direction-dependent number density fluctuations due to systematics must be controlled so that their variance is smaller than 10-6 (which corresponds to a 0.1% calibration). Additionally, we explore the implications of our results for attempts to use reconstructed ISW maps to shed light on the origin of large-angle CMB alignments. We find that there is only a weak correlation between the true and reconstructed angular momentum dispersion, which quantifies alignment, even for reconstructed ISW maps which are fairly accurate overall.

  3. A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy

    PubMed Central

    Agarwala, Richa; Applegate, David L.; Maglott, Donna; Schuler, Gregory D.; Schäffer, Alejandro A.

    2000-01-01

    This paper describes a fast and scalable strategy for constructing a radiation hybrid (RH) map from data on different RH panels. The maps on each panel are then integrated to produce a single RH map for the genome. Recurring problems in using maps from several sources are that the maps use different markers, the maps do not place the overlapping markers in same order, and the objective functions for map quality are incomparable. We use methods from combinatorial optimization to develop a strategy that addresses these issues. We show that by the standard objective functions of obligate chromosome breaks and maximum likelihood, software for the traveling salesman problem produces RH maps with better quality much more quickly than using software specifically tailored for RH mapping. We use known algorithms for the longest common subsequence problem as part of our map integration strategy. We demonstrate our methods by reconstructing and integrating maps for markers typed on the Genebridge 4 (GB4) and the Stanford G3 panels publicly available from the RH database. We compare map quality of our integrated map with published maps for GB4 panel and G3 panel by considering whether markers occur in the same order on a map and in DNA sequence contigs submitted to GenBank. We find that all of the maps are inconsistent with the sequence data for at least 50% of the contigs, but our integrated maps are more consistent. The map integration strategy not only scales to multiple RH maps but also to any maps that have comparable criteria for measuring map quality. Our software improves on current technology for doing RH mapping in areas of computation time and algorithms for considering a large number of markers for mapping. The essential impediments to producing dense high-quality RH maps are data quality and panel size, not computation. PMID:10720576

  4. A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes

    PubMed Central

    2011-01-01

    Background A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. Results The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes. Conclusion The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species. PMID:21906286

  5. A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes.

    PubMed

    Zhang, Yang; Zhang, Xiaojun; O'Hare, Thomas H; Payne, William S; Dong, Jennifer J; Scheuring, Chantel F; Zhang, Meiping; Huang, James J; Lee, Mi-Kyung; Delany, Mary E; Zhang, Hong-Bin; Dodgson, Jerry B

    2011-09-09

    A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes. The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species.

  6. Determination Of Slope Instability Using Spatially Integrated Mapping Framework

    NASA Astrophysics Data System (ADS)

    Baharuddin, I. N. Z.; Omar, R. C.; Roslan, R.; Khalid, N. H. N.; Hanifah, M. I. M.

    2016-11-01

    The determination and identification of slope instability are often rely on data obtained from in-situ soil investigation work where it involves the logistic of machineries and manpower, thus these aspects may increase the cost especially for remote locations. Therefore a method, which is able to identify possible slope instability without frequent ground walkabout survey, is needed. This paper presents the method used in prediction of slope instability using spatial integrated mapping framework which applicable for remote areas such as tropical forest and natural hilly terrain. Spatial data such as geology, topography, land use map, slope angle and elevation were used in regional analysis during desktop study. Through this framework, the occurrence of slope instability was able to be identified and was validate using a confirmatory site- specific analysis.

  7. Map Matching and Real World Integrated Sensor Data Warehousing (Presentation)

    SciTech Connect

    Burton, E.

    2014-02-01

    The inclusion of interlinked temporal and spatial elements within integrated sensor data enables a tremendous degree of flexibility when analyzing multi-component datasets. The presentation illustrates how to warehouse, process, and analyze high-resolution integrated sensor datasets to support complex system analysis at the entity and system levels. The example cases presented utilizes in-vehicle sensor system data to assess vehicle performance, while integrating a map matching algorithm to link vehicle data to roads to demonstrate the enhanced analysis possible via interlinking data elements. Furthermore, in addition to the flexibility provided, the examples presented illustrate concepts of maintaining proprietary operational information (Fleet DNA) and privacy of study participants (Transportation Secure Data Center) while producing widely distributed data products. Should real-time operational data be logged at high resolution across multiple infrastructure types, map matched to their associated infrastructure, and distributed employing a similar approach; dependencies between urban environment infrastructures components could be better understood. This understanding is especially crucial for the cities of the future where transportation will rely more on grid infrastructure to support its energy demands.

  8. The National Map 2.0 Tactical Plan: "Toward the (Integrated) National Map"

    USGS Publications Warehouse

    Zulick, Carl A.

    2008-01-01

    The National Map's 2-year goal, as described in this plan, is to provide a range of geospatial products and services that meet the basic goals of the original vision for The National Map while furthering the National Spatial Data Infrastructure that underpins U.S. Geological Survey (USGS) science. To accomplish this goal, the National Geospatial Program (NGP) will acquire, store, maintain, and distribute base map data. The management team for the NGP sets priorities for The National Map in three areas: Data and Products, Services, and Management. Priorities for fiscal years 2008 and 2009 (October 1, 2007 through September 30, 2009), involving the current data inventory, data acquisition, and the integration of data, are (1) incorporating current data from Federal, State, and local organizations into The National Map to the degree possible, given data availability and program resources; (2) collaborating with other USGS programs to incorporate data that support the USGS Science Strategy; (3) supporting the Department of the Interior (DOI) high-priority geospatial information needs; (4) emergency response; (5) homeland security, natural hazards; and (6) graphics products delivery. The management team identified known constraints, enablers, and drivers for the acquisition and integration of data. The NGP management team also identified customer-focused products and services of The National Map. Ongoing planning and management activities direct the development and delivery of these products and services. Management of work flow processes to support The National Map priorities are identified and established through a business-driven prioritization process. This tactical plan is primarily for use as a document to guide The National Map program for the next two fiscal years. The document is available to the public because of widespread interest in The National Map. The USGS collaborates with a broad range of customers and partners who are essential to the success of The

  9. Comparison of peanut gentics and physical maps provided insights on collinearity, reversions and translocations

    USDA-ARS?s Scientific Manuscript database

    Genetic and physical maps are the valuable resources for peanut research community in understanding genome organization and serving as the basis for map-based cloning and marker-assisted selection. Physical maps of two diploid wild peanut progenitor species, Arachis duranensis (A genome) and A. ipae...

  10. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

    PubMed Central

    2011-01-01

    Background Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123

  11. Learning about A level physics students’ understandings of particle physics using concept mapping

    NASA Astrophysics Data System (ADS)

    Gourlay, H.

    2017-01-01

    This paper describes a small-scale piece of research using concept mapping to elicit A level students’ understandings of particle physics. Fifty-nine year 12 (16- and 17 year-old) students from two London schools participated. The exercise took place during school physics lessons. Students were instructed how to make a concept map and were provided with 24 topic-specific key words. Students’ concept maps were analysed by identifying the knowledge propositions they represented, enumerating how many students had made each one, and by identifying errors and potential misconceptions, with reference to the specification they were studying. The only correct statement made by a majority of students in both schools was that annihilation takes place when matter and antimatter collide, although there was evidence that some students were unable to distinguish between annihilation and pair production. A high proportion of students knew of up, down and strange quarks, and that the electron is a lepton. However, some students appeared to have a misconception that everything is made of quarks. Students found it harder to classify tau particles than they did electrons and muons. Where students made incorrect links about muons and tau particles their concept maps suggested that they thought they were mesons or quarks.

  12. Computer Integrated Manufacturing: Physical Modelling Systems Design. A Personal View.

    ERIC Educational Resources Information Center

    Baker, Richard

    A computer-integrated manufacturing (CIM) Physical Modeling Systems Design project was undertaken in a time of rapid change in the industrial, business, technological, training, and educational areas in Australia. A specification of a manufacturing physical modeling system was drawn up. Physical modeling provides a flexibility and configurability…

  13. Discovering Integration through a Physical Phenomenon

    ERIC Educational Resources Information Center

    Burt, Derek; Magnes, Jenny; Schwarz, Gregory; Hartke, John

    2008-01-01

    This article outlines a method of conducting a laboratory designed to discover mathematical integration with students. The results are produced and verified in the laboratory by students. Understanding that an integral is defined by the area bounded by a function of x and the x-axis from a point a to a point b is challenging. Students often have…

  14. Integrating Physical Activity into Academic Pursuits

    ERIC Educational Resources Information Center

    Gaus, Mark D.; Simpson, Cynthia G.

    2009-01-01

    Children of today may be the first generation in the United States in more than 200 years to have a life expectancy shorter than their parents. Low levels of fitness caused by physical inactivity and poor nutritional habits of many of today's youth may be a contributing factor. Combating low fitness levels with physical activity is of utmost…

  15. Integrating Physical Activity into Academic Pursuits

    ERIC Educational Resources Information Center

    Gaus, Mark D.; Simpson, Cynthia G.

    2009-01-01

    Children of today may be the first generation in the United States in more than 200 years to have a life expectancy shorter than their parents. Low levels of fitness caused by physical inactivity and poor nutritional habits of many of today's youth may be a contributing factor. Combating low fitness levels with physical activity is of utmost…

  16. Integrating Condensed Matter Physics into a Liberal Arts Physics Curriculum

    NASA Astrophysics Data System (ADS)

    Collett, Jeffrey

    2008-03-01

    The emergence of nanoscale science into the popular consciousness presents an opportunity to attract and retain future condensed matter scientists. We inject nanoscale physics into recruiting activities and into the introductory and the core portions of the curriculum. Laboratory involvement and research opportunity play important roles in maintaining student engagement. We use inexpensive scanning tunneling (STM) and atomic force (AFM) microscopes to introduce students to nanoscale structure early in their college careers. Although the physics of tip-surface interactions is sophisticated, the resulting images can be interpreted intuitively. We use the STM in introductory modern physics to explore quantum tunneling and the properties of electrons at surfaces. An interdisciplinary course in nanoscience and nanotechnology course team-taught with chemists looks at nanoscale phenomena in physics, chemistry, and biology. Core quantum and statistical physics courses look at effects of quantum mechanics and quantum statistics in degenerate systems. An upper level solid-state physics course takes up traditional condensed matter topics from a structural perspective by beginning with a study of both elastic and inelastic scattering of x-rays from crystalline solids and liquid crystals. Students encounter reciprocal space concepts through the analysis of laboratory scattering data and by the development of the scattering theory. The course then examines the importance of scattering processes in band structure and in electrical and thermal conduction. A segment of the course is devoted to surface physics and nanostructures where we explore the effects of restricting particles to two-dimensional surfaces, one-dimensional wires, and zero-dimensional quantum dots.

  17. Integrated Health and Physical Education Program to Reduce Media Use and Increase Physical Activity in Youth

    ERIC Educational Resources Information Center

    Clocksin, Brian D.; Wattson, Doris L.; Williams, Daniel P.; Randsell, Lynda

    2009-01-01

    The purpose of this project was to compare an integrated health and physical education curriculum, focused on reducing media use and on increasing physical activity in middle school adolescents, to traditional and nonintegrated health and physical education curricula. Two middle schools' health and physical education classes were assigned to an…

  18. Automated computer vision interpretation for physical and genetic mapping experiments

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.

    1994-09-01

    Much of the high-throughput data currently generated in the molecular genetics laboratory is in the form of two dimensional images. In physical mapping, a high-density gridded filter containing thousands YACs or cosmids can be hybridized against a single labeled probe, such as the IRS-PCR products of a radiation hybrid (RH). In genetic mapping, hundreds of polymorphic dinucleotide repeat PCR experiments can be multiplexed into distinct lanes, size ranges, and fluorescent colors on a single run of an Applied Biosystems (ABl) 373A automated DNA sequencer. For all its advantages such high-throughput data introduces a new fundamental bottleneck: the greatly increased time, expense, and error of scoring these assays when relying solely on the human visual system. Toward this end, we have developed a novel computer vision automation architecture that addresses the needs of high-throughput data interpretation in the molecular genetics laboratory. A flexible knowledge-based approach is used to systematically detect and analyze signal features, motivated by how human experts perform the interpretation. This architecture enables customization to similar hybridization-and gel-based tasks. Our prototype system has thus far been tested on both hybridization data and ABl gel images.

  19. Physical maps and recombination frequency of six rice chromosomes.

    PubMed

    Wu, Jianzhong; Mizuno, Hiroshi; Hayashi-Tsugane, Mika; Ito, Yukiyo; Chiden, Yoshino; Fujisawa, Masaki; Katagiri, Satoshi; Saji, Shoko; Yoshiki, Shoji; Karasawa, Wataru; Yoshihara, Rie; Hayashi, Akiko; Kobayashi, Harumi; Ito, Kazue; Hamada, Masao; Okamoto, Masako; Ikeno, Maiko; Ichikawa, Yoko; Katayose, Yuichi; Yano, Masahiro; Matsumoto, Takashi; Sasaki, Takuji

    2003-12-01

    We constructed physical maps of rice chromosomes 1, 2, and 6-9 with P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-specific repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR)- and RIce RetroElement 7 (RIRE7)-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

  20. Level Spacings for Integrable Quantum Maps in Genus Zero

    NASA Astrophysics Data System (ADS)

    Zelditch, Steve

    We study the pair correlation function for a variety of completely integrable quantum maps in one degree of freedom. For simplicity we assume that the classical phase space M is the Riemann sphere P1 and that the classical map is a fixed-time map of a Hamilton flow. The quantization is then a unitary N × N matrix Ut,N and its pair correlation measure gives the distribution of spacings between eigenvalues in an interval of length comparable to the mean level spacing ( 1/N). The physicists' conjecture (Berry-Tabor conjecture) is that as , should converge to the pair correlation function of a Poisson process. For any 2-parameter family of Hamiltonians of the form with we prove that this conjecture is correct for almost all (α, β) along the subsequence of Planck constants . In the addendum to this paper [Z. Addendum], we further show that for polynomial phases φ the a.e. convergence to Poisson holds along the full sequence of Planck constants for the Cesaro means of .

  1. Mapping biological ideas: Concept maps as knowledge integration tools for evolution education

    NASA Astrophysics Data System (ADS)

    Schwendimann, Beat Adrian

    Many students leave school with a fragmented understanding of biology that does not allow them to connect their ideas to their everyday lives (Wandersee, 1989; Mintzes, Wandersee, & Novak, 1998; Mintzes, Wandersee, & Novak, 2000a). Understanding evolution ideas is seen as central to building an integrated knowledge of biology (Blackwell, Powell, & Dukes, 2003; Thagard & Findlay, 2010). However, the theory of evolution has been found difficult to understand as it incorporates a wide range of ideas from different areas (Bahar et al., 1999; Tsui & Treagust, 2003) and multiple interacting levels (Wilensky & Resnick, 1999; Duncan & Reiser, 2007; Hmelo-Silver et al., 2007). Research suggests that learners can hold a rich repertoire of co-existing alternative ideas of evolution (for example, Bishop & Anderson, 1990; Demastes, Good, & Peebles, 1996; Evans, 2008), especially of human evolution (for example, Nelson, 1986; Sinatra et al., 2003; Poling & Evans, 2004). Evolution ideas are difficult to understand because they often contradict existing alternative ideas (Mayr, 1982; Wolpert, 1994; Evans, 2008). Research suggests that understanding human evolution is a key to evolution education (for example, Blackwell et al., 2003; Besterman & Baggott la Velle, 2007). This dissertation research investigates how different concept mapping forms embedded in a collaborative technology-enhanced learning environment can support students' integration of evolution ideas using case studies of human evolution. Knowledge Integration (KI) (Linn et al., 2000; Linn et al., 2004) is used as the operational framework to explore concept maps as knowledge integration tools to elicit, add, critically distinguish, group, connect, and sort out alternative evolution ideas. Concept maps are a form of node-link diagram for organizing and representing connections between ideas as a semantic network (Novak & Gowin, 1984). This dissertation research describes the iterative development of a novel biology

  2. A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L.

    PubMed

    Zhang, Xiaojun; Scheuring, Chantel F; Zhang, Meiping; Dong, Jennifer J; Zhang, Yang; Huang, James J; Lee, Mi-Kyung; Abbo, Shahal; Sherman, Amir; Shtienberg, Dani; Chen, Weidong; Muehlbauer, Fred; Zhang, Hong-Bin

    2010-09-17

    Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.

  3. A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L

    PubMed Central

    2010-01-01

    Background Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. Results We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 ×) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. Conclusion The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes. PMID:20849583

  4. Cyber / Physical Security Vulnerability Assessment Integration

    SciTech Connect

    MacDonald, Douglas G.; Simpkins, Bret E.

    2012-07-28

    Abstract Both physical protection and cyber security domains offer solutions for the discovery of vulnerabilities through the use of various assessment processes and software tools. Each vulnerability assessment (VA) methodology provides the ability to identify and categorize vulnerabilities, and quantifies the risks within their own areas of expertise. Neither approach fully represents the true potential security risk to a site and/or a facility, nor comprehensively assesses the overall security posture. The technical approach to solving this problem was to identify methodologies and processes that blend the physical and cyber security assessments, and develop tools to accurately quantify the unaccounted for risk. SMEs from both the physical and the cyber security domains developed the blending methodologies, and cross trained each other on the various aspects of the physical and cyber security assessment processes. A local critical infrastructure entity volunteered to host a proof of concept physical/cyber security assessment, and the lessons learned have been leveraged by this effort. The four potential modes of attack an adversary can use in approaching a target are; Physical Only Attack, Cyber Only Attack, Physical Enabled Cyber Attack, and the Cyber Enabled Physical Attack. The Physical Only and the Cyber Only pathway analysis are two of the most widely analyzed attack modes. The pathway from an off-site location to the desired target location is dissected to ensure adversarial activity can be detected and neutralized by the protection strategy, prior to completion of a predefined task. This methodology typically explores a one way attack from the public space (or common area) inward towards the target. The Physical Enabled Cyber Attack and the Cyber Enabled Physical Attack are much more intricate. Both scenarios involve beginning in one domain to affect change in the other, then backing outward to take advantage of the reduced system effectiveness, before

  5. Comparing Two Forms of Concept Map Critique Activities to Facilitate Knowledge Integration Processes in Evolution Education

    ERIC Educational Resources Information Center

    Schwendimann, Beat A.; Linn, Marcia C.

    2016-01-01

    Concept map activities often lack a subsequent revision step that facilitates knowledge integration. This study compares two collaborative critique activities using a Knowledge Integration Map (KIM), a form of concept map. Four classes of high school biology students (n?=?81) using an online inquiry-based learning unit on evolution were assigned…

  6. Comparing Two Forms of Concept Map Critique Activities to Facilitate Knowledge Integration Processes in Evolution Education

    ERIC Educational Resources Information Center

    Schwendimann, Beat A.; Linn, Marcia C.

    2016-01-01

    Concept map activities often lack a subsequent revision step that facilitates knowledge integration. This study compares two collaborative critique activities using a Knowledge Integration Map (KIM), a form of concept map. Four classes of high school biology students (n?=?81) using an online inquiry-based learning unit on evolution were assigned…

  7. The roots of physics students' motivations: Fear and integrity

    NASA Astrophysics Data System (ADS)

    Van Dusen, Ben

    Too often, physics students are beset by feelings of failure and isolation rather than experiencing the creative joys of discovery that physics has to offer. This dissertation research was founded on the desire of a teacher to make physics class exciting and motivating to his students. This work explores how various aspects of learning environments interact with student motivation. This work uses qualitative and quantitative methods to explore how students are motivated to engage in physics and how they feel about themselves while engaging in physics. The collection of four studies in this dissertation culminates in a sociocultural perspective on motivation and identity. This perspective uses two extremes of how students experience physics as a lens for understanding motivation: fear and self-preservation versus integrity and self-expression. Rather than viewing motivation as a property of the student, or viewing students as inherently interested or disinterested in physics, the theoretical perspective on motivation and identity helps examine features of the learning environments that determine how students' experience themselves through physics class. This perspective highlights the importance of feeling a sense of belonging in the context of physics and the power that teachers have in shaping students' motivation through the construction of their classroom learning environments. Findings demonstrate how different ways that students experience themselves in physics class impact their performance and interest in physics. This dissertation concludes with a set of design principles that can foster integration and integrity among students in physics learning environments.

  8. Physical activity, physical fitness and academic achievement in adolescents: a self-organizing maps approach.

    PubMed

    Pellicer-Chenoll, Maite; Garcia-Massó, Xavier; Morales, Jose; Serra-Añó, Pilar; Solana-Tramunt, Mònica; González, Luis-Millán; Toca-Herrera, José-Luis

    2015-06-01

    The relationship among physical activity, physical fitness and academic achievement in adolescents has been widely studied; however, controversy concerning this topic persists. The methods used thus far to analyse the relationship between these variables have included mostly traditional lineal analysis according to the available literature. The aim of this study was to perform a visual analysis of this relationship with self-organizing maps and to monitor the subject's evolution during the 4 years of secondary school. Four hundred and forty-four students participated in the study. The physical activity and physical fitness of the participants were measured, and the participants' grade point averages were obtained from the five participant institutions. Four main clusters representing two primary student profiles with few differences between boys and girls were observed. The clustering demonstrated that students with higher energy expenditure and better physical fitness exhibited lower body mass index (BMI) and higher academic performance, whereas those adolescents with lower energy expenditure exhibited worse physical fitness, higher BMI and lower academic performance. With respect to the evolution of the students during the 4 years, ∼25% of the students originally clustered in a negative profile moved to a positive profile, and there was no movement in the opposite direction. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  9. Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

    PubMed Central

    Schaeffer, Stephen W.; Bhutkar, Arjun; McAllister, Bryant F.; Matsuda, Muneo; Matzkin, Luciano M.; O'Grady, Patrick M.; Rohde, Claudia; Valente, Vera L. S.; Aguadé, Montserrat; Anderson, Wyatt W.; Edwards, Kevin; Garcia, Ana C. L.; Goodman, Josh; Hartigan, James; Kataoka, Eiko; Lapoint, Richard T.; Lozovsky, Elena R.; Machado, Carlos A.; Noor, Mohamed A. F.; Papaceit, Montserrat; Reed, Laura K.; Richards, Stephen; Rieger, Tania T.; Russo, Susan M.; Sato, Hajime; Segarra, Carmen; Smith, Douglas R.; Smith, Temple F.; Strelets, Victor; Tobari, Yoshiko N.; Tomimura, Yoshihiko; Wasserman, Marvin; Watts, Thomas; Wilson, Robert; Yoshida, Kiyohito; Markow, Therese A.; Gelbart, William M.; Kaufman, Thomas C.

    2008-01-01

    The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events. PMID:18622037

  10. An Integration of Chemistry, Biology, and Physics: The Interdisciplinary Laboratory

    NASA Astrophysics Data System (ADS)

    van Hecke, Gerald R.; Karukstis, Kerry K.; Haskell, Richard C.; McFadden, Catherine S.; Sheldon Wettack, F.

    2002-07-01

    As a new venture to integrate research and education, a pilot section of a first-year laboratory sequence known as the Interdisciplinary Laboratory (ID Lab) was introduced on the Harvey Mudd campus during the 1999 2000 academic year and continues to be offered. The ID Lab attempts to bridge laboratory experiences from biology, chemistry, and physics for the first-year student. Taught by a team of faculty from these disciplines, the course seeks both to illustrate commonality of investigative methods and laboratory techniques in these sciences and to introduce discipline-specific principles. Experiments with a chemistry component include the Molecular Weight of Macromolecules, the Synthesis and Characterization of Liquid Crystals, A Structure Activity Investigation of Photosynthetic Electron Transport, a Genetic Map of a Bacterial Plasmid, and The Carbonate Content of Biological Hard Tissue. This article provides some details of the experiments conducted, information on the philosophy and mechanics of the course, and a discussion of student reaction to this innovative and novel course.

  11. Digital Geologic Mapping and Integration with the Geoweb: The Death Knell for Exclusively Paper Geologic Maps

    NASA Astrophysics Data System (ADS)

    House, P. K.

    2008-12-01

    The combination of traditional methods of geologic mapping with rapidly developing web-based geospatial applications ('the geoweb') and the various collaborative opportunities of web 2.0 have the potential to change the nature, value, and relevance of geologic maps and related field studies. Parallel advances in basic GPS technology, digital photography, and related integrative applications provide practicing geologic mappers with greatly enhanced methods for collecting, visualizing, interpreting, and disseminating geologic information. Even a cursory application of available tools can make field and office work more enriching and efficient; whereas more advanced and systematic applications provide new avenues for collaboration, outreach, and public education. Moreover, they ensure a much broader audience among an immense number of internet savvy end-users with very specific expectations for geospatial data availability. Perplexingly, the geologic community as a whole is not fully exploring this opportunity despite the inevitable revolution in portends. The slow acceptance follows a broad generational trend wherein seasoned professionals are lagging behind geology students and recent graduates in their grasp of and interest in the capabilities of the geoweb and web 2.0 types of applications. Possible explanations for this include: fear of the unknown, fear of learning curve, lack of interest, lack of academic/professional incentive, and (hopefully not) reluctance toward open collaboration. Although some aspects of the expanding geoweb are cloaked in arcane computer code, others are extremely simple to understand and use. A particularly obvious and simple application to enhance any field study is photo geotagging, the digital documentation of the locations of key outcrops, illustrative vistas, and particularly complicated geologic field relations. Viewing geotagged photos in their appropriate context on a virtual globe with high-resolution imagery can be an

  12. From Planetary Mapping to Map Production: Planetary Cartography as integral discipline in Planetary Sciences

    NASA Astrophysics Data System (ADS)

    Nass, Andrea; van Gasselt, Stephan; Hargitai, Hendrik; Hare, Trent; Manaud, Nicolas; Karachevtseva, Irina; Kersten, Elke; Roatsch, Thomas; Wählisch, Marita; Kereszturi, Akos

    2016-04-01

    Cartography is one of the most important communication channels between users of spatial information and laymen as well as the open public alike. This applies to all known real-world objects located either here on Earth or on any other object in our Solar System. In planetary sciences, however, the main use of cartography resides in a concept called planetary mapping with all its various attached meanings: it can be (1) systematic spacecraft observation from orbit, i.e. the retrieval of physical information, (2) the interpretation of discrete planetary surface units and their abstraction, or it can be (3) planetary cartography sensu strictu, i.e., the technical and artistic creation of map products. As the concept of planetary mapping covers a wide range of different information and knowledge levels, aims associated with the concept of mapping consequently range from a technical and engineering focus to a scientific distillation process. Among others, scientific centers focusing on planetary cartography are the United State Geological Survey (USGS, Flagstaff), the Moscow State University of Geodesy and Cartography (MIIGAiK, Moscow), Eötvös Loránd University (ELTE, Hungary), and the German Aerospace Center (DLR, Berlin). The International Astronomical Union (IAU), the Commission Planetary Cartography within International Cartographic Association (ICA), the Open Geospatial Consortium (OGC), the WG IV/8 Planetary Mapping and Spatial Databases within International Society for Photogrammetry and Remote Sensing (ISPRS) and a range of other institutions contribute on definition frameworks in planetary cartography. Classical cartography is nowadays often (mis-)understood as a tool mainly rather than a scientific discipline and an art of communication. Consequently, concepts of information systems, mapping tools and cartographic frameworks are used interchangeably, and cartographic workflows and visualization of spatial information in thematic maps have often been

  13. Path-integral approach to 't Hooft's derivation of quantum physics from classical physics

    SciTech Connect

    Blasone, Massimo; Jizba, Petr; Kleinert, Hagen

    2005-05-15

    We present a path-integral formulation of 't Hooft's derivation of quantum physics from classical physics. The crucial ingredient of this formulation is Gozzi et al.'s supersymmetric path integral of classical mechanics. We quantize explicitly two simple classical systems: the planar mathematical pendulum and the Roessler dynamical system.

  14. The MARINER Integrated Seismic and Geophysical Mapping Experiment (Invited)

    NASA Astrophysics Data System (ADS)

    Dunn, R. A.; Canales, J.; Sohn, R. A.; Paulatto, M.; Arai, R.; Szitkar, F.

    2013-12-01

    The MARINER (Mid-Atlantic Ridge INtegrated Experiments at Rainbow) seismic and geophysical mapping experiment was designed to examine the relationship between tectonic rifting, heat/melt supply, and oceanic core complex formation at a non-transform offset (NTO) of the Mid-Atlantic Ridge, 36°N, the site of the ultramafic-hosted Rainbow hydrothermal system. We present an overview of the components of the experiment and the various projects stemming from it. The 5-week experiment was carried out aboard the R/V M. G. Langseth in April-May 2013, and consisted of a 3D active-source seismic tomography experiment, 2D multi-channel seismic profiles, an on-going nine month passive micro-seismicity study, dense acoustic mapping of the seafloor (including depth and amplitude information), gravity field mapping, and magnetic field mapping. During the tomography experiment, we deployed 46 ocean bottom seismometers (OBS) over a 35 x 80 sq. km area centered on Rainbow. Twenty-six wide-angle seismic lines were carried out using the Langseth's 36-element source, generating ~175,000 seismic records. The MCS experiment, which was also recorded on 20 OBS, consisted of twenty-one densely spaced seismic lines using an 8-km-long hydrophone streamer. Bathymetry, gravity, and magnetic surveys were carried out over a broader, 80x105 sq. km, area centered on Rainbow. Overall, the experiment extends across two segments of the Mid-Atlantic Ridge separated by the Rainbow NTO massif. MARINER multi-beam bathymetry and acoustic imagery provide a broad view of the geologic and geophysical character of the ridge system, emphasizing the strong variability of ridge morphology, tectonics, and lava emplacement. The magnetization map shows a clear central anomaly with normal polarity, flanked by regions of negative polarity, consistent with the Brunhes-Matuyama reversal (~780,000 Ma). Rainbow itself lies in a region of weaker magnetization strength, which could be linked to a decrease in the depth of the

  15. The Atomic Relay: Integrating Physical Education and Science.

    ERIC Educational Resources Information Center

    Menelly, Daniel J.

    1997-01-01

    Presents a lesson plan for teaching abstract science concepts to gifted middle school students. The lesson integrates a physical education component into science instruction to reinforce the abstract notion that electrons emit energy in the form of visible light. (CR)

  16. Analysis of adiabatic trapping for quasi-integrable area-preserving maps

    NASA Astrophysics Data System (ADS)

    Bazzani, Armando; Frye, Christopher; Giovannozzi, Massimo; Hernalsteens, Cédric

    2014-04-01

    Trapping phenomena involving nonlinear resonances have been considered in the past in the framework of adiabatic theory. Several results are known for continuous-time dynamical systems generated by Hamiltonian flows in which the combined effect of nonlinear resonances and slow time variation of some system parameters is considered. The focus of this paper is on discrete-time dynamical systems generated by two-dimensional symplectic maps. The possibility of extending the results of neo-adiabatic theory to quasi-integrable area-preserving maps is discussed. Scaling laws are derived, which describe the adiabatic transport as a function of the system parameters using a probabilistic point of view. These laws can be particularly relevant for physical applications. The outcome of extensive numerical simulations showing the excellent agreement with the analytical estimates and scaling laws is presented and discussed in detail.

  17. Physical mapping of 49 microsatellite markers on chromosome 19 and correlation with the genetic linkage map

    SciTech Connect

    Reguigne-Arnould, I.; Mollicone, R.; Candelier, J.J.

    1996-03-05

    We have regionally localized 49 microsatellite markers developed by Genethon using a panel of previously characterized somatic cell hybrids that retain fragments from chromosome 19. The tight correlation observed between the physical and the genetic orders of the microsatellites provide cytogenetic anchorages to the genetic map data. We propose a position for the centromere just above D19S415, from the study of two hybrids, each of which retains one of the two derivatives of a balanced translocation t(1;19)(q11;q11). Microsatellites, which can be identified by a standard PCR protocol, are useful tools for the localization of disease genes and for the establishment of YAC or cosmid contigs. These markers can also judiciously be used for the characterization of new hybrid cell line panels. We report such a characterization of 11 clones, 8 of which were obtained by irradiation-fusion. Using the whole hybrid panel, we were able to define the order of 12 pairs of genetically colocalized microsatellites. As examples of gene mapping by the combined use of microsatellites and hybrid cell lines, we regionally assigned the PVS locus between the 19q13.2 markers D19S417 and D19S423 and confirmed the locations of fucosyltransferase loci FUT1, FUT2, and FUT5. 13 refs., 1 fig.

  18. Enhanced canopy fuel mapping by integrating lidar data

    USGS Publications Warehouse

    Peterson, Birgit E.; Nelson, Kurtis J.

    2016-10-03

    BackgroundThe Wildfire Sciences Team at the U.S. Geological Survey’s Earth Resources Observation and Science Center produces vegetation type, vegetation structure, and fuel products for the United States, primarily through the Landscape Fire and Resource Management Planning Tools (LANDFIRE) program. LANDFIRE products are used across disciplines for a variety of applications. The LANDFIRE data retain their currency and relevancy through periodic updating or remapping. These updating and remapping efforts provide opportunities to improve the LANDFIRE product suite by incorporating data from other sources. Light detection and ranging (lidar) is uniquely suitable for gathering information on vegetation structure and spatial arrangement because it can collect data in three dimensions. The Wildfire Sciences Team has several completed and ongoing studies focused on integrating lidar into vegetation and fuels mapping.

  19. Integrating Enhanced Satellite Data Maps Into Coastal Management

    NASA Astrophysics Data System (ADS)

    Stegmann, Petra M.; Foley, David G.; King, Chad; Schwing, Franklin B.; Price, Holly; Bograd, Steven J.; Palacios, Daniel M.

    2006-04-01

    Coastal areas continue to be popular destinations for tourists as well as for a large population who now reside year-round near coasts and whose size is predicted to grow steadily. Along with rapid growth in recreational and commercial marine activities, this increase in coastal development also brings issues related to urban runoff, water quality, beach access, and marine ecosystem health. All of these factors contribute to an increase in pressure on the living marine biota found in coastal waters. Coastal managers are therefore faced with the dual task of conserving and protecting marine resources as well as allowing for multiple uses within nearshore waters. A beneficial tool that has yet to be routinely integrated in discussions between regional planners and various stakeholders is a data map depicting representative oceanic conditions of coastal and adjacent waters. Classifying the state of the pelagic realm provides much needed information when deliberating such issues as the creation of marine reserves.

  20. D Topological Indoor Building Modeling Integrated with Open Street Map

    NASA Astrophysics Data System (ADS)

    Jamali, A.; Rahman, A. Abdul; Boguslawski, P.

    2016-09-01

    Considering various fields of applications for building surveying and various demands, geometry representation of a building is the most crucial aspect of a building survey. The interiors of the buildings need to be described along with the relative locations of the rooms, corridors, doors and exits in many kinds of emergency response, such as fire, bombs, smoke, and pollution. Topological representation is a challenging task within the Geography Information Science (GIS) environment, as the data structures required to express these relationships are particularly difficult to develop. Even within the Computer Aided Design (CAD) community, the structures for expressing the relationships between adjacent building parts are complex and often incomplete. In this paper, an integration of 3D topological indoor building modeling in Dual Half Edge (DHE) data structure and outdoor navigation network from Open Street Map (OSM) is presented.

  1. Integrative Acoustic Mapping Reveals Hudson RIver Sediment Processes an Habitats

    NASA Astrophysics Data System (ADS)

    Nitsche, F. O.; Bell, R.; Carbotte, S. M.; Ryan, W. B. F.; Slagle, A.; Chillrud, S.; Kenna, T.; Flood, R.; Ferrini, V.; Cerrato, R.; McHugh, C.; Strayer, D.

    2005-06-01

    Rivers and estuaries around the world are the focus of human settlements and activities. Needs for clean water, ecosystem preservation, commercial navigation, industrial development, and recreational access compete for the use of estuaries, and management of these resources requires a detailed understanding of estuarine morphology and sediment dynamics. This article presents an overview of the first estuary-wide study of a heavily used estuary, the Hudson River, based on high-resolution acoustic mapping of the river bottom. The integration of three high-resolution acoustic methods with extensive sampling reveals an unexpected complexity of bottom features and allows detailed classification of the benthic environment in terms of riverbed morphology, sediment type, and sedimentary processes.

  2. Constructing module maps for integrated analysis of heterogeneous biological networks

    PubMed Central

    Amar, David; Shamir, Ron

    2014-01-01

    Improved methods for integrated analysis of heterogeneous large-scale omic data are direly needed. Here, we take a network-based approach to this challenge. Given two networks, representing different types of gene interactions, we construct a map of linked modules, where modules are genes strongly connected in the first network and links represent strong inter-module connections in the second. We develop novel algorithms that considerably outperform prior art on simulated and real data from three distinct domains. First, by analyzing protein–protein interactions and negative genetic interactions in yeast, we discover epistatic relations among protein complexes. Second, we analyze protein–protein interactions and DNA damage-specific positive genetic interactions in yeast and reveal functional rewiring among protein complexes, suggesting novel mechanisms of DNA damage response. Finally, using transcriptomes of non–small-cell lung cancer patients, we analyze networks of global co-expression and disease-dependent differential co-expression and identify a sharp drop in correlation between two modules of immune activation processes, with possible microRNA control. Our study demonstrates that module maps are a powerful tool for deeper analysis of heterogeneous high-throughput omic data. PMID:24497192

  3. Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes.

    PubMed

    Wyrwa, Katarzyna; Książkiewicz, Michał; Szczepaniak, Anna; Susek, Karolina; Podkowiński, Jan; Naganowska, Barbara

    2016-09-01

    Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.

  4. Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding.

    PubMed

    Dou, Jinzhuang; Dou, Huaiqian; Mu, Chuang; Zhang, Lingling; Li, Yangping; Wang, Jia; Li, Tianqi; Li, Yuli; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

    2017-07-01

    Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. A bootstrap-based minimum spanning tree algorithm is developed for grouping and ordering of genome-wide markers and is implemented in a user-friendly, integrated software package (AMMO). We perform extensive analyses to validate the power and accuracy of our approach in the model plant Arabidopsis thaliana and human. We also demonstrate the utility of RadMap for enhancing the contiguity of a variety of whole-genome shotgun assemblies generated using either short Illumina reads (300 bp) or long PacBio reads (6-14 kb), with up to 15-fold improvement of N50 (∼816 kb-3.7 Mb) and high scaffolding accuracy (98.1-98.5%). RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies. Copyright © 2017 Dou et al.

  5. Whole-Genome Restriction Mapping by “Subhaploid”-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding

    PubMed Central

    Dou, Jinzhuang; Dou, Huaiqian; Mu, Chuang; Zhang, Lingling; Li, Yangping; Wang, Jia; Li, Tianqi; Li, Yuli; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

    2017-01-01

    Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based “in vitro” linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of “subhaploid” fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. A bootstrap-based minimum spanning tree algorithm is developed for grouping and ordering of genome-wide markers and is implemented in a user-friendly, integrated software package (AMMO). We perform extensive analyses to validate the power and accuracy of our approach in the model plant Arabidopsis thaliana and human. We also demonstrate the utility of RadMap for enhancing the contiguity of a variety of whole-genome shotgun assemblies generated using either short Illumina reads (300 bp) or long PacBio reads (6–14 kb), with up to 15-fold improvement of N50 (∼816 kb-3.7 Mb) and high scaffolding accuracy (98.1–98.5%). RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies. PMID:28468906

  6. Physical mapping of 43 STSs to human chromosome 6

    SciTech Connect

    Orphanos, V.; Santibanez-Koref, M.; McGown, G.; Hey, Y.; Rackstraw, C.; Boyle, J.M. )

    1994-03-15

    The authors have localized 43 sequence-tagged sites by deletion mapping using a chromosome 6 panel of 18 translocation hybrids. Thirty-four loci were mapped to the long arm of chromosome 6, and 9 were mapped to 6p. Many of the loci contain (CA)[sub n], dinucleotide repeated sequences and therefore will be useful markers for mapping genes on chromosome 6. 17 refs., 1 fig., 2 tabs.

  7. A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

    PubMed Central

    Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

    2012-01-01

    A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

  8. Physical mapping of chromosome 8p22 markers and their homozygous deletion in a metastatic prostate cancer

    SciTech Connect

    Bova, G.S.; Pin, S.S.; Isaacs, W.B. |

    1996-07-01

    Numerous studies have implicated the short arm of chromosome 8 as the site of one or more tumor suppressor genes inactivated in carcinogenesis of the prostate, colon, lung, and liver. Previously, we identified a homozygous deletion on chromosome 8p22 in a metastatic prostate cancer. To map this homozygous deletion physically, long-range restriction mapping was performed using yeast artificial chromosomes (YACs) spanning approximately 2 Mb of chromosome band 8p22. Subcloned genomic DNA and cDNA probes isolated by hybrid capture from these YACs were mapped in relation to one another, reinforcing map integrity. Mapped single-copy probes from the region were then applied to DNA isolated from a metastatic prostate cancer containing a chromosome 8p22 homozygous deletion and indicated that its deletion spans 730-970 kb. Candidate genes PRLTS (PDGF-receptor {beta}-like tumor suppressor) and CTSB (cathepsin B) are located outside the region of homozygous deletion. Genethon marker D8S549 is located approximately at the center of this region of homozygous deletion. Two new microsatellite polymorphisms, D8S1991 and D8S1992, also located within the region of homozygous deletion on chromosome 8p22, are described. Physical mapping places cosmid CI8-2644 telomeric to MSR (macrophage scavenger receptor), the reverse of a previously published map, altering the interpretation of published deletion studies. This work should prove helpful in the identification of candidate tumor suppressor genes in this region. 47 refs., 5 figs., 1 tab.

  9. Integrative Curriculum Program for Physical Education: Classroom on the Court

    ERIC Educational Resources Information Center

    Irwin, Carol C.; Irwin, Richard L.; Hays, Brandon

    2011-01-01

    Integrative curriculum has been noted as a best practice toward effective learning. Quality physical educators struggle and search for different ways to integrate other content areas (e.g.., language arts, math, and social studies) into their daily lessons; however, due to budgetary limitations, they must find ways to do so with educationally…

  10. Obstacles Perceived by Physical Education Teachers to Integrating ICT

    ERIC Educational Resources Information Center

    Villalba, Ana; González-Rivera, María Dolores; Díaz-Pulido, Belén

    2017-01-01

    Teachers find difficulties and barriers about integrating technology in the physical education classroom. Therefore, the aim of this study is to analyse the perception of PE teachers regarding obstacles to integrating ICT and its relation with their age. The methodology followed was quantitative and descriptive in nature. The participants were 400…

  11. Integrating Computational Chemistry into the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Johnson, Lewis E.; Engel, Thomas

    2011-01-01

    Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

  12. Integrative Curriculum Program for Physical Education: Classroom on the Court

    ERIC Educational Resources Information Center

    Irwin, Carol C.; Irwin, Richard L.; Hays, Brandon

    2011-01-01

    Integrative curriculum has been noted as a best practice toward effective learning. Quality physical educators struggle and search for different ways to integrate other content areas (e.g.., language arts, math, and social studies) into their daily lessons; however, due to budgetary limitations, they must find ways to do so with educationally…

  13. Integrating Computational Chemistry into the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Johnson, Lewis E.; Engel, Thomas

    2011-01-01

    Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

  14. Contract-Based Integration of Cyber-Physical Analyses

    DTIC Science & Technology

    2014-10-14

    1 Contract-Based Integration of Cyber-Physical Analyses Ivan Ruchkin Dionisio De Niz Sagar Chaki David Garlan October 14, 2014 14th International...Physical Analyses 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Dionisio de Niz Ivan Ruchkin; Sagar Chaki; David Garlan

  15. Contract-Based Integration of Cyber-Physical Analyses

    DTIC Science & Technology

    2014-10-14

    1 Contract-Based Integration of Cyber-Physical Analyses Ivan Ruchkin Dionisio De Niz Sagar Chaki David Garlan October 14, 2014 14th International...Physical Analyses 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Ivan Ruchkin, Dionisio De Niz, Sagar Chaki, David Garlan

  16. Integration and Physical Education: A Review of Research

    ERIC Educational Resources Information Center

    Marttinen, Risto Harri Juhani; McLoughlin, Gabriella; Fredrick, Ray, III; Novak, Dario

    2017-01-01

    The Common Core State Standards Initiative has placed an increased focus on mathematics and English language arts. A relationship between physical activity and academic achievement is evident, but research on integration of academic subjects with physical education is still unclear. This literature review examined databases for the years…

  17. Integration and Physical Education: A Review of Research

    ERIC Educational Resources Information Center

    Marttinen, Risto Harri Juhani; McLoughlin, Gabriella; Fredrick, Ray, III; Novak, Dario

    2017-01-01

    The Common Core State Standards Initiative has placed an increased focus on mathematics and English language arts. A relationship between physical activity and academic achievement is evident, but research on integration of academic subjects with physical education is still unclear. This literature review examined databases for the years…

  18. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

    USDA-ARS?s Scientific Manuscript database

    An ultra-dense consensus (UDC) genetic map of tetraploid cotton was constructed using six high-density component maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cut...

  19. Discovery of myosin genes by physical mapping in Dictyostelium.

    PubMed Central

    Titus, M A; Kuspa, A; Loomis, W F

    1994-01-01

    The diversity of the myosin family in a single organism, Dictyostelium discoideum, has been investigated by a strategy devised to rapidly identify and clone additional members of a gene family. An ordered array of yeast artificial chromosome clones that encompasses the Dictyostelium genome was probed at low stringency with conserved regions of the myosin motor domain to identify all possible myosin loci. The previously identified myosin loci (mchA, myoA-E) were detected by hybridization to the probes, as well as an additional seven previously unidentified loci (referred to as myoF-L). Clones corresponding to four of these additional loci (myoF, myoH-J) were obtained by using the isolated yeast artificial chromosomes as templates in a PCR employing degenerate primers specific for conserved regions of the myosin head. Sequence analysis and physical mapping of these clones confirm that these PCR products are derived from four previously unidentified myosin genes. Preliminary analysis of these sequences suggests that at least one of the genes (myoJ) encodes a member of a potentially different class of myosins. With the development of whole genome libraries for a variety of organisms, this approach can be used to rapidly explore the diversity of this and other gene families in a number of systems. PMID:7937787

  20. Validity and Responsiveness of Concept Map Assessment Scores in Physical Education

    ERIC Educational Resources Information Center

    Lee, Yun Soo; Jang, Yongkyu; Kang, Minsoo

    2015-01-01

    Concept map assessment has been applied to many education areas to measure students' knowledge structure. However, the proper and valid use of concept map assessment has not been examined in physical education. The purpose of this study was to evaluate the evidence of validity and responsiveness of the concept map assessment scores in physical…

  1. Validity and Responsiveness of Concept Map Assessment Scores in Physical Education

    ERIC Educational Resources Information Center

    Lee, Yun Soo; Jang, Yongkyu; Kang, Minsoo

    2015-01-01

    Concept map assessment has been applied to many education areas to measure students' knowledge structure. However, the proper and valid use of concept map assessment has not been examined in physical education. The purpose of this study was to evaluate the evidence of validity and responsiveness of the concept map assessment scores in physical…

  2. A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L.

    USDA-ARS?s Scientific Manuscript database

    Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire ...

  3. Physical Webbing: Collaborative Kinesthetic Three-Dimensional Mind Maps[R

    ERIC Educational Resources Information Center

    Williams, Marian H.

    2012-01-01

    Mind Mapping has predominantly been used by individuals or collaboratively in groups as a paper-based or computer-generated learning strategy. In an effort to make Mind Mapping kinesthetic, collaborative, and three-dimensional, an innovative pedagogical strategy, termed Physical Webbing, was devised. In the Physical Web activity, groups…

  4. EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome.

    PubMed

    Kota, R; Varshney, R K; Prasad, M; Zhang, H; Stein, N; Graner, A

    2008-08-01

    In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (pi) ranged from 0 to 40.0 x 10(-3) (average 3.1 x 10(-3)) and 0.52 x 10(-3) to 39.51 x 10(-3) (average 4.37 x 10(-3)) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps.

  5. High-throughput physical map anchoring via BAC-pool sequencing.

    PubMed

    Cviková, Kateřina; Cattonaro, Federica; Alaux, Michael; Stein, Nils; Mayer, Klaus Fx; Doležel, Jaroslav; Bartoš, Jan

    2015-04-11

    Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers. Here we present a novel approach for anchoring physical maps, based on sequencing three-dimensional pools of BAC clones from minimum tilling path. We used physical map of wheat chromosome arm 3DS to validate the method with two different DNA sequence datasets. The first comprised 567 genes ordered along the chromosome arm based on syntenic relationship of wheat with the sequenced genomes of Brachypodium, rice and sorghum. The second dataset consisted of 7,136 SNP-containing sequences, which were mapped genetically in Aegilops tauschii, the donor of the wheat D genome. Mapping of sequence reads from individual BAC pools to the first and the second datasets enabled unambiguous anchoring 447 and 311 3DS-specific sequences, respectively, or 758 in total. We demonstrate the utility of the novel approach for BAC contig anchoring based on mass parallel sequencing of three-dimensional pools prepared from minimum tilling path of physical map. The existing genetic markers as well as any other DNA sequence could be mapped to BAC clones in a single in silico experiment. The approach reduces significantly the cost and time needed for anchoring and is applicable to any genomic project involving the construction of anchored physical map.

  6. Data integration of Soil Survey Geographic Database data with layers of The National Map and data from archived geologic maps.

    NASA Astrophysics Data System (ADS)

    Perez Lespier, L. M.; Shoberg, T.

    2016-12-01

    This research integrates soil data from the Soil Survey Geographic Database (SSURGO) of the U.S. Department of Agriculture with layers from The National Map of the U.S. Geological Survey and bedrock geology data from archived geologic maps from the Missouri Geological Survey. The integration method involves geometry comparisons between alluvium based soil units from the SSURGO dataset with stream lines from National Hydrography Dataset of The National Map and alluvium units from the bedrock geology maps. The consistency of this integration process is analyzed by comparing the confidence limits of best fit parameters to the null set of pattern shift. Results imply good consistency with this method for areas with well-defined stream lines and distinct geologic units.

  7. Physically-Based Shallow Landslide Susceptibility Mapping, NW of Portugal

    NASA Astrophysics Data System (ADS)

    Teixeira, Manuel; Bateira, Carlos; Soares, Laura

    2013-04-01

    Two physically-based models - Shallow Landslide Stability Analysis (SHALSTAB) and Safety Factor (SF) - are applied in Serra da Peneda (northwest of Portugal) to evaluate shallow landslide susceptibility in Tibo drainage basin. This small basin is located in an area of granitic and metasedimentary substrate, covered by different types of surficial formations (weathering mantles and slope deposits). The application of the selected models requires the determination of a set of mechanical and hydrological parameters, and the use of high resolution topographic information to create an accurate DTM. To fulfill this goal we have applied the Shallow Landslide Stability Analysis (SHALSTAB) and the SF (Safety Factor) models. The shallow landslide area was inventoried on the field. The cohesion was assessed by back analysis and the other mechanical and hydrological soil parameters were assessed on the field survey. Several susceptibility scenarios were tested with SHALSTAB model. The best SHALSTAB scenario used to assess the susceptibility is achieved using the following parameters: cohesion (c) = 2000 N/m2, soil thickness (z) = 1,2 m, internal friction (?)=32o and soil weight (?s)=14,7 KN/m3. Shallow landslide susceptibility mapping using the SF model, was based on the cartography of the factors registered on the field survey and used the following parameters: cohesion (c) = 2000 - 6000 N/m2, soil thickness (z) =1,2 m, internal friction (?)=30 - 40o; soil volumic weight (?m) = 13,7 - 15,7 KN/m3 and Hydraulic conductivity = 0 - 3,9-03 kfs. SHALSTAB scenarios were validated by overlaying the shallow landslide area (scar concentration) and selected the better susceptibility modeling. The parameters used on the SF model applied spatially variable values registered in the field survey (using the superficial formation cartography). To validate the SF model we used the AUC (Area Under the Curve) method. The two models were compared by the scar concentration and landslide potential

  8. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses

    PubMed Central

    Bowers, John E.; Arias, Miguel A.; Asher, Rochelle; Avise, Jennifer A.; Ball, Robert T.; Brewer, Gene A.; Buss, Ryan W.; Chen, Amy H.; Edwards, Thomas M.; Estill, James C.; Exum, Heather E.; Goff, Valorie H.; Herrick, Kristen L.; Steele, Cassie L. James; Karunakaran, Santhosh; Lafayette, Gmerice K.; Lemke, Cornelia; Marler, Barry S.; Masters, Shelley L.; McMillan, Joana M.; Nelson, Lisa K.; Newsome, Graham A.; Nwakanma, Chike C.; Odeh, Rosana N.; Phelps, Cynthia A.; Rarick, Elizabeth A.; Rogers, Carl J.; Ryan, Sean P.; Slaughter, Keimun A.; Soderlund, Carol A.; Tang, Haibao; Wing, Rod A.; Paterson, Andrew H.

    2005-01-01

    Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice sequence and two sorghum physical maps that integrate genetic markers, bacterial artificial chromosome (BAC) fingerprints, and BAC hybridization data. The sorghum maps largely tile a genomic component containing 41% of BACs but 80% of single-copy genes that shows conserved microsynteny with rice and partially tile a nonsyntenic component containing 46% of BACs but only 13% of single-copy genes. The remaining BACs are centromeric (4%) or unassigned (8%). The two genomic components correspond to cytologically discernible “euchromatin” and “heterochromatin.” Gene and repetitive DNA distributions support this classification. Greater microcolinearity in recombinogenic (euchromatic) than nonrecombinogenic (heterochromatic) regions is consistent with the hypothesis that genomic rearrangements are usually deleterious, thus more likely to persist in nonrecombinogenic regions by virtue of Muller's ratchet. Interchromosomal centromeric rearrangements may have fostered diploidization of a polyploid cereal progenitor. Model plant sequences better guide studies of related genomes in recombinogenic than nonrecombinogenic regions. Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond. PMID:16141333

  9. Integration of feeding and spontaneous physical activity: role for orexin.

    PubMed

    Kotz, Catherine M

    2006-06-30

    Spontaneous physical activity is activity that is non-volitional, or subconscious, such as fidgeting and shifting in one's seat, and time spent moving (standing and ambulating). Recent evidence indicates that spontaneous physical activity, and the resulting thermogenesis (non-exercise activity thermogenesis) may be regulated by brain systems. A large number of brain areas, with their associated neurotransmitter populations and connectivity, participate in the regulation of feeding behavior by acting as energy sensing and modulating centers. Although less well characterized, it is likely that a multitude of neurotransmitters and brain areas act to mediate spontaneous physical activity. These two behaviors, feeding and spontaneous physical activity, affect energy intake and expenditure and thus are important to body weight. Interestingly, often the two behaviors are affected simultaneously; when feeding is affected, so too is spontaneous physical activity, and both food intake and physical activity (whether spontaneous or volitional) influence activity of brain areas important to both. Several brain areas and neuropeptides are important to feeding and spontaneous physical activity. The lateral hypothalamus is one area that appears important to both behaviors, as stimulation or lesion of this region produces alterations in feeding behavior and spontaneous physical activity. Orexin neurons, with their central location in the lateral hypothalamus, widespread projections and connectivity to other brain areas important to energy homeostasis, are well situated to perform an integrative function. This review focuses on how hypothalamic orexins participate in both feeding and spontaneous physical activity, and provides potential models for the integration of signals important to both.

  10. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

    PubMed

    Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

    2016-07-01

    The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  11. Alignment Between Genetic and Physical Maps of Gibberella zeae

    USDA-ARS?s Scientific Manuscript database

    We previously published a genetic map of Gibberella zeae (Fusarium graminearum) based on a cross between Kansas strain Z-3639 (lineage 7) and Japanese strain R-5470 (lineage 6). In this study, that genetic map was aligned with the third assembly of the genomic sequence of G. zeae strain PH-1 (linea...

  12. Integrating satellite imagery with simulation modeling to improve burn severity mapping

    Treesearch

    Eva C. Karau; Pamela G. Sikkink; Robert E. Keane; Gregory K. Dillon

    2014-01-01

    Both satellite imagery and spatial fire effects models are valuable tools for generating burn severity maps that are useful to fire scientists and resource managers. The purpose of this study was to test a new mapping approach that integrates imagery and modeling to create more accurate burn severity maps. We developed and assessed a statistical model that combines the...

  13. Fine structure of matrix Darboux-Toda integrable mapping

    NASA Astrophysics Data System (ADS)

    Leznov, A. N.; Yuzbashyan, E. A.

    1998-05-01

    The matrix Darboux-Toda mapping is represented as a product of a number of commutative mappings. The matrix Davey-Stewartson hierarchy is invariant with respect to each of these mappings. We thus introduce an entirely new type of discrete transformation for this hierarchy. The discrete transformation for the vector nonlinear Schrödinger system coincides with one of the mappings under necessary reduction conditions.

  14. Integrated information theory: from consciousness to its physical substrate.

    PubMed

    Tononi, Giulio; Boly, Melanie; Massimini, Marcello; Koch, Christof

    2016-07-01

    In this Opinion article, we discuss how integrated information theory accounts for several aspects of the relationship between consciousness and the brain. Integrated information theory starts from the essential properties of phenomenal experience, from which it derives the requirements for the physical substrate of consciousness. It argues that the physical substrate of consciousness must be a maximum of intrinsic cause-effect power and provides a means to determine, in principle, the quality and quantity of experience. The theory leads to some counterintuitive predictions and can be used to develop new tools for assessing consciousness in non-communicative patients.

  15. AthaMap, integrating transcriptional and post-transcriptional data

    PubMed Central

    Bülow, Lorenz; Engelmann, Stefan; Schindler, Martin; Hehl, Reinhard

    2009-01-01

    The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) for the whole Arabidopsis thaliana genome. AthaMap has now been extended to include data on post-transcriptional regulation. A total of 403 173 genomic positions of small RNAs have been mapped in the A. thaliana genome. These identify 5772 putative post-transcriptionally regulated target genes. AthaMap tools have been modified to improve the identification of common TFBS in co-regulated genes by subtracting post-transcriptionally regulated genes from such analyses. Furthermore, AthaMap was updated to the TAIR7 genome annotation, a graphic display of gene analysis results was implemented, and the TFBS data content was increased. AthaMap is freely available at http://www.athamap.de/. PMID:18842622

  16. Integrated optical Dirac physics via inversion symmetry breaking

    NASA Astrophysics Data System (ADS)

    Collins, Matthew J.; Zhang, Fan; Bojko, Richard; Chrostowski, Lukas; Rechtsman, Mikael C.

    2016-12-01

    Graphene and boron nitride are two-dimensional materials whose atoms are arranged in a honeycomb lattice. Their unique properties arise because their electrons behave like relativistic particles (without and with mass, respectively)—namely, they obey the Dirac equation. Here, we use a photonic analog of boron nitride to observe Dirac physics in a silicon integrated optical platform. This will allow for photonic applications of Dirac dispersions (gapped and ungapped) to be realized in an on-chip, integrated nanophotonic platform.

  17. A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms1[W][OPEN

    PubMed Central

    Ariyadasa, Ruvini; Mascher, Martin; Nussbaumer, Thomas; Schulte, Daniela; Frenkel, Zeev; Poursarebani, Naser; Zhou, Ruonan; Steuernagel, Burkhard; Gundlach, Heidrun; Taudien, Stefan; Felder, Marius; Platzer, Matthias; Himmelbach, Axel; Schmutzer, Thomas; Hedley, Pete E.; Muehlbauer, Gary J.; Scholz, Uwe; Korol, Abraham; Mayer, Klaus F.X.; Waugh, Robbie; Langridge, Peter; Graner, Andreas; Stein, Nils

    2014-01-01

    Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence. PMID:24243933

  18. Mental health following traumatic physical injury: an integrative literature review.

    PubMed

    Wiseman, Taneal; Foster, Kim; Curtis, Kate

    2013-11-01

    To investigate the state of knowledge on the relationship between physical trauma and mental health in patients admitted to hospital with traumatic physical injury. Adults who sustain traumatic physical injury can experience a range of mental health problems related to the injury and subsequent changes in physical health and function. However early screening and identification of mental health problems after traumatic physical injury is inconsistent and not routine during the hospital admission process for the physically injured patient. Integrative review methods were used. Data were sourced for the period 1995-2010 from EMBASE, CINAHL, MEDLINE and PsycINFO and hand searching of key references. Abstracts were screened by 3 researchers against inclusion/exclusion criteria. Forty-one papers met the inclusion criteria. Data were retrieved, appraised for quality, analysed, and synthesised into 5 main categories. Forty-one primary research papers on the relationship between mental health and traumatic physical injury were reviewed. Studies showed that post-traumatic stress disorder, depression and anxiety were frequent sequelae associated with traumatic physical injury. However, these conditions were poorly identified and treated in the acute hospital phase despite their effect on physical health. There is limited understanding of the experience of traumatic physical injury, particularly in relation to mental health. Greater translation of research findings to practice is needed in order to promote routine screening, early identification and referral to treatment for mental health problems in this patient group. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. Managing the physics of the economics of integrated health care.

    PubMed

    Zismer, Daniel K; Werner, Mark J

    2012-01-01

    The physics metaphor, as applied to the economics (and financial performance) of the integrated health system, seems appropriate when considered together with the nine principles of management framework provided. The nature of the integrated design enhances leaders' management potential as they consider organizational operations and strategy in the markets ahead. One question begged by this argument for the integrated design is the durability, efficiency and ultimate long-term survivability of the more "traditional" community health care delivery models, which, by design, are fragmented, internally competitive and less capital efficient. They also cannot exploit the leverage of teams, optimal access management or the pursuit of revenues made available in many forms. For those who wish to move from the traditional to the more integrated community health system designs (especially those who have not yet started the journey), the path requires: * Sufficient balance sheet capacity to fund the integration process-especially as the model requires physician practice acquisitions and electronic health record implementations * A well-prepared board13, 14 * A functional, durable and sustainable physician services enterprise design * A redesigned organizational and governance structure * Favorable internal financial incentives alignment design * Effective accountable physician leadership * Awareness that the system is not solely a funding strategy for acquired physicians, rather a fully -.. committed clinical and business model, one in which patient-centered integrated care is the core service (and not acute care hospital-based services) A willingness to create and exploit the implied and inherent potential of an integrated design and unified brand Last, it's important to remember that an integrated health system is a tool that creates a "new potential" (a physics metaphor reference, one last time). The design doesn't operate itself. Application of the management principles

  20. NEW APPROACHES: Using concept maps with trainee physics teachers

    NASA Astrophysics Data System (ADS)

    Adamczyk, Peter; Willson, Mike

    1996-11-01

    The technique of Concept Mapping described here is useful for identifying gaps in trainee teachers' knowledge, which may then be addressed to help those who must nowadays teach Science outside their own specialism.

  1. Condensed-matter physics: Vibrations mapped by an electron beam

    NASA Astrophysics Data System (ADS)

    Colliex, Christian

    2017-03-01

    The vibrational excitations of nanostructures have been mapped using state-of-the-art electron microscopy. The results improve our understanding of these excitations, which will aid the design of nanostructures. See Letter p.529

  2. Mapping data elements to terminological resources for integrating biomedical data sources.

    PubMed

    Mougin, Fleur; Burgun, Anita; Bodenreider, Olivier

    2006-11-24

    Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration. We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings. 82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed. Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.

  3. A complete set of marked telomeres in Saccharomyces cerevisiae for physical mapping and cloning

    SciTech Connect

    Louis, E.J.; Borts, R.H.

    1995-01-01

    Each telomere in a single strain (S288C) of Saccharomyces cerevisiae was marked with a URA3 containing integrating vector having telomeric TG{sub 1-3} sequences. Efficiency of integrative transformation was enhanced by creating single random double-strand breaks in the integrating vector using DNAseI in the presence of Mn{sup 2+} ions. A total of 327 transformants were screened by CHEF gels of intact chromosomal DNA. Transformants with homology to the vector at particular chromosomal bands were then screened by Southern analysis with several restriction enzymes to confirm telomeric locations. CHEF gels of NotI and/or SfiI digests were also analyzed to determine left or right arm locations. In some cases allelism of marked telomeres was determined genetically. Transformation was performed by lithium acetate and electroporation with varying results. Electroporation resulted in 50% (75/150) of the integrants at the internal URA3 location rather than telomeres. There were also two rearrangements involving URA3 and the telomere of another chromosome. Lithium acetate transformation resulted in fewer integrants at the internal URA3 location (5/84) and no rearrangements. All telomeres were marked with approximately the same efficiency ranging from 0 to 11 hits in the first 240 transformants. These marked telomeres can be used to complete the physical maps of chromosomes in which the telomere regions are absent. The marked telomeres can be cloned with the appropriate restriction enzymes, thus completing the cloning of individual chromosomes for sequencing projects. The analysis of these clones will lead to a better understanding of telomere region biology. The methodology can also be applied to telomeres of other organisms once they are cloned as telomeric YACs. 36 refs., 7 figs., 2 tabs.

  4. Integrating Key Competences in School Physical Education Programmes

    ERIC Educational Resources Information Center

    Lleixà, Teresa; González-Arévalo, Carles; Braz-Vieira, Marcelo

    2016-01-01

    In 2006, the European Union published its recommendations on competences for lifelong learning. Since then, key competences have been integrated into the official curriculum in Spain. The objectives of the present study are: a) to describe the strategies used most frequently by physical education teachers to incorporate key competences in their…

  5. Conceptual Integration of Chemical Equilibrium by Prospective Physical Sciences Teachers

    ERIC Educational Resources Information Center

    Ganaras, Kostas; Dumon, Alain; Larcher, Claudine

    2008-01-01

    This article describes an empirical study concerning the mastering of the chemical equilibrium concept by prospective physical sciences teachers. The main objective was to check whether the concept of chemical equilibrium had become an integrating and unifying concept for them, that is to say an operational and functional knowledge to explain and…

  6. Understanding Student Use of Differentials in Physics Integration Problems

    ERIC Educational Resources Information Center

    Hu, Dehui; Rebello, N. Sanjay

    2013-01-01

    This study focuses on students' use of the mathematical concept of differentials in physics problem solving. For instance, in electrostatics, students need to set up an integral to find the electric field due to a charged bar, an activity that involves the application of mathematical differentials (e.g., "dr," "dq"). In this…

  7. Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

    ERIC Educational Resources Information Center

    Bisbee, Gregory D.; Kaiser, Cheryl A.

    1997-01-01

    Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

  8. Systematic perturbation calculation of integrals with applications to physics.

    PubMed

    Amore, Paolo; Aranda, Alfredo; Sáenz, Ricardo; Fernández, Francisco M

    2005-01-01

    In this paper we generalize and improve a method for calculating the period of a classical oscillator and other integrals of physical interest, which was recently developed by some of the authors. We derive analytical expressions that prove to be more accurate than those commonly found in the literature, and test the convergence of the series produced by the approach.

  9. Conceptual Integration of Chemical Equilibrium by Prospective Physical Sciences Teachers

    ERIC Educational Resources Information Center

    Ganaras, Kostas; Dumon, Alain; Larcher, Claudine

    2008-01-01

    This article describes an empirical study concerning the mastering of the chemical equilibrium concept by prospective physical sciences teachers. The main objective was to check whether the concept of chemical equilibrium had become an integrating and unifying concept for them, that is to say an operational and functional knowledge to explain and…

  10. Understanding Student Use of Differentials in Physics Integration Problems

    ERIC Educational Resources Information Center

    Hu, Dehui; Rebello, N. Sanjay

    2013-01-01

    This study focuses on students' use of the mathematical concept of differentials in physics problem solving. For instance, in electrostatics, students need to set up an integral to find the electric field due to a charged bar, an activity that involves the application of mathematical differentials (e.g., "dr," "dq"). In this…

  11. Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

    ERIC Educational Resources Information Center

    Bisbee, Gregory D.; Kaiser, Cheryl A.

    1997-01-01

    Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

  12. Integrating Key Competences in School Physical Education Programmes

    ERIC Educational Resources Information Center

    Lleixà, Teresa; González-Arévalo, Carles; Braz-Vieira, Marcelo

    2016-01-01

    In 2006, the European Union published its recommendations on competences for lifelong learning. Since then, key competences have been integrated into the official curriculum in Spain. The objectives of the present study are: a) to describe the strategies used most frequently by physical education teachers to incorporate key competences in their…

  13. Tyramide-FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa.

    PubMed

    Romanov, Dmitry; Divashuk, Mikhail; Havey, Michael J; Khrustaleva, Ludmila

    2015-03-01

    Chromosome 5 of onion carries major quantitative trait loci (QTL) that control dry-matter content, pungency and storability of bulbs, amounts and types of epicuticular waxes, and resistances to abiotic factors, all of which are of interest to breeders. SNPs, SSRs, and RFLPs in expressed regions of the onion genome have been genetically mapped, and we used these clones and sequences from the NCBI database to develop DNA probes for in situ hybridization to integrate the genetic and physical maps of onion chromosome 5. We produced genomic amplicons from expressed regions of the onion genome that carried both exons and introns in order to increase the hybridization specificity of the probes and to enlarge the target DNA sizes. Tyramide-FISH technique was used to increase the detection sensitivity of relatively short target DNA regions, which range from 950 to 2100 bp. Through the integration of genetic and chromosomal maps, we were able to estimate the distribution of recombination events along onion chromosome 5. We demonstrated the efficiency of chromosomal in situ mapping of exon-intron genomic clones for the extremely large genome of onion.

  14. Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project.

    PubMed

    Clifford, R; Edmonson, M; Hu, Y; Nguyen, C; Scherpbier, T; Buetow, K H

    2000-08-01

    SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.

  15. A 2-Mb YAC/BAC-based physical map of the ovum mutant (Om) locus region on mouse chromosome 11.

    PubMed

    Cohen-Tannoudji, M; Vandormael-Pournin, S; Le Bras, S; Coumailleau, F; Babinet, C; Baldacci, P

    2000-09-15

    The embryonic lethal phenotype observed when DDK females are crossed with males from other strains results from a deleterious interaction between the egg cytoplasm and the paternal pronucleus soon after fertilization. We have previously mapped the Om locus responsible for this phenotype, called the DDK syndrome, to an approximately 2-cM region of chromosome 11. Here, we report the generation of a physical map of 28 yeast and bacterial artificial chromosome clones encompassing the entire genetic interval containing the Om locus. This contig, spanning approximately 2 Mb, was used to map precisely genes and genetic markers of the region. We determined the maximum physical interval for Om to be 1400 kb. In addition, 11 members of the Scya gene family were found to be organized into two clusters at the borders of the Om region. Two other genes (Rad51l3 and Schlafen 2) and one EST (D11Wsu78e) were also mapped in the Om region. This integrated map provides support for the identification of additional candidate genes for the DDK syndrome. Copyright 2000 Academic Press.

  16. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    PubMed Central

    2010-01-01

    Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). Results In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species. PMID:20969760

  17. Integrating In Silico Resources to Map a Signaling Network

    PubMed Central

    Liu, Hanqing; Beck, Tim N.; Golemis, Erica A.; Serebriiskii, Ilya G.

    2013-01-01

    The abundance of publicly available life science databases offer a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol to building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

  18. Optical and Physical Methods for Mapping Flooding with Satellite Imagery

    NASA Technical Reports Server (NTRS)

    Fayne, Jessica Fayne; Bolten, John; Lakshmi, Venkat; Ahamed, Aakash

    2016-01-01

    Flood and surface water mapping is becoming increasingly necessary, as extreme flooding events worldwide can damage crop yields and contribute to billions of dollars economic damages as well as social effects including fatalities and destroyed communities (Xaio et al. 2004; Kwak et al. 2015; Mueller et al. 2016).Utilizing earth observing satellite data to map standing water from space is indispensable to flood mapping for disaster response, mitigation, prevention, and warning (McFeeters 1996; Brakenridge and Anderson 2006). Since the early 1970s(Landsat, USGS 2013), researchers have been able to remotely sense surface processes such as extreme flood events to help offset some of these problems. Researchers have demonstrated countless methods and modifications of those methods to help increase knowledge of areas at risk and areas that are flooded using remote sensing data from optical and radar systems, as well as free publically available and costly commercial datasets.

  19. Contig Graph Tool: A graphical interface for Contig Physical Map assembly

    SciTech Connect

    Pecherer, R.M.

    1992-01-01

    A Contig Physical Map of a chromosome is a collection of DNA clones organized into ordered, overlapping sets called contigs which cover contiguous regions of the chromosome. Contigs may be assembled from a knowledge of the binary overlap relation between all clone pairs in a clone set which covers all or part of the chromosome, and contigs may be positioned along the chromosome by in situ hybridization using unique probes from each contig. Clone overlap is determined experimentally by factoring each clone into restriction fragments that are characterized by size and hybridization probe signals. Clones which overlap therefore share common restriction fragments, making overlap detectable. However, non-uniqueness of restriction fragments and experimental error lead to incorrect determination of the overlap relation and errors in the contig map. The Contig Graph Tool was developed to detect and correct overlap errors using editable visualizations of an abstract graph representation for clones and overlaps. This interactive tool is integrated with an electronic, laboratory notebook and introduces several concepts useful for solving problems with discrete, scientific visualization.

  20. Physical Activity Affects Brain Integrity in HIV+ Individuals.

    PubMed

    Ortega, Mario; Baker, Laurie M; Vaida, Florin; Paul, Robert; Basco, Brian; Ances, Beau M

    2015-11-01

    Prior research has suggested benefits of aerobic physical activity (PA) on cognition and brain volumes in HIV uninfected (HIV-) individuals, however, few studies have explored the relationships between PA and brain integrity (cognition and structural brain volumes) in HIV-infected (HIV+) individuals. Seventy HIV+ individuals underwent neuropsychological testing, structural neuroimaging, laboratory tests, and completed a PA questionnaire, recalling participation in walking, running, and jogging activities over the last year. A PA engagement score of weekly metabolic equivalent (MET) hr of activity was calculated using a compendium of PAs. HIV+ individuals were classified as physically active (any energy expended above resting expenditure, n=22) or sedentary (n=48). Comparisons of neuropsychological performance, grouped by executive and motor domains, and brain volumes were completed between groups. Physically active and sedentary HIV+ individuals had similar demographic and laboratory values, but the active group had higher education (14.0 vs. 12.6 years, p=.034). Physically active HIV+ individuals performed better on executive (p=.040, unadjusted; p=.043, adjusted) but not motor function (p=.17). In addition, among the physically active group the amount of physical activity (METs) positively correlated with executive (Pearson's r=0.45, p=0.035) but not motor (r=0.21; p=.35) performance. In adjusted analyses the physically active HIV+ individuals had larger putamen volumes (p=.019). A positive relationship exists between PA and brain integrity in HIV+ individuals. Results from the present study emphasize the importance to conduct longitudinal interventional investigation to determine if PA improves brain integrity in HIV+ individuals.

  1. Physical Activity Affects Brain Integrity in HIV + Individuals

    PubMed Central

    Ortega, Mario; Baker, Laurie M.; Vaida, Florin; Paul, Robert; Basco, Brian; Ances, Beau M.

    2015-01-01

    Prior research has suggested benefits of aerobic physical activity (PA) on cognition and brain volumes in HIV uninfected (HIV−) individuals, however, few studies have explored the relationships between PA and brain integrity (cognition and structural brain volumes) in HIV-infected (HIV +) individuals. Seventy HIV + individuals underwent neuropsychological testing, structural neuroimaging, laboratory tests, and completed a PA questionnaire, recalling participation in walking, running, and jogging activities over the last year. A PA engagement score of weekly metabolic equivalent (MET) hr of activity was calculated using a compendium of PAs. HIV + individuals were classified as physically active (any energy expended above resting expenditure, n = 22) or sedentary (n = 48). Comparisons of neuropsychological performance, grouped by executive and motor domains, and brain volumes were completed between groups. Physically active and sedentary HIV + individuals had similar demographic and laboratory values, but the active group had higher education (14.0 vs. 12.6 years, p = .034). Physically active HIV + individuals performed better on executive (p = .040, unadjusted; p = .043, adjusted) but not motor function (p = .17). In addition, among the physically active group the amount of physical activity (METs) positively correlated with executive (Pearson’s r = 0.45, p = 0.035) but not motor (r = 0.21; p = .35) performance. In adjusted analyses the physically active HIV + individuals had larger putamen volumes (p = .019). A positive relationship exists between PA and brain integrity in HIV + individuals. Results from the present study emphasize the importance to conduct longitudinal interventional investigation to determine if PA improves brain integrity in HIV + individuals. PMID:26581799

  2. Physical mapping of genomes using the landmark strategy

    SciTech Connect

    Charlebois, R.L.

    1993-12-31

    The success of an effort to produce an overlapping set of clones covering all of a complex genome depends, to a large degree, on the efficiency of detecting overlaps. Two kinds of approach exist for this purpose. The first involves a quantitative and statistical matching of restriction fragments, where the more extensive the overlap or the better the accuracy of fragment sizing, the more confident is the assignment. The second approach is more qualitative in nature, involving the use of distinct, unique reference points which when found to be shared between clones, demonstrates an overlap between them. The author and his colleagues have developed such a landmark-based overlap detection strategy, and they have used it to complete a map of the 4.1 Mbp genome of the archaeon Haloferaz volcanii. A second map, that of Halobacterium sp. GRB (2 Mbp), is nearly complete. In mapping genomes of this size using their method, there is but a minimal need for computer assistance. For larger, more complex genomes, the method is amenable to less tedious, more computer-intensive analysis. With the business of detecting overlaps simplified, finding solutions to the bigger problems in mapping, such as cloning the unclonable, can now occupy the brunt of one`s effort.

  3. A Differential Algebraic Integration Algorithm for Symplectic Mappings in Systems with Three-Dimensional Magnetic Field

    SciTech Connect

    Chang, P

    2004-09-15

    A differential algebraic integration algorithm is developed for symplectic mapping through a three-dimensional (3-D) magnetic field. The self-consistent reference orbit in phase space is obtained by making a canonical transformation to eliminate the linear part of the Hamiltonian. Transfer maps from the entrance to the exit of any 3-D magnetic field are then obtained through slice-by-slice symplectic integration. The particle phase-space coordinates are advanced by using the integrable polynomial procedure. This algorithm is a powerful tool to attain nonlinear maps for insertion devices in synchrotron light source or complicated magnetic field in the interaction region in high energy colliders.

  4. Trends in integrated circuit design for particle physics experiments

    NASA Astrophysics Data System (ADS)

    Atkin, E. V.

    2017-01-01

    Integrated circuits are one of the key complex units available to designers of multichannel detector setups. A whole number of factors makes Application Specific Integrated Circuits (ASICs) valuable for Particle Physics and Astrophysics experiments. Among them the most important ones are: integration scale, low power dissipation, radiation tolerance. In order to make possible future experiments in the intensity, cosmic, and energy frontiers today ASICs should provide new level of functionality at a new set of constraints and trade-offs, like low-noise high-dynamic range amplification and pulse shaping, high-speed waveform sampling, low power digitization, fast digital data processing, serialization and data transmission. All integrated circuits, necessary for physical instrumentation, should be radiation tolerant at an earlier not reached level (hundreds of Mrad) of total ionizing dose and allow minute almost 3D assemblies. The paper is based on literary source analysis and presents an overview of the state of the art and trends in nowadays chip design, using partially own ASIC lab experience. That shows a next stage of ising micro- and nanoelectronics in physical instrumentation.

  5. A comprehensive protein-centric ID mapping service for molecular data integration

    PubMed Central

    Huang, Hongzhan; Suzek, Baris E.; Mazumder, Raja; Zhang, Jian; Chen, Yongxing; Wu, Cathy H.

    2011-01-01

    Motivation: Identifier (ID) mapping establishes links between various biological databases and is an essential first step for molecular data integration and functional annotation. ID mapping allows diverse molecular data on genes and proteins to be combined and mapped to functional pathways and ontologies. We have developed comprehensive protein-centric ID mapping services providing mappings for 90 IDs derived from databases on genes, proteins, pathways, diseases, structures, protein families, protein interaction, literature, ontologies, etc. The services are widely used and have been regularly updated since 2006. Availability: www.uniprot.org/mappingandproteininformation-resource.org/pirwww/search/idmapping.shtml Contact: huang@dbi.udel.edu PMID:21478197

  6. Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization.

    PubMed

    Yim, Young-Sun; Davis, Georgia L; Duru, Ngozi A; Musket, Theresa A; Linton, Eric W; Messing, Joachim W; McMullen, Michael D; Soderlund, Carol A; Polacco, Mary L; Gardiner, Jack M; Coe, Edward H

    2002-12-01

    Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the 185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage lambda. The results indicate that the libraries are of high quality with low contamination by organellar and lambda-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6x coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 x Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 +/- 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction.

  7. Becoming physics people: Development of integrated physics identity through the Learning Assistant experience

    NASA Astrophysics Data System (ADS)

    Close, Eleanor W.; Conn, Jessica; Close, Hunter G.

    2016-06-01

    [This paper is part of the Focused Collection on Preparing and Supporting University Physics Educators.] In this study, we analyze the experience of students in the Physics Learning Assistant (LA) program at Texas State University in terms of the existing theoretical frameworks of community of practice and physics identity, and explore the implications suggested by these theories for LA program adoption and adaptation. Regression models from physics identity studies show that the physics identity construct strongly predicts intended choice of a career in physics. The goal of our current project is to understand the details of the impacts of participation in the LA experience on participants' practice and self-concept, in order to identify critical elements of LA program structure that positively influence physics identity and physics career intentions for students. Our analysis suggests that participation in the LA program impacts LAs in ways that support both stronger "physics student" identity and stronger "physics instructor" identity, and that these identities are reconciled into a coherent integrated physics identity. Increased comfort in interactions with peers, near peers, and faculty seems to be an important component of this identity development and reconciliation, suggesting that a focus on supporting community membership is useful for effective program design.

  8. Integration of Environmental Issues in a Physics Course: 'Physics by Inquiry' High School Teachers' Integration Models and Challenges

    NASA Astrophysics Data System (ADS)

    Kimori, David Abiya

    As we approach the second quarter of the twenty-first century, one may predict that the environment will be among the dominant themes in the political and educational discourse. Over the past three decades, particular perspectives regarding the environment have begun to emerge: (i) realization by human beings that we not only live on earth and use its resources at an increasingly high rate but we also actually belong to the earth and the total ecology of all living systems, (ii) there are strong interactions among different components of the large and complex systems that make up our environment, and (iii) the rising human population and its impact on the environment is a great concern (Hughes & Mason, 2014). Studies have revealed that although the students do not have a deep understanding of environmental issues and lack environmental awareness and attitudes necessary for protecting the environment, they have great concern for the environment (Chapman & Sharma, 2001; Fien, Yencken, & Sykes, 2002). However, addressing environmental issues in the classroom and other disciplines has never been an easy job for teachers (Pennock & Bardwell, 1994; Edelson, 2007). Using multiple case studies, this study investigated how three purposefully selected physics teachers teaching a 'Physics by Inquiry' course integrated environmental topics and issues in their classroom. Particularly this study looked at what integration models and practices the three physics teachers employed in integrating environmental topics and issues in their classroom and what challenges the teachers faced while integrating environmental topics in their classrooms. Data collection methods including field notes taken from observations, teachers' interviews and a collection of artifacts and documents were used. The data were coded analyzed and organized into codes and categories guided by Fogarty (1991) models of curriculum integration and Ham and Sewing (1988) four categories of barriers to environmental

  9. The new AP Physics exams: Integrating qualitative and quantitative reasoning

    NASA Astrophysics Data System (ADS)

    Elby, Andrew

    2015-04-01

    When physics instructors and education researchers emphasize the importance of integrating qualitative and quantitative reasoning in problem solving, they usually mean using those types of reasoning serially and separately: first students should analyze the physical situation qualitatively/conceptually to figure out the relevant equations, then they should process those equations quantitatively to generate a solution, and finally they should use qualitative reasoning to check that answer for plausibility (Heller, Keith, & Anderson, 1992). The new AP Physics 1 and 2 exams will, of course, reward this approach to problem solving. But one kind of free response question will demand and reward a further integration of qualitative and quantitative reasoning, namely mathematical modeling and sense-making--inventing new equations to capture a physical situation and focusing on proportionalities, inverse proportionalities, and other functional relations to infer what the equation ``says'' about the physical world. In this talk, I discuss examples of these qualitative-quantitative translation questions, highlighting how they differ from both standard quantitative and standard qualitative questions. I then discuss the kinds of modeling activities that can help AP and college students develop these skills and habits of mind.

  10. Physical Activity Among Adolescents with Cerebral Palsy: An Integrative Review.

    PubMed

    Koldoff, Elizabeth A; Holtzclaw, Barbara J

    2015-01-01

    Physical activity is necessary for optimum physical and psychosocial health in the general population. It is even more important for adolescents who struggle with impairments that limit motor function. Recommendations for best practice are needed as adolescents transition into adulthood. An integrative review was performed to determine the state of the science regarding 1) what factors impact physical activity in adolescents with cerebral palsy, and 2) how the needs of this population have been addressed regarding physical activity. A literature search of MEDLINE, CINAHL, and PubMed was conducted using the terms cerebral palsy, mobility or activity, and adolescents. Exclusion criteria were surgical or pharmacological interventions. Descriptive and intervention studies were included and evaluated for purpose, design, and key findings. Correcting the decline of physical activity in adolescents with CP may carry benefits over into adulthood. There are few studies that adapt physical activity to age and level of impairment. Several studies support approaching physical activity from a social model, focusing on participation of the person in the context of environment. There is a lack of research incorporating family-centered care. Many study designs are shallow and lack the proper instruments for assessing outcomes. Home and community based interventions need to be developed that are individualized. More studies are needed with stronger research designs and better instruments in order to generalize results for practice. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Correlation of physical and genetic maps of human chromosome 16

    SciTech Connect

    Sutherland, G.R.

    1990-01-01

    This project is now progressing strongly. Thirteen somatic cell hybrids containing rearranged {number sign}16 chromosomes have been constructed, bringing the total number of hybrids constructed by the group to 27 which divides chromosome 16 into 29 regions. 170 probes have been mapped into these regions. Although this is the second progress report for this contract it essentially contains all the work carried out since the first progress report covered a period of less than three months during which little had been done other than setting up. The project has been progressing very well and has led to numerous collaborations with other groups involved in mapping this chromosome or studying genes on it. 7 refs., 1 fig., 2 tabs.

  12. (Developing a physical map of human chromosome 22)

    SciTech Connect

    Simon, M.I.

    1991-01-01

    We have developed bacterial F-factor based systems for cloning large fragments of human DNA in E. coli. In addition to large size, these systems are capable of maintaining human DNA with a high degree of stability. The cosmid size clones are called Fosmids and the clones containing larger inserts (100--200 kb) are called bacterial artificial chromosomes (BACs). The ultimate test of the effectiveness of cloning and mapping technology is the degree to which it can be efficiently applied to solve complex mapping problems. We, therefore, plan to use the large fragment cloning procedure as well as a variety of other approaches to generate a complete map of overlapping clones corresponding to human chromosome 22. We have thus far prepared two human chromosome 22 specific Fosmid libraries and we are in the process of constructing a chromosome 22 specific BAC library composed of fragments larger than 100 kb. We will further optimize the technology so that libraries of fragments larger than 200 kb can be readily prepared.

  13. [Developing a physical map of human chromosome 22]. Progress report

    SciTech Connect

    Simon, M.I.

    1991-12-31

    We have developed bacterial F-factor based systems for cloning large fragments of human DNA in E. coli. In addition to large size, these systems are capable of maintaining human DNA with a high degree of stability. The cosmid size clones are called Fosmids and the clones containing larger inserts (100--200 kb) are called bacterial artificial chromosomes (BACs). The ultimate test of the effectiveness of cloning and mapping technology is the degree to which it can be efficiently applied to solve complex mapping problems. We, therefore, plan to use the large fragment cloning procedure as well as a variety of other approaches to generate a complete map of overlapping clones corresponding to human chromosome 22. We have thus far prepared two human chromosome 22 specific Fosmid libraries and we are in the process of constructing a chromosome 22 specific BAC library composed of fragments larger than 100 kb. We will further optimize the technology so that libraries of fragments larger than 200 kb can be readily prepared.

  14. Smartphone-based noise mapping: Integrating sound level meter app data into the strategic noise mapping process.

    PubMed

    Murphy, Enda; King, Eoin A

    2016-08-15

    The strategic noise mapping process of the EU has now been ongoing for more than ten years. However, despite the fact that a significant volume of research has been conducted on the process and related issues there has been little change or innovation in how relevant authorities and policymakers are conducting the process since its inception. This paper reports on research undertaken to assess the possibility for smartphone-based noise mapping data to be integrated into the traditional strategic noise mapping process. We compare maps generated using the traditional approach with those generated using smartphone-based measurement data. The advantage of the latter approach is that it has the potential to remove the need for exhaustive input data into the source calculation model for noise prediction. In addition, the study also tests the accuracy of smartphone-based measurements against simultaneous measurements taken using traditional sound level meters in the field. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Using MapMyFitness to Place Physical Activity into Neighborhood Context

    PubMed Central

    Hirsch, Jana A.; James, Peter; Robinson, Jamaica R. M.; Eastman, Kyler M.; Conley, Kevin D.; Evenson, Kelly R.; Laden, Francine

    2014-01-01

    It is difficult to obtain detailed information on the context of physical activity at large geographic scales, such as the entire United States, as well as over long periods of time, such as over years. MapMyFitness is a suite of interactive tools for individuals to track their workouts online or using global positioning system in their phones or other wireless trackers. This method article discusses the use of physical activity data tracked using MapMyFitness to examine patterns over space and time. An overview of MapMyFitness, including data tracked, user information, and geographic scope, is explored. We illustrate the utility of MapMyFitness data using tracked physical activity by users in Winston-Salem, NC, USA between 2006 and 2013. Types of physical activities tracked are described, as well as the percent of activities occurring in parks. Strengths of MapMyFitness data include objective data collection, low participant burden, extensive geographic scale, and longitudinal series. Limitations include generalizability, behavioral change as the result of technology use, and potential ethical considerations. MapMyFitness is a powerful tool to investigate patterns of physical activity across large geographic and temporal scales. PMID:24653982

  16. Physics of vertically integrated waveguide photodetectors and amplifiers. Final report

    SciTech Connect

    Wright, E.M.

    1993-11-01

    This report describes the efforts supported by LLNL under the Subcontract No. B239593 at the University of Arizona during the Fiscal Year 1992. A solid physical foundation has been developed for understanding the operation of vertically integrated photodetectors and amplifiers. This has been achieved through a combination of numerical simulation and development of simple coupled-mode theories. Coupled-mode theory has been used to elucidate the physics underlying the operation of vertically integrated photodetectors. In particular, the relation between the spatial transients observed in experiments and numerical simulations, and the non-power orthogonality of the underlying modes has been clarified. The coupled-mode theory has been extended to the case of coupled waveguide-amplifiers.

  17. A Physical Map of the Short Arm of Wheat Chromosome 1A

    PubMed Central

    Shatalina, Margarita; Frenkel, Zeev; Bertin, Isabelle; Philippe, Romain; Spielmeyer, Wolfgang; Šimková, Hana; Šafář, Jan; Cattonaro, Federica; Scalabrin, Simone; Magni, Federica; Vautrin, Sonia; Bergès, Hélène; Paux, Etienne; Fahima, Tzion; Doležel, Jaroslav; Korol, Abraham; Feuillet, Catherine; Keller, Beat

    2013-01-01

    Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS. PMID:24278269

  18. Using Concept Maps to Assess Interdisciplinary Integration of Green Engineering Knowledge

    ERIC Educational Resources Information Center

    Borrego, Maura; Newswander, Chad B.; McNair, Lisa D.; McGinnis, Sean; Paretti, Marie C.

    2009-01-01

    Engineering education, like many fields, has started to explore the benefits of concept maps as an assessment technique for knowledge integration. Because they allow students to graphically link topics and represent complex interconnections among diverse concepts, we argue that concept maps are particularly appropriate for assessing…

  19. Integrating polarimetric synthetic aperture radar and imaging spectrometry for wildland fuel mapping in southern California

    Treesearch

    P.E. Dennison; D.A. Roberts; J. Regelbrugge; S.L. Ustin

    2000-01-01

    Polarimetric synthetic aperture radar (SAR) and imaging spectrometry exemplify advanced technologies for mapping wildland fuels in chaparral ecosystems. In this study, we explore the potential of integrating polarimetric SAR and imaging spectrometry for mapping wildland fuels. P-band SAR and ratios containing P-band polarizations are sensitive to variations in stand...

  20. Transition Funding for the Shallow Water Integrated Mapping System (SWIMS) and Modular Microstructure Profiler (MMP)

    DTIC Science & Technology

    2014-09-30

    Mapping System ( SWIMS ) and Modular Microstructure Profiler (MMP) Matthew H. Alford Scripps Institution of Oceanography 9500 Gilman Drive, mail code...performance of operational and climate models, as well as for understanding local problems such as pollutant dispersal and biological productivity. SWIMS ...moored profiling instruments. OBJECTIVES • Transition the Shallow Water Integrated Mapping System ( SWIMS ) and Modular Microstructure Profiler

  1. Integrating Clinical Experiences in a TESOL Teacher Education Program: Curriculum Mapping as Process

    ERIC Educational Resources Information Center

    Baecher, Laura

    2012-01-01

    Across all certification areas, teacher education is being challenged to better integrate clinical experiences with coursework. This article describes the process of curriculum mapping and its impact on the organization of clinical experiences in a master's TESOL program over a 1-year redesign process. Although curriculum mapping has been employed…

  2. Construction of an integrated genetic map for Capsicum baccatum L.

    PubMed

    Moulin, M M; Rodrigues, R; Ramos, H C C; Bento, C S; Sudré, C P; Gonçalves, L S A; Viana, A P

    2015-06-18

    Capsicum baccatum L. is one of the five Capsicum domesticated species and has multiple uses in the food, pharmaceutical and cosmetic industries. This species is also a valuable source of genes for chili pepper breeding, especially genes for disease resistance and fruit quality. However, knowledge of the genetic structure of C. baccatum is limited. A reference map for C. baccatum (2n = 2x = 24) based on 42 microsatellite, 85 inter-simple sequence repeat, and 56 random amplified polymorphic DNA markers was constructed using an F2 population consisting of 203 individuals. The map was generated using the JoinMap software (version 4.0) and the linkage groups were formed and ordered using a LOD score of 3.0 and maximum of 40% recombination. The genetic map consisted of 12 major and four minor linkage groups covering a total genome distance of 2547.5 cM with an average distance of 14.25 cM between markers. Of the 152 pairs of microsatellite markers available for Capsicum annuum, 62 were successfully transferred to C. baccatum, generating polymorphism. Forty-two of these markers were mapped, allowing the introduction of C. baccatum in synteny studies with other species of the genus Capsicum.

  3. Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae.

    PubMed

    Zuriaga, Elena; Molina, Laura; Badenes, María Luisa; Romero, Carlos

    2012-06-01

    S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8 cM corresponding to ~364 Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus × domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.

  4. Mining plant genome browsers as a means for efficient connection of physical, genetic and cytogenetic mapping: An example using soybean

    PubMed Central

    Belarmino, Luis C.; da S. Oliveira, Ana R.; Brasileiro-Vidal, Ana C.; de A. Bortoleti, Kyria C.; Bezerra-Neto, João Pacífico; Abdelnoor, Ricardo V.; Benko-Iseppon, Ana M.

    2012-01-01

    Physical maps are important tools to uncover general chromosome structure as well as to compare different plant lineages and species, helping to elucidate genome structure, evolution and possibilities regarding synteny and colinearity. The increasing production of sequence data has opened an opportunity to link information from mapping studies to the underlying sequences. Genome browsers are invaluable platforms that provide access to these sequences, including tools for genome analysis, allowing the integration of multivariate information, and thus aiding to explain the emergence of complex genomes. The present work presents a tutorial regarding the use of genome browsers to develop targeted physical mapping, providing also a general overview and examples about the possibilities regarding the use of Fluorescent In Situ Hybridization (FISH) using bacterial artificial chromosomes (BAC), simple sequence repeats (SSR) and rDNA probes, highlighting the potential of such studies for map integration and comparative genetics. As a case study, the available genome of soybean was accessed to show how the physical and in silico distribution of such sequences may be compared at different levels. Such evaluations may also be complemented by the identification of sequences beyond the detection level of cytological methods, here using members of the aquaporin gene family as an example. The proposed approach highlights the complementation power of the combination of molecular cytogenetics and computational approaches for the anchoring of coding or repetitive sequences in plant genomes using available genome browsers, helping in the determination of sequence location, arrangement and number of repeats, and also filling gaps found in computational pseudochromosome assemblies. PMID:22802719

  5. Maximizing Information Diffusion in the Cyber-physical Integrated Network.

    PubMed

    Lu, Hongliang; Lv, Shaohe; Jiao, Xianlong; Wang, Xiaodong; Liu, Juan

    2015-11-11

    Nowadays, our living environment has been embedded with smart objects, such as smart sensors, smart watches and smart phones. They make cyberspace and physical space integrated by their abundant abilities of sensing, communication and computation, forming a cyber-physical integrated network. In order to maximize information diffusion in such a network, a group of objects are selected as the forwarding points. To optimize the selection, a minimum connected dominating set (CDS) strategy is adopted. However, existing approaches focus on minimizing the size of the CDS, neglecting an important factor: the weight of links. In this paper, we propose a distributed maximizing the probability of information diffusion (DMPID) algorithm in the cyber-physical integrated network. Unlike previous approaches that only consider the size of CDS selection, DMPID also considers the information spread probability that depends on the weight of links. To weaken the effects of excessively-weighted links, we also present an optimization strategy that can properly balance the two factors. The results of extensive simulation show that DMPID can nearly double the information diffusion probability, while keeping a reasonable size of selection with low overhead in different distributed networks.

  6. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology

    PubMed Central

    Ramšak, Živa; Baebler, Špela; Rotter, Ana; Korbar, Matej; Mozetič, Igor; Usadel, Björn; Gruden, Kristina

    2014-01-01

    GoMapMan (http://www.gomapman.org) is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species. GoMapMan is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis and three crop species (potato, tomato and rice) are included. The main features of GoMapMan are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes. PMID:24194592

  7. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology.

    PubMed

    Ramsak, Živa; Baebler, Špela; Rotter, Ana; Korbar, Matej; Mozetic, Igor; Usadel, Björn; Gruden, Kristina

    2014-01-01

    GoMapMan (http://www.gomapman.org) is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species. GoMapMan is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis and three crop species (potato, tomato and rice) are included. The main features of GoMapMan are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.

  8. Physical Education Teachers' Subjective Theories about Integrating Information and Communication Technology (ICT) into Physical Education

    ERIC Educational Resources Information Center

    Kretschmann, Rolf

    2015-01-01

    As well as other school subjects, physical education (PE) is emerging in terms of integrating information and communication technology (ICT) into regular classes. Such innovative teaching practices that implement ICT in PE involve diverse parties that are affected by these teaching processes. Students, principals, districts, parents,…

  9. Pre-Service Physics and Chemistry Teachers' Conceptual Integration of Physics and Chemistry Concepts

    ERIC Educational Resources Information Center

    Tuysuz, Mustafa; Bektas, Oktay; Geban, Omer; Ozturk, Gokhan; Yalvac, Bugrahan

    2016-01-01

    This study examines the pre-service teachers' opinions about conceptual integration (CI) and their understanding of it. A qualitative phenomenology design was used in the study. Data was collected through in-depth semi-structured interviews comprising ten guiding questions. Three pre-service physics and three pre-service chemistry teachers…

  10. Pre-Service Physics and Chemistry Teachers' Conceptual Integration of Physics and Chemistry Concepts

    ERIC Educational Resources Information Center

    Tuysuz, Mustafa; Bektas, Oktay; Geban, Omer; Ozturk, Gokhan; Yalvac, Bugrahan

    2016-01-01

    This study examines the pre-service teachers' opinions about conceptual integration (CI) and their understanding of it. A qualitative phenomenology design was used in the study. Data was collected through in-depth semi-structured interviews comprising ten guiding questions. Three pre-service physics and three pre-service chemistry teachers…

  11. Persistent Mappings in Cross-Domain Analogical Learning of Physics Domains

    DTIC Science & Technology

    2009-01-01

    retrieval? 6.1 Materials The problems were selected from a variety of physics resources, (Shearer et al. 1971; Giancoli 1991; Ogata 1997; Fogiel...of electricity. In Mental Models, by D. Gentner and A.L. Stevens. Eltham, London: Greenwich University Press. Giancoli , D. (1991). Physics ...PERSISTENT MAPPINGS IN CROSS-DOMAIN ANALOGICAL LEARNING OF PHYSICS DOMAINS Matthew Klenk (matthew.klenk.ctr@nrl.navy.mil) Navy Center for

  12. Spectroscopic mapping of the physical properties of supernova remnant N 49

    NASA Astrophysics Data System (ADS)

    Pauletti, D.; Copetti, M. V. F.

    2016-10-01

    Context. Physical conditions inside a supernova remnant can vary significantly between different positions. However, typical observational data of supernova remnants are integrated data or contemplate specific portions of the remnant. Aims: We study the spatial variation in the physical properties of the N 49 supernova remnant based on a spectroscopic mapping of the whole nebula. Methods: Long-slit spectra were obtained with the slit (~4' × 1.03″) aligned along the east-west direction from 29 different positions spaced by 2″ in declination. A total of 3248 1D spectra were extracted from sections of 2″ of the 2D spectra. More than 60 emission lines in the range 3550 Å to 8920 Å were measured in these spectra. Maps of the fluxes and of intensity ratios of these emission lines were built with a spatial resolution of 2″ × 2″. Results: An electron density map has been obtained using the [S II] λ6716 /λ6731 line ratio. Values vary from ~500 cm-3 at the northeast region to more than 3500 cm-3 at the southeast border. We calculated the electron temperature using line ratio sensors for the ions S+, O++, O+, and N+. Values are about 3.6 × 104 K for the O++ sensor and about 1.1 × 104 K for other sensors. The Hα/Hβ ratio map presents a ring structure with higher values that may result from collisional excitation of hydrogen. We detected an area with high values of [N II] λ6583/Hα extending from the remnant center to its northeastern border, which may be indicating an overabundance of nitrogen in the area due to contamination by the progenitor star. We found a radial dependence in many line intensity ratio maps. We observed an increase toward the remnant borders of the intensity ratio of any two lines in which the numerator comes before in the sequence [O III] λ5007, [O III] λ4363, [Ar III] λ7136, [Ne III] λ3869, [O II] λ7325, [O II] λ3727, He II λ4686, Hβ λ4861, [N II] λ6583, He I λ6678, [S II] λ6731, [S II] λ6716, [O i] λ6300, [Ca II]

  13. Mapping the Big Picture. Integrating Curriculum & Assessment K-12.

    ERIC Educational Resources Information Center

    Jacobs, Heidi Hayes

    Although teachers may work in the same building for years, they usually have slight knowledge about what goes on in each other's classrooms. In a similar way, there is little knowledge at one school level about what happens at other levels. This book presents a way for teachers to make maps as a way to communicate about curriculum development.…

  14. Reverberation Mapping and the Physics of Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Netzer, Hagai; Peterson, Bradley M.

    Reverberation mapping of the broad line gas in AGN has revolutionized our understanding of these objects. It produced several reliable determinations of the black-hole mass in low-luminosity objects and recent results enables to deduce, for the first time, the L-M relationship in AGN. Yet, despite of the availability of several superb data sets, there is not a single self-consistent solution for the gas distribution and the line emissivity in any such object. We are probably facing a fundamental limitation of the MEM and other deconvolution techniques and future modelling should concentrate on simulations and forward solutions, rather than on inversion methods. The talk will address the emerging new picture of AGN, the success and limitation of present techniques and the future prospects of AGN time-series analysis.

  15. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

    PubMed

    Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

    2014-01-20

    Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

  16. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

    PubMed Central

    2014-01-01

    Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

  17. Canonical integration and analysis of periodic maps using non-standard analysis and life methods

    SciTech Connect

    Forest, E.; Berz, M.

    1988-06-01

    We describe a method and a way of thinking which is ideally suited for the study of systems represented by canonical integrators. Starting with the continuous description provided by the Hamiltonians, we replace it by a succession of preferably canonical maps. The power series representation of these maps can be extracted with a computer implementation of the tools of Non-Standard Analysis and analyzed by the same tools. For a nearly integrable system, we can define a Floquet ring in a way consistent with our needs. Using the finite time maps, the Floquet ring is defined only at the locations s/sub i/ where one perturbs or observes the phase space. At most the total number of locations is equal to the total number of steps of our integrator. We can also produce pseudo-Hamiltonians which describe the motion induced by these maps. 15 refs., 1 fig.

  18. A new family of four-dimensional symplectic and integrable mappings

    NASA Astrophysics Data System (ADS)

    Capel, H. W.; Sahadevan, R.

    2001-01-01

    We investigate the generalisations of the Quispel, Roberts and Thompson (QRT) family of mappings in the plane leaving a rational quadratic expression invariant to the case of four variables. We assume invariance of the rational expression under a cyclic permutation of variables and we impose a symplectic structure with Poisson brackets of the Weyl type. All mappings satisfying these conditions are shown to be integrable either as four-dimensional mappings with two explicit integrals which are in involution with respect to the symplectic structure and which can also be inferred from the periodic reductions of the double-discrete versions of the modified Korteweg-deVries ( ΔΔMKdV) and sine-Gordon ( ΔΔsG) equations or by reduction to two-dimensional mappings with one integral of the symmetric QRT family.

  19. An Integrated Simulation Module for Cyber-Physical Automation Systems.

    PubMed

    Ferracuti, Francesco; Freddi, Alessandro; Monteriù, Andrea; Prist, Mariorosario

    2016-05-05

    The integration of Wireless Sensors Networks (WSNs) into Cyber Physical Systems (CPSs) is an important research problem to solve in order to increase the performances, safety, reliability and usability of wireless automation systems. Due to the complexity of real CPSs, emulators and simulators are often used to replace the real control devices and physical connections during the development stage. The most widespread simulators are free, open source, expandable, flexible and fully integrated into mathematical modeling tools; however, the connection at a physical level and the direct interaction with the real process via the WSN are only marginally tackled; moreover, the simulated wireless sensor motes are not able to generate the analogue output typically required for control purposes. A new simulation module for the control of a wireless cyber-physical system is proposed in this paper. The module integrates the COntiki OS JAva Simulator (COOJA), a cross-level wireless sensor network simulator, and the LabVIEW system design software from National Instruments. The proposed software module has been called "GILOO" (Graphical Integration of Labview and cOOja). It allows one to develop and to debug control strategies over the WSN both using virtual or real hardware modules, such as the National Instruments Real-Time Module platform, the CompactRio, the Supervisory Control And Data Acquisition (SCADA), etc. To test the proposed solution, we decided to integrate it with one of the most popular simulators, i.e., the Contiki OS, and wireless motes, i.e., the Sky mote. As a further contribution, the Contiki Sky DAC driver and a new "Advanced Sky GUI" have been proposed and tested in the COOJA Simulator in order to provide the possibility to develop control over the WSN. To test the performances of the proposed GILOO software module, several experimental tests have been made, and interesting preliminary results are reported. The GILOO module has been applied to a smart home

  20. An Integrated Linkage Map for Cultivated Peanut Derived from Two RILs Populations

    USDA-ARS?s Scientific Manuscript database

    A comparable integrated map for cultivated peanut (Arachis hypogaea L.) was constructed from the integration of two recombinant inbred line (RIL) populations in which two runner type cultivars, one Spanish type cultivar and one breeding line derived from a cross of Virginia type and hirsuta type wer...

  1. Mapping the goal space: personality integration and higher-order goals.

    PubMed

    Hirsh, Jacob B

    2014-04-01

    By situating goals at the heart of human cognitive function, Huang & Bargh (H&B) provide a useful platform for understanding the process of personality integration as the gradual mapping of implicit motives into a coherently organized self-system. This integrative process is a critical feature of human development that must be accounted for by any complete goal theory.

  2. Use of an Innovation Component Configuration Map to Measure Technology Integration Practices of Higher Education Faculty

    ERIC Educational Resources Information Center

    Javeri, Manisha; Persichitte, Kay

    2004-01-01

    This presentation will focus on the use of a custom developed Innovation Component Configuration Map (ICCM) to measure technology integration practices of faculty in Schools, Colleges, and Departments of Education (SCDEs). This study investigated the relationship between the level of technology integration fidelity (high, moderate or low) by SCDE…

  3. A physically based criterion for hydraulic hazard mapping

    NASA Astrophysics Data System (ADS)

    Milanesi, Luca; Pilotti, Marco; Petrucci, Olga

    2013-04-01

    Hydraulic hazard maps are widely used for land use and emergency planning. Due to their practical consequences, it is important that their meaning is effectively transferred and shared by the stakeholders; to this purpose maps should communicate hazard levels moving from the potential consequences on specified targets. For these reasons flood maps showing only the extension of the inundated areas or flow features as depth and/or velocity may reveal themselves as ineffective instruments. The selection of the specific target to analyse must, in our opinion, be site-specific and reflect land use and/or the hydraulics features of the phenomenon. In case of sudden processes, such as torrential floods or debris flows, hazard levels should be referred to human life, because emergency plans may not mitigate risk; on the contrary, when the time scale of the flood wave propagation is sufficiently larger than the warning system one, the focus might move to the economic value of properties, since human-focused criteria may result in too severe land planning restrictions. This contribution starts exploring, from a theoretical point of view, human hazard levels as drowning, toppling and friction stability limits, which are the main failure mechanisms of human stability in flows. The proposed approach considers the human body, set on a slope and hit by a current of known density, as a combination of cylinders with different dimensions. The drowning threshold is identified through a limiting water depth, while toppling and translation are studied respectively through a moment and momentum balance. The involved forces are the friction at the bottom, the destabilizing drag force exerted by the current, the human weight and buoyancy. Several threshold curves on the velocity-depth plane can be identified as a function of different masses and heights for children and adults. Because of its dependence from the fluid density, this methodology may be applied also to define hazard

  4. Sensor integration in a low cost land mobile mapping system.

    PubMed

    Madeira, Sergio; Gonçalves, José A; Bastos, Luísa

    2012-01-01

    Mobile mapping is a multidisciplinary technique which requires several dedicated equipment, calibration procedures that must be as rigorous as possible, time synchronization of all acquired data and software for data processing and extraction of additional information. To decrease the cost and complexity of Mobile Mapping Systems (MMS), the use of less expensive sensors and the simplification of procedures for calibration and data acquisition are mandatory features. This article refers to the use of MMS technology, focusing on the main aspects that need to be addressed to guarantee proper data acquisition and describing the way those aspects were handled in a terrestrial MMS developed at the University of Porto. In this case the main aim was to implement a low cost system while maintaining good quality standards of the acquired georeferenced information. The results discussed here show that this goal has been achieved.

  5. Sensor Integration in a Low Cost Land Mobile Mapping System

    PubMed Central

    Madeira, Sergio; Gonçalves, José A.; Bastos, Luísa

    2012-01-01

    Mobile mapping is a multidisciplinary technique which requires several dedicated equipment, calibration procedures that must be as rigorous as possible, time synchronization of all acquired data and software for data processing and extraction of additional information. To decrease the cost and complexity of Mobile Mapping Systems (MMS), the use of less expensive sensors and the simplification of procedures for calibration and data acquisition are mandatory features. This article refers to the use of MMS technology, focusing on the main aspects that need to be addressed to guarantee proper data acquisition and describing the way those aspects were handled in a terrestrial MMS developed at the University of Porto. In this case the main aim was to implement a low cost system while maintaining good quality standards of the acquired georeferenced information. The results discussed here show that this goal has been achieved. PMID:22736985

  6. Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.

    PubMed

    Ferguson, Andrew L; Panagiotopoulos, Athanassios Z; Debenedetti, Pablo G; Kevrekidis, Ioannis G

    2011-04-07

    Nonlinear dimensionality reduction techniques can be applied to molecular simulation trajectories to systematically extract a small number of variables with which to parametrize the important dynamical motions of the system. For molecular systems exhibiting free energy barriers exceeding a few k(B)T, inadequate sampling of the barrier regions between stable or metastable basins can lead to a poor global characterization of the free energy landscape. We present an adaptation of a nonlinear dimensionality reduction technique known as the diffusion map that extends its applicability to biased umbrella sampling simulation trajectories in which restraining potentials are employed to drive the system into high free energy regions and improve sampling of phase space. We then propose a bootstrapped approach to iteratively discover good low-dimensional parametrizations by interleaving successive rounds of umbrella sampling and diffusion mapping, and we illustrate the technique through a study of alanine dipeptide in explicit solvent.

  7. Physical and material science aspects of integrated optoelectronics

    NASA Astrophysics Data System (ADS)

    Ermakov, Oleg N.

    2007-05-01

    Physical, material science and technological aspects (adequate material and substrate choice, different physical effects and limitations of modern simulation methods) are discussed. Analysis of modern microelectronics and optoelectronics development trends shows that rigid boundaries between microoelectronics and optoelectronics are smearing. Wide materials range previously used only in optoelectronics ( A 3 B 5 - , A2 B 6 -, A 4 B 4 - compounds, their sold alloys, diamond, organic material etc.) are now of interest for LSI designers also. Although wide range of different substrates types (organic and inorganic, single crystalline and amorphous, rigid and flexible) are now used in optoelectronics optically transparent and electrically insulating substrates are preferable for integrated optoelectronics. One type of such substrates namely sapphire is of essential practical interest now because silicon on sapphire (SOS) structures are used for LSI implementation and gallium nitride and its alloys on sapphire stwctures (GNS) are used for super bright LEDs, LDs and photodetectors fabrication. Special attention is paid to optical properties of organic structures as very promising media both for integrated optoelectronics and microelectronics. Different physical effects (band structure, quantum, disorder, strain, carrier heating effects) as well as limitations of modern simulation methods are discussed.

  8. Assess, Map and Predict the Integrity, Resilience, and ...

    EPA Pesticide Factsheets

    This project will provide knowledge and adaptive management techniques to both maintain healthy waters and to improve degraded systems. It will provide scientific support for the National Aquatic Resource Surveys. Results will provide a basis for informed decision making and tools applicable to EPA program office and regional needs at national regional, and local scales. The research products, tools, models, and maps produced will be an excellent means to communicate management options with stakeholders. To share information about SSWR research projects

  9. A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.

    PubMed

    Palti, Yniv; Genet, Carine; Gao, Guangtu; Hu, Yuqin; You, Frank M; Boussaha, Mekki; Rexroad, Caird E; Luo, Ming-Cheng

    2012-06-01

    DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.

  10. Calibrating the FloodMap Model to Improve the Integrated HydroProg-FloodMap Real-Time Multimodel Ensemble System for Forecasting Inundation

    NASA Astrophysics Data System (ADS)

    Świerczyńska, M. G.; Yu, D.; Miziński, B.; Niedzielski, T.; Latocha, A.; Parzóch, K.

    2015-12-01

    HydroProg is a novel system (research project no. 2011/01/D/ST10/04171 of the National Science Centre of Poland) which produces early warnings against peak flows. It works in real time and uses outputs from multiple hydrologic models to compute the multimodel ensemble prediction of riverflow, i.e. the hydrograph. The system has been experimentally implemented for the upper Nysa Kłodzka river basin (SW Poland). We also integrated the system with the well-established hydrodynamic model, known as FloodMap, to forecast flood inundation (HydroProg computes hydrograph prediction and FloodMap maps the hydrograph prognosis into terrain). The HydroProg-FloodMap solution works at five sites. The real-time experimental forecasts are available at http://www.klodzko.hydroprog.uni.wroc.pl/. The FloodMap model is calibrated at each site on a basis of the available Digital Elevation Model (DEM) or Digital Surface Model (DSM) and hydrograph data. However, since the launch of the HydroProg-FloodMap solution no true data on inundation has been available to check the model outputs against observation, and hence to redo the calibration if necessary. If we consider past events, which occurred before the launch of the system, there exists the observed inundation map for the Żelazno site. It was produced by geomorphological mapping of consequences of the flood in June 2009. The aim of the study is therefore to use this specific data set for a single site, calibrate the FloodMap model using inundation data, and identify the physical-geographical characteristics of terrain under which we are allowed to extrapolate the parameters to the other four sites. We conducted a spatial analysis of land use (based on Polish national database of topographical objects) and topography (based on DEM/DSM from the Light Detection and Ranging (LiDAR)) in order to identify similarities of the studied areas and hence to improve the estimates of the Manning's roughness coefficient.

  11. The Irish Seabed Mapping Programme: INFOMAR - Integrated Mapping Survey for the Sustainable Developments of Ireland's Marine Resources. Progress to Date.

    NASA Astrophysics Data System (ADS)

    Sacchetti, F.; Benetti, S.; Fitzpatrick, F.

    2006-12-01

    During the last six years, the Geological Survey of Ireland and the Marine Institute of Ireland worked together on the multimillion Irish National Seabed Survey project with the purpose of mapping the Irish marine territory using a suite of remote sensing equipment, from multibeam to seismic, achieving 87% coverage of the marine zone. Ireland was the first country in the world to carry out an extensive mapping project of their extended Exclusive Economic Zone. The Irish National Seabed Survey is now succeeded by the multiyear INFOMAR Programme. INFOMAR will concentrate initially on mapping twenty-six selected priority bays, three sea areas and the fisheries-protection "Biologically Sensitive Area", and then will complete 100% mapping of the remainder of the EEZ. Designed to incorporate all elements of an integrated mapping programme, the key data acquisition will include hydrography, oceanographic, geological and heritage data. These data sets discharge Ireland's obligations under international treaties to which she is signatory and the uses of these data are vast and multipurpose: from management plans for inshore fishing, aquaculture, coastal protection and engineering works, to environmental impact assessments related to licensing activity and support to the evolving needs of integrated coastal zone management. INFOMAR also includes a data management, exchange and integration programme for the establishment of a National Marine Data Discovery and Exchange Service; providing improved dissemination of information to researchers, policy makers, the public and private sector and the adoption of standard operating procedures in data management to facilitate inter-agency data integration. During the first year of activity, INFOMAR carried out an integrated survey from the national research vessel, the RV Celtic Explorer, acquiring hydrographic, geophysical and groundtruthing data from Bantry and Dunmanus Bays, located off the South West coast of Ireland. Airborne Li

  12. Parallel computation of a maximum-likelihood estimator of a physical map.

    PubMed Central

    Bhandarkar, S M; Machaka, S A; Shete, S S; Kota, R N

    2001-01-01

    Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity that provides the motivation for parallel computing. Parallelization strategies for a maximum-likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails a gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a stochastic optimization algorithm such as simulated annealing or microcanonical annealing. A two-level parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the stochastic optimization algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a distributed-memory multiprocessor cluster running the parallel virtual machine (PVM) environment are presented using simulated and real hybridization data. PMID:11238392

  13. An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations.

    PubMed

    Qin, Hongde; Feng, Suping; Chen, Charles; Guo, Yufang; Knapp, Steven; Culbreath, Albert; He, Guohao; Wang, Ming Li; Zhang, Xinyou; Holbrook, C Corley; Ozias-Akins, Peggy; Guo, Baozhu

    2012-03-01

    Construction and improvement of a genetic map for peanut (Arachis hypogaea L.) continues to be an important task in order to facilitate quantitative trait locus (QTL) analysis and the development of tools for marker-assisted breeding. The objective of this study was to develop a comparative integrated map from two cultivated × cultivated recombinant inbred line (RIL) mapping populations and to apply in mapping Tomato spotted wilt virus (TSWV) resistance trait in peanut. A total of 4,576 simple sequence repeat (SSR) markers from three sources: published SSR markers, newly developed SSR markers from expressed sequence tags (EST) and from bacterial artificial chromosome end-sequences were used for screening polymorphisms. Two cleaved amplified polymorphic sequence markers were also included to differentiate ahFAD2A alleles and ahFAD2B alleles. A total of 324 markers were anchored on this integrated map covering 1,352.1 cM with 21 linkage groups (LGs). Combining information from duplicated loci between LGs and comparing with published diploid maps, seven homoeologous groups were defined and 17 LGs (A1-A10, B1-B4, B7, B8, and B9) were aligned to corresponding A-subgenome or B-subgenome of diploid progenitors. One reciprocal translocation was confirmed in the tetraploid-cultivated peanut genome. Several chromosomal rearrangements were observed by comparing with published cultivated peanut maps. High consistency with cultivated peanut maps derived from different populations may support this integrated map as a reliable reference map for peanut whole genome sequencing assembling. Further two major QTLs for TSWV resistance were identified for each RILs, which illustrated the application of this map.

  14. 77 FR 9226 - Physical Systems Integration, LLC; Supplemental Notice That Initial Market-Based Rate Filing...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-16

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Physical Systems Integration, LLC; Supplemental Notice That Initial Market... in the above-referenced proceeding of Physical Systems Integration, LLC's application for...

  15. Prioritization maps: The integration of environmental risks to manage water quality in harbor areas.

    PubMed

    Valdor, Paloma F; Gómez, Aina G; Ondiviela, Bárbara; Puente, Araceli; Juanes, José A

    2016-10-15

    A method to integrate the environmental risk of the multiple effects from uses and activities developed in harbor areas is presented. Consequences are considered as the effects derived from all identified hazards. Vulnerability is expressed in terms of functional relations between environmental susceptibility against a disturbance and the state of protection of the receptors at risk. Consequences and vulnerability are integrated obtaining a spatial variation of risk: prioritization maps. The maps are developed by 4 main stages: (1) environmental hazard identification; (2) estimation of the consequences; (3) estimation of vulnerability and, (4) integration of environmental risks. To adapt prioritization maps to the peculiarities of the study area, three different methods for the integration of the effects are proposed: average-value, worst-case and weighted methods. The implementation to a real case (Tarragona harbor, NE Spain) confirms its usefulness as a risk analysis tool to communicate and support water quality management in harbors. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Modeling photonic crystals by boundary integral equations and Dirichlet-to-Neumann maps

    SciTech Connect

    Yuan Jianhua; Lu Yayan Antoine, Xavier

    2008-04-20

    Efficient numerical methods for analyzing photonic crystals (PhCs) can be developed using the Dirichlet-to-Neumann (DtN) maps of the unit cells. The DtN map is an operator that takes the wave field on the boundary of a unit cell to its normal derivative. In frequency domain calculations for band structures and transmission spectra of finite PhCs, the DtN maps allow us to reduce the computation to the boundaries of the unit cells. For two-dimensional (2D) PhCs with unit cells containing circular cylinders, the DtN maps can be constructed from analytic solutions (the cylindrical waves). In this paper, we develop a boundary integral equation method for computing DtN maps of general unit cells containing cylinders with arbitrary cross sections. The DtN map method is used to analyze band structures for 2D PhCs with elliptic and other cylinders.

  17. Mapping the Prevalence of Physical Inactivity in U.S. States, 1984-2015.

    PubMed

    An, Ruopeng; Xiang, Xiaoling; Yang, Yan; Yan, Hai

    2016-01-01

    Physical inactivity is a leading cause of morbidity, disability and premature mortality in the U.S. and worldwide. This study aimed to map the prevalence of physical inactivity across U.S. states over the past three decades, and estimate the over-time adjusted changes in the prevalence of physical inactivity in each state. Individual-level data (N = 6,701,954) were taken from the 1984-2015 Behavioral Risk Factor Surveillance System (BRFSS), an annually repeated cross-sectional survey of state-representative adult population. Prevalence of self-reported leisure-time physical inactivity was estimated by state and survey year, accounting for the BRFSS sampling design. Logistic regressions were performed to estimate the changes in the prevalence of physical inactivity over the study period for each state, adjusting for individual characteristics including sex, age, race/ethnicity, education, marital status, and employment status. The prevalence of leisure-time physical inactivity varied substantially across states and survey years. In general, the adjusted prevalence of physical inactivity gradually declined over the past three decades in a majority of states. However, a substantial proportion of American adults remain physically inactive. Among the 50 states and District of Columbia, 45 had over a fifth of their adult population without any leisure-time physical activity, and 8 had over 30% without physical activity in 2015. Moreover, the adjusted prevalence of physical inactivity in several states (Arizona, North Carolina, North Dakota, Utah, West Virginia, and Wyoming) remained largely unchanged or even increased (Minnesota and Ohio) over the study period. Although the prevalence of physical inactivity declined over the past three decades in a majority of states, the rates remain substantially high and vary considerably across states. Closely monitoring and tracking physical activity level using the state physical activity maps can help guide policy and program

  18. Mapping the Prevalence of Physical Inactivity in U.S. States, 1984-2015

    PubMed Central

    Xiang, Xiaoling; Yang, Yan; Yan, Hai

    2016-01-01

    Background Physical inactivity is a leading cause of morbidity, disability and premature mortality in the U.S. and worldwide. This study aimed to map the prevalence of physical inactivity across U.S. states over the past three decades, and estimate the over-time adjusted changes in the prevalence of physical inactivity in each state. Methods Individual-level data (N = 6,701,954) were taken from the 1984–2015 Behavioral Risk Factor Surveillance System (BRFSS), an annually repeated cross-sectional survey of state-representative adult population. Prevalence of self-reported leisure-time physical inactivity was estimated by state and survey year, accounting for the BRFSS sampling design. Logistic regressions were performed to estimate the changes in the prevalence of physical inactivity over the study period for each state, adjusting for individual characteristics including sex, age, race/ethnicity, education, marital status, and employment status. Results The prevalence of leisure-time physical inactivity varied substantially across states and survey years. In general, the adjusted prevalence of physical inactivity gradually declined over the past three decades in a majority of states. However, a substantial proportion of American adults remain physically inactive. Among the 50 states and District of Columbia, 45 had over a fifth of their adult population without any leisure-time physical activity, and 8 had over 30% without physical activity in 2015. Moreover, the adjusted prevalence of physical inactivity in several states (Arizona, North Carolina, North Dakota, Utah, West Virginia, and Wyoming) remained largely unchanged or even increased (Minnesota and Ohio) over the study period. Conclusions Although the prevalence of physical inactivity declined over the past three decades in a majority of states, the rates remain substantially high and vary considerably across states. Closely monitoring and tracking physical activity level using the state physical activity

  19. Physical mapping of complex genomes by sampled sequencing: A theoretical analysis

    SciTech Connect

    Kupfer, K.; Smith, M.; Quackenbush, J.

    1995-05-01

    A method for high-throughput, high-resolution physical mapping of complex genomes and human chromosomes called Genomic Sequence Sampling (GSS) has recently been proposed. This mapping strategy employs high-density cosmid contig assembly over 200-kb to 1-Mb regions of the target genome coupled with DNA sequencing of the cosmid ends. The relative order and spacing of the sequence fragments is determined from the template contig, resulting in a physical map of 1-to 5-kb resolution that contains a substantial portion of the entire sequence at one-pass accuracy. The purpose of this paper is to determine the theoretical parameters for GSS mapping, to evaluate the effectiveness of the contig-building strategy, and to calculate the expected fraction of the target genome that can be recovered as mapped sequence. A novel aspect of the cosmid fingerprinting and contig-building strategy involves determining the orientation of the genomic inserts relative to the cloning vectors, so that the sampled sequence fragments can be mapped with high resolution. The algorithm is based upon complete restriction enzyme digestion, contig assembly by matching fragments, and end-orientation of individual cosmids by determining the best consistent fit of the labeled cosmid end fragments in the consensus restriction map. 32 refs., 7 figs.

  20. An integrated physical and biological model for anaerobic lagoons.

    PubMed

    Wu, Binxin; Chen, Zhenbin

    2011-04-01

    A computational fluid dynamics (CFD) model that integrates physical and biological processes for anaerobic lagoons is presented. In the model development, turbulence is represented using a transition k-ω model, heat conduction and solar radiation are included in the thermal model, biological oxygen demand (BOD) reduction is characterized by first-order kinetics, and methane yield rate is expressed as a linear function of temperature. A test of the model applicability is conducted in a covered lagoon digester operated under tropical climate conditions. The commercial CFD software, ANSYS-Fluent, is employed to solve the integrated model. The simulation procedures include solving fluid flow and heat transfer, predicting local resident time based on the converged flow fields, and calculating the BOD reduction and methane production. The simulated results show that monthly methane production varies insignificantly, but the time to achieve a 99% BOD reduction in January is much longer than that in July.

  1. Integrating particle physical geometry into composting degradation kinetics.

    PubMed

    Wang, Yongjiang; Ai, Ping

    2016-01-01

    The study was carried out to integrate physical geometry of compost particle with degradation kinetics to model biological reactions, which revealing additional dynamic approaches. A sphere and its circumscribing cube were used to represent compost particles. An inner sphere, representing anaerobic zone, was introduced to describe variations of substrate volume without sufficient oxygen supply. Degradation of soluble substrates and hydrolysis of insoluble substrates were associated with the particle geometry. Transportation of soluble substrates produced from hydrolysis was expressed using Fick's law. Through the integration of degradation kinetics with geometry models, degradation models could describe varying volume of composting materials involving aerobic or anaerobic digestion and transportation of soluble substrates in a unit compost particle.

  2. Making Laboratories Count -- Better Integration of Laboratories in Physics Courses

    NASA Astrophysics Data System (ADS)

    Sizemore, Jim

    2011-10-01

    The quality of K-12 education leaves something to be desired and presents higher education faculty with the challenge of instructing under-prepared students. However, by their own admission, students from many institutions inform us that laboratory sections in science classes, including physics, consist mostly of showing up, going through the motions, and getting grades that boost their overall grade. This work presents laboratories that challenge students to take their laboratory work more seriously including specific rubrics enforcing SOLVE and Bloom's Taxonomy, pre-lab preparation work, and quizzes on pre-lab preparation. Early results are encouraging revealing greater student progress with better integration of laboratory with the rest of a complete physics course.

  3. Ultrasound thermal mapping based on a hybrid method combining physical and statistical models.

    PubMed

    Chen, Ben-Ting; Shieh, Jay; Huang, Chang-Wei; Chen, Wen-Shiang; Chen, Shing-Ru; Chen, Chuin-Shan

    2014-01-01

    Non-invasive temperature measurement of tissues deep inside the body has great potential for clinical applications, such as temperature monitoring during thermal therapy and early diagnosis of diseases. We developed a novel method for both temperature estimation and thermal mapping that uses ultrasound B-mode radiofrequency data. The proposed method is a hybrid that combines elements of physical and statistical models to achieve higher precision and resolution of temperature variations and distribution. We propose a dimensionless combined index (CI) that combines the echo shift differential and signal intensity difference with a weighting factor relative to the distance from the heat source. In vitro experiments verified that the combined index has a strong linear relationship with temperature variation and can be used to effectively estimate temperature with an average relative error <5%. This algorithm provides an alternative for imaging guidance-based techniques during thermal therapy and could easily be integrated into existing ultrasound systems. Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  4. Using Playground Maps for Movement

    ERIC Educational Resources Information Center

    Colvin, A. Vonnie

    2016-01-01

    Many schools now decorate their outside hard surface areas with maps. These maps provide color and excitement to a playground and are a terrific teaching tool for geography. But these maps can easily be integrated into physical education as well to promote both physical activity as well as knowledge of geography. The purpose of this article is to…

  5. Using Playground Maps for Movement

    ERIC Educational Resources Information Center

    Colvin, A. Vonnie

    2016-01-01

    Many schools now decorate their outside hard surface areas with maps. These maps provide color and excitement to a playground and are a terrific teaching tool for geography. But these maps can easily be integrated into physical education as well to promote both physical activity as well as knowledge of geography. The purpose of this article is to…

  6. Object Individuation and Physical Reasoning in Infancy: An Integrative Account

    PubMed Central

    Baillargeon, Renée; Stavans, Maayan; Wu, Di; Gertner, Yael; Setoh, Peipei; Kittredge, Audrey K.; Bernard, Amélie

    2012-01-01

    Much of the research on object individuation in infancy has used a task in which two different objects emerge in alternation from behind a large screen, which is then removed to reveal either one or two objects. In their seminal work, Xu and Carey (1996) found that it is typically not until the end of the first year that infants detect a violation when a single object is revealed. Since then, a large number of investigations have modified the standard task in various ways and found that young infants succeed with some but not with other modifications, yielding a complex and unwieldy picture. In this article, we argue that this confusing picture can be better understood by bringing to bear insights from a related subfield of infancy research, physical reasoning. By considering how infants reason about object information within and across physical events, we can make sense of apparently inconsistent findings from different object-individuation tasks. In turn, object-individuation findings deepen our understanding of how physical reasoning develops in infancy. Integrating the insights from physical-reasoning and object-individuation investigations thus enriches both subfields and brings about a clearer account of how infants represent objects and events. PMID:23204946

  7. A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

    PubMed Central

    Qiu, Gao-Feng; Xiong, Liang-Wei; Han, Zhi-Ke; Liu, Zhi-Qiang; Feng, Jian-Bin; Wu, Xu-Gan; Yan, Yin-Long; Shen, Hong; Huang, Long; Chen, Li

    2017-01-01

    The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs. PMID:28045132

  8. Integrative Analysis of the Physical Transport Network into Australia

    PubMed Central

    Cope, Robert C.; Ross, Joshua V.; Wittmann, Talia A.; Prowse, Thomas A. A.; Cassey, Phillip

    2016-01-01

    Effective biosecurity is necessary to protect nations and their citizens from a variety of threats, including emerging infectious diseases, agricultural or environmental pests and pathogens, and illegal wildlife trade. The physical pathways by which these threats are transported internationally, predominantly shipping and air traffic, have undergone significant growth and changes in spatial distributions in recent decades. An understanding of the specific pathways and donor-traffic hotspots created by this integrated physical transport network is vital for the development of effective biosecurity strategies into the future. In this study, we analysed the physical transport network into Australia over the period 1999–2012. Seaborne and air traffic were weighted to calculate a “weighted cumulative impact” score for each source region worldwide, each year. High risk source regions, and those source regions that underwent substantial changes in risk over the study period, were determined. An overall risk ranking was calculated by integrating across all possible weighting combinations. The source regions having greatest overall physical connectedness with Australia were Singapore, which is a global transport hub, and the North Island of New Zealand, a close regional trading partner with Australia. Both those regions with large amounts of traffic across multiple vectors (e.g., Hong Kong), and those with high levels of traffic of only one type (e.g., Bali, Indonesia with respect to passenger flights), were represented among high risk source regions. These data provide a baseline model for the transport of individuals and commodities against which the effectiveness of biosecurity controls may be assessed, and are a valuable tool in the development of future biosecurity policy. PMID:26881782

  9. Integrative Analysis of the Physical Transport Network into Australia.

    PubMed

    Cope, Robert C; Ross, Joshua V; Wittmann, Talia A; Prowse, Thomas A A; Cassey, Phillip

    2016-01-01

    Effective biosecurity is necessary to protect nations and their citizens from a variety of threats, including emerging infectious diseases, agricultural or environmental pests and pathogens, and illegal wildlife trade. The physical pathways by which these threats are transported internationally, predominantly shipping and air traffic, have undergone significant growth and changes in spatial distributions in recent decades. An understanding of the specific pathways and donor-traffic hotspots created by this integrated physical transport network is vital for the development of effective biosecurity strategies into the future. In this study, we analysed the physical transport network into Australia over the period 1999-2012. Seaborne and air traffic were weighted to calculate a "weighted cumulative impact" score for each source region worldwide, each year. High risk source regions, and those source regions that underwent substantial changes in risk over the study period, were determined. An overall risk ranking was calculated by integrating across all possible weighting combinations. The source regions having greatest overall physical connectedness with Australia were Singapore, which is a global transport hub, and the North Island of New Zealand, a close regional trading partner with Australia. Both those regions with large amounts of traffic across multiple vectors (e.g., Hong Kong), and those with high levels of traffic of only one type (e.g., Bali, Indonesia with respect to passenger flights), were represented among high risk source regions. These data provide a baseline model for the transport of individuals and commodities against which the effectiveness of biosecurity controls may be assessed, and are a valuable tool in the development of future biosecurity policy.

  10. Integrating Satellite Imagery with Simulation Modeling to Improve Burn Severity Mapping

    NASA Astrophysics Data System (ADS)

    Karau, Eva C.; Sikkink, Pamela G.; Keane, Robert E.; Dillon, Gregory K.

    2014-07-01

    Both satellite imagery and spatial fire effects models are valuable tools for generating burn severity maps that are useful to fire scientists and resource managers. The purpose of this study was to test a new mapping approach that integrates imagery and modeling to create more accurate burn severity maps. We developed and assessed a statistical model that combines the Relative differenced Normalized Burn Ratio, a satellite image-based change detection procedure commonly used to map burn severity, with output from the Fire Hazard and Risk Model, a simulation model that estimates fire effects at a landscape scale. Using 285 Composite Burn Index (CBI) plots in Washington and Montana as ground reference, we found that an integrated model explained more variability in CBI ( R 2 = 0.47) and had lower mean squared error (MSE = 0.28) than image ( R 2 = 0.42 and MSE = 0.30) or simulation-based models ( R 2 = 0.07 and MSE = 0.49) alone. Overall map accuracy was also highest for maps created with the Integrated Model (63 %). We suspect that Simulation Model performance would greatly improve with higher quality and more accurate spatial input data. Results of this study indicate the potential benefit of combining satellite image-based methods with a fire effects simulation model to create improved burn severity maps.

  11. Integrating satellite imagery with simulation modeling to improve burn severity mapping.

    PubMed

    Karau, Eva C; Sikkink, Pamela G; Keane, Robert E; Dillon, Gregory K

    2014-07-01

    Both satellite imagery and spatial fire effects models are valuable tools for generating burn severity maps that are useful to fire scientists and resource managers. The purpose of this study was to test a new mapping approach that integrates imagery and modeling to create more accurate burn severity maps. We developed and assessed a statistical model that combines the Relative differenced Normalized Burn Ratio, a satellite image-based change detection procedure commonly used to map burn severity, with output from the Fire Hazard and Risk Model, a simulation model that estimates fire effects at a landscape scale. Using 285 Composite Burn Index (CBI) plots in Washington and Montana as ground reference, we found that an integrated model explained more variability in CBI (R (2) = 0.47) and had lower mean squared error (MSE = 0.28) than image (R (2) = 0.42 and MSE = 0.30) or simulation-based models (R (2) = 0.07 and MSE = 0.49) alone. Overall map accuracy was also highest for maps created with the Integrated Model (63 %). We suspect that Simulation Model performance would greatly improve with higher quality and more accurate spatial input data. Results of this study indicate the potential benefit of combining satellite image-based methods with a fire effects simulation model to create improved burn severity maps.

  12. Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project

    PubMed Central

    Clifford, Robert; Edmonson, Michael; Hu, Ying; Nguyen, Cu; Scherpbier, Titia; Buetow, Kenneth H.

    2000-01-01

    SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use. [The sequence data described in this paper have been submitted to the db SNP data library under accession nos. SS8196–SS18418.] PMID:10958644

  13. Efficacy of Physical Integration, Disability Awareness, and Adventure Programming on Adolescents' Acceptance of Individuals with Disabilities.

    ERIC Educational Resources Information Center

    Sable, Janet R.

    1995-01-01

    This study examined the effect of three physically integrated camping programs (physical integration alone or with disability awareness or inclusionary adventure programs) on adolescents' acceptance of peers with disabilities. Pretests and posttests indicated that physical integration did not make significant attitudinal changes, but both other…

  14. Mapping Watershed Integrity for the Conterminous United States

    EPA Science Inventory

    Watersheds provide a variety of ecosystem services valued by society. Production of these services is partially a function of the degree to which watersheds are altered by human activities. In a recent manuscript, Flotemersch and others (in preparation), defined watershed integr...

  15. MAPPING WATERSHED INTEGRITY FOR THE CONTERMINOUS UNITED STATES.

    EPA Science Inventory

    Watersheds provide a variety of ecosystem services valued by society. Production of these services is sensitive to watershed alteration by human activities. Flotemersch and others (2015), defined watershed integrity (WI) as the “capacity of a watershed to support and maint...

  16. MAPPING WATERSHED INTEGRITY FOR THE CONTERMINOUS UNITED STATES.

    EPA Science Inventory

    Watersheds provide a variety of ecosystem services valued by society. Production of these services is sensitive to watershed alteration by human activities. Flotemersch and others (2015), defined watershed integrity (WI) as the “capacity of a watershed to support and maint...

  17. Mapping Watershed Integrity for the Conterminous United States

    EPA Science Inventory

    Watersheds provide a variety of ecosystem services valued by society. Production of these services is partially a function of the degree to which watersheds are altered by human activities. In a recent manuscript, Flotemersch and others (in preparation), defined watershed integr...

  18. Measuring community integration using Geographic Information Systems (GIS) and participatory mapping for people who were once homeless.

    PubMed

    Chan, Dara V; Helfrich, Christine A; Hursh, Norman C; Sally Rogers, E; Gopal, Sucharita

    2014-05-01

    Measures of community integration rely on self-report assessments that often quantify physical or social participation, but fail to capture the individual׳s spatial presence in the community. The current study documents the activity space, or area of daily experiences, of 37 individuals who were once homeless through participatory mapping and Geographic Information Systems (GIS). Contrary to expectations, there was no significant relationship between activity space size and community integration measures, except a negative association with physical integration. Further analysis revealed, however, that continued use of homeless services, geographically spread throughout the city, was associated with larger activity space size, but may be counterproductive to social and psychological integration efforts. Analysis of the types of locations identified revealed high importance given to leisure locations and ongoing involvement with medical and mental health locations. Finally, community integration outcomes did not differ significantly by demographics or housing type, but rather degree of family involvement and feeling like home, factors that may have more potential for change. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus).

    PubMed

    Menotti-Raymond, M; David, V A; Roelke, M E; Chen, Z Q; Menotti, K A; Sun, S; Schäffer, A A; Tomlin, J F; Agarwala, R; O'Brien, S J; Murphy, W J

    2003-01-01

    We report construction of second-generation integrated genetic linkage and radiation hybrid (RH) maps in the domestic cat (Felis catus) that exhibit a high level of marker concordance and provide near-full genome coverage. A total of 864 markers, including 585 coding loci (type I markers) and 279 polymorphic microsatellite loci (type II markers), are now mapped in the cat genome. We generated the genetic linkage map utilizing a multigeneration interspecies backcross pedigree between the domestic cat and the Asian leopard cat (Prionailurus bengalensis). Eighty-one type I markers were integrated with 247 type II markers from a first-generation map to generate a map of 328 loci (320 autosomal and 8 X-linked) distributed in 47 linkage groups, with an average intermarker spacing of 8 cM. Genome coverage spans approximately 2,650 cM, allowing an estimate for the genetic length of the sex-averaged map as 3,300 cM. The 834-locus second-generation domestic cat RH map was generated from the incorporation of 579 type I and 255 type II loci. Type I markers were added using targeted selection to cover either genomic regions underrepresented in the first-generation map or to refine breakpoints in human/feline synteny. The integrated linkage and RH maps reveal approximately 110 conserved segments ordered between the human and feline genomes, and provide extensive anchored reference marker homologues that connect to the more gene dense human and mouse sequence maps, suitable for positional cloning applications.

  20. 3-D or median map? Earthquake scenario ground-motion maps from physics-based models versus maps from ground-motion prediction equations

    NASA Astrophysics Data System (ADS)

    Porter, K.

    2015-12-01

    There are two common ways to create a ground-motion map for a hypothetical earthquake: using ground motion prediction equations (by far the more common of the two) and using 3-D physics-based modeling. The former is very familiar to engineers, the latter much less so, and the difference can present a problem because engineers tend to trust the familiar and distrust novelty. Maps for essentially the same hypothetical earthquake using the two different methods can look very different, while appearing to present the same information. Using one or the other can lead an engineer or disaster planner to very different estimates of damage and risk. The reasons have to do with depiction of variability, spatial correlation of shaking, the skewed distribution of real-world shaking, and the upward-curving relationship between shaking and damage. The scientists who develop the two kinds of map tend to specialize in one or the other and seem to defend their turf, which can aggravate the problem of clearly communicating with engineers.The USGS Science Application for Risk Reduction's (SAFRR) HayWired scenario has addressed the challenge of explaining to engineers the differences between the two maps, and why, in a disaster planning scenario, one might want to use the less-familiar 3-D map.

  1. Accuracy assessment of topographic mapping using UAV image integrated with satellite images

    NASA Astrophysics Data System (ADS)

    Azmi, S. M.; Ahmad, Baharin; Ahmad, Anuar

    2014-02-01

    Unmanned Aerial Vehicle or UAV is extensively applied in various fields such as military applications, archaeology, agriculture and scientific research. This study focuses on topographic mapping and map updating. UAV is one of the alternative ways to ease the process of acquiring data with lower operating costs, low manufacturing and operational costs, plus it is easy to operate. Furthermore, UAV images will be integrated with QuickBird images that are used as base maps. The objective of this study is to make accuracy assessment and comparison between topographic mapping using UAV images integrated with aerial photograph and satellite image. The main purpose of using UAV image is as a replacement for cloud covered area which normally exists in aerial photograph and satellite image, and for updating topographic map. Meanwhile, spatial resolution, pixel size, scale, geometric accuracy and correction, image quality and information contents are important requirements needed for the generation of topographic map using these kinds of data. In this study, ground control points (GCPs) and check points (CPs) were established using real time kinematic Global Positioning System (RTK-GPS) technique. There are two types of analysis that are carried out in this study which are quantitative and qualitative assessments. Quantitative assessment is carried out by calculating root mean square error (RMSE). The outputs of this study include topographic map and orthophoto. From this study, the accuracy of UAV image is ± 0.460 m. As conclusion, UAV image has the potential to be used for updating of topographic maps.

  2. Mapping strategies: Chromosome 16 workshop

    SciTech Connect

    Not Available

    1989-01-01

    The following topics from a workshop on chromosome 16 are briefly discussed: genetic map of chromosome 16; chromosome breakpoint map of chromosome 16; integrated physical/genetic map of chromosome 16; pulsed field map of the 16p13.2--p13.3 region (3 sheets); and a report of the HGM10 chromosome 16 committee.

  3. An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago

    PubMed Central

    2013-01-01

    Background White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linkage analysis among unrelated mapping populations. Such integrative analysis requires tools for homoeologue matching among populations. Development of these tools provides for a consistent framework map of the white clover genome, and facilitates in silico alignment with the model forage legume, Medicago truncatula. Results This is the first report of integration of independent linkage maps in white clover, and adds to the literature on methyl filtered GeneThresher®-derived microsatellite (simple sequence repeat; SSR) markers for linkage mapping. Gene-targeted SSR markers were discovered in a GeneThresher® (TrGT) methyl-filtered database of 364,539 sequences, which yielded 15,647 SSR arrays. Primers were designed for 4,038 arrays and of these, 465 TrGT-SSR markers were used for parental consensus genetic linkage analysis in an F1 mapping population (MP2). This was merged with an EST-SSR consensus genetic map of an independent population (MP1), using markers to match homoeologues and develop a multi-population integrated map of the white clover genome. This integrated map (IM) includes 1109 loci based on 804 SSRs over 1274 cM, covering 97% of the genome at a moderate density of one locus per 1.2 cM. Eighteen candidate genes and one morphological marker were also placed on the IM. Despite being derived from disparate populations and marker sources, the component maps and the derived IM had consistent representations of the white clover genome for marker order and genetic length. In silico analysis at an E-value threshold of 1e-20 revealed substantial co-linearity with the Medicago truncatula genome, and indicates a translocation between T. repens groups 2 and 6 relative to

  4. Application of Intervention Mapping to the Development of a Complex Physical Therapist Intervention.

    PubMed

    Jones, Taryn M; Dear, Blake F; Hush, Julia M; Titov, Nickolai; Dean, Catherine M

    2016-12-01

    Physical therapist interventions, such as those designed to change physical activity behavior, are often complex and multifaceted. In order to facilitate rigorous evaluation and implementation of these complex interventions into clinical practice, the development process must be comprehensive, systematic, and transparent, with a sound theoretical basis. Intervention Mapping is designed to guide an iterative and problem-focused approach to the development of complex interventions. The purpose of this case report is to demonstrate the application of an Intervention Mapping approach to the development of a complex physical therapist intervention, a remote self-management program aimed at increasing physical activity after acquired brain injury. Intervention Mapping consists of 6 steps to guide the development of complex interventions: (1) needs assessment; (2) identification of outcomes, performance objectives, and change objectives; (3) selection of theory-based intervention methods and practical applications; (4) organization of methods and applications into an intervention program; (5) creation of an implementation plan; and (6) generation of an evaluation plan. The rationale and detailed description of this process are presented using an example of the development of a novel and complex physical therapist intervention, myMoves-a program designed to help individuals with an acquired brain injury to change their physical activity behavior. The Intervention Mapping framework may be useful in the development of complex physical therapist interventions, ensuring the development is comprehensive, systematic, and thorough, with a sound theoretical basis. This process facilitates translation into clinical practice and allows for greater confidence and transparency when the program efficacy is investigated. © 2016 American Physical Therapy Association.

  5. Students' network integration vs. persistence in introductory physics courses

    NASA Astrophysics Data System (ADS)

    Zwolak, Justyna; Brewe, Eric

    2017-01-01

    Society is constantly in flux, which demands the continuous development of our educational system to meet new challenges and impart the appropriate knowledge/skills to students. In order to improve student learning, among other things, the way we are teaching has significantly changed over the past few decades. We are moving away from traditional, lecture-based teaching towards more interactive, engagement-based strategies. A current, major challenge for universities is to increase student retention. While students' academic and social integration into an institution seems to be vital for student retention, research on the effect of interpersonal interactions is rare. I use of network analysis to investigate academic and social experiences of students in and beyond the classroom. In particular, there is a compelling case that transformed physics classes, such as Modeling Instruction (MI), promote persistence by the creation of learning communities that support the integration of students into the university. I will discuss recent results on pattern development in networks of MI students' interactions throughout the semester, as well as the effect of students' position within the network on their persistence in physics.

  6. Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences.

    PubMed

    Lee, Heung-Ryul; Bae, Ik-Hyun; Park, Soung-Woo; Kim, Hyoun-Joung; Min, Woong-Ki; Han, Jung-Heon; Kim, Ki-Taek; Kim, Byung-Dong

    2009-01-31

    Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

  7. Mitotic-Chromosome-Based Physical Mapping of the Culex quinquefasciatus Genome

    PubMed Central

    Naumenko, Anastasia N.; Timoshevskiy, Vladimir A.; Kinney, Nicholas A.; Kokhanenko, Alina A.; deBruyn, Becky S.; Lovin, Diane D.; Stegniy, Vladimir N.; Severson, David W.; Sharakhov, Igor V.; Sharakhova, Maria V.

    2015-01-01

    The genome assembly of southern house mosquito Cx. quinquefasciatus is represented by a high number of supercontigs with no order or orientation on the chromosomes. Although cytogenetic maps for the polytene chromosomes of this mosquito have been developed, their utilization for the genome mapping remains difficult because of the low number of high-quality spreads in chromosome preparations. Therefore, a simple and robust mitotic-chromosome-based approach for the genome mapping of Cx. quinquefasciatus still needs to be developed. In this study, we performed physical mapping of 37 genomic supercontigs using fluorescent in situ hybridization on mitotic chromosomes from imaginal discs of 4th instar larvae. The genetic linkage map nomenclature was adopted for the chromosome numbering based on the direct positioning of 58 markers that were previously genetically mapped. The smallest, largest, and intermediate chromosomes were numbered as 1, 2, and 3, respectively. For idiogram development, we analyzed and described in detail the morphology and proportions of the mitotic chromosomes. Chromosomes were subdivided into 19 divisions and 72 bands of four different intensities. These idiograms were used for mapping the genomic supercontigs/genetic markers. We also determined the presence of length polymorphism in the q arm of sex-determining chromosome 1 in Cx. quinquefasciatus related to the size of ribosomal locus. Our physical mapping and previous genetic linkage mapping resulted in the chromosomal assignment of 13% of the total genome assembly to the chromosome bands. We provided the first detailed description, nomenclature, and idiograms for the mitotic chromosomes of Cx. quinquefasciatus. Further application of the approach developed in this study will help to improve the quality of the southern house mosquito genome. PMID:25768920

  8. Mitotic-chromosome-based physical mapping of the Culex quinquefasciatus genome.

    PubMed

    Naumenko, Anastasia N; Timoshevskiy, Vladimir A; Kinney, Nicholas A; Kokhanenko, Alina A; deBruyn, Becky S; Lovin, Diane D; Stegniy, Vladimir N; Severson, David W; Sharakhov, Igor V; Sharakhova, Maria V

    2015-01-01

    The genome assembly of southern house mosquito Cx. quinquefasciatus is represented by a high number of supercontigs with no order or orientation on the chromosomes. Although cytogenetic maps for the polytene chromosomes of this mosquito have been developed, their utilization for the genome mapping remains difficult because of the low number of high-quality spreads in chromosome preparations. Therefore, a simple and robust mitotic-chromosome-based approach for the genome mapping of Cx. quinquefasciatus still needs to be developed. In this study, we performed physical mapping of 37 genomic supercontigs using fluorescent in situ hybridization on mitotic chromosomes from imaginal discs of 4th instar larvae. The genetic linkage map nomenclature was adopted for the chromosome numbering based on the direct positioning of 58 markers that were previously genetically mapped. The smallest, largest, and intermediate chromosomes were numbered as 1, 2, and 3, respectively. For idiogram development, we analyzed and described in detail the morphology and proportions of the mitotic chromosomes. Chromosomes were subdivided into 19 divisions and 72 bands of four different intensities. These idiograms were used for mapping the genomic supercontigs/genetic markers. We also determined the presence of length polymorphism in the q arm of sex-determining chromosome 1 in Cx. quinquefasciatus related to the size of ribosomal locus. Our physical mapping and previous genetic linkage mapping resulted in the chromosomal assignment of 13% of the total genome assembly to the chromosome bands. We provided the first detailed description, nomenclature, and idiograms for the mitotic chromosomes of Cx. quinquefasciatus. Further application of the approach developed in this study will help to improve the quality of the southern house mosquito genome.

  9. Systematic method of generating new integrable systems via inverse Miura maps

    SciTech Connect

    Tsuchida, Takayuki

    2011-05-15

    We provide a new natural interpretation of the Lax representation for an integrable system; that is, the spectral problem is the linearized form of a Miura transformation between the original system and a modified version of it. On the basis of this interpretation, we formulate a systematic method of identifying modified integrable systems that can be mapped to a given integrable system by Miura transformations. Thus, this method can be used to generate new integrable systems from known systems through inverse Miura maps; it can be applied to both continuous and discrete systems in 1 + 1 dimensions as well as in 2 + 1 dimensions. The effectiveness of the method is illustrated using examples such as the nonlinear Schroedinger (NLS) system, the Zakharov-Ito system (two-component KdV), the three-wave interaction system, the Yajima-Oikawa system, the Ablowitz-Ladik lattice (integrable space-discrete NLS), and two (2 + 1)-dimensional NLS systems.

  10. Surround Integration Organizes a Spatial Map during Active Sensation.

    PubMed

    Pluta, Scott R; Lyall, Evan H; Telian, Greg I; Ryapolova-Webb, Elena; Adesnik, Hillel

    2017-06-21

    During active sensation, sensors scan space in order to generate a representation of the outside world. However, since spatial coding in sensory systems is typically addressed by measuring receptive fields in a fixed, sensor-based coordinate frame, the cortical representation of scanned space is poorly understood. To address this question, we probed spatial coding in the rodent whisker system using a combination of two-photon imaging and electrophysiology during active touch. We found that surround whiskers powerfully transform the cortical representation of scanned space. On the single-neuron level, surround input profoundly alters response amplitude and modulates spatial preference in the cortex. On the population level, surround input organizes the spatial preference of neurons into a continuous map of the space swept out by the whiskers. These data demonstrate how spatial summation over a moving sensor array is critical to generating population codes of sensory space. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. A physical map of important QTLs, functional markers and genes available for sesame breeding programs.

    PubMed

    Dossa, Komivi

    2016-10-01

    Sesame is one of the oldest oilseed crops grown mainly in Africa and Asia. Although genetic and genomic studies on sesame have started late, the past 5 years have witnessed extensive progresses in these areas on this crop. Important genomic sequence resources such as functional markers, genes and QTLs linked to agronomically important traits, have been generated through linkage mapping and association analysis to assist sesame improvement programs. However, most of these data are scattered in different maps making them hard to be exploited efficiently in breeding programs. In this study, we report a comprehensive physical map gathering 151 published genomic sequence resources which highlighted some hotspot functional regions in the sesame genome. Moreover, 83,135 non-redundant SSRs have been supplied along with their physical position and motif composition. This will assist future research in fine mapping or pinpointing more functional genes based on the already published QTLs and functional markers. This physical map represents a good landmark for further non-overlapping genetic and genomic studies working towards sesame improvement.

  12. Dense gene physical maps of the non-model species Drosophila subobscura.

    PubMed

    Orengo, Dorcas J; Puerma, Eva; Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2017-06-01

    The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.

  13. Physical and cognitive effects of virtual reality integrated training.

    PubMed

    Stone, Richard T; Watts, Kristopher P; Zhong, Peihan; Wei, Chen-Shuang

    2011-10-01

    The objective of this study was to evaluate the cognitive and physical impact of virtual reality (VR) integrated training versus traditional training methods in the domain of weld training. Weld training is very important in various industries and represents a complex skill set appropriate for advanced training intervention. As such, there has been a long search for the most successful and most cost-effective method for training new welders. Participants in this study were randomly assigned to one of two separate training courses taught by sanctioned American Welding Society certified welding instructors; the duration of each course was 2 weeks. After completing the training for a specific weld type, participants were given the opportunity to test for the corresponding certification. Participants were evaluated in terms of their cognitive and physical parameters, total training time exposure, and welding certification awards earned. Each of the four weld types taught in this study represented distinct levels of difficulty and required the development of specialized knowledge and skills. This study demonstrated that participants in the VR integrated training group (VR50) performed as well as, and in some cases, significantly outperformed, the traditional welding (TW) training group.The VR50 group was found to have a 41.6% increase in overall certifications earned compared with the TW group. VR technology is a valuable tool for the production of skilled welders in a shorter time and often with more highly developed skills than their traditionally trained counterparts. These findings strongly support the use ofVR integrated training in the welding industry.

  14. ODP-PLOT and MAP-PLOT: Software for integration of geosciences data set

    NASA Astrophysics Data System (ADS)

    Gaillot, P.

    2002-12-01

    Since 17 years, Ocean Drilling Program (ODP) supports multidisciplinary researches to explore the structure and history of Earth beneath the oceans. After more than 200 Legs, complementary data sets covering different time and space scales have been obtained and distributed world-wide using ODP-Janus and LDEO-BRG data base servers. In Earth Sciences, more than any other science, the ensemble of these data is characterized by heterogeneous format and graphical representation mode. In order to fully and quickly put value into this information, we present a set of Unix/Linux-based C programs for conversion and integration of data sets acquired during ODP legs. Using Leg 199 datasets, we show examples of the capabilities of these programs. ODP-PLOT displays data with respect to depth and/or time. The program includes depth-time shifting, filtering and plotting of core summary, analysis (structure) and measurements (physical properties, geochemistry ...) of samples, in-situ continuous logs, magneto- and bio-stratigraphy, specific sediment analysis (lithology, grain size, texture, porosity...), core and borehole wall images. MAP-PLOT is used to easily display datasets onto 2-D maps. Outputs of both programs can be in post-script (ps), portable document format (pdf) or standard image format (GIF, JPEG, ...). Based on command line operations and customization of parameter files, these programs can be included in other Shell- or database- scripts, automating plotting procedures of data request. As an open source software, these programs can be customized to answer any specific plotting need.

  15. Learning Movement Culture: Mapping the Landscape between Physical Education and School Sport

    ERIC Educational Resources Information Center

    Ward, Gavin

    2014-01-01

    This article examines Movement Culture as an approach to support teachers in exploring the integration of Sport as a medium for learning within Physical Education. By avoiding the need to draw clearly defined lines between Physical Education and Sport, Movement Culture embraces both. It acknowledges the need for subject matter in Physical…

  16. Learning Movement Culture: Mapping the Landscape between Physical Education and School Sport

    ERIC Educational Resources Information Center

    Ward, Gavin

    2014-01-01

    This article examines Movement Culture as an approach to support teachers in exploring the integration of Sport as a medium for learning within Physical Education. By avoiding the need to draw clearly defined lines between Physical Education and Sport, Movement Culture embraces both. It acknowledges the need for subject matter in Physical…

  17. Physical and genetic map of the Lactococcus lactis subsp. cremoris MG1363 chromosome: comparison with that of Lactococcus lactis subsp. lactis IL 1403 reveals a large genome inversion.

    PubMed Central

    Le Bourgeois, P; Lautier, M; van den Berghe, L; Gasson, M J; Ritzenthaler, P

    1995-01-01

    A physical and genetic map of the chromosome of the Lactococcus lactis subsp. cremoris reference strain MG1363 was established. The physical map was constructed for NotI, ApaI, and SmaI enzymes by using a strategy that combines creation of new rare restriction sites by the random-integration vector pRL1 and ordering of restriction fragments by indirect end-labeling experiments. The MG1363 chromosome appeared to be circular and 2,560 kb long. Seventy-seven chromosomal markers were located on the physical map by hybridization experiments. Integration via homologous recombination of pRC1-derived plasmids allowed a more precise location of some lactococcal genes and determination of their orientation on the chromosome. The MG1363 chromosome contains six rRNA operons; five are clustered within 15% of the chromosome and transcribed in the same direction. Comparison of the L. lactis subsp. cremoris MG1363 physical map with those of the two L. lactis subsp. lactis strains IL1403 and DL11 revealed a high degree of restriction polymorphism. At the genetic organization level, despite an overall conservation of gene organization, strain MG1363 presents a large inversion of half of the genome in the region containing the rRNA operons. PMID:7751295

  18. Integrating physical and financial approaches to manage environmental financial risk

    NASA Astrophysics Data System (ADS)

    Characklis, Gregory; Meyer, Eliot; Foster, Benjamin

    2017-04-01

    Physical and/or engineered solutions have long been used to manage risks associated with adverse environmental events. Examples include reservoirs as a tool for mitigating drought-related supply risk, levees for managing flood risk and dredging of inland waterways to ensure navigability during low flow periods. These measures can reduce many types of risk (e.g., loss of life), but are often employed as a means of protecting against financial losses. When the focus is on managing environmental financial risk, physical solutions can be effective, but also costly. In many cases, non-physical tools can provide a less expensive means of managing financial risk, with these often taking the form of financial instruments such as hedging contracts, contingency funds or insurance. Some of these instruments, such as flood insurance, are widely available, but historically many environmental financial risks have been managed primarily (or solely) via physical solutions without much consideration of alternatives, thereby opening opportunities for innovation in developing financial solutions. Recent research has demonstrated that financial instruments can play a significant role in managing drought-related financial risk in sectors as diverse as water utilities, energy generation and inland navigation. Nonetheless, this work has largely considered the use of these instruments within systems in which physical solutions are already in place (but failing to achieve desired performance). The next step in the evolution of managing environmental financial risk involves developing methods for designing risk management strategies that do not assume an established physical system. Here the goal is to identify the relative role that physical solutions and financial instruments should play as they are integrated into a comprehensive risk management strategy. This is not a straightforward challenge as one approach reduces the risk of financial losses and the other redistributes those losses

  19. Physical Activity, Physical Fitness and Academic Achievement in Adolescents: A Self-Organizing Maps Approach

    ERIC Educational Resources Information Center

    Pellicer-Chenoll, Maite; Garcia-Massó, Xavier; Morales, Jose; Serra-Añó, Pilar; Solana-Tramunt, Mònica; González, Luis-Millán; Toca-Herrera, José-Luis

    2015-01-01

    The relationship among physical activity, physical fitness and academic achievement in adolescents has been widely studied; however, controversy concerning this topic persists. The methods used thus far to analyse the relationship between these variables have included mostly traditional lineal analysis according to the available literature. The…

  20. Physical Activity, Physical Fitness and Academic Achievement in Adolescents: A Self-Organizing Maps Approach

    ERIC Educational Resources Information Center

    Pellicer-Chenoll, Maite; Garcia-Massó, Xavier; Morales, Jose; Serra-Añó, Pilar; Solana-Tramunt, Mònica; González, Luis-Millán; Toca-Herrera, José-Luis

    2015-01-01

    The relationship among physical activity, physical fitness and academic achievement in adolescents has been widely studied; however, controversy concerning this topic persists. The methods used thus far to analyse the relationship between these variables have included mostly traditional lineal analysis according to the available literature. The…

  1. Integrating visual information across camera movements with a visual-motor calibration map

    SciTech Connect

    Prokopowicz, P.N.; Cooper, P.R.

    1996-12-31

    Facing the competing demands for wider field of view and higher spatial resolution, computer vision will evolve toward greater use of foveal sensors and frequent camera movements. Integration of visual information across movements becomes a fundamental problem. We show that integration is possible using a biologically-inspired representation we call the visual-motor calibration map. The map is a memory-based model of the relationship between camera movements and corresponding pixel locations before and after any movement. The map constitutes a self-calibration that can compensate for non-uniform sampling, lens distortion, mechanical misalignments, and arbitrary pixel reordering. Integration takes place entirely in a retinotopic frame, using a short-term, predictive visual memory.

  2. Mapping the physical location of Telecenter using the geospatial information systems: A requirement of spatial digital mapping

    NASA Astrophysics Data System (ADS)

    Bohari, Abdul Manaf; Hin, Cheng Wei; Fuad, Nurwahida

    2016-08-01

    Recently, a study of Telecenter lifetime value is vital to academician, government and non-profit organization where Telecenter has great contribute to the nation development of rural community. Telecenter as important location of enhance the relationship of socio-economic, where placed all non-profit activity into single location platform. Consistently, previous studies mentioned Telecenter have significance contribution toward the nation, however, research and knowledge still lacking regarding the location factors that affecting the Telecenter specifically on spatial aspects of physical location environment. This research aimed to understand the requirement of spatial digital mapping the physical location of Telecenter, according to location of user and it environment, by using the geospatial information systems references, as called grid coordinate systems. The suggestion and implications of this study are briefly explored where spatial location factor plays important role in determine the lifetime value of Telecenter.

  3. GRAD-MAP: A Joint Physics and Astronomy Diversity Initiative at the University of Maryland

    NASA Astrophysics Data System (ADS)

    Megson, Peter; Anderson, Neil; Jameson, Katie; Price, Lora; Roberg-Clark, Gareth; Rogoszinksi, Zeeve; Sheppard, Kyle; Taylor, Corbin; Uher, Tim; Wilkins, Ashlee; Hammer, Donna

    Graduate Resources for Advancing Diversity with Maryland's Astronomy and Physics (GRAD-MAP), builds connections between UMD and mid-Atlantic HBCUs, Minority-Serving Institutions, and community colleges, and uses seminars, forums, and workshops to foster a diverse community of undergraduates prepared to succeed in graduate school, and is now in its third year. GRAD-MAP launched with a three-pronged approach: 1) Collaborative Seminars, 2) A Winter Workshop, and 3) A Spring Symposium. This program allows GRAD-MAP to do more than just increase the numbers of minority students participating in astronomy and physics research (or, worse, simply shuffle around students who already are or would be); it is committed to identifying students who are otherwise underserved or overlooked by the traditional academic pipeline, not only to get them on the path to be successful undergraduate researchers and eventual graduate applicants, but also to make the climate of academic physics and astronomy more inclusive to them and all other underrepresented minority students. We will describe the key elements of our program, and highlight successes and lessons learned; GRAD-MAP can serve as a model for other universities committed to diversity and inclusion. Supported by NSF PIRE and CAREER programs, Maryland Space Grant Consortium, and UMD Departments of Physics and Astronomy.

  4. Missouri Assessment Program (MAP), Spring 2000: High School Health/Physical Education, Released Items, Grade 9.

    ERIC Educational Resources Information Center

    Missouri State Dept. of Elementary and Secondary Education, Jefferson City.

    This document presents 10 released items from the Health/Physical Education Missouri Assessment Program (MAP) test given in the spring of 2000 to ninth graders. Items from the test sessions include: selected-response (multiple choice), constructed-response, and a performance event. The selected-response items consist of individual questions…

  5. Missouri Assessment Program (MAP), Spring 2000: Elementary Health/Physical Education, Released Items, Grade 5.

    ERIC Educational Resources Information Center

    Missouri State Dept. of Elementary and Secondary Education, Jefferson City.

    This document presents 10 released items from the Health/Physical Education Missouri Assessment Program (MAP) test given in the spring of 2000 to fifth graders. Items from the test sessions include: selected-response (multiple choice), constructed-response, and a performance event. The selected-response items consist of individual questions…

  6. A First Generation BAC Physical Map of the Rainbow Trout Genome

    USDA-ARS?s Scientific Manuscript database

    The physical map was constructed using the high-information content fingerprinting (HICF) method of Luo et al. (2003; Genomics, 82, 378-389). All the clones from the Swanson YY doubled haploid male BAC library (10X coverage; 184,704 clones) were fingerprinted and edited using FPMiner software. App...

  7. Integration of data-driven and physically-based methods to assess shallow landslides susceptibility

    NASA Astrophysics Data System (ADS)

    Lajas, Sara; Oliveira, Sérgio C.; Zêzere, José Luis

    2016-04-01

    Approaches used to assess shallow landslides susceptibility at the basin scale are conceptually different depending on the use of statistic or deterministic methods. The data-driven methods are sustained in the assumption that the same causes are likely to produce the same effects and for that reason a present/past landslide inventory and a dataset of factors assumed as predisposing factors are crucial for the landslide susceptibility assessment. The physically-based methods are based on a system controlled by physical laws and soil mechanics, where the forces which tend to promote movement are compared with forces that tend to promote resistance to movement. In this case, the evaluation of susceptibility is supported by the calculation of the Factor of safety (FoS), and dependent of the availability of detailed data related with the slope geometry and hydrological and geotechnical properties of the soils and rocks. Within this framework, this work aims to test two hypothesis: (i) although conceptually distinct and based on contrasting procedures, statistic and deterministic methods generate similar shallow landslides susceptibility results regarding the predictive capacity and spatial agreement; and (ii) the integration of the shallow landslides susceptibility maps obtained with data-driven and physically-based methods, for the same study area, generate a more reliable susceptibility model for shallow landslides occurrence. To evaluate these two hypotheses, we select the Information Value data-driven method and the physically-based Infinite Slope model to evaluate shallow landslides in the study area of Monfalim and Louriceira basins (13.9 km2), which is located in the north of Lisbon region (Portugal). The landslide inventory is composed by 111 shallow landslides and was divide in two independent groups based on temporal criteria (age ≤ 1983 and age > 1983): (i) the modelling group (51 cases) was used to define the weights for each predisposing factor

  8. Spatial data software integration - Merging CAD/CAM/mapping with GIS and image processing

    NASA Technical Reports Server (NTRS)

    Logan, Thomas L.; Bryant, Nevin A.

    1987-01-01

    The integration of CAD/CAM/mapping with image processing using geographic information systems (GISs) as the interface is examined. Particular emphasis is given to the development of software interfaces between JPL's Video Image Communication and Retrieval (VICAR)/Imaged Based Information System (IBIS) raster-based GIS and the CAD/CAM/mapping system. The design and functions of the VICAR and IBIS are described. Vector data capture and editing are studied. Various software programs for interfacing between the VICAR/IBIS and CAD/CAM/mapping are presented and analyzed.

  9. An integrated approach for automated cover-type mapping of large inaccessible areas in Alaska

    USGS Publications Warehouse

    Fleming, Michael D.

    1988-01-01

    The lack of any detailed cover type maps in the state necessitated that a rapid and accurate approach to be employed to develop maps for 329 million acres of Alaska within a seven-year period. This goal has been addressed by using an integrated approach to computer-aided analysis which combines efficient use of field data with the only consistent statewide spatial data sets available: Landsat multispectral scanner data, digital elevation data derived from 1:250 000-scale maps, and 1:60 000-scale color-infrared aerial photographs.

  10. Spatial data software integration - Merging CAD/CAM/mapping with GIS and image processing

    NASA Technical Reports Server (NTRS)

    Logan, Thomas L.; Bryant, Nevin A.

    1987-01-01

    The integration of CAD/CAM/mapping with image processing using geographic information systems (GISs) as the interface is examined. Particular emphasis is given to the development of software interfaces between JPL's Video Image Communication and Retrieval (VICAR)/Imaged Based Information System (IBIS) raster-based GIS and the CAD/CAM/mapping system. The design and functions of the VICAR and IBIS are described. Vector data capture and editing are studied. Various software programs for interfacing between the VICAR/IBIS and CAD/CAM/mapping are presented and analyzed.

  11. Mental and Physical (MAP) Training: a neurogenesis-inspired intervention that enhances health in humans.

    PubMed

    Shors, Tracey J; Olson, Ryan L; Bates, Marsha E; Selby, Edward A; Alderman, Brandon L

    2014-11-01

    New neurons are generated in the hippocampus each day and their survival is greatly enhanced through effortful learning (Shors, 2014). The numbers of cells produced can be increased by physical exercise (van Praag, Kempermann, & Gage, 1999). These findings inspired us to develop a clinical intervention for humans known as Mental and Physical Training, or MAP Training. Each session consists of 30min of mental training with focused attention meditation (20min sitting and 10min walking). Meditation is an effortful training practice that involves learning about the transient nature of thoughts and thought patterns, and acquiring skills to recognize them without necessarily attaching meaning and/or emotions to them. The mental training component is followed by physical training with 30min of aerobic exercise performed at moderate intensity. During this component, participants learn choreographed dance routines while engaging in aerobic exercise. In a pilot "proof-of-concept" study, we provided supervised MAP Training (2 sessions per week for 8weeks) to a group of young mothers in the local community who were recently homeless, most of them having previously suffered from physical and sexual abuse, addiction, and depression. Preliminary data suggest that MAP Training improves dependent measures of aerobic fitness (as assessed by maximal rate of oxygen consumed) while decreasing symptoms of depression and anxiety. Similar changes were not observed in a group of recently homeless women who did not participate in MAP Training. It is not currently possible to determine whether new neurons in the human brain increase in number as a result of MAP Training. Rather these preliminary results of MAP Training illustrate how neuroscientific research can be translated into novel clinical interventions that benefit human health and wellness.

  12. Integrated cytogenetic BAC map of the genome of the gray, short-tailed opossum, Monodelphis domestica.

    PubMed

    Duke, S E; Samollow, P B; Mauceli, E; Lindblad-Toh, K; Breen, M

    2007-01-01

    The generation of high-quality genome assemblies for numerous species is advancing at a rapid pace. As the number of genome assemblies increases, so does our ability to investigate genome relationships and their contributions to unraveling complex biological, evolutionary, and biomedical processes. A key process in the generation of a genome assembly is to determine and verify the precise physical location and order of the large sequence blocks (scaffolds) that result from the assembly. For organisms of relatively recent common ancestry this process may be achieved largely through comparative sequence alignment. However, as the evolutionary distance between species lengthens, the use of comparative sequence alignment becomes increasingly less reliable. Simultaneous cytogenetic mapping, using multicolor fluorescence in-situ hybridization (FISH) analysis, offers an alternative means to define the cytogenetic location and relative order of DNA sequences, thereby anchoring the genome sequence to the karyotype. In this article we report the molecular cytogenetic locations of 415 bacterial artificial chromosome (BAC) clones that served to anchor sequence scaffolds of the gray, short-tailed opossum (Monodelphis domestica) to its karyotype, which enabled accurate integration of these regions into the genome assembly.

  13. A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome

    PubMed Central

    Tomkins, Jeffrey P.; Wood, Todd C.; Stacey, Minviluz G.; Loh, John T.; Judd, Adam; Goicoechea, Jose L.; Stacey, Gary; Sadowsky, Michael J.; Wing, Rod A.

    2001-01-01

    Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes the development of a physical framework for the genome of Bradyrhizobium japonicum, the nitrogen-fixing symbiont of soybean. A BAC library for B. japonicum was constructed that provides a 77-fold genome coverage based on an estimated genome size of 8.7 Mb. The library contains 4608 clones with an average insert size of 146 kb. To generate a physical map, the entire library was fingerprinted with HindIII, and the fingerprinted clones were assembled into contigs using the Fingerprint Contig software (FPC; Sanger Centre, UK). The FPC analysis placed 3410 clones in six large contigs. The ends of 1152 BAC inserts were sequenced to generate a sequence-tagged connector (STC) framework. To join and orient the contigs, high-density BAC colony filters were probed with 41 known gene probes and 17 end sequences from contig boundaries. STC sequences were searched against the public databases using FASTA and BLASTX algorithms. Query results allowed the identification of 113 high probability matches with putative functional identities that were placed on the physical map. Combined with the hybridization data, a high-resolution physical map with 194 positioned markers represented in two large contigs was developed, providing a marker every 45 kb. Of these markers, 177 are known or putative B. japonicum genes. Additionally, 1338 significant BLASTX results (E < 10−4) were manually sorted by function to produce a functionally categorized database of relevant B. japonicum STC sequences that can also be traced to specific locations in the physical map. PMID:11483585

  14. Physical and genetic mapping in the grasses Lolium perenne and Festuca pratensis.

    PubMed Central

    King, J; Armstead, I P; Donnison, I S; Thomas, H M; Jones, R N; Kearsey, M J; Roberts, L A; Thomas, A; Morgan, W G; King, I P

    2002-01-01

    A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line 2n = 2x = 14. In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1. PMID:12019245

  15. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.)

    PubMed Central

    2011-01-01

    Background Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with <30 or >250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. Conclusion BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing. PMID:21595870

  16. Application of integrated methods in mapping waste disposal areas

    NASA Astrophysics Data System (ADS)

    Soupios, Pantelis; Papadopoulos, Nikos; Papadopoulos, Ilias; Kouli, Maria; Vallianatos, Filippos; Sarris, Apostolos; Manios, Thrassyvoulos

    2007-11-01

    An integrated suite of environmental methods was used to characterize the hydrogeological, geological and tectonic regime of the largest waste disposal landfill of Crete Island, the Fodele municipal solid waste site (MSW), to determine the geometry of the landfill (depth and spatial extent of electrically conductive anomalies), to define the anisotropy caused by bedrock fabric fractures and to locate potential zones of electrically conductive contamination. A combination of geophysical methods and chemical analysis was implemented for the characterization and management of the landfill. Five different types of geophysical surveys were performed: (1) 2D electrical resistance tomography (ERT), (2) electromagnetic measurements using very low frequencies (VLF), (3) electromagnetic conductivity (EM31), (4) seismic refraction measurements (SR), and (5) ambient noise measurements (HVSR). The above geophysical methods were used with the aim of studying the subsurface properties of the landfill and to define the exact geometrical characteristics of the site under investigation.

  17. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).

    PubMed

    Dohm, Juliane C; Lange, Cornelia; Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Borchardt, Dietrich; Schulz, Britta; Lehrach, Hans; Weisshaar, Bernd; Himmelbauer, Heinz

    2012-05-01

    Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.

  18. Refined genetic mapping of a gene for familial juvenile nephronophthisis (NPH1) and physical mapping of linked markers

    SciTech Connect

    Hildebrandt, F.; Singh-Sawhney, I.; Schnieders, B.

    1995-01-20

    We have recently assigned a gene for familial juvenile nephronophthisis (NPH1) to chromosome 2q between microsatellite markers at loci D2S135 and D2S110. Here we have extended and refined our previous linkage analysis by studying five additional NPH families and by testing five additional markers. By haplotype analysis in a large family yielding proof of linkage, D2S135 and D2S283 were defined with certainty as flanking the NPH1 critical region within a 14-cM interval. These data now allow cytogenetic assignment of the NPH1 critical region to 2q11.1-q21.1. Furthermore, haplotype analysis in 12 small families helped to define as flanking markers D2S293 and D2S363, which span an 8-cM interval. Multipoint linkage analysis by the location score method resulted in a maximum multipoint lod score of 10.30. The {sub max}-1 support interval spans 6.9 cM and is flanked by marker loci D2S293 and D2S363. Since IL1A maps to this region and has been cytogenetically mapped to 2q13 in the literature, NPH1 can be assigned more closely to 2q13 or adjacent bands. Contigs of CEPH mega-YAC clones in the region were established by screening the clones with microsatellite markers, adding marker IL1A to the physical map as a novel assignment. We conclude that the NPH1 gene most probably localizes to an interval of 6.9 cM between marker loci D2S293 and D2S363 in the vicinity of 2q13. This contig mapping provides the basis for cloning of this interval and for isolation of the NPH1 gene. 18 refs., 3 figs., 1 tab.

  19. Hudson Canyon benthic habitats characterization and mapping by integrated analysis of multidisciplinary data

    NASA Astrophysics Data System (ADS)

    Pierdomenico, Martina; Guida, Vincent G.; Rona, Peter A.; Macelloni, Leonardo; Scranton, Mary I.; Asper, Vernon; Diercks, Arne

    2013-04-01

    Hudson Canyon, about 180 km SE of New York City, is the largest eastern U.S. submarine canyon and is under consideration for HAPC (Habitat Area of Particular Concern) status, representing a fisheries and biodiversity hot spot. Interest in the area, within the perspective of ecosystem based management, marine spatial planning, habitat and species conservation, led to a joint project between NOAA Northeast Fisheries, U.S. Geological Survey (USGS), Mississippi Mineral Research Institute (MMRI), National Institute for Undersea Science and Technology (NIUST), Stony Brook and Rutgers Universities for the study of benthic habitats, that includes the assembly of existing data with newly collected ones: acoustic mapping, visual ground-truthing, hydrographic, sedimentological, and trawl data collections. Acoustic mapping, performed using AUV-mounted multibeam sonar, provided ultra-high resolution bathymetric and backscatter imagery (3m and 1m respectively) at all water depths for identification of geomorphological features and for the characterization of surficial sediments along the two thirds of the shelf portion of the canyon. Identification of benthic and demersal communities was accomplished by visual ground thruthing with underwater vehicle video and still cameras, and from trawl catch data. A CTD-rosette sampler provided water column salinity-temperature profiles and water samples for dissolved methane analysis in the vicinity of suspected bottom sources. Analysis of data revealed a complex of topographic structures and hydrological patterns that provide a wide range of physical habitats in a relatively small area. A mosaic of sandy and muddy substrates, gravel beds, rock outcrops, and semilithified clay outcrops host rich and varied faunal assemblages, including deepwater corals and sponge communities. Pockmark fields, occurring below 300 m depth, suggest that methane-based chemosynthetic carbonate deposition contributes to creation of specific hard bottom habitats

  20. The Field-Testing of a Novel Integrated Mapping Protocol for Neglected Tropical Diseases

    PubMed Central

    Pelletreau, Sonia; Nyaku, Mawuli; Dembele, Massitan; Sarr, Boubacar; Budge, Philip; Ross, Rachael; Mathieu, Els

    2011-01-01

    Background Vertical control and elimination programs focused on specific neglected tropical diseases (NTDs) can achieve notable success by reducing the prevalence and intensity of infection. However, many NTD-endemic countries have not been able to launch or scale-up programs because they lack the necessary baseline data for planning and advocacy. Each NTD program has its own mapping guidelines to collect missing data. Where geographic overlap among NTDs exists, an integrated mapping approach could result in significant resource savings. We developed and field-tested an innovative integrated NTD mapping protocol (Integrated Threshold Mapping (ITM) Methodology) for lymphatic filariasis (LF), trachoma, schistosomiasis and soil-transmitted helminths (STH). Methodology/Principal Findings The protocol is designed to be resource-efficient, and its specific purpose is to determine whether a threshold to trigger public health interventions in an implementation unit has been attained. The protocol relies on World Health Organization (WHO) recommended indicators in the disease-specific age groups. For each disease, the sampling frame was the district, but for schistosomiasis, the sub-district rather than the ecological zone was used. We tested the protocol by comparing it to current WHO mapping methodologies for each of the targeted diseases in one district each in Mali and Senegal. Results were compared in terms of public health intervention, and feasibility, including cost. In this study, the ITM methodology reached the same conclusions as the WHO methodologies regarding the initiation of public health interventions for trachoma, LF and STH, but resulted in more targeted intervention recommendations for schistosomiasis. ITM was practical, feasible and demonstrated an overall cost saving compared with the standard, non-integrated, WHO methodologies. Conclusions/Significance This integrated mapping tool could facilitate the implementation of much-needed programs in endemic

  1. An integrated pan-tropical biomass map using multiple reference datasets.

    PubMed

    Avitabile, Valerio; Herold, Martin; Heuvelink, Gerard B M; Lewis, Simon L; Phillips, Oliver L; Asner, Gregory P; Armston, John; Ashton, Peter S; Banin, Lindsay; Bayol, Nicolas; Berry, Nicholas J; Boeckx, Pascal; de Jong, Bernardus H J; DeVries, Ben; Girardin, Cecile A J; Kearsley, Elizabeth; Lindsell, Jeremy A; Lopez-Gonzalez, Gabriela; Lucas, Richard; Malhi, Yadvinder; Morel, Alexandra; Mitchard, Edward T A; Nagy, Laszlo; Qie, Lan; Quinones, Marcela J; Ryan, Casey M; Ferry, Slik J W; Sunderland, Terry; Laurin, Gaia Vaglio; Gatti, Roberto Cazzolla; Valentini, Riccardo; Verbeeck, Hans; Wijaya, Arief; Willcock, Simon

    2016-04-01

    We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets. © 2015 John Wiley & Sons Ltd.

  2. GRAD-MAP: A Physics and Astronomy Diversity Initiative at the University of Maryland

    NASA Astrophysics Data System (ADS)

    Smith, Robyn; Rogoszinski, Zeeve; Sheppard, Kyle; Taylor, Corbin; Wilkins, Ashlee; Vogel, Stuart; Rolston, Steve; Hammer, Donna; Gezari, Suvi; Williams, Jimmy

    2017-01-01

    Graduate Resources for Advancing Diversity with Maryland's Astronomy and Physics (GRAD-MAP) builds connections with mid-Atlantic HBCUs, Minority-Serving Institutions (MSIs), and community colleges using seminars, forums, and workshops to foster a diverse community: undergraduates prepared to succeed in graduate school, inclusion-minded graduate student mentors, and faculty versed in the experiences of students at MSIs. In its fourth year, GRAD-MAP remains a graduate-student-powered initiative with a four-pronged approach: 1) Fall Collaborative Seminars, 2) Winter Workshop, 3) Spring Symposium, and 4) Summer Scholars Program. This coherent programming allows GRAD-MAP to do more than just increase the number of minority students or simply shuffle around students who already are, or would be, active in research. GRAD-MAP is committed to identifying students who are underserved or overlooked by the traditional academic pipeline. Our goal is not only to get them on the path to be successful undergraduate researchers and eventual graduate applicants, but also to make substantial, sustainable efforts toward a more inclusive climate in physics and astronomy. We will describe the key elements of our program, highlight successes and lessons learned, and describe formal evaluation currently underway with the intent that GRAD-MAP could serve as a model for other universities committed to diversity and inclusion.

  3. A physical map of the X chromosome of Drosophila melanogaster: Cosmid contigs and sequence tagged sites

    SciTech Connect

    Madueno, E.; Modolell, J.; Papagiannakis, G.

    1995-04-01

    A physical map of the euchromatic X chromosome of Drosophila melanogaster has been constructed by assembling contiguous arrays of cosmids that were selected by screening a library with DNA isolated from microamplified chromosomal divisions. This map, consisting of 893 cosmids, covers {approximately}64% of the euchromatic part of the chromosome. In addition, 568 sequence tagged sites (STS), in aggregate representing 120 kb of sequenced DNA, were derived from selected cosmids. Most of these STSs, spaced at an average distance of {approximately} 35 kb along the euchromatic region of the chromosome, represent DNA tags that can be used as entry points to the fruitfly genome. Furthermore, 42 genes have been placed on the physical map, either through the hybridization of specific probes to the cosmids or through the fact that they were represented among the STSs. These provide a link between the physical and the genetic maps of D. melanogaster. Nine novel genes have been tentatively identified in Drosophila on the basis of matches between STS sequences and sequences from other species. 32 refs., 3 figs., 4 tabs.

  4. A Physical Map of the X Chromosome of Drosophila Melanogaster: Cosmid Contigs and Sequence Tagged Sites

    PubMed Central

    Madueno, E.; Papagiannakis, G.; Rimmington, G.; Saunders, RDC.; Savakis, C.; Siden-Kiamos, I.; Skavdis, G.; Spanos, L.; Trenear, J.; Adam, P.; Ashburner, M.; Benos, P.; Bolshakov, V. N.; Coulson, D.; Glover, D. M.; Herrmann, S.; Kafatos, F. C.; Louis, C.; Majerus, T.; Modolell, J.

    1995-01-01

    A physical map of the euchromatic X chromosome of Drosophila melanogaster has been constructed by assembling contiguous arrays of cosmids that were selected by screening a library with DNA isolated from microamplified chromosomal divisions. This map, consisting of 893 cosmids, covers ~64% of the euchromatic part of the chromosome. In addition, 568 sequence tagged sites (STS), in aggregate representing 120 kb of sequenced DNA, were derived from selected cosmids. Most of these STSs, spaced at an average distance of ~35 kb along the euchromatic region of the chromosome, represent DNA tags that can be used as entry points to the fruitfly genome. Furthermore, 42 genes have been placed on the physical map, either through the hybridization of specific probes to the cosmids or through the fact that they were represented among the STSs. These provide a link between the physical and the genetic maps of D. melanogaster. Nine novel genes have been tentatively identified in Drosophila on the basis of matches between STS sequences and sequences from other species. PMID:7789765

  5. The Effectiveness of Concept Maps in Teaching Physics Concepts Applied to Engineering Education: Experimental Comparison of the Amount of Learning Achieved with and without Concept Maps

    ERIC Educational Resources Information Center

    Martinez, Guadalupe; Perez, Angel Luis; Suero, Maria Isabel; Pardo, Pedro J.

    2013-01-01

    A study was conducted to quantify the effectiveness of concept maps in learning physics in engineering degrees. The following research question was posed: What was the difference in learning results from the use of concept maps to study a particular topic in an engineering course? The study design was quasi-experimental and used a post-test as a…

  6. The Effectiveness of Concept Maps in Teaching Physics Concepts Applied to Engineering Education: Experimental Comparison of the Amount of Learning Achieved with and without Concept Maps

    ERIC Educational Resources Information Center

    Martinez, Guadalupe; Perez, Angel Luis; Suero, Maria Isabel; Pardo, Pedro J.

    2013-01-01

    A study was conducted to quantify the effectiveness of concept maps in learning physics in engineering degrees. The following research question was posed: What was the difference in learning results from the use of concept maps to study a particular topic in an engineering course? The study design was quasi-experimental and used a post-test as a…

  7. The need for sustained and integrated high-resolution mapping of dynamic coastal environments

    USGS Publications Warehouse

    Stockdon, Hilary F.; Lillycrop, Jeff W.; Howd, Peter A.; Wozencraft, Jennifer M.

    2007-01-01

    The evolution of the United States' coastal zone response to both human activities and natural processes is dynamic. Coastal resource and population protection requires understanding, in detail, the processes needed for change as well as the physical setting. Sustained coastal area mapping allows change to be documented and baseline conditions to be established, as well as future behavior to be predicted in conjunction with physical process models. Hyperspectral imagers and airborne lidars, as well as other recent mapping technology advances, allow rapid national scale land use information and high-resolution elevation data collection. Coastal hazard risk evaluation has critical dependence on these rich data sets. A fundamental storm surge model parameter in predicting flooding location, for example, is coastal elevation data, and a foundation in identifying the most vulnerable populations and resources is land use maps. A wealth of information for physical change process study, coastal resource and community management and protection, and coastal area hazard vulnerability determination, is available in a comprehensive national coastal mapping plan designed to take advantage of recent mapping technology progress and data distribution, management, and collection.

  8. Physical mapping and molecular cloning of mung bean yellow mosaic virus DNA.

    PubMed

    Morinaga, T; Ikegami, M; Miura, K

    1990-01-01

    Viral single-stranded DNA of mung bean yellow mosaic virus (MYMV) was converted to the double-stranded state in vitro, and physical mapping was carried out. The genome of MYMV was found to consist of two major components (designated as DNA 1 and DNA 2). In addition, some minor components were detected. Molecular cloning of the major components was carried out, using in vitro double-stranded DNA and replicative intermediate DNAs. DNA 1 is about 2.72 and DNA 2 about 2.67 kilobase pairs. No similarities were observed when the two restriction maps of DNA 1 and 2 were compared.

  9. Assessing integration of clinical and public health skills in preventive medicine residencies: using competency mapping.

    PubMed

    Wells, Eden V; Sarigiannis, Amy N; Boulton, Matthew L

    2012-06-01

    We evaluated the utility of a competency mapping process for assessing the integration of clinical and public health skills in a newly developed Community Health Center (CHC) rotation at the University of Michigan School of Public Health Preventive Medicine residency. Learning objectives for the CHC rotation were derived from the Accreditation Council for Graduate Medical Education core clinical preventive medicine competencies. CHC learning objectives were mapped to clinical preventive medicine competencies specific to the specialty of public health and general preventive medicine. Objectives were also mapped to The Council on Linkages Between Academia and Public Health Practice's tier 2 Core Competencies for Public Health Professionals. CHC learning objectives mapped to all 4 (100%) of the public health and general preventive medicine clinical preventive medicine competencies. CHC population-level learning objectives mapped to 32 (94%) of 34 competencies for public health professionals. Utilizing competency mapping to assess clinical-public health integration in a new CHC rotation proved to be feasible and useful. Clinical preventive medicine learning objectives for a CHC rotation can also address public health competencies.

  10. Assessing integration of clinical and public health skills in preventive medicine residencies: using competency mapping.

    PubMed

    Wells, Eden V; Sarigiannis, Amy N; Boulton, Matthew L

    2012-06-01

    To evaluate the utility of a competency mapping process for assessing the integration of clinical and public health skills in a newly developed Community Health Center (CHC) rotation at the University of Michigan School of Public Health Preventive Medicine residency. Learning objectives for the CHC rotation were derived from the Accreditation Council for Graduate Medical Education core clinical preventive medicine competencies. CHC learning objectives were mapped to clinical preventive medicine competencies specific to the specialty of public health and general preventive medicine. Objectives were also mapped to The Council on Linkages Between Academia and Public Health Practice's Tier-2 Core Competencies for Public Health Professionals. CHC learning objectives mapped to all four (100%) of the public health and general preventive medicine clinical preventive medicine competencies. CHC population-level learning objectives mapped to 32 (94%) of 34 competencies for public health professionals. Utilizing competency mapping to assess clinical-public health integration in a new CHC rotation proved to be feasible and useful. Clinical preventive medicine learning objectives for a CHC rotation can also address public health competencies. Copyright © 2012 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  11. Assessing Integration of Clinical and Public Health Skills in Preventive Medicine Residencies: Using Competency Mapping

    PubMed Central

    Sarigiannis, Amy N.; Boulton, Matthew L.

    2012-01-01

    Objectives. We evaluated the utility of a competency mapping process for assessing the integration of clinical and public health skills in a newly developed Community Health Center (CHC) rotation at the University of Michigan School of Public Health Preventive Medicine residency. Methods. Learning objectives for the CHC rotation were derived from the Accreditation Council for Graduate Medical Education core clinical preventive medicine competencies. CHC learning objectives were mapped to clinical preventive medicine competencies specific to the specialty of public health and general preventive medicine. Objectives were also mapped to The Council on Linkages Between Academia and Public Health Practice’s tier 2 Core Competencies for Public Health Professionals. Results. CHC learning objectives mapped to all 4 (100%) of the public health and general preventive medicine clinical preventive medicine competencies. CHC population-level learning objectives mapped to 32 (94%) of 34 competencies for public health professionals. Conclusions. Utilizing competency mapping to assess clinical–public health integration in a new CHC rotation proved to be feasible and useful. Clinical preventive medicine learning objectives for a CHC rotation can also address public health competencies. PMID:22690972

  12. Integrating Community Volcanic Hazard Mapping, Geographic Information Systems, and Modeling to Reduce Volcanic Hazard Vulnerability

    NASA Astrophysics Data System (ADS)

    Bajo Sanchez, Jorge V.

    This dissertation is composed of an introductory chapter and three papers about vulnerability and volcanic hazard maps with emphasis on lahars. The introductory chapter reviews definitions of the term vulnerability by the social and natural hazard community and it provides a new definition of hazard vulnerability that includes social and natural hazard factors. The first paper explains how the Community Volcanic Hazard Map (CVHM) is used for vulnerability analysis and explains in detail a new methodology to obtain valuable information about ethnophysiographic differences, hazards, and landscape knowledge of communities in the area of interest: the Canton Buenos Aires situated on the northern flank of the Santa Ana (Ilamatepec) Volcano, El Salvador. The second paper is about creating a lahar hazard map in data poor environments by generating a landslide inventory and obtaining potential volumes of dry material that can potentially be carried by lahars. The third paper introduces an innovative lahar hazard map integrating information generated by the previous two papers. It shows the differences in hazard maps created by the communities and experts both visually as well as quantitatively. This new, integrated hazard map was presented to the community with positive feedback and acceptance. The dissertation concludes with a summary chapter on the results and recommendations.

  13. Effects of Various Types of Situps on Integrated MAP's of the Abdominal Musculature.

    ERIC Educational Resources Information Center

    Noble, Larry

    The electrical activity of the abdominal muscles was tested during situps to determine the effect upon integrated muscle action potential (MAP). The following types of situps were used in testing 18 college males: (1) trunk curls; (2) AAHPER situp; (3) YMCA situp; (4) modified AAHPER situp; and (5) modified YMCA situp. All situps were performed…

  14. Developing stressor-watershed function relationships to refine the national maps of watershed integrity

    EPA Science Inventory

    Abstract ESA 2017Developing stressor-watershed function relationships to refine the national maps of watershed integrityJohnson, Z.C., S.G. Leibowitz, and R.A. Hill. To be submitted to the Ecological Society of America Annual Meeting, Portland, OR. August 2017.Human-induced ecolo...

  15. Breaking Concept Boundaries to Enhance Creative Potential: Using Integrated Concept Maps for Conceptual Self-Awareness

    ERIC Educational Resources Information Center

    Kao, Gloria Yi-Ming; Lin, Sunny S. J.; Sun, Chuen-Tsai

    2008-01-01

    The authors address the role of computer support for building conceptual self-awareness--that is, enabling students to think outside of concept boundaries in hope of enhancing creative potential. Based on meta-cognition theory, we developed an integrated concept mapping system (ICMSys) to improve users' conceptual self-awareness in addition to…

  16. Breaking Concept Boundaries to Enhance Creative Potential: Using Integrated Concept Maps for Conceptual Self-Awareness

    ERIC Educational Resources Information Center

    Kao, Gloria Yi-Ming; Lin, Sunny S. J.; Sun, Chuen-Tsai

    2008-01-01

    The authors address the role of computer support for building conceptual self-awareness--that is, enabling students to think outside of concept boundaries in hope of enhancing creative potential. Based on meta-cognition theory, we developed an integrated concept mapping system (ICMSys) to improve users' conceptual self-awareness in addition to…

  17. Integrated environmental mapping and monitoring, a methodological approach to optimise knowledge gathering and sampling strategy.

    PubMed

    Nilssen, Ingunn; Ødegård, Øyvind; Sørensen, Asgeir J; Johnsen, Geir; Moline, Mark A; Berge, Jørgen

    2015-07-15

    New technology has led to new opportunities for a holistic environmental monitoring approach adjusted to purpose and object of interest. The proposed integrated environmental mapping and monitoring (IEMM) concept, presented in this paper, describes the different steps in such a system from mission of survey to selection of parameters, sensors, sensor platforms, data collection, data storage, analysis and to data interpretation for reliable decision making. The system is generic; it can be used by authorities, industry and academia and is useful for planning- and operational phases. In the planning process the systematic approach is also ideal to identify areas with gap of knowledge. The critical stages of the concept is discussed and exemplified by two case studies, one environmental mapping and one monitoring case. As an operational system, the IEMM concept can contribute to an optimised integrated environmental mapping and monitoring for knowledge generation as basis for decision making. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Fostering Scientific Thinking by Prospective Teachers in a Course That Integrates Physics and Literacy Learning

    ERIC Educational Resources Information Center

    van Zee, Emily H.; Jansen, Henri; Winograd, Kenneth; Crowl, Michele; Devitt, Adam

    2013-01-01

    We designed a physics course for prospective elementary and middle school teachers to foster aspects of scientific thinking recommended in reform documents. Because the elementary school curriculum focuses heavily on literacy, we also explicitly integrated physics and literacy learning in this course. By integrating physics and literacy learning,…

  19. Fostering Scientific Thinking by Prospective Teachers in a Course That Integrates Physics and Literacy Learning

    ERIC Educational Resources Information Center

    van Zee, Emily H.; Jansen, Henri; Winograd, Kenneth; Crowl, Michele; Devitt, Adam

    2013-01-01

    We designed a physics course for prospective elementary and middle school teachers to foster aspects of scientific thinking recommended in reform documents. Because the elementary school curriculum focuses heavily on literacy, we also explicitly integrated physics and literacy learning in this course. By integrating physics and literacy learning,…

  20. Wakeful rest promotes the integration of spatial memories into accurate cognitive maps.

    PubMed

    Craig, Michael; Dewar, Michaela; Harris, Mathew A; Della Sala, Sergio; Wolbers, Thomas

    2016-02-01

    Flexible spatial navigation, e.g. the ability to take novel shortcuts, is contingent upon accurate mental representations of environments-cognitive maps. These cognitive maps critically depend on hippocampal place cells. In rodents, place cells replay recently travelled routes, especially during periods of behavioural inactivity (sleep/wakeful rest). This neural replay is hypothesised to promote not only the consolidation of specific experiences, but also their wider integration, e.g. into accurate cognitive maps. In humans, rest promotes the consolidation of specific experiences, but the effect of rest on the wider integration of memories remained unknown. In the present study, we examined the hypothesis that cognitive map formation is supported by rest-related integration of new spatial memories. We predicted that if wakeful rest supports cognitive map formation, then rest should enhance knowledge of overarching spatial relations that were never experienced directly during recent navigation. Forty young participants learned a route through a virtual environment before either resting wakefully or engaging in an unrelated perceptual task for 10 min. Participants in the wakeful rest condition performed more accurately in a delayed cognitive map test, requiring the pointing to landmarks from a range of locations. Importantly, the benefit of rest could not be explained by active rehearsal, but can be attributed to the promotion of consolidation-related activity. These findings (i) resonate with the demonstration of hippocampal replay in rodents, and (ii) provide the first evidence that wakeful rest can improve the integration of new spatial memories in humans, a function that has, hitherto, been associated with sleep. © 2015 Wiley Periodicals, Inc.

  1. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha).

    PubMed

    McKinney, G J; Seeb, L W; Larson, W A; Gomez-Uchida, D; Limborg, M T; Brieuc, M S O; Everett, M V; Naish, K A; Waples, R K; Seeb, J E

    2016-05-01

    Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.

  2. Physical map of human Xq27-qter: Localizing the region of the fragile X mutation

    SciTech Connect

    Poustka, A.; Dietrich, A.; Langenstein, G. ); Toniolo, D. ); Warren, S.T. ); Lehrach, H. )

    1991-10-01

    The authors describe a physical map of the end of the long arm of the human X chromosome encompassing the region from Xq27.2 to the q telomere, inclusive of the chromosomal band Xq28. This region is of particular interest, since it contains the highest density of genes associated with genetic diseases. The map covers a total of 12 megabases (Mb) of DNA and extends from the telomere to 3 Mb beyond the most likely position of the fragile X mutation, defined by a cluster of translocation breakpoints in somatic cell hybrids. The map determines order and position of loci throughout the Xq28 region and localizes cell line breakpoints marking the fragile X region to an interval of 300-700 kilobases between 8 and 8.7. Mb proximal of the Xq telomere.

  3. ASCA Temperature Maps for Merging and Relaxed Clusters and Physics of the Cluster Gas

    NASA Technical Reports Server (NTRS)

    Markevitch, M.; Sarazin, C.; Nevalainen, J.; Vikhlinin, A.; Forman, W.

    1999-01-01

    ASCA temperature maps for several galaxy clusters undergoing strong mergers will be presented. From these maps, it is possible to estimate velocities of the colliding subclusters. I will discuss several interesting implications of these estimates for the physics of the cluster gas and the shape of the gravitational potential. I will also present temperature maps and profiles for several relaxed clusters selected for X-ray mass determination, and present the mass values derived without the assumption of isothermality. The accurate mass-temperature and luminosity-temperature relations will be discussed. This talk will review how AXAF will revolutionize X-ray astronomy through its radically better imaging and spectroscopic resolution. Examples from many fields of astrophysics will be given.

  4. Analyzing diffraction gratings by a boundary integral equation Neumann-to-Dirichlet map method.

    PubMed

    Wu, Yumao; Lu, Ya Yan

    2009-11-01

    For analyzing diffraction gratings, a new method is developed based on dividing one period of the grating into homogeneous subdomains and computing the Neumann-to-Dirichlet (NtD) maps for these subdomains by boundary integral equations. For a subdomain, the NtD operator maps the normal derivative of the wave field to the wave field on its boundary. The integral operators used in this method are simple to approximate, since they involve only the standard Green's function of the Helmholtz equation in homogeneous media. The method retains the advantages of existing boundary integral equation methods for diffraction gratings but avoids the quasi-periodic Green's functions that are expensive to evaluate.

  5. Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf.

    PubMed

    Sierro, Nicolas; van Oeveren, Jan; van Eijk, Michiel J T; Martin, Florian; Stormo, Keith E; Peitsch, Manuel C; Ivanov, Nikolai V

    2013-09-01

    Genomics-based breeding of economically important crops such as banana, coffee, cotton, potato, tobacco and wheat is often hampered by genome size, polyploidy and high repeat content. We adapted sequence-based whole-genome profiling (WGP™) technology to obtain insight into the polyploidy of the model plant Nicotiana tabacum (tobacco). N. tabacum is assumed to originate from a hybridization event between ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis approximately 200,000 years ago. This resulted in tobacco having a haploid genome size of 4500 million base pairs, approximately four times larger than the related tomato (Solanum lycopersicum) and potato (Solanum tuberosum) genomes. In this study, a physical map containing 9750 contigs of bacterial artificial chromosomes (BACs) was constructed. The mean contig size was 462 kbp, and the calculated genome coverage equaled the estimated tobacco genome size. We used a method for determination of the ancestral origin of the genome by annotation of WGP sequence tags. This assignment agreed with the ancestral annotation available from the tobacco genetic map, and may be used to investigate the evolution of homoeologous genome segments after polyploidization. The map generated is an essential scaffold for the tobacco genome. We propose the combination of WGP physical mapping technology and tag profiling of ancestral lines as a generally applicable method to elucidate the ancestral origin of genome segments of polyploid species. The physical mapping of genes and their origins will enable application of biotechnology to polyploid plants aimed at accelerating and increasing the precision of breeding for abiotic and biotic stress resistance.

  6. Overview of National Thematic Data Integration (An Experience on One Map Mangrove Sulawesi)

    NASA Astrophysics Data System (ADS)

    Rudiastuti, A. W.; Yuwono, D. M.; Niendyawati; Pramono, G. H.; Rahmanto, B. D.

    2016-11-01

    Playing role as coastal shield with enormous economic value and ecological functions, mangrove forest management is always challenging to be studied. As either the largest archipelagic countryor the largest mangrove forest habitat around the globe, Indonesia needs a national mangrove forest baseline data and its updating for coastal management. Many stakeholders and institutions, including Geospatial Information Agency (BIG), had conducted mangrove mapping and updating. However, in order to achieve one mangrove national data, coordination and synergy among stakeholders and institutions such as: the Ministry of Environment and Forestry as mangrove custodian, Indonesian National Institute of Aeronautics and Space, Ministry of Marine and Fisheries, and BIG aligned with the National Mangrove Working Group is needed. A fundamental step for national mangrove forest management is the establishment of National One Map Mangrove Program by means of coordination, synchronization, and integration of mangrove geospatial data from various stakeholders. This paper will discuss the technical process of data integration and field survey in order to produce One Map Mangrove Sulawesi with the same geo-reference, database, and also standard and specification. The result of One Map Mangrove Sulawesi Program comprises of information about mangrove current status, existing area, and its distribution in Sulawesi.Beside the geospatial data from Ministry of Environment and Forestry and other institutions, the primary data used to map mangrove forest in Sulawesi is SPOT 6 and SPOT 7(year 2014 - 2015) imageries yielded map scale of 1: 25,000. On screen digitation using NIR, Red and Green bands and Normalized Difference Vegetation Index (NDVI)image transformation are applied for the initial canopy density classification. Field survey was doneto obtain field data forvegetation analysis, image classification andre-interpretation. In 2015, the process of producing One Map Mangrove Sulawesi has

  7. Genetic and physical mapping of the genomic region spanning CMT4A

    SciTech Connect

    Othmane, K.B.; Loeb, D.; Roses, A.D.

    1994-09-01

    Autosomal recessive Charcot-Marie-Tooth disease (CMT4) is a severe childhood neuropathy classified into three types: A, B, and C. We previously mapped CMT4A to chromosome 8q13-q21 in four large Tunisian families. Analysis of recombination events suggested the order: cent.-D8S279-(D8S286,D8S164, CMT4A)-D8S84-tel. Families with types B and C were subsequently typed and linkage for these types was excluded for the CMT4A region and other known CMT loci. Recently, the gene for a major peripheral myelin protein (PMP2) was mapped by FISH to chromosome 8q21-q22 and therefore appeared to be a strong candidate gene for CMT4A. We used SSCP analysis, DNA sequencing, FISH and YAC mapping analysis, and demonstrated that PMP2 is not the defect in CMT4A. Using physical mapping data, we sublocalized a new genethon marker (D8S548) to the CMT4A region between D8S286 and D8S164. All affected CMT4A patients were homozygotes for this polymorphic microsatellite as expected from its physical localization. We screened the CEPH megabase YAC library using the closest markers; over 30 YACs were isolated and characterized by PFGE. FISH analysis revealed about 16% chimeras. The YACs span the 8 cM region between D8S279 and PMP2 (mapped distal to D8S84), with a current 1 cM gap between D8S164 and D8S84. We are currently using Alu-PCR and vectorette to develop end clones in order to identify new YACs in the region and further close this gap. Alu-PCR fragments have identified several new microsatellites in the region which can be used for additional mapping of the CMT4A gene.

  8. Creating and Mapping Flash Flood Social and Physical Vulnerability Index of Riyadh, Saudi Arabia

    NASA Astrophysics Data System (ADS)

    Tauhidur Rahman, Muhammad; Aldosary, Adel S.; Nahiduzzaman, Khondokar Mohammad

    2014-05-01

    Over the past couple of years, the frequency and magnitude of flash floods are increasing in the Kingdom of Saudi Arabia. For effective planning and mitigation purposes, it is necessary to identify and visualize areas that are vulnerable to the flooding. In this paper, we will first create a flash flood social and physical vulnerability index for the city of Riyadh based on physical and social-economic data. Building upon the index, the areas of Riyadh that are highly vulnerable to flash floods will be identified and mapped using Geographic Information Systems (GIS). Finally, possible mitigation measures that can be used to reduce the impacts of flooding will be discussed in details.

  9. A Systematic Review of Mapping Strategies for the Sonification of Physical Quantities

    PubMed Central

    Dubus, Gaël; Bresin, Roberto

    2013-01-01

    The field of sonification has progressed greatly over the past twenty years and currently constitutes an established area of research. This article aims at exploiting and organizing the knowledge accumulated in previous experimental studies to build a foundation for future sonification works. A systematic review of these studies may reveal trends in sonification design, and therefore support the development of design guidelines. To this end, we have reviewed and analyzed 179 scientific publications related to sonification of physical quantities. Using a bottom-up approach, we set up a list of conceptual dimensions belonging to both physical and auditory domains. Mappings used in the reviewed works were identified, forming a database of 495 entries. Frequency of use was analyzed among these conceptual dimensions as well as higher-level categories. Results confirm two hypotheses formulated in a preliminary study: pitch is by far the most used auditory dimension in sonification applications, and spatial auditory dimensions are almost exclusively used to sonify kinematic quantities. To detect successful as well as unsuccessful sonification strategies, assessment of mapping efficiency conducted in the reviewed works was considered. Results show that a proper evaluation of sonification mappings is performed only in a marginal proportion of publications. Additional aspects of the publication database were investigated: historical distribution of sonification works is presented, projects are classified according to their primary function, and the sonic material used in the auditory display is discussed. Finally, a mapping-based approach for characterizing sonification is proposed. PMID:24358192

  10. Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

    PubMed Central

    Kim, HyeRan; Miguel, Phillip San; Nelson, William; Collura, Kristi; Wissotski, Marina; Walling, Jason G.; Kim, Jun Pyo; Jackson, Scott A.; Soderlund, Carol; Wing, Rod A.

    2007-01-01

    A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5–16.5%. The sum of expansions and contractions observed in regions >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged ∼2 million years ago. PMID:17339227

  11. Comparative physical maps of the human and mouse Meckel syndrome critical regions.

    PubMed

    Hentges, Kathryn E; Kyttälä, Mira; Justice, Monica J; Peltonen, Leena

    2004-04-01

    Meckel syndrome (MKS-OMIM 24900) is an autosomal recessive disease characterized by cystic kidneys, occipital encephalocele, polydactyly, and fibrotic changes of the liver, typically resulting in postnatal death. A Meckel syndrome critical region (MKS1) maps to human Chromosome (Chr) 17, in a region of homology to mouse Chr 11. Here we report the comparison of human Chr 17q23 with mouse Chr 11. We have generated physical maps of the human and mouse MKS1 critical regions. Additionally, we have created a transcript map of the MKS1 critical region in both species. By comparing these physical maps, we observe a high degree of similarity in gene order in the human and mouse Meckel syndrome critical regions. We have also examined the expression patterns of genes in the MKS1 region to assess their potential as MKS1 candidates. Finally, we have analyzed genes present in the other Meckel syndrome critical regions, MKS2 and MKS3, to determine whether any of the candidate genes for the three MKS loci have similar gene functions or are members of a common biological pathway.

  12. Expansion of polynomial Lie group integrals in terms of certain maps on surfaces, and factorizations of permutations

    NASA Astrophysics Data System (ADS)

    Novaes, Marcel

    2017-02-01

    Using the diagrammatic approach to integrals over Gaussian random matrices, we find a representation for polynomial Lie group integrals as infinite sums over certain maps on surfaces. The maps involved satisfy a specific condition: they have some marked vertices, and no closed walks that avoid these vertices. We also formulate our results in terms of permutations, arriving at new kinds of factorization problems.

  13. Mapping Physical Characteristics of the Columbia River Mouth Using Transmittered Diving Waterbirds

    DTIC Science & Technology

    2013-09-30

    18 2 OBJECTIVES The objectives of this project are to: • Investigate the use of cormorants (Phalacrocorax spp.) as platforms to measure...conductivity, temperature, and depth across the MCR • Investigate the use of cormorants to collect river/sea bed imagery across the MCR • Collaborate with...bed form, or other physical features for the MCR. APPROACH The spatial distribution of individual foraging cormorants can be precisely mapped

  14. A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens

    PubMed Central

    2013-01-01

    Background Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited and the pathogenic mechanism of this disease is still not clear. To facilitate genetic, molecular and genomic studies of this fungal pathogen, we constructed the first BAC-based physical map and performed the first genome survey for this species. Results High molecular weight genomic DNA was isolated from young mycelia of the Villosiclava virens strain UV-8b and a high-quality, large-insert and deep-coverage Bacterial Artificial Chromosome (BAC) library was constructed with the restriction enzyme HindIII. The BAC library consisted of 5,760 clones, which covers 22.7-fold of the UV-8b genome, with an average insert size of 140 kb and an empty clone rate of lower than 1%. BAC fingerprinting generated successful fingerprints for 2,290 BAC clones. Using the fingerprints, a whole genome-wide BAC physical map was constructed that contained 194 contigs (2,035 clones) spanning 51.2 Mb in physical length. Bidirectional-end sequencing of 4,512 BAC clones generated 6,560 high quality BAC end sequences (BESs), with a total length of 3,030,658 bp, representing 8.54% of the genome sequence. Analysis of the BESs revealed general genome information, including 51.52% GC content, 22.51% repetitive sequences, 376.12/Mb simple sequence repeat (SSR) density and approximately 36.01% coding regions. Sequence comparisons to other available fungal genome sequences through BESs showed high similarities to Metarhizium anisopliae, Trichoderma reesei, Nectria haematococca and Cordyceps militaris, which were generally in agreement with the 18S rRNA gene analysis results. Conclusion This study provides the first BAC-based physical map and genome information for the important rice fungal pathogen Villosiclava virens. The BAC clones, physical map and genome information will

  15. Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells

    PubMed Central

    Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

    2013-01-01

    A major challenge of the postgenomic era is to understand how human genes function together in normal and disease states. In microorganisms, high-density genetic interaction (GI) maps are a powerful tool to elucidate gene functions and pathways. We have developed an integrated methodology based on pooled shRNA screening in mammalian cells for genome-wide identification of genes with relevant phenotypes and systematic mapping of all GIs among them. We recently demonstrated the potential of this approach in an application to pathways controlling the susceptibility of human cells to the toxin ricin. Here we present the complete quantitative framework underlying our strategy, including experimental design, derivation of quantitative phenotypes from pooled screens, robust identification of hit genes using ultra-complex shRNA libraries, parallel measurement of tens of thousands of GIs from a single double-shRNA experiment, and construction of GI maps. We describe the general applicability of our strategy. Our pooled approach enables rapid screening of the same shRNA library in different cell lines and under different conditions to determine a range of different phenotypes. We illustrate this strategy here for single- and double-shRNA libraries. We compare the roles of genes for susceptibility to ricin and Shiga toxin in different human cell lines and reveal both toxin-specific and cell line-specific pathways. We also present GI maps based on growth and ricin-resistance phenotypes, and we demonstrate how such a comparative GI mapping strategy enables functional dissection of physical complexes and context-dependent pathways. PMID:23739767

  16. Indoor Map Aided Wi-Fi Integrated Lbs on Smartphone Platforms

    NASA Astrophysics Data System (ADS)

    Yu, C.; El-Sheimy, N.

    2017-09-01

    In this research, an indoor map aided INS/Wi-Fi integrated location based services (LBS) applications is proposed and implemented on smartphone platforms. Indoor map information together with measurements from an inertial measurement unit (IMU) and Received Signal Strength Indicator (RSSI) value from Wi-Fi are collected to obtain an accurate, continuous, and low-cost position solution. The main challenge of this research is to make effective use of various measurements that complement each other without increasing the computational burden of the system. The integrated system in this paper includes three modules: INS, Wi-Fi (if signal available) and indoor maps. A cascade structure Particle/Kalman filter framework is applied to combine the different modules. Firstly, INS position and Wi-Fi fingerprint position integrated through Kalman filter for estimating positioning information. Then, indoor map information is applied to correct the error of INS/Wi-Fi estimated position through particle filter. Indoor tests show that the proposed method can effectively reduce the accumulation positioning errors of stand-alone INS systems, and provide stable, continuous and reliable indoor location service.

  17. Deriving global flood hazard maps of fluvial floods through a physical model cascade

    NASA Astrophysics Data System (ADS)

    Pappenberger, F.; Dutra, E.; Wetterhall, F.; Cloke, H.

    2012-05-01

    Global flood hazard maps can be used in the assessment of flood risk in a number of different applications, including (re)insurance and large scale flood preparedness. Such global hazard maps can be generated using large scale physically based models of rainfall-runoff and river routing, when used in conjunction with a number of post-processing methods. In this study, the European Centre for Medium Range Weather Forecasts (ECMWF) land surface model is coupled to ERA-Interim reanalysis meteorological forcing data, and resultant runoff is passed to a river routing algorithm which simulates floodplains and flood flow across the global land area. The global hazard map is based on a 30 yr (1979-2010) simulation period. A Gumbel distribution is fitted to the annual maxima flows to derive a number of flood return periods. The return periods are calculated initially for a 25 × 25 km grid, which is then reprojected onto a 1 × 1 km grid to derive maps of higher resolution and estimate flooded fractional area for the individual 25 × 25 km cells. Several global and regional maps of flood return periods ranging from 2 to 500 yr are presented. The results compare reasonably to a benchmark data set of global flood hazard. The developed methodology can be applied to other datasets on a global or regional scale.

  18. Deriving global flood hazard maps of fluvial floods through a physical model cascade

    NASA Astrophysics Data System (ADS)

    Pappenberger, F.; Dutra, E.; Wetterhall, F.; Cloke, H. L.

    2012-11-01

    Global flood hazard maps can be used in the assessment of flood risk in a number of different applications, including (re)insurance and large scale flood preparedness. Such global hazard maps can be generated using large scale physically based models of rainfall-runoff and river routing, when used in conjunction with a number of post-processing methods. In this study, the European Centre for Medium Range Weather Forecasts (ECMWF) land surface model is coupled to ERA-Interim reanalysis meteorological forcing data, and resultant runoff is passed to a river routing algorithm which simulates floodplains and flood flow across the global land area. The global hazard map is based on a 30 yr (1979-2010) simulation period. A Gumbel distribution is fitted to the annual maxima flows to derive a number of flood return periods. The return periods are calculated initially for a 25 × 25 km grid, which is then reprojected onto a 1 × 1 km grid to derive maps of higher resolution and estimate flooded fractional area for the individual 25 × 25 km cells. Several global and regional maps of flood return periods ranging from 2 to 500 yr are presented. The results compare reasonably to a benchmark data set of global flood hazard. The developed methodology can be applied to other datasets on a global or regional scale.

  19. Deriving global flood hazard maps of fluvial floods through a physical model cascade

    NASA Astrophysics Data System (ADS)

    Pappenberger, Florian; Dutra, Emanuel; Wetterhall, Fredrik; Cloke, Hannah L.

    2013-04-01

    Global flood hazard maps can be used in the assessment of flood risk in a number of different applications, including (re)insurance and large scale flood preparedness. Such global hazard maps can be generated using large scale physically based models of rainfall-runoff and river routing, when used in conjunction with a number of post-processing methods. In this study, the European Centre for Medium Range Weather Forecasts (ECMWF) land surface model is coupled to ERA-Interim reanalysis meteorological forcing data, and resultant runoff is passed to a river routing algorithm which simulates floodplains and flood flow across the global land area. The global hazard map is based on a 30 yr (1979-2010) simulation period. A Gumbel distribution is fitted to the annual maxima flows to derive a number of flood return periods. The return periods are calculated initially for a 25 × 25 km grid, which is then reprojected onto a 1 × 1 km grid to derive maps of higher resolution and estimate flooded fractional area for the individual 25 × 25 km cells. Several global and regional maps of flood return periods ranging from 2 to 500 yr are presented. The results compare reasonably to a benchmark data set of global flood hazard. The developed methodology can be applied to other datasets on a global or regional scale.

  20. Refinement of the Spinal Muscular Atrophy Locus by Genetic and Physical Mapping

    PubMed Central

    Wang, C. H.; Kleyn, P. W.; Vitale, E.; Ross, B. M.; Lien, L.; Xu, J.; Carter, T. A.; Brzustowicz, L. M.; Obici, S.; Selig, S.; Pavone, L.; Parano, E.; Penchaszadeh, G. K.; Munsat, T.; Kunkel, L. M.; Gilliam, T. C.

    1995-01-01

    We report the mapping and characterization of 12 microsatellite markers including 11 novel markers. All markers were generated from overlapping YAC clones that span the spinal muscular atrophy (SMA) locus. PCR amplification of 32 overlapping YAC clones shows that 9 of the new markers (those set in italics) map to the interval between the two previous closest flanking markers (D5S629 and D5S557): cen - D5S6 - D5S125 - D5S435 - D5S1407-D5S629-D5S1410-D5S1411/D5S1412-D5S1413-D5S1414-D5Z8-D5Z9-CATT1-D5Z10/D5Z6-D5S557-D5S1408-D5S1409-D5S637-D5S351-MAP1B-tel. Four of these new markers detect multiple loci in and out of the SMA gene region. Genetic analysis of recombinant SMA families indicates that D5S1413 is a new proximal flanking locus for the SMA gene. Interestingly, among the 40 physically mapped loci, the 14 multilocus markers map contiguously to a genomic region that overlaps, and perhaps helps define, the minimum genetic region encompassing the SMA gene(s). ImagesFigure 2Figure 5 PMID:7825579

  1. Refinement of the spinal muscular atrophy locus by genetic and physical mapping

    SciTech Connect

    Wang, C.H.; Kleyn, P.W.; Vitale, E.; Ross, B.M.; Xu, J.; Carter, T.A.; Brzustowicz, L.M.; Obici, S.; Lien, L.; Selig, S.

    1995-01-01

    We report the mapping and characterization of 12 microsatellite markers including 11 novel markers. All markers were generated from overlapping YAC clones that span the spinal muscular atrophy (SMA) locus. PCR amplification of 32 overlapping YAC clones show that 9 of the new markers (those set in italics) map to the interval between the two previous closest flanking markers (D5S629 and D5S557):cen - D5S6 - D5S125 - D5S435 - D5S1407 - D5S629 - D5S1410 - D5S1411/D5S1412 - D5S1413 - D5S1414 - D5Z8 - D5Z9 - CATT1 - D5Z10/D5Z6 - D5S557 - D5S1408 - D5S1409 - D5S637 - D5S351 - MAP1B - tel. Four of these new markers detect multiple loci in and out of the SMA gene region. Genetic analysis of recombinant SMA families indicates that D5S1413 is a new proximal flanking locus for the SMA gene. Interestingly, among the 40 physically mapped loci, the 14 multilocus markers map contiguously to a genomic region that overlaps, and perhaps helps define, the minimum genetic region encompassing the SMA gene(s). 24 refs., 5 figs., 1 tab.

  2. Integral field spectroscopy of planetary nebulae: mapping the line diagnostics and hydrogen-poor zones with VLT FLAMES

    NASA Astrophysics Data System (ADS)

    Tsamis, Y. G.; Walsh, J. R.; Péquignot, D.; Barlow, M. J.; Danziger, I. J.; Liu, X.-W.

    2008-05-01

    Results from the first dedicated study of Galactic planetary nebulae (PNe) by means of optical integral field spectroscopy with the Very Large Telescope Fibre Large Array Multi Element Spectrograph Argus integral field unit are presented. Three typical Galactic disc PNe have been mapped with the 11.5 × 7.2-arcsec2 Argus array: 2D spectral maps of the main shell of NGC5882 and of large areas of NGC 6153 and NGC 7009 with 297 spatial pixels per target were obtained at subarcsec resolutions. A corresponding number of 297 spectra per target were obtained in the 396.4-507.8nm range. Spatially resolved maps of emission lines and of nebular physical properties such as electron temperatures, densities and ionic abundances were produced. The abundances of helium and of doubly ionized carbon and oxygen, relative to hydrogen, were derived from optical recombination lines (ORLs), while those of O2+ were also derived from the classic collisionally excited lines (CELs). The occurrence of the abundance discrepancy problem, pertaining to oxygen, was investigated by mapping the ratio of ORL/CEL abundances for O2+ [the abundance discrepancy factor (ADF)] across the face of the PNe. The ADF varies between targets and also with position within the targets, attaining values of ~40 in the case of NGC 6153 and ~30 in the case of NGC 7009. Correlations of the ADF with geometric distance from the central star and plasma surface brightness (for NGC 6153), as well as with [OIII] electron temperature, plasma ionization state and other physical properties of the targets are established. Very small values of the temperature fluctuation parameter in the plane of the sky, t2A(O2+), are found in all cases. It is argued that these results provide further evidence for the existence in run-of-the-mill PNe of a distinct nebular component consisting of hydrogen-deficient, super-metal-rich plasma. The zones containing this posited component appear as undulations in the CII and OII ORL abundance

  3. Integration of diverse remote sensing data sets for geologic mapping and resource exploration

    NASA Technical Reports Server (NTRS)

    Kruse, Fred A.; Dietz, John B.

    1991-01-01

    The use of high-quality multispectral images in the visible, near-infrared, shortwave infrared, thermal infrared, and microwave regions of the spectrum for producing thematic maps showing details of the surface geology is reported. The airborne data sets used in the study include the Airborne Visible/Infrared Imaging Spectrometer, the Thermal Infrared Multispectral Scanner, and the airborne SAR. Ancillary data include a digital elevation model, National High Altitude Photography, Landsat Multispectral Scanner data, Landsat Thematic Mapper data, laboratory and field spectral measurements, and traditional geologic mapping. The integrated, multispectral images are shown to provide new geologic information that can be used in mineral deposit models to provide exploration targets.

  4. How integrated are neurology and palliative care services? Results of a multicentre mapping exercise.

    PubMed

    van Vliet, Liesbeth M; Gao, Wei; DiFrancesco, Daniel; Crosby, Vincent; Wilcock, Andrew; Byrne, Anthony; Al-Chalabi, Ammar; Chaudhuri, K Ray; Evans, Catherine; Silber, Eli; Young, Carolyn; Malik, Farida; Quibell, Rachel; Higginson, Irene J

    2016-05-10

    Patients affected by progressive long-term neurological conditions might benefit from specialist palliative care involvement. However, little is known on how neurology and specialist palliative care services interact. This study aimed to map the current level of connections and integration between these services. The mapping exercise was conducted in eight centres with neurology and palliative care services in the United Kingdom. The data were provided by the respective neurology and specialist palliative care teams. Questions focused on: i) catchment and population served; ii) service provision and staffing; iii) integration and relationships. Centres varied in size of catchment areas (39-5,840 square miles) and population served (142,000-3,500,000). Neurology and specialist palliative care were often not co-terminus. Service provisions for neurology and specialist palliative care were also varied. For example, neurology services varied in the number and type of provided clinics and palliative care services in the settings they work in. Integration was most developed in Motor Neuron Disease (MND), e.g., joint meetings were often held, followed by Parkinsonism (made up of Parkinson's Disease (PD), Multiple-System Atrophy (MSA) and Progressive Supranuclear Palsy (PSP), with integration being more developed for MSA and PSP) and least in Multiple Sclerosis (MS), e.g., most sites had no formal links. The number of neurology patients per annum receiving specialist palliative care reflected these differences in integration (range: 9-88 MND, 3-25 Parkinsonism, and 0-5 MS). This mapping exercise showed heterogeneity in service provision and integration between neurology and specialist palliative care services, which varied not only between sites but also between diseases. This highlights the need and opportunities for improved models of integration, which should be rigorously tested for effectiveness.

  5. Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics.

    PubMed

    Yant, Levi

    2012-02-01

    How does evolution forge adaptive responses? Are many changes required or few? Just how complex are the transcriptional networks that control development? Diverse questions like these are being newly addressed by next-generation sequencing-based techniques. Facilitating a mechanistic understanding, these approaches reveal the direct in vivo interactions between transcription factors and their physical targets, combined with genome-scale readouts to comprehensively map adaptive gene regulatory networks (GRNs). Here I focus on pioneering work from the last 3 years that has leveraged these data to investigate diverse aspects of GRN circuitry controlling the reproductive transition in plants. These approaches have revealed surprising new functions for long-investigated key players in developmental programs and laid bare the basis for pleiotropy in many others, suggesting widespread process integration at the transcriptional level. Evolutionary questions begged by the recent deluge of GRN mapping data are being assessed anew, both by emerging work outside Arabidopsis thaliana and novel analyses within. These studies have swiftly exposed the distinctive power and adaptability of genome-wide GRN mapping and illustrate that this unique data type holds tremendous promise for plant biology.

  6. Data layer integration for the national map of the united states

    USGS Publications Warehouse

    Usery, E.L.; Finn, M.P.; Starbuck, M.

    2009-01-01

    The integration of geographic data layers in multiple raster and vector formats, from many different organizations and at a variety of resolutions and scales, is a significant problem for The National Map of the United States being developed by the U.S. Geological Survey. Our research has examined data integration from a layer-based approach for five of The National Map data layers: digital orthoimages, elevation, land cover, hydrography, and transportation. An empirical approach has included visual assessment by a set of respondents with statistical analysis to establish the meaning of various types of integration. A separate theoretical approach with established hypotheses tested against actual data sets has resulted in an automated procedure for integration of specific layers and is being tested. The empirical analysis has established resolution bounds on meanings of integration with raster datasets and distance bounds for vector data. The theoretical approach has used a combination of theories on cartographic transformation and generalization, such as T??pfer's radical law, and additional research concerning optimum viewing scales for digital images to establish a set of guiding principles for integrating data of different resolutions.

  7. Putting people on the map through an approach that integrates social data in conservation planning.

    PubMed

    Stephanson, Sheri L; Mascia, Michael B

    2014-10-01

    Conservation planning is integral to strategic and effective operations of conservation organizations. Drawing upon biological sciences, conservation planning has historically made limited use of social data. We offer an approach for integrating data on social well-being into conservation planning that captures and places into context the spatial patterns and trends in human needs and capacities. This hierarchical approach provides a nested framework for characterizing and mapping data on social well-being in 5 domains: economic well-being, health, political empowerment, education, and culture. These 5 domains each have multiple attributes; each attribute may be characterized by one or more indicators. Through existing or novel data that display spatial and temporal heterogeneity in social well-being, conservation scientists, planners, and decision makers may measure, benchmark, map, and integrate these data within conservation planning processes. Selecting indicators and integrating these data into conservation planning is an iterative, participatory process tailored to the local context and planning goals. Social well-being data complement biophysical and threat-oriented social data within conservation planning processes to inform decisions regarding where and how to conserve biodiversity, provide a structure for exploring socioecological relationships, and to foster adaptive management. Building upon existing conservation planning methods and insights from multiple disciplines, this approach to putting people on the map can readily merge with current planning practices to facilitate more rigorous decision making. © 2014 Society for Conservation Biology.

  8. The case of the QRS-T angles versus QRST integral maps.

    PubMed

    van Oosterom, Adriaan

    2014-01-01

    This contribution discusses the QRS-T angle as well as the QRST integral map. Both of these topics have been tested in their application in extracting the major features of depolarization and repolarization: their spatio-temporal behaviour, and how much of their global or local nature might be deduced from signals that can be observed clinically. Recently, it is in particular the QRS-T angle that has received considerable attention, a method that stems directly from vectorcardiography, a subdomain of electrocardiography. The QRST integral map is a display of a map on the body surface of the integrals over time of the ECG signals observed at sets of electrodes. The common biophysical background of both techniques is highlighted. In particular it is explained why, in healthy myocardium, both provide a similar view on the global timing of the depolarization and repolarization of all cardiac myocytes, more specifically, on the dispersion of their action potential durations. In the presence of ischemia, the view obtained is of the integral over time of the transmembrane potentials, which comprises a 'mixture' of their timing and magnitude. The analysis of results of a simulation study emphasizes the large discrepancies that may be observed between the QRS-T angle in the frontal plane and its 3D variant. It is shown that the required vector representation of the signals may be derived from the 12-lead ECG by using the transfer matrix proposed in 1990 by Kors and colleagues.

  9. Aerotriangulation Supported by Camera Station Position Determined via Physical Integration of LIDAR and SLR Digital Camera

    NASA Astrophysics Data System (ADS)

    Mitishita, E.; Martins, M.; Centeno, J.; Hainosz, F.

    2011-09-01

    Nowadays lidar and photogrammetric surveys have been used together in many mapping procedures due to their complementary characteristics. Lidar survey is capable to promptly acquire reliable elevation information that is sometimes difficult via photogrammetric procedure. On the other hand, photogrammetric survey is easily able to get semantic information of the objects. Accessibility, availability, the increasing sensor size and quick image acquisition and processing are properties that have raised the use of SLR digital cameras in photogrammetry. Orthoimage generation is a powerful photogrammetric mapping procedure, where the advantages of the integration of lidar and image datasets are very well characterized. However, to perform this application both datasets must be within a common reference frame. In this paper, a procedure to have digital images positioned and oriented in the same lidar frame via a combination of direct and indirect georeferencing is studied. The SLR digital camera was physically connected with the lidar system to calculate the camera station's position in lidar frame. After that, the aerotriangulation supported by camera station's position is performed to get image's exterior orientation parameters (EOP).

  10. Concepts of integrated satellite surveys. [thematic mapping of land use in Ethiopia, Sudan, and Morocco

    NASA Technical Reports Server (NTRS)

    Howard, J. A.

    1974-01-01

    The United Nations initially contracted with NASA to carry out investigations in three countries; but now as the result of rapidly increasing interest, ERTS imagery has been/is being used in 7 additional projects related to agriculture, forestry, land-use, soils, landforms and hydrology. Initially the ERTS frames were simply used to provide a synoptic view of a large area of a developing country as a basis to regional surveys. From this, interest has extended to using reconstituted false color imagery and latterly, in co-operation with Purdue University, the use of computer generated false color mosaics and computer generated large scale maps. As many developing countries are inadequately mapped and frequently rely on outdated maps, the ERTS imagery is considered to provide a very wide spectrum of valuable data. Thematic maps can be readily prepared at a scale of 1:250,000 using standard NASA imagery. These provide coverage of areas not previously mapped and provide supplementary information and enable existing maps to be up-dated. There is also increasing evidence that ERTS imagery is useful for temporal studies and for providing a new dimension in integrated surveys.

  11. Benthic habitat mapping in a Portuguese Marine Protected Area using EUNIS: An integrated approach

    NASA Astrophysics Data System (ADS)

    Henriques, Victor; Guerra, Miriam Tuaty; Mendes, Beatriz; Gaudêncio, Maria José; Fonseca, Paulo

    2015-06-01

    A growing demand for seabed and habitat mapping has taken place over the past years to support the maritime integrated policies at EU and national levels aiming at the sustainable use of sea resources. This study presents the results of applying the hierarchical European Nature Information System (EUNIS) to classify and map the benthic habitats of the Luiz Saldanha Marine Park, a marine protected area (MPA), located in the mainland Portuguese southwest coast, in the Iberian Peninsula. The habitat map was modelled by applying a methodology based on EUNIS to merge biotic and abiotic key habitat drivers. The modelling in this approach focused on predicting the association of different data types: substrate, bathymetry, light intensity, waves and currents energy, sediment grain size and benthic macrofauna into a common framework. The resulting seamless medium scale habitat map discriminates twenty six distinct sublittoral habitats, including eight with no match in the current classification, which may be regarded as new potential habitat classes and therefore will be submitted to EUNIS. A discussion is provided examining the suitability of the current EUNIS scheme as a standardized approach to classify marine benthic habitats and map their spatial distribution at medium scales in the Portuguese coast. In addition the factors that most affected the results available in the predictive habitat map and the role of the environmental factors on macrofaunal assemblage composition and distribution are outlined.

  12. Promoting Virtue or Punishing Fraud: Mapping Contrasts in the Language of 'Scientific Integrity'.

    PubMed

    Horbach, S P J M; Halffman, W

    2016-12-19

    Even though integrity is widely considered to be an essential aspect of research, there is an ongoing debate on what actually constitutes research integrity. The understanding of integrity ranges from the minimal, only considering falsification, fabrication and plagiarism, to the maximum, blending into science ethics. Underneath these obvious contrasts, there are more subtle differences that are not as immediately evident. The debate about integrity is usually presented as a single, universal discussion, with shared concerns for researchers, policymakers and 'the public'. In this article, we show that it is not. There are substantial differences between the language of research integrity in the scientific arena and in the public domain. Notably, scientists and policymakers adopt different approaches to research integrity. Scientists tend to present integrity as a virtue that must be kindled, while policy documents and newspapers stress norm enforcement. Rather than performing a conceptual analysis through philosophical reasoning and discussion, we aimed to clarify the discourse of 'scientific integrity' by studying its usage in written documents. To this end, large numbers of scientific publications, policy documents and newspaper articles were analysed by means of scientometric and content analysis techniques. The texts were analysed on their usage of the term 'integrity' and of frequently co-occurring terms and concepts. A comparison was made between the usage in the various media, as well as between different periods in which they were published through co-word analysis, mapping co-occurrence networks of significant terms and themes.

  13. High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

    PubMed Central

    George, Phillip; Sharakhova, Maria V.; Sharakhov, Igor V.

    2012-01-01

    Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform3,4. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies5. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented4,6. Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations7,8. Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome

  14. The Effect of Collaborative Concept Mapping on Elementary Preservice Teachers' Anxiety, Efficacy, and Achievement in Physical Science.

    ERIC Educational Resources Information Center

    Czerniak, Charlene M.; Haney, Jodi J.

    1998-01-01

    Examines the effects of using concept-mapping activities in a physical science class for elementary science teachers on physical science achievement, self-efficacy, and anxiety toward learning and teaching physical science. Discusses implications for teacher education. Contains 54 references. (WRM)

  15. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  16. Integrated mapping analysis of the Werner syndrome region of chromosome 8.

    PubMed

    Oshima, J; Yu, C E; Boehnke, M; Weber, J L; Edelhoff, S; Wagner, M J; Wells, D E; Wood, S; Disteche, C M; Martin, G M

    1994-09-01

    The Werner syndrome locus (WRN) is located at 8p11-p12. To facilitate eventual cloning of the WRN gene, a 10,000-rad radiation-reduced hybrid (RH) cell panel was generated to map genetic markers, sequence-tagged sites (STSs), and genes in this region. A hamster cell line carrying an intact human chromosome 8 was fused with another hamster cell line. Two sets of hybrid cell panels from 2 separate fusions were generated; each panel consisted of 50 independent clones; 33 and 34 cell lines from the 2 fusions retained human chromsome material as determined by inter-Alu PCR. The combined panel was genotyped for 52 markers spanning the entire chromosome, including 10 genes, 29 anonymous polymorphic loci, and 13 STSs. Seventeen of these markers have not been previously described. Markers near the centromere were retained at a higher frequency than more distal markers. Fluorescence in situ hybridization was also used to localize and order a subset of the markers. A RH map of the WRN region was constructed using a maximum likelihood method, giving the following most likely order: D8S131-D8S339 (GSR)-D8S124-D8S278-D8S259-(D8S71)-D8S283- D8S87-D8S105-D8S135 (FGFR1)-D8S135PB-D8S255-ANK1. A genetic map of 15 short tandem repeat polymorphic loci in the WRN region was also constructed. The marker orders from the genetic and RH maps were consistent. In addition, an integrated map of 24 loci in the WRN region was generated using information from both genetic and RH mapping methods. A 1000:1 framework map for 6 loci (LPL-D8S136-D8S137-D8S87-FGFR1-ANK1) was determined by genetic mapping, and the resulting locus order was fixed during analysis of the RH genotype data. The resulting integrated map contained more markers than could confidently be ordered by either genetic or RH mapping alone.

  17. 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

  18. Physical mapping of chromosome 4J of Thinopyrum bessarabicum using gamma radiation-induced aberrations.

    PubMed

    Pu, Jing; Wang, Qing; Shen, Yuefeng; Zhuang, Lifang; Li, Chenxu; Tan, Mengfa; Bie, Tongde; Chu, Chenggen; Qi, Zengjun

    2015-07-01

    Gamma radiation induced a series of structural aberrations involving Thinopyrum bessarabicum chromosome 4J. The aberrations allowed for deletion mapping of 101 4J-specific markers and fine mapping of blue-grained gene BaThb. Irradiation can induce translocations and deletions to assist physically locating genes and markers on chromosomes. In this study, a 12-Gy dosage of (60)Co-γ was applied to pollen and eggs of a wheat (Triticum aestivum) landrace Chinese Spring (CS)-Thinopyrum bessarabicum chromosome 4J disomic addition line (DA4J), and the gametes from irradiated plants were fertilized with normal CS eggs or pollen to produce M1 seeds. Based on genomic in situ hybridization analysis of 261 M1 plants, we identified 74 lines carrying structural aberrations involving chromosome 4J with the higher aberration rate in treated pollen (31.2 %) than in the treated eggs (21.3 %). We further identified 43 (53.8 %) lines with structural aberrations on chromosome 4J by analyzing another 80 M1 plants with 74 4J-specific markers, indicating that combining molecular and cytological methods was more efficient for detecting chromosome aberrations. Marker analysis thus was performed prior to cytogenetic identification on M2-M4 seeds to detect chromosome structural aberrations. Sixty-eight M3 lines with structural aberrations on chromosome 4J and six previously obtained chromosome 4J alien lines were then analyzed using 101 chromosome 4J-specific markers. After combining marker results with chromosome aberrations in each line, chromosome 4J was physically divided into 24 segmental blocks with 7 in the short arm and 17 in the long arm. The blue-grained gene BaThb was further mapped into the region corresponding to block 4JL-11. The chromosome aberrations and the physical map developed in this research provide useful stocks and tools for introgression of genes on chromosome 4J into wheat.

  19. Magnetic Field Mapping and Integral Transfer Function Matching of the Prototype Dipoles for the NSLS-II at BNL

    SciTech Connect

    He, P.; Jain, A., Gupta, R., Skaritka, J., Spataro, C., Joshi, P., Ganetis, G., Anerella, M., Wanderer, P.

    2011-03-28

    The National Synchrotron Light Source-II (NSLS-II) storage ring at Brookhaven National Laboratory (BNL) will be equipped with 54 dipole magnets having a gap of 35 mm, and 6 dipoles having a gap of 90 mm. Each dipole has a field of 0.4 T and provides 6 degrees of bending for a 3 GeV electron beam. The large aperture magnets are necessary to allow the extraction of long-wavelength light from the dipole magnet to serve a growing number of users of low energy radiation. The dipoles must not only have good field homogeneity (0.015% over a 40 mm x 20 mm region), but the integral transfer functions and integral end harmonics of the two types of magnets must also be matched. The 35 mm aperture dipole has a novel design where the yoke ends are extended up to the outside dimension of the coil using magnetic steel nose pieces. This design increases the effective length of the dipole without increasing the physical length. These nose pieces can be tailored to adjust the integral transfer function as well as the homogeneity of the integrated field. One prototype of each dipole type has been fabricated to validate the designs and to study matching of the two dipoles. A Hall probe mapping system has been built with three Group 3 Hall probes mounted on a 2-D translation stage. The probes are arranged with one probe in the midplane of the magnet and the others vertically offset by {+-}10 mm. The field is mapped around a nominal 25 m radius beam trajectory. The results of measurements in the as-received magnets, and with modifications made to the nose pieces are presented.

  20. Mapping virtual addresses to different physical addresses for value disambiguation for thread memory access requests

    DOEpatents

    Gala, Alan; Ohmacht, Martin

    2014-09-02

    A multiprocessor system includes nodes. Each node includes a data path that includes a core, a TLB, and a first level cache implementing disambiguation. The system also includes at least one second level cache and a main memory. For thread memory access requests, the core uses an address associated with an instruction format of the core. The first level cache uses an address format related to the size of the main memory plus an offset corresponding to hardware thread meta data. The second level cache uses a physical main memory address plus software thread meta data to store the memory access request. The second level cache accesses the main memory using the physical address with neither the offset nor the thread meta data after resolving speculation. In short, this system includes mapping of a virtual address to a different physical addresses for value disambiguation for different threads.

  1. Implementation and Outcomes of a Responsibility-Based Physical Activity Program Integrated Into an Intact High School Physical Education Class

    ERIC Educational Resources Information Center

    Wright, Paul M.; Burton, Suzanne

    2008-01-01

    Underserved youth are at risk for numerous threats to their physical and psychological well-being. To navigate the challenges they face, they need a variety of positive life skills. This study systematically explored the implementation and short-term outcomes of a responsibility-based physical activity program that was integrated into an intact…

  2. Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids)

    PubMed Central

    2010-01-01

    Background Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed. Results An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed. Conclusions This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the

  3. Physical and genetic mapping of the muscle phosphofructokinase gene (PFKM): Reassignment to human chromosome 12q

    SciTech Connect

    Howard, T.D.; Akots, G.; Bowden, D.W.

    1996-05-15

    Phosphofructokinase (PFK) is a key rate-limiting enzyme in glycolysis and represents a major control point in the metabolism of glucose. There are at least three known isoforms of PFK in humans, referred to as the muscle, platelet, and liver forms, each of which is differentially expressed in various tissues. The gene for muscle phosphofructokinase, PFKM, is mutated in Tarui disease and conceivably contributes to non-insulin-dependent diabetes mellitus (NIDDM). Based on physical and genetic mapping, we have found that the gene for PFKM does not map to chromosome 1 as previously described, but instead maps to chromosome 12. PCR analysis with a somatic cell hybrid mapping panel using primers derived from intron 6 and exon 18 of the PFKM gene showed consistent amplification of cell lines containing chromosome 12 (concordance, 100%). Fluorescence in situ hybridization analysis with CEPH YAC 762G4, isolated with exon 18 primers, indicated that this clone maps to 12q13, centromeric to the diacylglycerol kinase gene (DAGK) at 12q13.3. A highly informative genetic marker isolated from YAC 762G4 was used to map PFKM genetically between the CHLC framework markers D12S1090 and D12S390. This placement for 762G4 was significantly proximal to the recently reported locus for a third gene for maturity onset diabetes of the young (MODY). The PFKM-associated microsatellite will be a valuable tool in the evaluation of PFKM in diabetic populations as well as in linkage analysis in families with Tarui disease. 23 refs., 3 figs., 2 tabs.

  4. Physical Confirmation and Mapping of Overlapping Rat Mammary Carcinoma Susceptibility QTLs, Mcs2 and Mcs6

    PubMed Central

    Sanders, Jennifer; Haag, Jill D.; Samuelson, David J.

    2011-01-01

    Only a portion of the estimated heritability of breast cancer susceptibility has been explained by individual loci. Comparative genetic approaches that first use an experimental organism to map susceptibility QTLs are unbiased methods to identify human orthologs to target in human population-based genetic association studies. Here, overlapping rat mammary carcinoma susceptibility (Mcs) predicted QTLs, Mcs6 and Mcs2, were physically confirmed and mapped to identify the human orthologous region. To physically confirm Mcs6 and Mcs2, congenic lines were established using the Wistar-Furth (WF) rat strain, which is susceptible to developing mammary carcinomas, as the recipient (genetic background) and either Wistar-Kyoto (WKy, Mcs6) or Copenhagen (COP, Mcs2), which are resistant, as donor strains. By comparing Mcs phenotypes of WF.WKy congenic lines with distinct segments of WKy chromosome 7 we physically confirmed and mapped Mcs6 to ∼33 Mb between markers D7Rat171 and gUwm64-3. The predicted Mcs2 QTL was also physically confirmed using segments of COP chromosome 7 introgressed into a susceptible WF background. The Mcs6 and Mcs2 overlapping genomic regions contain multiple annotated genes, but none have a clear or well established link to breast cancer susceptibility. Igf1 and Socs2 are two of multiple potential candidate genes in Mcs6. The human genomic region orthologous to rat Mcs6 is on chromosome 12 from base positions 71,270,266 to 105,502,699. This region has not shown a genome-wide significant association to breast cancer risk in pun studies of breast cancer susceptibility. PMID:21625632

  5. Physical localization and genetic mapping of the fertility restoration gene Rfo in canola (Brassica napus L.).

    PubMed

    Feng, Jiuhuan; Primomo, Valerio; Li, Zenglu; Zhang, Yongping; Jan, Chao-Chien; Tulsieram, Lomas; Xu, Steven S

    2009-04-01

    The Ogu cytoplasm for male sterility and its fertility restorer gene Rfo in canola (Brassica napus L.) were originally introgressed from radish (Raphanus sativus L.) and have been widely used for canola hybrid production and breeding. The objective of this study was to determine the physical location of the Rfo locus in the canola genome using fluorescence in situ hybridization and genetic mapping. For physical localization of the Rfo gene, two bacterial artificial chromosome (BAC) clones, G62 and B420, which were closely linked to the Rfo gene, were used as probes to hybridize with the somatic metaphase chromosomes of a canola hybrid variety, PHI-46 (46H02), containing the Rfo fragment. The results showed that both clones were physically located at the end of one large metacentric chromosome. By simultaneous use of two BAC clones and 45S rDNA repeated sequences as the probes, we demonstrated that the large metacentric chromosome probed with the two BAC clones did not carry 45S rDNA repeated sequences. The chromosome was 3.65 +/- 0.74 microm in average length (20 cells) and ranked second in size among the chromosomes without 45S rDNAs. The centromere index of the chromosome (20 cells) was calculated as 43.74 +/- 4.19. A comparison with previously reported putative karyotypes of B. napus (AACC) and its diploid ancestors Brassica rapa L. (AA) and Brassica oleracea L. (CC) suggests that the chromosome carrying the Rfo fragment might belong to one of three large metacentric chromosomes of the C genome. Genetic mapping has confirmed the localization of the Rfo fragment to the distal region of linkage group N19, which corresponds to the C genome in B. napus. This study has provided the evidence of the location of the Rfo gene on canola chromosomes and established a basic framework for further physical mapping and manipulation of the gene.

  6. Adding maps (GPS) to accelerometry data to improve study participants' recall of physical activity: a methodological advance in physical activity research.

    PubMed

    Brown, Barbara B; Wilson, Laura; Tribby, Calvin P; Werner, Carol M; Wolf, Jean; Miller, Harvey J; Smith, Ken R

    2014-07-01

    Obtaining the 'when, where and why' of healthy bouts of moderate-to-vigorous physical activity (MVPA) provides insights into natural PA. In Salt Lake City, Utah, adults wore accelerometer and Global Positioning System (GPS) loggers for a week in a cross-sectional study to establish baseline travel and activity patterns near a planned Complete Street intervention involving a new rail line, new sidewalks and a bike path. At the end of the week, research assistants met with the 918 participants who had at least three 10 h days of good accelerometer readings. Accelerometer and GPS data were uploaded and integrated within a custom application, and participants were provided with maps and time information for past MVPA bouts of ≥3 min to help them recall bout details. Participants said that 'getting someplace' was, on average, a more important motivation for their bouts than leisure or exercise. A series of recall tests showed that participants recalled most bouts they were asked about, regardless of the duration of the bout, suggesting that participant perceptions of their shorter lifestyle bouts can be studied with this methodology. Visual prompting with a map depicting where each bout took place yielded more accurate recall than prompting with time cues alone. These techniques provide a novel way to understand participant memories of the context and subjective assessments associated with healthy bouts of PA. Prompts with time-stamped maps that illustrate places of MVPA offer an effective method to improve understanding of activity and its supportive sociophysical contexts. 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.

  7. Multi-Sensor Integration to Map Odor Distribution for the Detection of Chemical Sources

    PubMed Central

    Gao, Xiang; Acar, Levent

    2016-01-01

    This paper addresses the problem of mapping odor distribution derived from a chemical source using multi-sensor integration and reasoning system design. Odor localization is the problem of finding the source of an odor or other volatile chemical. Most localization methods require a mobile vehicle to follow an odor plume along its entire path, which is time consuming and may be especially difficult in a cluttered environment. To solve both of the above challenges, this paper proposes a novel algorithm that combines data from odor and anemometer sensors, and combine sensors’ data at different positions. Initially, a multi-sensor integration method, together with the path of airflow was used to map the pattern of odor particle movement. Then, more sensors are introduced at specific regions to determine the probable location of the odor source. Finally, the results of odor source location simulation and a real experiment are presented. PMID:27384568

  8. Multi-Sensor Integration to Map Odor Distribution for the Detection of Chemical Sources.

    PubMed

    Gao, Xiang; Acar, Levent

    2016-07-04

    This paper addresses the problem of mapping odor distribution derived from a chemical source using multi-sensor integration and reasoning system design. Odor localization is the problem of finding the source of an odor or other volatile chemical. Most localization methods require a mobile vehicle to follow an odor plume along its entire path, which is time consuming and may be especially difficult in a cluttered environment. To solve both of the above challenges, this paper proposes a novel algorithm that combines data from odor and anemometer sensors, and combine sensors' data at different positions. Initially, a multi-sensor integration method, together with the path of airflow was used to map the pattern of odor particle movement. Then, more sensors are introduced at specific regions to determine the probable location of the odor source. Finally, the results of odor source location simulation and a real experiment are presented.

  9. Feasibility of a GNSS-Probe for Creating Digital Maps of High Accuracy and Integrity

    NASA Astrophysics Data System (ADS)

    Vartziotis, Dimitris; Poulis, Alkis; Minogiannis, Alexandros; Siozos, Panayiotis; Goudas, Iraklis; Samson, Jaron; Tossaint, Michel

    The “ROADSCANNER” project addresses the need for increased accuracy and integrity Digital Maps (DM) utilizing the latest developments in GNSS, in order to provide the required datasets for novel applications, such as navigation based Safety Applications, Advanced Driver Assistance Systems (ADAS) and Digital Automotive Simulations. The activity covered in the current paper is the feasibility study, preliminary tests, initial product design and development plan for an EGNOS enabled vehicle probe. The vehicle probe will be used for generating high accuracy, high integrity and ADAS compatible digital maps of roads, employing a multiple passes methodology supported by sophisticated refinement algorithms. Furthermore, the vehicle probe will be equipped with pavement scanning and other data fusion equipment, in order to produce 3D road surface models compatible with standards of road-tire simulation applications. The project was assigned to NIKI Ltd under the 1st Call for Ideas in the frame of the ESA - Greece Task Force.

  10. [Application of biotope mapping model integrated with vegetation cover continuity attributes in urban biodiversity conservation].

    PubMed

    Gao, Tian; Qiu, Ling; Chen, Cun-gen

    2010-09-01

    Based on the biotope classification system with vegetation structure as the framework, a modified biotope mapping model integrated with vegetation cover continuity attributes was developed, and applied to the study of the greenbelts in Helsingborg in southern Sweden. An evaluation of the vegetation cover continuity in the greenbelts was carried out by the comparisons of the vascular plant species richness in long- and short-continuity forests, based on the identification of woodland continuity by using ancient woodland indicator species (AWIS). In the test greenbelts, long-continuity woodlands had more AWIS. Among the forests where the dominant trees were more than 30-year-old, the long-continuity ones had a higher biodiversity of vascular plants, compared with the short-continuity ones with the similar vegetation structure. The modified biotope mapping model integrated with the continuity features of vegetation cover could be an important tool in investigating urban biodiversity, and provide corresponding strategies for future urban biodiversity conservation.

  11. Clay content mapping through integration of geophysical proximal and remote sensing data

    NASA Astrophysics Data System (ADS)

    Garfagnoli, Francesca; André, Frédéric; Grandjean, Gilles; Lambot, Sébastien; Ciampalini, Andrea; Moretti, Sandro

    2013-04-01

    Soil sustainable exploitation planning and land resource evaluation require up-to-date and accurate maps of soil properties. In that respect, geophysical techniques present particular interests given their non-invasiveness and their fast data acquisition capacity, which permit to characterize large areas with fine spatial and/or temporal resolutions. We investigated the relevancy of combining data from airborne hyperspectral (Hs), electromagnetic induction (EMI) and far-field ground-penetrating radar (GPR) for mapping soil properties, in particular soil clay content, at the field scale. Data from the three techniques were acquired at a test site in Mugello (Italy) characterized by relatively strong spatial variations of soil texture. Soil samples were collected for determining actual clay contents. For the frequencies used in this study (200-2000 MHz), the GPR surface reflection is mainly determined by soil dielectric permittivity, itself primarily influenced by soil moisture. In contrast, EMI is mostly sensitive to soil electrical conductivity, which integrates several soil properties including in particular soil moisture and clay content. Taking advantage of the complementary information provided by the two instruments, the GPR and EMI data were combined and correlated to local ground-truth measurements of clay content to provide high-resolution clay content maps over the entire field area. Besides, a relationship was also observed between Hs data and clay content measurements, which permitted to produce a Hs-derived clay content map. EMI-GPR and Hs maps showed close spatial patterns and a relatively high correlation was observed between both clay content estimates, as well as between clay content estimates and ground-truth clay content measurements. Future analyses will entail more advanced Bayesian data fusion techniques for combining EMI-GPR and Hs information. These results demonstrated great promise for integrated, digital soil mapping applications.

  12. Ensemble Integration of Forest Disturbance Maps for the Landscape Change Monitoring System (LCMS)

    NASA Astrophysics Data System (ADS)

    Cohen, W. B.; Healey, S. P.; Yang, Z.; Zhu, Z.; Woodcock, C. E.; Kennedy, R. E.; Huang, C.; Steinwand, D.; Vogelmann, J. E.; Stehman, S. V.; Loveland, T. R.

    2014-12-01

    The recent convergence of free, high quality Landsat data and acceleration in the development of dense Landsat time series algorithms has spawned a nascent interagency effort known as the Landscape Change Monitoring System (LCMS). LCMS is being designed to map historic land cover changes associated with all major disturbance agents and land cover types in the US. Currently, five existing algorithms are being evaluated for inclusion in LCMS. The priorities of these five algorithms overlap to some degree, but each has its own strengths. This has led to the adoption of a novel approach, within LCMS, to integrate the map outputs (i.e., base learners) from these change detection algorithms using empirical ensemble models. Training data are derived from independent datasets representing disturbances such as: harvest, fire, insects, wind, and land use change. Ensemble modeling is expected to produce significant increases in predictive accuracy relative to the results of the individual base learners. The non-parametric models used in LCMS also provide a framework for matching output ensemble maps to independent sample-based statistical estimates of disturbance area. Multiple decision trees "vote" on class assignment, and it is possible to manipulate vote thresholds to ensure that ensemble maps reflect areas of disturbance derived from sources such as national-scale ground or image-based inventories. This talk will focus on results of the first ensemble integration of the base learners for six Landsat scenes distributed across the US. We will present an assessment of base learner performance across different types of disturbance against an independently derived, sample-based disturbance dataset (derived from the TimeSync Landsat time series visualization tool). The goal is to understand the contributions of each base learner to the quality of the ensemble map products. We will also demonstrate how the ensemble map products can be manipulated to match sample-based annual

  13. Mapping of submerged aquatic vegetation with a physically based process chain

    NASA Astrophysics Data System (ADS)

    Heege, Thomas; Bogner, Anke; Pinnel, Nicole

    2004-02-01

    Mapping the submerse vegetation is of prime importance for the ecological evaluation of an entire lake. Remote sensing techniques are efficient for such mapping tasks, if the retrieval algorithms and processing methods are robust and mostly independent from additional ground truth measurements. The Modular Inversion Program (MIP) follows this concept. It is a processing tool designed for the recovery of hydro-biological parameters from multi- and hyper-spectral remote sensing data. The architecture of the program consists of physical inversion schemes that derive bio-physical parameters from the measured radiance signal at the sensor. Program modules exist for the retrieval of aerosols, sun glitter correction, atmospheric corrections, retrieval of water constituents among others. For the purpose of mapping the bottom coverage in optically shallow waters, two modules have been added to MIP. The first module calculates the bottom reflectance using the subsurface reflectance, the depth and an approximation of the water constituent concentrations as input. The second module fractionalizes the bottom reflectance to three endmembers of specific reflectance spectra by linear unmixing. The three endmembers are specific reflectance spectra of bottom sediments, small growing macrophytes (Characeae) and tall macrophytes such as Potamogeton perfoliatus & P. pectinatus. The processing system has been tested with data collected from the multi-spectral airborne scanner Daedalus AADS1268 at Lake Constance, Germany, for multi- temporal analysis.

  14. Somatic cell hybrid and long-range physical mapping of 11p13 microdissected genomic clones.

    PubMed Central

    Davis, L M; Senger, G; Lüdecke, H J; Claussen, U; Horsthemke, B; Zhang, S S; Metzroth, B; Hohenfellner, K; Zabel, B; Shows, T B

    1990-01-01

    Microdissection and microcloning of banded human metaphase chromosomes have been used to construct a genomic library of 20,000 clones that is highly enriched for chromosome 11p13 DNA sequences. Clones from this library have been mapped on a panel of human-rodent somatic cell hybrids that divides the region from distal p12 to proximal p14 into seven physical intervals, A total of 1500 clones has been isolated, 250 clones have been characterized, and 58 clones have been mapped. Six of the clones were used to complete a long-range physical map of 7.5 megabases through the region. Two of the clones are localized to the Wilms tumor (WT) region, three are localized to the aniridia (AN2) region, and two are localized to the region between WT and AN2. The library represents DNA sequences spanning a distance of approximately 13 x 10(6) base pairs, with an average density of one clone per 37,000 base pairs. Images PMID:2169618

  15. Integration of imagery and cartographic data through a common map base

    NASA Technical Reports Server (NTRS)

    Clark, J.

    1983-01-01

    Several disparate data types are integrated by using control points as the basis for spatially registering the data to a map base. The data are reprojected to match the coordinates of the reference UTM (Universal Transverse Mercator) map projection, as expressed in lines and samples. Control point selection is the most critical aspect of integrating the Thematic Mapper Simulator MSS imagery with the cartographic data. It is noted that control points chosen from the imagery are subject to error from mislocated points, either points that did not correlate well to the reference map or minor pixel offsets because of interactive cursorring errors. Errors are also introduced in map control points when points are improperly located and digitized, leading to inaccurate latitude and longitude coordinates. Nonsystematic aircraft platform variations, such as yawl, pitch, and roll, affect the spatial fidelity of the imagery in comparison with the quadrangles. Features in adjacent flight paths do not always correspond properly owing to the systematic panorama effect and alteration of flightline direction, as well as platform variations.

  16. A Map/INS/Wi-Fi Integrated System for Indoor Location-Based Service Applications.

    PubMed

    Yu, Chunyang; Lan, Haiyu; Gu, Fuqiang; Yu, Fei; El-Sheimy, Naser

    2017-06-02

    In this research, a new Map/INS/Wi-Fi integrated system for indoor location-based service (LBS) applications based on a cascaded Particle/Kalman filter framework structure is proposed. Two-dimension indoor map information, together with measurements from an inertial measurement unit (IMU) and Received Signal Strength Indicator (RSSI) value, are integrated for estimating positioning information. The main challenge of this research is how to make effective use of various measurements that complement each other in order to obtain an accurate, continuous, and low-cost position solution without increasing the computational burden of the system. Therefore, to eliminate the cumulative drift caused by low-cost IMU sensor errors, the ubiquitous Wi-Fi signal and non-holonomic constraints are rationally used to correct the IMU-derived navigation solution through the extended Kalman Filter (EKF). Moreover, the map-aiding method and map-matching method are innovatively combined to constrain the primary Wi-Fi/IMU-derived position through an Auxiliary Value Particle Filter (AVPF). Different sources of information are incorporated through a cascaded structure EKF/AVPF filter algorithm. Indoor tests show that the proposed method can effectively reduce the accumulation of positioning errors of a stand-alone Inertial Navigation System (INS), and provide a stable, continuous and reliable indoor location service.

  17. A Map/INS/Wi-Fi Integrated System for Indoor Location-Based Service Applications

    PubMed Central

    Yu, Chunyang; Lan, Haiyu; Gu, Fuqiang; Yu, Fei; El-Sheimy, Naser

    2017-01-01

    In this research, a new Map/INS/Wi-Fi integrated system for indoor location-based service (LBS) applications based on a cascaded Particle/Kalman filter framework structure is proposed. Two-dimension indoor map information, together with measurements from an inertial measurement unit (IMU) and Received Signal Strength Indicator (RSSI) value, are integrated for estimating positioning information. The main challenge of this research is how to make effective use of various measurements that complement each other in order to obtain an accurate, continuous, and low-cost position solution without increasing the computational burden of the system. Therefore, to eliminate the cumulative drift caused by low-cost IMU sensor errors, the ubiquitous Wi-Fi signal and non-holonomic constraints are rationally used to correct the IMU-derived navigation solution through the extended Kalman Filter (EKF). Moreover, the map-aiding method and map-matching method are innovatively combined to constrain the primary Wi-Fi/IMU-derived position through an Auxiliary Value Particle Filter (AVPF). Different sources of information are incorporated through a cascaded structure EKF/AVPF filter algorithm. Indoor tests show that the proposed method can effectively reduce the accumulation of positioning errors of a stand-alone Inertial Navigation System (INS), and provide a stable, continuous and reliable indoor location service. PMID:28574471

  18. Correlation of physical and genetic maps of human chromosome 16. Annual progress report, October 1, 1990--July 31, 1991

    SciTech Connect

    Sutherland, G.R.

    1991-12-31

    This project aimed to divide chromosome 16 into approximately 50 intervals of {approximately}2Mb in size by constructing a series of mouse/human somatic cell hybrids each containing a rearranged chromosome 16. Using these hybrids, DNA probes would be regionally mapped by Southern blot or PCR analysis. Preference would be given to mapping probes which demonstrated polymorphisms for which the CEPH panel of families had been typed. This would allow a correlation of the physical and linkage maps of this chromosome. The aims have been substantially achieved. 49 somatic cell hybrids have been constructed which have allowed definition of 46, and potentially 57, different physical intervals on the chromosome. 164 loci have been fully mapped into these intervals. A correlation of the physical and genetic maps of the chromosome is in an advanced stage of preparation. The somatic cell hybrids constructed have been widely distributed to groups working on chromosome 16 and other genome projects.

  19. Integrated Gravity Mapping System (IGMS) Study Program for Aircraft and Land Vehicles. Volume 1.

    DTIC Science & Technology

    1982-03-01

    Office (SP24) for the US Navy, under the management of Sperry Systems Management. 1.3 Scope 1.3.1 General The Integrated Gravity Mapping System (IGMS...program plan outlined on Figure 2-1 incorporates the experiences gained on the GSS ADM system for Sperry /SSPC/USN, which was delivered and installed...5 5 * . .SS * use of a smaller militarized computer. Improvement observed as a result of efforts conducted under the Sperry /SSPO program will be

  20. A natural user interface to integrate citizen science and physical exercise

    PubMed Central

    Palermo, Eduardo; Laut, Jeffrey; Nov, Oded; Porfiri, Maurizio

    2017-01-01

    Citizen science enables volunteers to contribute to scientific projects, where massive data collection and analysis are often required. Volunteers participate in citizen science activities online from their homes or in the field and are motivated by both intrinsic and extrinsic factors. Here, we investigated the possibility of integrating citizen science tasks within physical exercises envisaged as part of a potential rehabilitation therapy session. The citizen science activity entailed environmental mapping of a polluted body of water using a miniature instrumented boat, which was remotely controlled by the participants through their physical gesture tracked by a low-cost markerless motion capture system. Our findings demonstrate that the natural user interface offers an engaging and effective means for performing environmental monitoring tasks. At the same time, the citizen science activity increases the commitment of the participants, leading to a better motion performance, quantified through an array of objective indices. The study constitutes a first and necessary step toward rehabilitative treatments of the upper limb through citizen science and low-cost markerless optical systems. PMID:28231261

  1. A natural user interface to integrate citizen science and physical exercise.

    PubMed

    Palermo, Eduardo; Laut, Jeffrey; Nov, Oded; Cappa, Paolo; Porfiri, Maurizio

    2017-01-01

    Citizen science enables volunteers to contribute to scientific projects, where massive data collection and analysis are often required. Volunteers participate in citizen science activities online from their homes or in the field and are motivated by both intrinsic and extrinsic factors. Here, we investigated the possibility of integrating citizen science tasks within physical exercises envisaged as part of a potential rehabilitation therapy session. The citizen science activity entailed environmental mapping of a polluted body of water using a miniature instrumented boat, which was remotely controlled by the participants through their physical gesture tracked by a low-cost markerless motion capture system. Our findings demonstrate that the natural user interface offers an engaging and effective means for performing environmental monitoring tasks. At the same time, the citizen science activity increases the commitment of the participants, leading to a better motion performance, quantified through an array of objective indices. The study constitutes a first and necessary step toward rehabilitative treatments of the upper limb through citizen science and low-cost markerless optical systems.

  2. Intraoperative Monitoring and Mapping of the Functional Integrity of the Brainstem

    PubMed Central

    Fernández-Conejero, Isabel

    2016-01-01

    The risk of iatrogenic damage is very high in surgical interventions in or around the brainstem. However, surgical techniques and intraoperative neuromonitoring (ION) have evolved sufficiently to increase the likelihood of successful functional outcomes in many patients. We present a critical review of the methodologies available for intraoperative monitoring and mapping of the brainstem. There are three main groups of techniques that can be used to assess the functional integrity of the brainstem: 1) mapping, which provides rapid anatomical identification of neural structures using electrical stimulation with a hand-held probe, 2) monitoring, which provides real-time information about the functional integrity of the nervous tissue, and 3) techniques involving the examination of brainstem reflexes in the operating room, which allows for the evaluation of the reflex responses that are known to be crucial for most brainstem functions. These include the blink reflex, which is already in use, and other brainstem reflexes that are being explored, such as the masseter H-reflex. This is still under development but is likely to have important functional consequences. Today an abundant armory of ION methods is available for the monitoring and mapping of the functional integrity of the brainstem during surgery. ION methods are essential in surgery either in or around the brainstem; they facilitate the removal of lesions and contribute to notable improvements in the functional outcomes of patients. PMID:27449909

  3. Integrating conventional classifiers with a GIS expert system to increase the accuracy of invasive species mapping

    NASA Astrophysics Data System (ADS)

    Masocha, Mhosisi; Skidmore, Andrew K.

    2011-06-01

    Mapping the cover of invasive species using remotely sensed data alone is challenging, because many invaders occur as mid-level canopy species or as subtle understorey species and therefore contribute little to the spectral signatures captured by passive remote sensing devices. In this study, two common non-parametric classifiers namely, the neural network and support vector machine were used to map four cover classes of the invasive shrub Lantana camara in a protected game reserve and the adjacent area under communal land management in Zimbabwe. These classifiers were each combined with a geographic information system (GIS) expert system, in order to test whether the new hybrid classifiers yielded significantly more accurate invasive species cover maps than the single classifiers. The neural network, when used on its own, mapped the cover of L. camara with an overall accuracy of 71% and a Kappa index of agreement of 0.61. When the neural network was combined with an expert system, the overall accuracy and Kappa index of agreement significantly increased to 83% and 0.77, respectively. Similarly, the support vector machine achieved an overall accuracy of 64% with a Kappa index of agreement of 0.52, whereas the hybrid support vector machine and expert system classifier achieved a significantly higher overall accuracy of 76% and a Kappa index of agreement of 0.67. These results suggest that integrating conventional image classifiers with an expert system increases the accuracy of invasive species mapping.

  4. GIS integration of the 1:2880 Stabile cadastre map sheets from Bukovina

    NASA Astrophysics Data System (ADS)

    Crǎciunescu, Vasile; Niè›U, Constantin; Timár, Gábor; Boicu, Alin; Rus, Ioan

    2010-05-01

    Starting with 1975, the North-West part of the Moldavia Principality was occupied by the Habsburg Monarchy and become known as Duchy of Bukovina. During the 143 years of Austrian rule (1775 - 1918), this territory was the subject of several topographic and cadastral surveys. The paper will focus on the cadastral maps produced under the Stabile cadaster (also known as Franciscan cadastre). In the Habsburg Empire, this cadastral survey was started in 1817, at an order of the Emperor Francis I of Austria, as a base for his land taxation reform. In Bukovina, the land registration system was introduced in 1832. The base maps, known as Katastralmappe or Parzellenplan, were drawn under the 1:2880 scale, using Viennese Klafter (fathom) as length unit (1 Viennese Klafter = 1.89648 meters). Each taxation parish (usually centered on the most important cities/villages) was surveyed and mapped individually. The map sheets were accompanied by several registers (e.g. register of building plots, register of land plots) with informations regarding the cadastral parcels. Today, such documents represent a valuable resource in reconstructing the natural and built environment. The study presents the way this maps can be georeferenced and integrated into modern GIS applications, for precise digitization, spatial analysis and 3D reconstruction. The base of the georeference is the knowledge of the projection and datum parameters of the survey in Bukovina as well as the sheet labeling system.

  5. A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map.

    PubMed

    Solignac, Michel; Mougel, Florence; Vautrin, Dominique; Monnerot, Monique; Cornuet, Jean-Marie

    2007-01-01

    The honey bee is a key model for social behavior and this feature led to the selection of the species for genome sequencing. A genetic map is a necessary companion to the sequence. In addition, because there was originally no physical map for the honey bee genome project, a meiotic map was the only resource for organizing the sequence assembly on the chromosomes. We present the genetic (meiotic) map here and describe the main features that emerged from comparison with the sequence-based physical map. The genetic map of the honey bee is saturated and the chromosomes are oriented from the centromeric to the telomeric regions. The map is based on 2,008 markers and is about 40 Morgans (M) long, resulting in a marker density of one every 2.05 centiMorgans (cM). For the 186 megabases (Mb) of the genome mapped and assembled, this corresponds to a very high average recombination rate of 22.04 cM/Mb. Honey bee meiosis shows a relatively homogeneous recombination rate along and across chromosomes, as well as within and between individuals. Interference is higher than inferred from the Kosambi function of distance. In addition, numerous recombination hotspots are dispersed over the genome. The very large genetic length of the honey bee genome, its small physical size and an almost complete genome sequence with a relatively low number of genes suggest a very promising future for association mapping in the honey bee, particularly as the existence of haploid males allows easy bulk segregant analysis.

  6. A standard cytogenetic photomap for the mosquito Anopheles stephensi (Diptera: Culicidae): application for physical mapping.

    PubMed

    Sharakhova, Maria V; Xia, Ai; McAlister, Sarah I; Sharakhov, Igor V

    2006-09-01

    To facilitate physical genome mapping, we have developed a new cytogenetic photomap for Anopheles stephensi (Liston) (Diptera: Culicidae), an important malaria vector in Asia. The high-resolution images of the ovarian polytene chromosomes have been straightened and divided by numbered divisions and lettered subdivisions. The exact chromosomal locations of eight DNA probes have been determined by fluorescent in situ hybridization. Using the DNA sequences, we have established correspondence between chromosomal arms among An. stephensi, Anopheles gambiae (Patton), and Anopheles funestus (Giles). The results support previous cytogenetic observations of arm translocations taking place during diversification of the species. To make the cytogenetic map useful for population genetics studies, we have indicated the chromosomal positions for the breakpoints of 19 polymorphic inversions.

  7. Interfacing 1990 US Census TIGER map files with New S graphics software. [Topologically Integrated Geographic Encoding and Referencing (TIGER)

    SciTech Connect

    Rizzardi, M.; Mohr, M.S.; Merrill, D.W.; Selvin, S. California Univ., Berkeley, CA . School of Public Health)

    1992-07-01

    In 1990, the United States Bureau of the Census released detailed geographic base files known as TIGER/Line (Topologically Integrated Geographic Encoding and Referencing) which contain detail on the physical features and census tract boundaries of every county in the United States. The TIGER database is attractive for two reasons. First, it is publicly available through the Bureau of the Census on tape or cd-rom for a minimal fee. Second, it contains 24 billion characters of data which describe geographic features of interest to the Census Bureau such as coastlines, hydrography, transportation networks, political boundaries, etc. Unfortunately, the large TIGER database only provides raw alphanumeric data; no utility software, graphical or otherwise, is included. On the other hand New S, a popular statistical software package by AT T, has easily operated functions that permit advanced graphics in conjunction with data analysis. New S has the ability to plot contours, lines, segments, and points. However, of special interest is the New S function map and its options. Using the map function, which requires polygons as input, census tracts can be quickly selected, plotted, shaded, etc. New S graphics combined with the TIGER database has obvious potential. This paper reports on our efforts to use the TIGER map files with New S, especially to construct census tract maps of counties. While census tract boundaries are inherently polygonal, they are not organized as such in the TIGER database. This conversion of the TIGER line'' format into New S polygon/polyline'' format is one facet of the work reported here. Also we discuss the selection and extraction of auxiliary geographic information from TIGER files for graphical display using New S.

  8. Evidence, Theory and Context: Using intervention mapping to develop a worksite physical activity intervention

    PubMed Central

    McEachan, Rosemary RC; Lawton, Rebecca J; Jackson, Cath; Conner, Mark; Lunt, Jennifer

    2008-01-01

    Background The workplace is an ideal setting for health promotion. Helping employees to be more physically active can not only improve their physical and mental health, but can also have economic benefits such as reduced sickness absence. The current paper describes the development of a three month theory-based intervention that aims to increase levels of moderate intensity physical activity amongst employees in sedentary occupations. Methods The intervention was developed using an intervention mapping protocol. The intervention was also informed by previous literature, qualitative focus groups, an expert steering group, and feedback from key contacts within a range of organisations. Results The intervention was designed to target awareness (e.g. provision of information), motivation (e.g. goal setting, social support) and environment (e.g. management support) and to address behavioural (e.g. increasing moderate physical activity in work) and interpersonal outcomes (e.g. encourage colleagues to be more physically active). The intervention can be implemented by local facilitators without the requirement for a large investment of resources. A facilitator manual was developed which listed step by step instructions on how to implement each component along with a suggested timetable. Conclusion Although time consuming, intervention mapping was found to be a useful tool for developing a theory based intervention. The length of this process has implications for the way in which funding bodies allow for the development of interventions as part of their funding policy. The intervention will be evaluated in a cluster randomised trial involving 1350 employees from 5 different organisations, results available September 2009. PMID:18808709

  9. Genomic composition and evolution of Aedes aegypti chromosomes revealed by the analysis of physically mapped supercontigs

    PubMed Central

    2014-01-01

    Background An initial comparative genomic study of the malaria vector Anopheles gambiae and the yellow fever mosquito Aedes aegypti revealed striking differences in the genome assembly size and in the abundance of transposable elements between the two species. However, the chromosome arms homology between An. gambiae and Ae. aegypti, as well as the distribution of genes and repetitive elements in chromosomes of Ae. aegypti, remained largely unexplored because of the lack of a detailed physical genome map for the yellow fever mosquito. Results Using a molecular landmark-guided fluorescent in situ hybridization approach, we mapped 624 Mb of the Ae. aegypti genome to mitotic chromosomes. We used this map to analyze the distribution of genes, tandem repeats and transposable elements along the chromosomes and to explore the patterns of chromosome homology and rearrangements between Ae. aegypti and An. gambiae. The study demonstrated that the q arm of the sex-determining chromosome 1 had the lowest gene content and the highest density of minisatellites. A comparative genomic analysis with An. gambiae determined that the previously proposed whole-arm synteny is not fully preserved; a number of pericentric inversions have occurred between the two species. The sex-determining chromosome 1 had a higher rate of genome rearrangements than observed in autosomes 2 and 3 of Ae. aegypti. Conclusions The study developed a physical map of 45% of the Ae. aegypti genome and provided new insights into genomic composition and evolution of Ae. aegypti chromosomes. Our data suggest that minisatellites rather than transposable elements played a major role in rapid evolution of chromosome 1 in the Aedes lineage. The research tools and information generated by this study contribute to a more complete understanding of the genome organization and evolution in mosquitoes. PMID:24731704

  10. A high-resolution physically-based global flood hazard map

    NASA Astrophysics Data System (ADS)

    Kaheil, Y.; Begnudelli, L.; McCollum, J.

    2016-12-01

    We present the results from a physically-based global flood hazard model. The model uses a physically-based hydrologic model to simulate river discharges, and 2D hydrodynamic model to simulate inundation. The model is set up such that it allows the application of large-scale flood hazard through efficient use of parallel computing. For hydrology, we use the Hillslope River Routing (HRR) model. HRR accounts for surface hydrology using Green-Ampt parameterization. The model is calibrated against observed discharge data from the Global Runoff Data Centre (GRDC) network, among other publicly-available datasets. The parallel-computing framework takes advantage of the river network structure to minimize cross-processor messages, and thus significantly increases computational efficiency. For inundation, we implemented a computationally-efficient 2D finite-volume model with wetting/drying. The approach consists of simulating flood along the river network by forcing the hydraulic model with the streamflow hydrographs simulated by HRR, and scaled up to certain return levels, e.g. 100 years. The model is distributed such that each available processor takes the next simulation. Given an approximate criterion, the simulations are ordered from most-demanding to least-demanding to ensure that all processors finalize almost simultaneously. Upon completing all simulations, the maximum envelope of flood depth is taken to generate the final map. The model is applied globally, with selected results shown from different continents and regions. The maps shown depict flood depth and extent at different return periods. These maps, which are currently available at 3 arc-sec resolution ( 90m) can be made available at higher resolutions where high resolution DEMs are available. The maps can be utilized by flood risk managers at the national, regional, and even local levels to further understand their flood risk exposure, exercise certain measures of mitigation, and/or transfer the residual

  11. Mapping the telomere integrated genome of human herpesvirus 6A and 6B.

    PubMed

    Arbuckle, Jesse H; Pantry, Shara N; Medveczky, Maria M; Prichett, Joshua; Loomis, Kristin S; Ablashi, Dharam; Medveczky, Peter G