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Sample records for integrated physical mapping

  1. Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants

    PubMed Central

    Ariyadasa, Ruvini; Stein, Nils

    2012-01-01

    In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map construction and its integration with high-density genetic maps have benefited from NGS and high-throughput array platforms. This paper addresses the current advancements of BAC-based physical mapping and high-throughput map integration strategies to obtain densely anchored well-ordered physical maps. The resulted maps are of immediate utility while providing a template to harness the maximum benefits of the current NGS platforms. PMID:22500080

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. 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

  4. An integrated BAC/BIBAC-based physical and genetic map of the cotton genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Integrated genome-wide genetic and physical maps are crucial to many aspects of cotton genome research. We report a genome-wide BAC/BIBAC-based physical and genetic map of the upland cotton genome using a high-resolution and high-throughput capillary-based fingerprinting method. The map was constr...

  5. Second-Generation Genetic Linkage Map of Catfish and Its Integration with the BAC-Based Physical Map

    PubMed Central

    Ninwichian, Parichart; Peatman, Eric; Liu, Hong; Kucuktas, Huseyin; Somridhivej, Benjaporn; Liu, Shikai; Li, Ping; Jiang, Yanliang; Sha, Zhenxia; Kaltenboeck, Ludmilla; Abernathy, Jason W.; Wang, Wenqi; Chen, Fei; Lee, Yoona; Wong, Lilian; Wang, Shaolin; Lu, Jianguo; Liu, Zhanjiang

    2012-01-01

    Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ∼52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds. PMID:23050234

  6. Algorithms for computing and integrating physical maps using unique probes.

    PubMed

    Jain, M; Myers, E W

    1997-01-01

    Current physical mapping projects based on STS-probes involve additional clues such as the fact that some probes are anchored to a known map and that others come from the ends of clones. Because of the disparate combinatorial contributions of these varied data items, it is difficult to design a "tailored" algorithm that incorporates them all. Moreover, it is inevitable that new experiments will provide new kinds of data, making obsolete any such algorithm. We show how to convert the physical mapping problem into a 0/1 linear programming (LP) problem. We further show how one can incorporate additional clues as additional constraints in the LP formulation. We give a simple relaxation of the 0/1 LP problem, which solves problems of the same scale as previously reported tailored algorithms, to equal or greater optimization levels. We also present a theorem proving that when the data is 100% accurate, then the relaxed and integer solutions coincide. The LP algorithm suffices to solve problems on the order of 80-100 probes--the typical size of the 2- or 3-connected contigs of Arratia et al. (1991). We give a heuristic algorithm which attempts to order and link the set of LP-solved contigs. Unlike previous work, this algorithm only links and orders contigs when the join is 90% or more likely to be correct. It is our view that there is no value in computing an optimal solution with respect to some criteria over very noisy data as this optimal solution rarely corresponds to the true solution. The paper involves extensive empirical trials over real and simulated data. PMID:9385539

  7. A 4103 marker integrated physical and comparative map of the horse genome

    PubMed Central

    Raudsepp, Terje; Gustafson-Seabury, Ashley; Durkin, Keith; Wagner, Michelle L.; Goh, Glenda; Seabury, Christopher M.; Brinkmeyer-Langford, Candice; Lee, Eun-Joon; Agarwala, Richa; Rice, Edward Stallknecht; Schäffer, Alejandro A.; Skow, Loren C.; Tozaki, Teruaki; Yasue, Hiroshi; Penedo, M. Cecilia T.; Lyons, Leslie A.; Khazanehdari, Kamal A.; Binns, Matthew M.; MacLeod, James N.; Distl, Ottmar; Guérin, Gérard; Leeb, Tosso; Mickelson, James R.; Chowdhary, Bhanu P.

    2008-01-01

    A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n=64) has been developed using the 5000rad horse × hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH, 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase-pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species. PMID:18931483

  8. Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A comprehensive integrated genomic framework is considered a centerpiece of genomic research. In collaboration with the USDA-ARS (SHRS) and Mars Inc., the Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of the T. cacao genome. Three BAC libraries contai...

  9. 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.

  10. 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.

  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. PMID:24610029

  12. 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.

  13. Comparison of methods for integrating biological and physical data for marine habitat mapping and classification

    NASA Astrophysics Data System (ADS)

    Shumchenia, E. J.; King, J. W.

    2010-09-01

    An important first step in marine spatial planning and ecosystem-based management efforts is the creation of benthic habitat maps that allow scientists and managers to understand the distribution of living and non-living resources on the seafloor. However, the location of boundaries between and composition of habitats is highly dependent on the approach taken to integrate abiotic and biotic information. The purpose of this study was to test "top-down" and "bottom-up" approaches for integrating physical and biological data derived from commonly used sub-tidal benthic mapping tools to create a habitat map compatible with the US Coastal and Marine Ecological Classification Standard (CMECS). We found that a top-down framework, where we tested for differences in macrofauna assemblages among side scan sonar facies, defined two broad-scale and general habitats. Using the bottom-up approach, where patterns in abiotic and biotic variables were examined with multivariate statistics (BEST, LINKTREE, ANOSIM, SIMPER), we generated seven biotopes based on the macrofauna abundance, percent sand, water depth, and backscatter standard deviation that corresponded well to, but provided more fine-scale detail than the top-down habitats. We were able to use the statistical relationship between abiotic variables and macrofauna assemblages in the LINKTREE to predict the spatial distribution of assemblages over ˜50% of the study area. We created a local catalogue of biotopes specific to our study area that contributes to the CMECS library. In addition, we were able to fully map CMECS Geoform, Surface Geology, and Biotic Cover Components. This mapping effort represented real progress toward reconciling the "data density mismatch" between physical and biological mapping methods, and it provided further evidence that using a bottom-up methodology preserves species-environment relationships.

  14. An updated USMARC genetic map for the pig integrated with the pig physical map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ten years ago, we published our last comprehensive genetic map for the pig. This map contained 1,042 markers (mostly microsatellites) and spanned 2,286 cM of the autosomal genome, ~98% estimated coverage based on information available at the time. Since that time, USMARC has continued to add genetic...

  15. Integration of 28 STSs into the physical map of human chromosome 18

    SciTech Connect

    Gerken, S.; White, R.; Bradley, P.

    1994-12-01

    Genes on human chromosome 18 are associated with familial glucocorticoid deficiency (MC2R), pemphigus vulgaris (DSG3) and foliaceus (DSG1), familial amyloidosis (TTR), colorectal carcinoma (DCC), erythropoietic protoporphyria (FECH), follicular lymphoma (BCL2, FVT1), and congenital methemoglobinemia (CYB5). As the resolution of human genetic maps improves, linkage between other diseases and specific regions of chromosome 18 will occur. A physical map of human chromosome 18 will prove useful in identifying candidate genes that are associated with these disorders. Using various physical and genetic mapping techniques, over 35 genes and 19 expressed sequence tags (ESTs) are assigned to human chromosome 18. Most of these genes and several of the ESTs were sublocalized using a well-defined panel of somatic cell hybrids that contain different segments of human chromosome 18. Despite recent efforts, progress in mapping human chromosome 18 has lagged behind that achieved for other chromosomes. Thus, the purpose of this study was to integrate 9 new transcriptional tags [8 brain ESTs (8) and the melanocortin 4 receptor (MC4R) (3)] and 19 simple sequence repeats (SSRs) into the physical map of human chromosome 18. The SSRs were isolated by screening genomic DNA libraries constructed in M13mp18 vectors with oligonucleotide probes that detected dinucleotide d(CA)- and tetranucleotide-repeat motifs. DNA sequences of clones that contained microsatellite repeats were obtained by thermal-cycle sequencing, and STSs were developed from clones that contained numerous repeats. STSs that identified highly polymorphic loci in eight unrelated CEPH parents were used for genotyping. Results of linkage analyses and estimates of heterozygosity for these markers will be reported. 9 refs., 1 fig., 1 tab.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  17. 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. PMID:11238414

  18. Fundamentals of Physical Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    PubMed Central

    Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G.; Dunham, Rex; Liu, Zhanjiang

    2015-01-01

    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 present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits. PMID:25428894

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

    PubMed

    Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G; Dunham, Rex; Liu, Zhanjiang

    2015-02-01

    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 present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits. PMID:25428894

  1. An integrated physical map of 210 markers assigned to the short arm of human chromosome 11

    SciTech Connect

    Redeker, E.; Hoovers, J.M.N.; Alders, M.

    1994-06-01

    Using a panel of patient cell lines with chromosomal breakpoints, the authors constructed a physical map for the short arm of human chromosome 11. They focused on 11p15, a chromosome band harboring at least 25 known genes and associated with the Beckwith-Wiedemann syndrome, several childhood tumors, and genomic imprinting. This underlines the need for a physical map for this region. They divided the short arm of chromosome 11 into 18 breakpoint regions, and a large series of new and previously described genes and markers was mapped within these intervals using fluorescence in situ hybridization. Cosmid fingerprint analysis showed that 19 of these markers were included in cosmid contigs. A detailed 10-Mb pulsed-field physical map of the region 11p15.3-pter was constructed. These three different approaches enabled the high-resolution mapping of 210 markers, including 22 known genes. 64 refs., 6 figs., 3 tabs.

  2. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Upland cotton (G. hirsutum L.) is the leading fiber crop worldwide. Genetic improvement of fiber quality and yield is facilitated by a variety of genomics tools. An integrated genetic and physical map is needed to better characterize quantitative trait loci and to allow for the positional cloning ...

  3. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.).

    PubMed

    Cloutier, Sylvie; Ragupathy, Raja; Miranda, Evelyn; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Ward, Kerry; Rowland, Gordon; Duguid, Scott; Banik, Mitali

    2012-12-01

    Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence. PMID:22890805

  4. AN INTEGRATED MAP FOR MAIZE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Maize Mapping Project (MMP) is focused on developing genetic, physical, and database resources for the maize genome. A key resource being developed by the MMP is a well-integrated genetic and physical map that will expedite the identification of DNA sequences underlying key traits that have been...

  5. 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. PMID:25603894

  6. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome

    PubMed Central

    Han, Yuepeng; Zheng, Danman; Vimolmangkang, Sornkanok; Khan, Muhammad A.; Beever, Jonathan E.; Korban, Schuyler S.

    2011-01-01

    A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143 cM, with an average density of 2.5 cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421 Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97 kb to 4.0 Mb, with an average of 995 kb. The average physical length of anchored contigs on each linkage group was ∼24.8 Mb, ranging from 17.0 Mb to 37.73 Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple. PMID:21743103

  7. Efficient high-resolution genetic mapping of mouse interspersed repetitive sequence PCR products, toward integrated genetic and physical mapping of the mouse genome.

    PubMed Central

    McCarthy, L; Hunter, K; Schalkwyk, L; Riba, L; Anson, S; Mott, R; Newell, W; Bruley, C; Bar, I; Ramu, E

    1995-01-01

    The ability to carry out high-resolution genetic mapping at high throughput in the mouse is a critical rate-limiting step in the generation of genetically anchored contigs in physical mapping projects and the mapping of genetic loci for complex traits. To address this need, we have developed an efficient, high-resolution, large-scale genome mapping system. This system is based on the identification of polymorphic DNA sites between mouse strains by using interspersed repetitive sequence (IRS) PCR. Individual cloned IRS PCR products are hybridized to a DNA array of IRS PCR products derived from the DNA of individual mice segregating DNA sequences from the two parent strains. Since gel electrophoresis is not required, large numbers of samples can be genotyped in parallel. By using this approach, we have mapped > 450 polymorphic probes with filters containing the DNA of up to 517 backcross mice, potentially allowing resolution of 0.14 centimorgan. This approach also carries the potential for a high degree of efficiency in the integration of physical and genetic maps, since pooled DNAs representing libraries of yeast artificial chromosomes or other physical representations of the mouse genome can be addressed by hybridization of filter representations of the IRS PCR products of such libraries. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 PMID:7777502

  8. 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

    2013-11-01

    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

  9. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. 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.

  12. 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.

  13. Integration and validation of the physical map of chromosome 21 using a high resolution somatic cell hybrid panel, STS mapping, and rare cleavage

    SciTech Connect

    Patterson, D.; Graw, S.; Gardiner, K.

    1994-09-01

    We are constructing a minimal tiling path of chromosome 21 based on the 810 YAC set described by Chumakov et al., the YACs isolated by the Chromosome 21 Joint YAC Screening Effort, and several additional YAC, cosmid, and P1 libraries. We are integrating the STS and YAC contig data with the high resolution somatic cell hybrid map of chromosome 21 to validate that the YACs chosen as part of the tilling path accurately represent the chromosomal region from which they are derived, to resolve problems of homology between chromosome 21 and other acrocentric chromosomes, to help resolve STS order, to integrate additional markers, especially genes, into the map, and to help in registration of the STS and YAC maps with the cytogenetic and genetic linkage maps. The physical boundaries of 23 different somatic cell hybrids have been determined. This appears to require reordering of some of the STSs on chromosome 21 and suggests the necessity of isolation of additional DNA markers and clones. A remarkable clustering of chromosome 21 breakpoints is observed. Rec-A Assisted Restriction Endonuclease (RARE) cleavage is being used to assess whether YACs accurately reflect this genomic region of origin and to assess the extent of overlap of YACs. This information will aid in the most efficient generation of high quality reagents for sequencing chromosome 21.

  14. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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,...

  16. 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

  17. 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.

  18. 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.

  19. Genetic and physical map correlation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. A high-resolution integrated physical, cytogenetic, and genetic map of human chromosome 11: distal p13 to proximal p15.1.

    PubMed

    Fantes, J A; Oghene, K; Boyle, S; Danes, S; Fletcher, J M; Bruford, E A; Williamson, K; Seawright, A; Schedl, A; Hanson, I

    1995-01-20

    We describe a detailed physical map of human chromosome 11, extending from the distal part of p13 through the entirety of p14 to proximal p15.1. The primary level of mapping is based on chromosome breakpoints that divide the region into 20 intervals. At higher resolution YACs cover approximately 12 Mb of the region, and in many places overlapping cosmids are ordered in contiguous arrays. The map incorporates 18 known genes, including precise localization of the GTF2H1 gene encoding the 62-kDa subunit of TFIIH. We have also localized four expressed sequences of unknown function. The physical map incorporates genetic markers that allow relationships between physical and genetic distance to be examined, and similarly includes markers from a radiation hybrid map of 11. The cytogenetic location of cosmids has been examined on high-resolution banded chromosomes by fluorescence in situ hybridization, and FLpter values have been determined. The map therefore fully integrates physical, genic, genetic, and cytogenetic information and should provide a robust framework for the rapid and accurate assignment of new markers at a high level of resolution in this region of 11p. PMID:7789978

  1. Statistical methods in physical mapping

    SciTech Connect

    Nelson, D.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.

  2. Linkage map integration

    SciTech Connect

    Collins, A.; Teague, J.; Morton, N.E.; Keats, B.J.

    1996-08-15

    The algorithms that drive the map+ program for locus-oriented linkage mapping are presented. They depend on the enhanced location database program ldb+ to specify an initial comprehensive map that includes all loci in the summary lod file. Subsequently the map may be edited or order constrained and is automatically improved by estimating the location of each locus conditional on the remainder, beginning with the most discrepant loci. Operating characteristics permit rapid and accurate construction of linkage maps with several hundred loci. The map+ program also performs nondisjunction mapping with tests of nonstandard recombination. We have released map+ on Internet as a source program in the C language together with the location database that now includes the LODSOURCE database. 28 refs., 5 tabs.

  3. Integration of High-Resolution Physical and Genetic Map Reveals Differential Recombination Frequency between Chromosomes and the Genome Assembling Quality in Cucumber

    PubMed Central

    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. PMID

  4. A triallelic genetic male sterility locus in Brassica napus: an integrative strategy for its physical mapping and possible local chromosome evolution around it

    PubMed Central

    Lu, Wei; Liu, Jun; Xin, Qiang; Wan, Lili; Hong, Dengfeng; Yang, Guangsheng

    2013-01-01

    Background and Aims Spontaneous male sterility is an advantageous trait for both constructing efficient pollination control systems and for understanding the developmental process of the male reproductive unit in many crops. A triallelic genetic male-sterile locus (BnMs5) has been identified in Brassica napus; however, its complicated genome structure has greatly hampered the isolation of this locus. The aim of this study was to physically map BnMs5 through an integrated map-based cloning strategy and analyse the local chromosomal evolution around BnMs5. Methods A large F2 population was used to integrate the existing genetic maps around BnMs5. A map-based cloning strategy in combination with comparative mapping among B. napus, Arabidopsis, Brassica rapa and Brassica oleracea was employed to facilitate the identification of a target bacterial artificial chromosome (BAC) clone covering the BnMs5 locus. The genomic sequences from the Brassica species were analysed to reveal the regional chromosomal evolution around BnMs5. Key Results BnMs5 was finally delimited to a 0·3-cM genetic fragment from an integrated local genetic map, and was anchored on the B. napus A8 chromosome. Screening of a B. napus BAC clone library and identification of the positive clones validated that JBnB034L06 was the target BAC clone. The closest flanking markers restrict BnMs5 to a 21-kb region on JBnB034L06 containing six predicted functional genes. Good collinearity relationship around BnMs5 between several Brassica species was observed, while violent chromosomal evolutionary events including insertions/deletions, duplications and single nucleotide mutations were also found to have extensively occurred during their divergence. Conclusions This work represents major progress towards the molecular cloning of BnMs5, as well as presenting a powerful, integrative method to mapping loci in plants with complex genomic architecture, such as the amphidiploid B. napus. PMID:23243189

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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…

  11. 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.

  12. 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.

  13. 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)

  14. 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.

  15. 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

  16. Physics Integration KErnels (PIKE)

    Energy Science and Technology Software Center (ESTSC)

    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 containsmore » 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.« less

  17. 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.

  18. Physical mapping of human chromosome 16

    SciTech Connect

    Sutherland, G.R.

    1992-01-01

    Project aims for the past year have been to refine the cytogenetic based physical map of human chromosome 16. This has been achieved by extending the panel of mouse/human hybrids of chromosome 16 to over sixty hybrids and mapping approximately 250 DNA makers. The high resolution of this physical map, with an average distance between breakpoints of less than 1.6 Mb, and the availability of at least one STS in the majority of these intervals, will be the basis for constructing extensive contigs of cloned DNA.

  19. Transitional Spaces: Mapping Physical Change

    ERIC Educational Resources Information Center

    Sprake, Juliet; Thomas, Helen

    2007-01-01

    Museums and buildings are both considered immutable by the majority of people who use them. A small team from Goldsmiths College, the V&A + RIBA Architecture Partnership and Pimlico School set out to challenge this preconception. The Victoria & Albert museum was taken as a case study to investigate how buildings are a physical manifestation of an…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling of 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 genom...

  1. 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.

  2. Integrating the physically handicapped child.

    PubMed

    Bleck, E E

    1979-03-01

    This paper will serve several purposes: (1) to provide information on the incidence of physically handicapped children (exclusive of the blind and deaf) who are likely to be integrated into schools for normal non-physically impaired children, (2) to describe briefly the major handicapping conditions and their educational implications, (3) to comment on why integration has come about and why it promises to enrich the lives of normal children, (4) to suggest how physicians, physical therapists, and occupational therapists might help to make schools programs successful, (5) to comment briefly on financial implications of this program and to suggest ways in which the complexity of the medical management might be simplified, (6) to provide factual knowledge about the handicapped child and his potential to teachers who are already on the firing line to "improve" the academic achievement of the alleged normal child. PMID:155177

  3. 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

  4. 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. PMID:23526058

  5. Four strikes against physical mapping of DNA.

    PubMed

    Goldberg, P W; Golumbic, M C; Kaplan, H; Shamir, R

    1995-01-01

    Physical mapping is a central problem in molecular biology and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NP-complete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the k-consecutive ones problem for k > or = 2. These models have been chosen to reflect various features typical in biological data, including false-negative and positive errors, small width of the map, and chimericism. PMID:7497116

  6. Integrating order and distance relationships from heterogeneous maps.

    PubMed

    Graves, M

    1993-01-01

    There is no automatic mechanism to integrate information between heterogeneous genome maps. Currently, integration is a difficult, manual process. We have developed a process for knowledge base design, and we use this to integrate order and distance relationships between genetic linkage, radiation hybrid, and physical maps. Until now, the only way to develop a persistent, knowledge-intensive application was to either develop a new knowledge base from scratch or coerce the application to fit an existing knowledge base. This was not from lack of interest by the knowledge base or database community, but merely from a lack of theoretical tools powerful enough to tackle the problem. We import formalisms from knowledge representation, natural language semantics, programming language research, and databases. These form a strong, theoretical foundation for knowledge base design upon which we have implemented the knowledge base design tool called WEAVE. PMID:7584331

  7. 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.

  8. Determinant Expressions for Discrete Integrable Maps

    NASA Astrophysics Data System (ADS)

    Sogo, Kiyoshi

    2006-08-01

    Explicit formulas for several discrete integrable maps with periodic boundary condition are obtained, which give the sequential time developments in a form of the quotient of successive determinants of tri-diagonal matrices. We can expect that such formulas make the corresponding numerical simulations simple and stable. The cases of discrete Lotka-Volterra and discrete KdV equations are demonstrated by using the common algorithm computing determinants of tri-diagonal matrices.

  9. 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.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  10. 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 detailed…

  11. Computational methods for physical mapping of chromosomes

    SciTech Connect

    Torney, D.C.; Schenk, K.R. ); Whittaker, C.C. Los Alamos National Lab., NM ); White, S.W. )

    1990-01-01

    A standard technique for mapping a chromosome is to randomly select pieces, to use restriction enzymes to cut these pieces into fragments, and then to use the fragments for estimating the probability of overlap of these pieces. Typically, the order of the fragments within a piece is not determined, and the observed fragment data from each pair of pieces must be permuted N1 {times} N2 ways to evaluate the probability of overlap, N1 and N2 being the observed number of fragments in the two selected pieces. We will describe computational approaches used to substantially reduce the computational complexity of the calculation of overlap probability from fragment data. Presently, about 10{sup {minus}4} CPU seconds on one processor of an IBM 3090 is required for calculation of overlap probability from the fragment data of two randomly selected pieces, with an average of ten fragments per piece. A parallel version has been written using IBM clustered FORTRAN. Parallel measurements for 1, 6, and 12 processors will be presented. This approach has proven promising in the mapping of chromosome 16 at Los Alamos National Laboratory. We will also describe other computational challenges presented by physical mapping. 4 refs., 4 figs., 1 tab.

  12. An integrated YAC contig map for human chromosome 3

    SciTech Connect

    Gemmill, R.M.; Scott, P.; Cypser, J.

    1994-09-01

    An integrated physical map of human chromosome 3, containing 590 primary markers and 694 corresponding megabase-sized YACs, has been developed from the fusion of two large datasets. YACs identified with 462 physically localized hybridization-based probes and 120 genetically linked polymorphic STSs form the basis of the contigs. Many additional chromosome 3-specific YACs were identified by Alu-PCR hybridization and fingerprint analyses. Contigs defined entirely by primary marker content (level 1) provide >70% coverage. Since the markers used are chromosome 3-specific and have been previously localized by genetic or regional positioning, the reliability of the data at this level is extremely high. Alu-PCR and fingerprint analyses identified overlapping YACs which have permitted fusion and extension of these primary contigs. Selected incorporation of these data has resulted in an integrated coverage of over 80% at level 3. This level corresponds to the use of a single YAC to bridge gaps between YACs or contigs identified by primary markers. Limiting level 3 connections such that the STS or hybridization probe-containing YACs are derived from a common chromosomal segment has helped to ensure their authenticity. The chromosome is now represented by a number of very large YAC contigs whose order is known. Some of the gaps which separate these contigs can be bridged using Alu-PCR and fingerprint data at level 4, although these connections require STS confirmation. The map generated by fusion of the hybridization and STS based datasets is a major advance over maps possible from either dataset alone, both in terms of overall coverage and reliability, and should provide the foundation for development of a transcriptional map and a higher resolution physical map.

  13. 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.

  14. 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)

  15. 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.

  16. A First Generation Bac-Based Physical Map of the Channel Catfish Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 kar...

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

    PubMed

    Ulitsky, Igor; Shlomi, Tomer; Kupiec, Martin; Shamir, Ron

    2008-01-01

    Recent technological breakthroughs allow the quantification of hundreds of thousands of genetic interactions (GIs) in Saccharomyces cerevisiae. The interpretation of these data is often difficult, but it can be improved by the joint analysis of GIs along with complementary data types. Here, we describe a novel methodology that integrates genetic and physical interaction data. We use our method to identify a collection of functional modules related to chromosomal biology and to investigate the relations among them. We show how the resulting map of modules provides clues for the elucidation of function both at the level of individual genes and at the level of functional modules. PMID:18628749

  18. 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.

  19. 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. PMID:26442503

  20. 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…

  1. 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)

  2. 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.

  3. Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  4. Physical mapping of human chromosomes by repetitive sequence fingerprinting.

    PubMed Central

    Stallings, R L; Torney, D C; Hildebrand, C E; Longmire, J L; Deaven, L L; Jett, J H; Doggett, N A; Moyzis, R K

    1990-01-01

    We have developed an approach for identifying overlapping cosmid clones by exploiting the high density of repetitive sequences in complex genomes. Individual clones are fingerprinted, using a combination of restriction enzyme digestions followed by hybridization with selected classes of repetitive sequences. This "repeat fingerprinting" technique allows small regions of clone overlap (10-20%) to be unambiguously assigned. We demonstrate the utility of this approach, using the fingerprinting of 3145 cosmid clones (1.25 x coverage), containing one or more (GT)n repeats, from human chromosome 16. A statistical analysis was used to link these clones into 460 contiguous sequences (contigs), averaging 106 kilobases (kb) in length and representing approximately 54% (48.7 Mb) of the euchromatic arms of this chromosome. These values are consistent with theoretical calculations and indicate that 150- to 200-kb contigs can be generated with 1.5 x coverage. This strategy requires the fingerprinting of approximately one-fourth as many cosmids as random strategies requiring 50% minimum overlap for overlap detection. By "nucleating" at specific regions in the human genome, and exploiting the high density of interspersed sequences, this approach allows (i) the rapid generation of large (greater than 100-kb) contigs in the early stages of contig mapping and (ii) the production of a contig map with useful landmarks for rapid integration of the genetic and physical maps. Images PMID:2385591

  5. 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.

  6. A physical map of the bovine genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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…

  8. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

    PubMed Central

    2013-01-01

    Background As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. PMID:23800011

  9. 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…

  10. The Construction of Mental Maps Based on a Fragmentary View of Physical Maps

    ERIC Educational Resources Information Center

    Zimmer, Hubert D.

    2004-01-01

    Participants acquired spatial knowledge of a fictitious island by studying either (a) a complete physical map, (b) a sequence of part maps each showing the outline of the island and a subset of the landmarks, or (c) a sequence of sentences each describing a part map. During test, they verified the direction between 2 landmarks. Spatial knowledge…

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. Multiscale mapping: Physical concepts and mathematical techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. Maize centromere mapping: A comparison of physical and genetic strategies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The location of chromosome centromeres in various maize genetic maps relative to physical maps has not been consistently and clearly identified due to the paucity of markers and low recombination in the highly heterochromatic centromeric and flanking regions. Centromere positions on seven maize chro...

  19. 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

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

    SciTech Connect

    Sutherland, G.R.

    1992-08-01

    Project aims for the past year have been to refine the cytogenetic based physical map of human chromosome 16. This has been achieved by extending the panel of mouse/human hybrids of chromosome 16 to over sixty hybrids and mapping approximately 250 DNA makers. The high resolution of this physical map, with an average distance between breakpoints of less than 1.6 Mb, and the availability of at least one STS in the majority of these intervals, will be the basis for constructing extensive contigs of cloned DNA.

  1. The first generation of a BAC-based physical map of Brassica rapa

    PubMed Central

    Mun, Jeong-Hwan; Kwon, Soo-Jin; Yang, Tae-Jin; Kim, Hye-Sun; Choi, Beom-Soon; Baek, Seunghoon; Kim, Jung Sun; Jin, Mina; Kim, Jin A; Lim, Myung-Ho; Lee, Soo In; Kim, Ho-Il; Kim, Hyungtae; Lim, Yong Pyo; Park, Beom-Seok

    2008-01-01

    Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. Results A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. Conclusion The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community. PMID:18549474

  2. The construction of a physical map for human chromosome 19

    SciTech Connect

    Carrano, A.V.; Alleman, J.; Amemiya, C.; Ashworth, L.K.; Aslanidis, C.; Branscomb, E.W.; Combs, J.; Chen, C.; Christensen, M.; Copeland, A.; Fertitta, A.; Garcia, E.; de Jong, P.J.; Kwan, C.; Lamerdin, J.; Mohrenweiser, H.; Olsen, A.; Slezak, T.; Trask, B.; Tynan, K.

    1990-11-05

    Unlike a genetic map which provides information on the relative position of genes or markers based upon the frequency of genetic recombination, a physical map provides a topographical picture of DNA, i.e. distances in base pairs between landmarks. The landmarks may be genes, gene markers, anonymous sequences, or cloned DNA fragments. Perhaps the most useful type of physical map is one that consists of an overlapping set of cloned DNA fragments (contigs) that span the chromosome. Once genes are assigned to this contig map, sequencing of the genomic DNA can be prioritized to complete the most interesting regions first. While, in practice, complete coverage of a complex genome in recombinant clones may not be possible to achieve, many gaps in a clone map may be closed by using multiple cloning vectors or uncloned large DNA fragments such as those separated by electrophoretic methods. Human chromosome 19 contains about 60 million base pairs of DNA and represents about 2% of the haploid genome. Our initial interest in chromosome 19 originated from the presence of three DNA repair genes which we localized to a region of this chromosome. Our approach to constructing a physical map of human chromosome 19 involves four steps: building a foundation of overlapping cosmid contigs; bridging the gaps in the cosmid map with hybridization-based methods to walk onto DNA cloned in yeast and cosmids: orienting the contigs relative to each other and linking them to the cytological map; and coupling the contig map with the genetic map. The methods we use and the current status of the map are summarized in this report. 6 refs., 1 fig.

  3. 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. PMID:24815217

  4. 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

  5. An integrative approach to genomic introgression mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Near-Isogenic Lines (NILs) are valuable genetic resources for many crop species, including soybean. The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here we compare some existing and emerging methodologies for genetic intro...

  6. Integrative Physiology: On Mapping the Organism.

    ERIC Educational Resources Information Center

    Engelberg, Joseph

    1983-01-01

    The physiological literature exhibits a variety of diagrammatic conventions to represent cause-and-effect relationships (organismal maps). One scheme, based on mathematical studies of physiological systems, is described. The scheme involves the use of solid and dotted arrows, the former representing stimulation, the latter inhibition. (JN)

  7. 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

  8. 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

  9. A physical map of the human pseudoautosomal region.

    PubMed Central

    Brown, W R

    1988-01-01

    A physical map of the human pseudoautosomal region has been constructed using pulsed field gel electrophoresis and the infrequently cutting restriction enzymes BssHIII, EagI, SstII, NotI, MluI and NruI. This map extends 2.3 Mbp from the telomere to sex-chromosome-specific DNA, includes at least seven CpG islands and locates four genetically mapped loci. Five of the CpG islands are organized into two clusters. One cluster is adjacent to the telomere, the other extends into sex-chromosome-specific DNA. There is congruence between the genetic and physical maps which implies that the frequency of recombination is approximately uniform throughout the DNA. Images PMID:2847916

  10. DEVELOPMENT OF AN INTEGRATED LABORATORY INFORMATION MANAGEMENT SYSTEM FOR THE MAIZE MAPPING PROJECT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, the system must...

  11. Integrable mappings of the plane preserving biquadratic invariant curves II

    NASA Astrophysics Data System (ADS)

    Iatrou, Apostolos; Roberts, John A. G.

    2002-03-01

    We review recently introduced curve-dependent McMillan maps which are mappings of the plane that preserve biquadratic foliations. We show that they are measure preserving and thus integrable. We discuss the geometry of these maps including their fixed points and their stability. We consider the normal forms of symmetric and asymmetric biquadratic curves and the normal forms for their associated McMillan maps. We further discuss the dynamics on biquadratic curves by considering the possibility of parametrizing them by Jacobian elliptic or rational functions.

  12. 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.

  13. 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.

  14. 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.

  15. 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…

  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. Physical map of the genome of Rhodobacter capsulatus SB 1003.

    PubMed Central

    Fonstein, M; Zheng, S; Haselkorn, R

    1992-01-01

    A map of the chromosome of Rhodobacter capsulatus was constructed by overlapping the large restriction fragments generated by endonucleases AseI and XbaI. The analyses were done by hybridization of single fragments with the restriction fragments blotted from pulsed-field gels and by grouping cosmids of a genomic library of R. capsulatus into contigs, corresponding to the restriction fragments, and further overlapping of the contigs. A technical difficulty due to a repeated sequence made it necessary to use hybridization with cloned genes and prior knowledge of the genetic map in order to close the physical circle in a unique way. In all, 41 restriction sites were mapped on the 3.6-Mb circular genome and 22 genes were positioned at 26 loci of the map. Cosmid clones were grouped in about 80 subcontigs, forming two groups, one corresponding to the chromosome of R. capsulatus and the other corresponding to a 134-kb plasmid. cos site end labeling and partial digestion of cosmids were used to construct a high-resolution EcoRV map of the 134-kb plasmid. The same method can be extended to the entire chromosome. The cosmid clones derived in this work can be used as a hybridization panel for the physical mapping of new genes as soon as they are cloned. Images PMID:1597421

  18. Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping.

    PubMed

    Wang, Xiaoming; Kudrna, David A; Pan, Yonglong; Wang, Hao; Liu, Lin; Lin, Haiyan; Zhang, Jianwei; Song, Xiang; Goicoechea, Jose Luis; Wing, Rod A; Zhang, Qifa; Luo, Meizhong

    2014-04-01

    Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html). PMID:24424778

  19. Genetic and physical mapping of the bovine X chromosome.

    PubMed

    Yeh, C C; Taylor, J F; Gallagher, D S; Sanders, J O; Turner, J W; Davis, S K

    1996-03-01

    Three hundred eighty reciprocal backcross and F(2) full sib progeny from 33 families produced by embryo transfer from 77 Angus (Bos taurus), Brahman (Bos indicus), and F1 parents and grandparents were used to construct genetic maps of the bovine X and Y chromosomes. Ml individuals were scored for 15 microsatellite loci, with an average of 608 informative meioses per locus. The length of the bovine X chromosome genetic map was 118.7 cM (female only) and of the pseudoautosomal region was 13.0 cM (male only). The 15-marker framework map in Kosambi centimorgans is [BM6017-6.1 -TGLA89-35.8-TEXAN13-3.4-TGLA128-1.3 -BM2713 -21.1 -BM4604-2.4-BR215 - 12.9-TGLA68-10.0-BM4321 - 1.0-HEL14-4.9-TGLA15-2.3-INRA12O- 12.5-TGLA325- 1.6-MAF45-3.2-INRA3O], with an average interval of 7.91 cM. Clones containing pseudoautosomal or sex-linked microsatellites were isolated from a bovine bacterial artificial chromosome library and were physically mapped to bovine metaphase chromosomes by fluorescence in situ hybridization to orient the X and Y chromosome maps. BAC57, containing the pseudoautosomal microsatellite INRA3O, mapped to the distal end of the long arm of the X chromosome at q42-ter and to the short arm of the Y chromosome at p13-ter. This confirms the published assignment of this region to Ypl2-ter, but challenges the published assignment of Xpl4-ter and thus reorients the X chromosome physical map. BAC2O4, containing the X-linked microsatellite BM4604, mapped to the middle of the long arm of the X chromosome at q26-q31. The position of the physically mapped markers indicates either a lack of microsatellite markers for a large (30 to 50 cM) region of the short arm of the X chromosome or heterogeneity of recombination along the X chromosome. PMID:8833151

  20. A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.

    PubMed

    Steen, R G; Kwitek-Black, A E; Glenn, C; Gullings-Handley, J; Van Etten, W; Atkinson, O S; Appel, D; Twigger, S; Muir, M; Mull, T; Granados, M; Kissebah, M; Russo, K; Crane, R; Popp, M; Peden, M; Matise, T; Brown, D M; Lu, J; Kingsmore, S; Tonellato, P J; Rozen, S; Slonim, D; Young, P; Jacob, H J

    1999-06-01

    The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F2 intercrosses (SHRSP x BN and FHH x ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod >/= 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). [Bihoreau et al. (1997); James and Tanigami, RHdb (http:www.ebi.ac.uk/RHdb/index.html); Wilder (http://www.nih.gov/niams/scientific/ratgbase); Serikawa et al. (1992); RATMAP server (http://ratmap.gen.gu.se)] RH maps (v. 2.0) have been posted on our web sites at http://goliath.ifrc.mcw.edu/LGR/index.html or http://curatools.curagen.com/ratmap. Both web sites provide an RH mapping server where investigators can localize their own RH vectors relative to this map. The raw data have been deposited in the RHdb database. Taken together, these maps provide the basic tools for rat genomics. The RH map provides the means to rapidly localize genetic markers, genes, and ESTs within the rat genome. These maps provide the basic tools for rat genomics. They will facilitate studies of multifactorial disease and functional genomics, allow construction of physical maps, and provide a scaffold for both directed and large-scale sequencing efforts and comparative genomics in this important experimental organism. PMID:10400928

  1. Integrating statistical rock physics and sedimentology for quantitative seismic interpretation

    NASA Astrophysics Data System (ADS)

    Avseth, Per; Mukerji, Tapan; Mavko, Gary; Gonzalez, Ezequiel

    This paper presents an integrated approach for seismic reservoir characterization that can be applied both in petroleum exploration and in hydrological subsurface analysis. We integrate fundamental concepts and models of rock physics, sedimentology, statistical pattern recognition, and information theory, with seismic inversions and geostatistics. Rock physics models enable us to link seismic amplitudes to geological facies and reservoir properties. Seismic imaging brings indirect, noninvasive, but nevertheless spatially exhaustive information about the reservoir properties that are not available from well data alone. Classification and estimation methods based on computational statistical techniques such as nonparametric Bayesian classification, Monte Carlo simulations and bootstrap, help to quantitatively measure the interpretation uncertainty and the mis-classification risk at each spatial location. Geostatistical stochastic simulations incorporate the spatial correlation and the small scale variability which is hard to capture with only seismic information because of the limits of resolution. Combining deterministic physical models with statistical techniques has provided us with a successful way of performing quantitative interpretation and estimation of reservoir properties from seismic data. These formulations identify not only the most likely interpretation but also the uncertainty of the interpretation, and serve as a guide for quantitative decision analysis. The methodology shown in this article is applied successfully to map petroleum reservoirs, and the examples are from relatively deeply buried oil fields. However, we suggest that this approach can also be carried out for improved characterization of shallow hydrologic aquifers using shallow seismic or GPR data.

  2. 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. PMID:26357233

  3. 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.

  4. A high utility integrated map of the pig genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. 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

  6. 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. PMID:25662411

  7. Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum.

    PubMed

    Xu, Zhanyou; van den Berg, Marco A; Scheuring, Chantel; Covaleda, Lina; Lu, Hong; Santos, Felipe A; Uhm, Taesik; Lee, Mi-Kyung; Wu, Chengcang; Liu, Steve; Zhang, Hong-Bin

    2005-01-01

    Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40-70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP-dROX, we assembled a physical map for P.chrysogenum, with 2-3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes. PMID:15767275

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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. PMID:27017185

  13. Integrated modeling, data transfers, and physical models

    NASA Astrophysics Data System (ADS)

    Brookshire, D. S.; Chermak, J. M.

    2003-04-01

    Difficulties in developing precise economic policy models for water reallocation and re-regulation in various regional and transboundary settings has been exacerbated not only by climate issues but also by institutional changes reflected in the promulgation of environmental laws, changing regional populations, and an increased focus on water quality standards. As complexity of the water issues have increased, model development at a micro-policy level is necessary to capture difficult institutional nuances and represent the differing national, regional and stakeholders' viewpoints. More often than not, adequate "local" or specific micro-data are not available in all settings for modeling and policy decisions. Economic policy analysis increasingly deals with this problem through data transfers (transferring results from one study area to another) and significant progress has been made in understanding the issue of the dimensionality of data transfers. This paper explores the conceptual and empirical dimensions of data transfers in the context of integrated modeling when the transfers are not only from the behavioral, but also from the hard sciences. We begin by exploring the domain of transfer issues associated with policy analyses that directly consider uncertainty in both the behavioral and physical science settings. We then, through a stylized, hybrid, economic-engineering model of water supply and demand in the Middle Rio Grand Valley of New Mexico (USA) analyze the impacts of; (1) the relative uncertainty of data transfers methods, (2) the uncertainty of climate data and, (3) the uncertainly of population growth. These efforts are motivated by the need to address the relative importance of more accurate data both from the physical sciences as well as from demography and economics for policy analyses. We evaluate the impacts by empirically addressing (within the Middle Rio Grand model): (1) How much does the surrounding uncertainty of the benefit transfer

  14. Mapping of topological quantum circuits to physical hardware.

    PubMed

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

    2014-01-01

    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. PMID:24722360

  15. Mapping of Topological Quantum Circuits to Physical Hardware

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    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.

  16. 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...

  17. 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.

  18. 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…

  19. 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…

  20. 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

  1. Physical mapping of human chromosome segment 9q34

    SciTech Connect

    Cutone, S.; Turner, A.; Rutter, M.

    1994-09-01

    A high resolution physical map of the {approximately}15 Mb that constitute human chromosome region 9q34 is being constructed. YACs have been identified with 138 9q34 markers including 40 genetic markers (STS, SSR), 8 known genes and 90 exons isolated from cosmids localized to 9q34 by FISH or localized to 9q34 by hybridization to somatic cell hybrid mapping panels. In addition, Alu-PCR products (62) and end clones (29) from 9q34 YACs have been utilized to identify additional overlapping clones in the region. A total of 229 markers have identified 257 YACs (62 unique and 195 redundant) that have been organized into 41 contigs and cover > 12 Mb of this region. Fifteen of these contigs are sub-localized within 9q34 based on the presence of a genetic marker, and 26 contigs are localized only to 9q34 based on the origin of the marker they contain. The location of these contigs in 9q34 is being independently confirmed by FISH of YAC Alu-PCR products. Contig extension is being pursued through hybridization of individual YAC Alu-PCR products to Alu-PCR products of clones in a chromosome 9 YAC library and by chromosome walking from YAC end clones. This has resulted in the extension of 14 contigs and the reduction of 5 smaller contigs to 2 larger contigs. In addition, a 1.7 Mb complete, overlapping contig has been constructed in the TSC1 candidate region. It is anticipated that a cloned physical map of 9q34 will aid in the identification of this and other disease genes localized to this chromosome segment.

  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. 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.

  4. 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

  5. A Lithology Based Map Unit Schema For Onegeology Regional Geologic Map Integration

    NASA Astrophysics Data System (ADS)

    Moosdorf, N.; Richard, S. M.

    2012-12-01

    A system of lithogenetic categories for a global lithological map (GLiM, http://www.ifbm.zmaw.de/index.php?id=6460&L=3) has been compiled based on analysis of lithology/genesis categories for regional geologic maps for the entire globe. The scheme is presented for discussion and comment. Analysis of units on a variety of regional geologic maps indicates that units are defined based on assemblages of rock types, as well as their genetic type. In this compilation of continental geology, outcropping surface materials are dominantly sediment/sedimentary rock; major subdivisions of the sedimentary category include clastic sediment, carbonate sedimentary rocks, clastic sedimentary rocks, mixed carbonate and clastic sedimentary rock, colluvium and residuum. Significant areas of mixed igneous and metamorphic rock are also present. A system of global categories to characterize the lithology of regional geologic units is important for Earth System models of matter fluxes to soils, ecosystems, rivers and oceans, and for regional analysis of Earth surface processes at global scale. Because different applications of the classification scheme will focus on different lithologic constituents in mixed units, an ontology-type representation of the scheme that assigns properties to the units in an analyzable manner will be pursued. The OneGeology project is promoting deployment of geologic map services at million scale for all nations. Although initial efforts are commonly simple scanned map WMS services, the intention is to move towards data-based map services that categorize map units with standard vocabularies to allow use of a common map legend for better visual integration of the maps (e.g. see OneGeology Europe, http://onegeology-europe.brgm.fr/ geoportal/ viewer.jsp). Current categorization of regional units with a single lithology from the CGI SimpleLithology (http://resource.geosciml.org/201202/ Vocab2012html/ SimpleLithology201012.html) vocabulary poorly captures the

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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…

  8. 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…

  9. Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 25 genetic marker-anchor...

  10. 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.

  11. 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…

  12. Integrating biodiversity distribution knowledge: toward a global map of life.

    PubMed

    Jetz, Walter; McPherson, Jana M; Guralnick, Robert P

    2012-03-01

    Global knowledge about the spatial distribution of species is orders of magnitude coarser in resolution than other geographically-structured environmental datasets such as topography or land cover. Yet such knowledge is crucial in deciphering ecological and evolutionary processes and in managing global change. In this review, we propose a conceptual and cyber-infrastructure framework for refining species distributional knowledge that is novel in its ability to mobilize and integrate diverse types of data such that their collective strengths overcome individual weaknesses. The ultimate aim is a public, online, quality-vetted 'Map of Life' that for every species integrates and visualizes available distributional knowledge, while also facilitating user feedback and dynamic biodiversity analyses. First milestones toward such an infrastructure have now been implemented. PMID:22019413

  13. 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…

  14. An Integrative Method for Accurate Comparative Genome Mapping

    PubMed Central

    Swidan, Firas; Rocha, Eduardo P. C; Shmoish, Michael; Pinter, Ron Y

    2006-01-01

    We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying “maximal similar segments,” and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes. PMID:16933978

  15. The distribution of transgene insertion sites in barley determined by physical and genetic mapping.

    PubMed Central

    Salvo-Garrido, Haroldo; Travella, Silvia; Bilham, Lorelei J; Harwood, Wendy A; Snape, John W

    2004-01-01

    The exact site of transgene insertion into a plant host genome is one feature of the genetic transformation process that cannot, at present, be controlled and is often poorly understood. The site of transgene insertion may have implications for transgene stability and for potential unintended effects of the transgene on plant metabolism. To increase our understanding of transgene insertion sites in barley, a detailed analysis of transgene integration in independently derived transgenic barley lines was carried out. Fluorescence in situ hybridization (FISH) was used to physically map 23 transgene integration sites from 19 independent barley lines. Genetic mapping further confirmed the location of the transgenes in 11 of these lines. Transgene integration sites were present only on five of the seven barley chromosomes. The pattern of transgene integration appeared to be nonrandom and there was evidence of clustering of independent transgene insertion events within the barley genome. In addition, barley genomic regions flanking the transgene insertion site were isolated for seven independent lines. The data from the transgene flanking regions indicated that transgene insertions were preferentially located in gene-rich areas of the genome. These results are discussed in relation to the structure of the barley genome. PMID:15280249

  16. 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

  17. Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome

    PubMed Central

    2012-01-01

    Background Sequencing projects using a clone-by-clone approach require the availability of a robust physical map. The SNaPshot technology, based on pair-wise comparisons of restriction fragments sizes, has been used recently to build the first physical map of a wheat chromosome and to complete the maize physical map. However, restriction fragments sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs and mis-assembled BACs in such large and repetitive genomes. Whole Genome Profiling (WGP™) was developed recently as a new sequence-based physical mapping technology and has the potential to limit this problem. Results A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to establish a WGP physical map and to compare it to a map obtained with the SNaPshot technology. We first adapted the WGP-based assembly methodology to cope with the complexity of the wheat genome. Then, the results showed that the WGP map covers the same length than the SNaPshot map but with 30% less contigs and, more importantly with 3.5 times less mis-assembled BACs. Finally, we evaluated the benefit of integrating WGP tags in different sequence assemblies obtained after Roche/454 sequencing of BAC pools. We showed that while WGP tag integration improves assemblies performed with unpaired reads and with paired-end reads at low coverage, it does not significantly improve sequence assemblies performed at high coverage (25x) with paired-end reads. Conclusions Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome. Moreover, WGP tag integration in sequence assemblies improves low quality assembly. However, to achieve a high quality draft sequence assembly, a sequencing depth of 25x paired-end reads is required, at which point WGP tag integration does not provide additional scaffolding value. Finally, we suggest that WGP

  18. 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

  19. 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.

  20. 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…

  1. 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. PMID:25953972

  2. Paper versus Pixel: Effectiveness of Paper versus Electronic Maps to Teach Map Reading Skills in an Introductory Physical Geography Course

    ERIC Educational Resources Information Center

    Pedersen, Paula; Farrell, Pat; McPhee, Eric

    2005-01-01

    This article addresses the lack of outcome-based research on the integration of technology into pedagogy at the undergraduate college level. It describes a study performed at a Midwestern university, testing the relative effectiveness of paper and electronic topographic maps for teaching map-reading skills, and considers the relationship between…

  3. 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

  4. Integrated Applied Programs in Physical Sciences.

    ERIC Educational Resources Information Center

    Byrd, J. William

    1980-01-01

    Data gathered from a national survey mailed to 55 industries employing large numbers of technical personnel support the notion that the employment market should be broadened for persons receiving their academic training in physics. Alternative curriculum strategies and course subjects are suggested for preparing physicists for industrial…

  5. 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

  6. Mapping White Matter Integrity in Elderly People with HIV

    PubMed Central

    Nir, Talia M.; Jahanshad, Neda; Busovaca, Edgar; Wendelken, Lauren; Nicolas, Krista; Thompson, Paul M.; Valcour, Victor G.

    2013-01-01

    People with HIV are living longer as combination antiretroviral therapy (cART) becomes more widely available. However, even when plasma viral load is reduced to untraceable levels, chronic HIV infection is associated with neurological deficits and brain atrophy beyond that of normal aging. HIV is often marked by cortical and subcortical atrophy, but the integrity of the brain’s white matter (WM) pathways also progressively declines. Few studies focus on older cohorts where normal aging may be compounded with HIV infection to influence deficit patterns. In this relatively large diffusion tensor imaging (DTI) study, we investigated abnormalities in WM fiber integrity in 56 HIV+ adults with access to cART (mean age: 63.9 ± 3.7 years), compared to 31 matched healthy controls (65.4 ± 2.2 years). Statistical 3D maps revealed the independent effects of HIV diagnosis and age on fractional anisotropy (FA) and diffusivity, but we did not find any evidence for an age by diagnosis interaction in our current sample. Compared to healthy controls, HIV patients showed pervasive FA decreases and diffusivity increases throughout WM. We also assessed neuropsychological (NP) summary z-score associations. In both patients and controls, fiber integrity measures were associated with NP summary scores. The greatest differences were detected in the corpus callosum and in the projection fibers of the corona radiata. These deficits are consistent with published NP deficits and cortical atrophy patterns in elderly people with HIV. PMID:23362139

  7. 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.

  8. Molecular cloning and physical mapping of murine cytomegalovirus DNA.

    PubMed Central

    Ebeling, A; Keil, G M; Knust, E; Koszinowski, U H

    1983-01-01

    Murine cytomegalovirus (MCMV) Smith strain DNA is cleaved by restriction endonuclease HindIII into 16 fragments, ranging in size from 0.64 to 22.25 megadaltons. Of the 16 HindIII fragments, 15 were cloned in plasmid pACYC177 in Escherichia coli HB101 (recA). The recombinant plasmid clones were characterized by cleavage with the enzymes XbaI and EcoRI. In addition, fragments generated by double digestion of cloned fragments with HindIII and XbaI were inserted into the plasmid vector pACYC184. The results obtained after hybridization of 32P-labeled cloned fragments to Southern blots of MCMV DNA cleaved with HindIII, XbaI, EcoRI, BamHI, ApaI, ClaI, EcoRV, or KpnI allowed us to construct complete physical maps of the viral DNA for the restriction endonucleases HindIII, XbaI, and EcoRI. On the basis of the cloning and mapping experiments, it was calculated that the MCMV genome spans about 235 kilobase pairs, corresponding to a molecular weight of 155,000,000. All fragments were found to be present in equimolar concentrations, and no cross-hybridization between any of the fragments was seen. We conclude that the MCMV DNA molecule consists of a long unique sequence without large terminal or internal repeat regions. Thus, the structural organization of the MCMV genome is fundamentally different from that of the human cytomegalovirus or herpes simplex virus genome. Images PMID:6312075

  9. 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)

  10. A linkage and physical map of chromosome 22, and some applications to gene mapping.

    PubMed

    Julier, C; Lathrop, G M; Reghis, A; Szajnert, M F; Lalouel, J M; Kaplan, J C

    1988-02-01

    A genetic map of human chromosome 22 has been derived from physical assignments and multilocus linkage analysis. It consists of the loci for the immunoglobulin lambda light-chain variable (IGLV) and immunoglobulin lambda light-chain constant (IGLC) regions, myoglobin (MB), the sis proto-oncogene (SIS), and an arbitrary probe (D22S1). The first RFLPs at the loci for SIS, IGLV, and MB are described. The most likely gene order on the basis of multilocus analysis was cen-(IGLV-IGLC)-D22S1-MB-SIS. This map provides further evidence for localization of the P1 polymorphism of the P blood group to chromosome 22, close to the SIS locus. Analysis of families segregating recessive congenital methemoglobinemia (RCM), a disease in which the cytochrome b5 reductase is defective, as well as of families with cases of hereditary low levels of cytochrome b5 reductase activity, confirmed that the locus responsible for RCM is on chromosome 22. Biochemical studies had already suggested that mutation at the cytochrome b5 reductase locus (DIA1) is responsible for RCM. We found no evidence of genetic heterogeneity between the families segregating RCM and the families exhibiting cases of low cytochrome b5 reductase activity. Linkage analysis indicated that the most probable location of DIA1 lies between MB and SIS. PMID:2893546

  11. 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.

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

    PubMed

    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. PMID:24827321

  13. 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. PMID:27168155

  14. 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.

  15. HEALTHY BOUTS OF ACTIVITY: INTEGRATING GPS AND ACCELEROMETRY FOR MAP-PROMPTED BOUT RECALLS

    PubMed Central

    Brown, Barbara B.; Wilson, Laura; Tribby, Calvin P.; Werner, Carol M.; Wolf, Jean; Miller, Harvey J.; Smith, Ken R.

    2015-01-01

    Objective Obtaining the “when, where, and why” of healthy bouts of moderate-to-vigorous physical activity (MVPA) provides insights into natural physical activity Design In Salt Lake City, Utah, adults wore accelerometer and 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. Results At the end of the week research assistants met with the 918 participants who had at least three 10-hour 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 minutes 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 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. Conclusion These techniques provide a novel way to understand participant memories of the context and subjective assessments associated with healthy bouts of physical activity. Prompts with time-stamped maps that illustrate places of moderate-to-vigorous physical activity offer an effective method to improve understanding of activity and its supportive socio-physical contexts. PMID:24815545

  16. Accelerator physics analysis with an integrated toolkit

    SciTech Connect

    Holt, J.A.; Michelotti, L.; Satogata, T.

    1992-08-01

    Work is in progress on an integrated software toolkit for linear and nonlinear accelerator design, analysis, and simulation. As a first application, ``beamline`` and ``MXYZPTLK`` (differential algebra) class libraries, were used with an X Windows graphics library to build an user-friendly, interactive phase space tracker which, additionally, finds periodic orbits. This program was used to analyse a theoretical lattice which contains octupoles and decapoles to find the 20th order, stable and unstable periodic orbits and to explore the local phase space structure.

  17. 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…

  18. 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…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. Integrating social and physical sciences in water management

    NASA Astrophysics Data System (ADS)

    Lund, Jay R.

    2015-08-01

    Water management has always required more than physical science. This paper reviews the accomplishments of integrating social with physical sciences for water management in the last 50 years. Particular successes are highlighted to illustrate how fundamentals from both physical science and social science have been brought together to improve the performance of water management systems. Some forward-looking lessons for managing practical and academic interdisciplinary research for water management are also provided.

  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.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. An Integrated Linkage, Chromosome, and Genome Map for the Yellow Fever Mosquito Aedes aegypti

    PubMed Central

    Timoshevskiy, Vladimir A.; Severson, David W.; deBruyn, Becky S.; Black, William C.; Sharakhov, Igor V.; Sharakhova, Maria V.

    2013-01-01

    Background Aedes aegypti, the yellow fever mosquito, is an efficient vector of arboviruses and a convenient model system for laboratory research. Extensive linkage mapping of morphological and molecular markers localized a number of quantitative trait loci (QTLs) related to the mosquito's ability to transmit various pathogens. However, linking the QTLs to Ae. aegypti chromosomes and genomic sequences has been challenging because of the poor quality of polytene chromosomes and the highly fragmented genome assembly for this species. Methodology/Principal Findings Based on the approach developed in our previous study, we constructed idiograms for mitotic chromosomes of Ae. aegypti based on their banding patterns at early metaphase. These idiograms represent the first cytogenetic map developed for mitotic chromosomes of Ae. aegypti. One hundred bacterial artificial chromosome clones carrying major genetic markers were hybridized to the chromosomes using fluorescent in situ hybridization. As a result, QTLs related to the transmission of the filarioid nematode Brugia malayi, the avian malaria parasite Plasmodium gallinaceum, and the dengue virus, as well as sex determination locus and 183 Mbp of genomic sequences were anchored to the exact positions on Ae. aegypti chromosomes. A linear regression analysis demonstrated a good correlation between positions of the markers on the physical and linkage maps. As a result of the recombination rate variation along the chromosomes, 12 QTLs on the linkage map were combined into five major clusters of QTLs on the chromosome map. Conclusion This study developed an integrated linkage, chromosome, and genome map—iMap—for the yellow fever mosquito. Our discovery of the localization of multiple QTLs in a few major chromosome clusters suggests a possibility that the transmission of various pathogens is controlled by the same genomic loci. Thus, the iMap will facilitate the identification of genomic determinants of traits responsible

  5. 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

  6. Alignment Between Genetic and Physical Maps of Gibberella zeae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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. PMID:26801360

  8. Mapping algorithm for 360-deg profilometry with time delayed integration imaging

    NASA Astrophysics Data System (ADS)

    Asundi, Anand K.; Zhou, Wensen

    1999-02-01

    A direct phase-to-radial distance mapping algorithm for 360 deg profilometry with time delay and integration imaging is presented. This method, based on an inherent mapping relationship, is capable of speedy and accurate measurement without the determination of any geometric parameter. The capability of the mapping algorithm is demonstrated by measuring a plane and a shoe.

  9. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

    PubMed

    Paux, Etienne; Legeai, Fabrice; Guilhot, Nicolas; Adam-Blondon, Anne-Françoise; Alaux, Michaël; Salse, Jérôme; Sourdille, Pierre; Leroy, Philippe; Feuillet, Catherine

    2008-02-01

    Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes. PMID:18038165

  10. 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. PMID:27225071

  11. 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

  12. AthaMap, integrating transcriptional and post-transcriptional data.

    PubMed

    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

  13. Mapping the properties of blue compact dwarf galaxies: integral field spectroscopy with PMAS

    NASA Astrophysics Data System (ADS)

    Cairós, L. M.; Caon, N.; Zurita, C.; Kehrig, C.; Roth, M.; Weilbacher, P.

    2010-09-01

    Context. Blue compact dwarf (BCD) galaxies are low-luminosity, low-metal content dwarf systems undergoing violent bursts of star formation. They present a unique opportunity to probe galaxy formation and evolution and to investigate the process of star formation in a relatively simple scenario. Spectrophotometric studies of BCDs are essential to disentangle and characterize their stellar populations. Aims: We perform integral field spectroscopy of a sample of BCDs with the aim of analyzing their morphology, the spatial distribution of some of their physical properties (excitation, extinction, and electron density) and their relationship with the distribution and evolutionary state of the stellar populations. Methods: Integral field spectroscopy observations of the sample galaxies were carried out with the Potsdam Multi-Aperture Spectrophotometer (PMAS) at the 3.5 m telescope at Calar Alto Observatory. An area 16 arcsec × 16 arcsec in size was mapped with a spatial sampling of 1 arcsec × 1 arcsec. We obtained data in the 3590-6996 Å spectral range, with a linear dispersion of 3.2 Å per pixel. From these data we built two-dimensional maps of the flux of the most prominent emission lines, of two continuum bands, of the most relevant line ratios, and of the gas velocity field. Integrated spectra of the most prominent star-forming regions and of whole objects within the FOV were used to derive their physical parameters and the gas metal abundances. Results: Six galaxies display the same morphology both in emission line and in continuum maps; only in two objects, Mrk 32 and Tololo 1434+032, the distributions of the ionized gas and of the stars differ considerably. In general the different excitation maps for a same object display the same pattern and trace the star-forming regions, as expected for objects ionized by hot stars; only the outer regions of Mrk 32, I Zw 123 and I Zw 159 display higher [S II]/Hα values, suggestive of shocks. Six galaxies display an

  14. Integrative transcriptome, proteome, phosphoproteome and genetic mapping reveals new aspects in a fiberless mutant of cotton

    PubMed Central

    Ma, Qi-Feng; Wu, Chun-Hui; Wu, Man; Pei, Wen-Feng; Li, Xing-Li; Wang, Wen-Kui; Zhang, Jinfa; Yu, Ji-Wen; Yu, Shu-Xun

    2016-01-01

    To investigate the molecular mechanisms of fiber initiation in cotton (Gossypium spp.), an integrated approach combining transcriptome, iTRAQ-based proteome and genetic mapping was taken to compare the ovules of the Xuzhou 142 wild type (WT) with its fuzzless-lintless (fl) mutant at −3 and 0 day post-anthesis. A total of 1,953 mRNAs, 187 proteins, and 131 phosphoproteins were differentially expressed (DE) between WT and fl, and the levels of transcripts and their encoded proteins and phosphoproteins were highly congruent. A functional analysis suggested that the abundance of proteins were mainly involved in amino sugar, nucleotide sugar and fatty acid metabolism, one carbon pool for folate metabolism and flavonoid biosynthesis. qRT-PCR, Western blotting, and enzymatic assays were performed to confirm the regulation of these transcripts and proteins. A molecular mapping located the lintless gene li3 in the fl mutant on chromosome 26 for the first time. A further in-silico physical mapping of DE genes with sequence variations between fl and WT identified one and four candidate genes in the li3 and n2 regions, respectively. Taken together, the transcript abundance, phosphorylation status of proteins at the fiber initiation stage and candidate genes have provided insights into regulatory processes underlying cotton fiber initiation. PMID:27075604

  15. Integrative transcriptome, proteome, phosphoproteome and genetic mapping reveals new aspects in a fiberless mutant of cotton.

    PubMed

    Ma, Qi-Feng; Wu, Chun-Hui; Wu, Man; Pei, Wen-Feng; Li, Xing-Li; Wang, Wen-Kui; Zhang, Jinfa; Yu, Ji-Wen; Yu, Shu-Xun

    2016-01-01

    To investigate the molecular mechanisms of fiber initiation in cotton (Gossypium spp.), an integrated approach combining transcriptome, iTRAQ-based proteome and genetic mapping was taken to compare the ovules of the Xuzhou 142 wild type (WT) with its fuzzless-lintless (fl) mutant at -3 and 0 day post-anthesis. A total of 1,953 mRNAs, 187 proteins, and 131 phosphoproteins were differentially expressed (DE) between WT and fl, and the levels of transcripts and their encoded proteins and phosphoproteins were highly congruent. A functional analysis suggested that the abundance of proteins were mainly involved in amino sugar, nucleotide sugar and fatty acid metabolism, one carbon pool for folate metabolism and flavonoid biosynthesis. qRT-PCR, Western blotting, and enzymatic assays were performed to confirm the regulation of these transcripts and proteins. A molecular mapping located the lintless gene li3 in the fl mutant on chromosome 26 for the first time. A further in-silico physical mapping of DE genes with sequence variations between fl and WT identified one and four candidate genes in the li3 and n2 regions, respectively. Taken together, the transcript abundance, phosphorylation status of proteins at the fiber initiation stage and candidate genes have provided insights into regulatory processes underlying cotton fiber initiation. PMID:27075604

  16. Integrated mapping of groundwater drought risk in the Southern African Development Community (SADC) region

    NASA Astrophysics Data System (ADS)

    Villholth, Karen G.; Tøttrup, Christian; Stendel, Martin; Maherry, Ashton

    2013-06-01

    Groundwater drought denotes the condition and hazard during a prolonged meteorological drought when groundwater resources decline and become unavailable or inaccessible for human use. Groundwater drought risk refers to the combined physical risk and human vulnerability associated with diminished groundwater availability and access during drought. An integrated management support tool, GRiMMS, is presented, for the mapping and assessment of relative groundwater drought risk in the Southern African Development Community (SADC) region. Based on composite mapping analysis of region-wide gridded relative indices of meteorological drought risk, hydrogeological drought proneness and human groundwater drought vulnerability, the mapping results highlight consistent areas across the region with highest groundwater drought risk and populations in the order of 39 million at risk of groundwater drought at present. Projective climate-model results suggest a potentially significant negative impact of climate change on groundwater drought risk. The tool provides a means for further attention to the key, but neglected, role of groundwater in drought management in Africa.

  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. Identification of Ischemic Lesions Based on Difference Integral Maps, Comparison of Several ECG Intervals

    NASA Astrophysics Data System (ADS)

    Švehlíková, J.; Kania, M.; Turzová, M.; Hebláková, E.; Tyšler, M.; Maniewski, R.

    2009-01-01

    Ischemic changes in small areas of myocardium can be detected from difference integral maps computed from body surface potentials measured on the same subject in situations with and without manifestation of ischemia. The proposed method for their detection is the inverse solution with 2 dipoles. Surface potentials were recorded at rest and during stress on 10 patients and 3 healthy subjects. Difference integral maps were computed for 4 intervals of integration of electrocardiographic signal (QRST, QRSU, STT and STU) and their properties and applicability as input data for inverse identification of ischemic lesions were compared. The results showed that better (more reliable) inverse solutions can be obtained from difference integral maps computed either from QRST or from STT interval of integration. The average correlation between these maps was 97%. The use of the end of U wave instead of the end of T wave for interval of integration did not improve the results.

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

    EPA Science Inventory

    This paper integrates economic, biological, and physical models to explore the efficient combination and spatial allocation of conservation efforts to protect water quality and increase salmonid populations in the Grande Ronde basin, Oregon. We focus on the effects of shade on wa...

  20. 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…

  1. 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…

  2. 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…

  3. Integrating Computer Simulations into High School Physics Teaching.

    ERIC Educational Resources Information Center

    Ronen, Miky; And Others

    1992-01-01

    Describes a project aimed at examining the problems involved in a large scale integration of computerized simulations into the present structure of physics teaching in Israeli high schools. Assessment by students, teachers, and the project team indicated general satisfaction with the project. Discusses difficulties of implementing computer-based…

  4. Integrating Physical Activity Data Technologies into Elementary School Classrooms

    ERIC Educational Resources Information Center

    Lee, Victor R.; Thomas, Jonathan M.

    2011-01-01

    This paper describes an iteration of a design-based research project that involved integrating commercial physical activity data (PAD) sensors, such as heart rate monitors and pedometers, as technologies that could be used in two fifth grade classrooms. By working in partnership with two participating teachers and seeking out immediate resources…

  5. The construction of a tetraploid cotton genome-wide comprehensive reference map and the comparison with cotton physical mapping information

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The integration of multiple genomic maps provides a higher density of markers and greater genome coverage, which not only facilitates the identification and positioning of QTLs and candidate genes, but also provides a basic structure for the genome sequence assembly. However, the diversity in marke...

  6. INTEGRATION OF GENETIC AND RADIATION HYBRID MAPS OF THE PIG: THE SECOND GENERATION IMPRH MAPS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More than 4500 markers, ESTs and genes have been mapped on IMpRH radiation hybrid panel and submitted to IMpRH Server before 30 March 2002, whereas 757 markers only were mapped on the first generation map (Hawken et al, 1999). To take advantage of the different resolutions observed on the genetic an...

  7. Integrating in silico resources to map a signaling network.

    PubMed

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

    2014-01-01

    The abundance of publicly available life science databases offers 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 we 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 for 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

  8. 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

  9. Integrating grid-based and topological maps for mobile robot navigation

    SciTech Connect

    Thrun, S.; Buecken, A.

    1996-12-31

    Research on mobile robot navigation has produced two major paradigms for mapping indoor environments: grid-based and topological. While grid-based methods produce accurate metric maps, their complexity often prohibits efficient planning and problem solving in large-scale indoor environments. Topological maps, on the other hand, can be used much more efficiently, yet accurate and consistent topological maps are considerably difficult to learn in large-scale environments. This paper describes an approach that integrates both paradigms: grid-based and topological. Grid-based maps are learned using artificial neural networks and Bayesian integration. Topological maps are generated on top of the grid-based maps, by partitioning the latter into coherent regions. By combining both paradigms-grid-based and topological, the approach presented here gains the best of both worlds: accuracy/consistency and efficiency. The paper gives results for autonomously operating a mobile robot equipped with sonar sensors in populated multi-room environments.

  10. 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.

  11. 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

  12. Map_plot and bgg_plot: software for integration of geoscience datasets

    NASA Astrophysics Data System (ADS)

    Gaillot, Philippe; Punongbayan, Jane T.; Rea, Brice

    2004-02-01

    Since 1985, the Ocean Drilling Program (ODP) has been supporting multidisciplinary research in exploring the structure and history of Earth beneath the oceans. After more than 200 Legs, complementary datasets covering different geological environments, periods and space scales have been obtained and distributed world-wide using the ODP-Janus and Lamont Doherty Earth Observatory-Borehole Research Group (LDEO-BRG) database servers. In Earth Sciences, more than in any other science, the ensemble of these data is characterized by heterogeneous formats and graphical representation modes. In order to fully and quickly assess this information, a set of Unix/Linux and Generic Mapping Tool-based C programs has been designed to convert and integrate datasets acquired during the present ODP and the future Integrated ODP (IODP) Legs. Using ODP Leg 199 datasets, we show examples of the capabilities of the proposed programs. The program map_plot is used to easily display datasets onto 2-D maps. The program bgg_plot (borehole geology and geophysics plot) displays data with respect to depth and/or time. The latter program includes depth shifting, filtering and plotting of core summary information, continuous and discrete-sample core measurements (e.g. physical properties, geochemistry, etc.), in situ continuous logs, magneto- and bio-stratigraphies, specific sedimentological analyses (lithology, grain size, texture, porosity, etc.), as well as core and borehole wall images. Outputs from both programs are initially produced in PostScript format that can be easily converted to Portable Document Format (PDF) or standard image formats (GIF, JPEG, etc.) using widely distributed conversion programs. 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 requests. As an open source software, these programs can be customized and interfaced to fulfill any specific

  13. Julius Edgar Lilienfeld Prize Lecture: Mapping the Universe: Physics Writ Large

    NASA Astrophysics Data System (ADS)

    Geller, Margaret

    2013-03-01

    The age of mapping the universe began in earnest in the late twentieth century. I will describe the enormous strides we have made in mapping the galaxy distribution and in understanding its nature and history. I will show how techniques for measuring the (primarily dark) matter distribuion in massive systems of galaxies are an astrophysical route to tests of fundamental physics.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  15. 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.

  16. An Incremental Map Building Approach via Static Stixel Integration

    NASA Astrophysics Data System (ADS)

    Muffert, M.; Anzt, S.; Franke, U.

    2013-10-01

    This paper presents a stereo-vision based incremental mapping approach for urban regions. As input, we use the 3D representation called multi-layered Stixel World which is computed from dense disparity images. More and more, researchers of Driver Assistance Systems rely on efficient and compact 3D representations like the Stixel World. The developed mapping approach takes into account the motion state of obstacles, as well as free space information obtained from the Stixel World. The presented work is based on the well known occupancy grid mapping technique and is formulated with evidential theory. A detailed sensor model is described which is used to determine the information whether a grid cell is occupied, free or has an unknown state. The map update is solved in a time recursive manner by using the Dempster`s Rule of Combination. 3D results of complex inner city regions are shown and are compared with Google Earth images.

  17. Safe task planning integrating uncertainties and local maps federations

    SciTech Connect

    Lambert, A.; Fort-Piat, N.L.

    2000-06-01

    This paper deals with the generation of safe tasks for displacement missions of a nonholonomic mobile robot in a mapped indoor environment. The goal of this study is to plan safe actions (path-following) as well as observations (they call it local maps federation [LMF]), leading the robot to configurations where pertinent features can be sensed, thus attaining best localization relative to its environment. A path-planning method dealing with uncertainties is proposed, where both uncertainties in localization and in control of a nonholonomic mobile robot are managed. Maps uncertainties are handled using the local map concept, which is introduced as a set of the best landmarks used for planning and executing robust motion movements. The safeness of the proposed method is due to the mixing between the planning phase and the navigation phase.

  18. 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.

  19. 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.

  20. New physical map of bacteriophage T5 DNA.

    PubMed Central

    Rhoades, M

    1982-01-01

    The locations of 103 cleavage sites, produced by 13 restriction endonucleases, were mapped on the DNA of bacteriophage T5. Single- and double-digest fragment sizes were determined by agarose gel electrophoresis, using restriction fragments of phi X174 DNA and lambda DNA as molecular weight standards. Map coordinates were determined by a computer-based least-squares procedures (J. Schroeder and F. Blattner, Gene [Amst] 4:167-174, 1978). The fragment sizes predicted by the final map are all within 2% of the measured values. Based on this analysis, T5st(+) DNA contains 121,300 base pairs (Mr, 80.3 X 10(6) and has a terminal repetition of 10,160 base pairs (Mr, 6.7 X 10(6)). Restriction endonuclease analysis after treatment with exonuclease III and a single-strand-specific endonuclease allowed precise localization of five of the natural single-chain interruptions in T5 DNA. Revised locations for several T5 deletions were also determined. Images PMID:6287031

  1. (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.

  2. [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.

  3. Beam Physics of Integrable Optics Test Accelerator at Fermilab

    SciTech Connect

    Nagaitsev, S.; Valishev, A.; Danilov, V.V.; Shatilov, D.N.; /Novosibirsk, IYF

    2012-05-01

    Fermilab's Integrable Optics Test Accelerator (IOTA) is an electron storage ring designed for testing advanced accelerator physics concepts, including implementation of nonlinear integrable beam optics and experiments on optical stochastic cooling. The machine is currently under construction at the Advanced Superconducting Test Accelerator facility. In this report we present the goals and the current status of the project, and describe the details of machine design. In particular, we concentrate on numerical simulations setting the requirements on the design and supporting the choice of machine parameters.

  4. 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. PMID:27115622

  5. 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

  6. 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

    2015-01-01

    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. PMID:26125877

  7. 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

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

    PubMed

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

    2015-01-01

    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. PMID:26569254

  9. Understanding student use of differentials in physics integration problems

    NASA Astrophysics Data System (ADS)

    Hu, Dehui; Rebello, N. Sanjay

    2013-12-01

    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 paper we aim to explore students’ reasoning about the differential concept in physics problems. We conducted group teaching or learning interviews with 13 engineering students enrolled in a second-semester calculus-based physics course. We amalgamated two frameworks—the resources framework and the conceptual metaphor framework—to analyze students’ reasoning about differential concept. Categorizing the mathematical resources involved in students’ mathematical thinking in physics provides us deeper insights into how students use mathematics in physics. Identifying the conceptual metaphors in students’ discourse illustrates the role of concrete experiential notions in students’ construction of mathematical reasoning. These two frameworks serve different purposes, and we illustrate how they can be pieced together to provide a better understanding of students’ mathematical thinking in physics.

  10. 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…

  11. 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…

  12. Integrating historical topographic maps and SRTM data to derive the bathymetry of a tropical reservoir

    NASA Astrophysics Data System (ADS)

    Alcântara, Enner; Novo, Evlyn; Stech, José; Assireu, Arcilan; Nascimento, Renata; Lorenzzetti, João; Souza, Arley

    2010-08-01

    SummaryThis paper proposes a fast and inexpensive method for estimating the bathymetry of hydroelectric reservoirs. Brazil has more than 30 large hydroelectric reservoirs with a combined volume exceeding one billion cubic meters. The hydroelectric sector is responsible for 97% of the energy production in Brazil and is the largest hydroelectric park in the world. Among the variables affecting the environmental impacts of reservoirs, depth plays a major role because it influences the aquatic system hydrodynamics. Reservoir depth distribution (i.e., the bathymetry) is also a fundamental factor controlling the physical-chemical and biological properties of the system. However, the acquisition of bathymetric information for the large reservoirs in Brazil is not a simple task because: (1) most of the topographic maps available in the area of the lake have a very small scale (1:100,000 and smaller), (2) larger charts are the property of the hydropower companies and are classified, and (3) the size of the reservoirs prevent the use of bathymetric surveys. The proposed method of integrating historical and Shuttle Radar Topography Mission (SRTM) topographic data allowed for the estimation of the bathymetry of the Itumbiara reservoir with R2 = 0.98 ( n = 100, ρ = 0.00) and RMSE = 3.78 m. For researchers who need a rapid and simple method to develop bathymetric maps of hydroelectric reservoirs, the proposed method can provide a simple and fast alternative to more data intensive methods.

  13. 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…

  14. 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,…

  15. Integrated and composite genome maps: the bovine example

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Combinations of genome maps representing different types of information are needed to link economically important phenotypic variation with underlying genomic variation in farmed animals. For the cow, data from two linkage populations and three radiation hybrid (RH) panels were combined to construc...

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

    PubMed

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

    2016-01-01

    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

  17. 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

  18. Integrated genetic map of Anopheles gambiae: use of RAPD polymorphisms for genetic, cytogenetic and STS landmarks.

    PubMed

    Dimopoulos, G; Zheng, L; Kumar, V; della Torre, A; Kafatos, F C; Louis, C

    1996-06-01

    Randomly amplified polymorphic DNA (RAPD) markers have been integrated in the genetic and cytogenetic maps of the malaria vector mosquito, Anopheles gambiae. Fifteen of these markers were mapped by recombination, relative to microsatellite markers that had been mapped previously. Thirty-four gel-purified RAPD bands were cloned and sequenced, generating sequence tagged sites (STSs) that can be used as entry points to the A. gambiae genome. Thirty one of these STSs were localized on nurse cell polytene chromosomes through their unique hybridization signal in in situ hybridization experiments. Five STSs map close to the breakpoints of polymorphic inversions, which are notable features of the Anopheles genome. The usefulness and limitations of this integrated mosquito map are discussed. PMID:8725241

  19. 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

  20. Toward efficient riparian restoration: integrating economic, physical, and biological models.

    PubMed

    Watanabe, Michio; Adams, Richard M; Wu, Junjie; Bolte, John P; Cox, Matt M; Johnson, Sherri L; Liss, William J; Boggess, William G; Ebersole, Joseph L

    2005-04-01

    This paper integrates economic, biological, and physical models to explore the efficient combination and spatial allocation of conservation efforts to protect water quality and increase salmonid populations in the Grande Ronde basin, Oregon. We focus on the effects of shade on water temperatures and the subsequent impacts on endangered juvenile salmonid populations. The integrated modeling system consists of a physical model that links riparian conditions and hydrological characteristics to water temperature; a biological model that links water temperature and riparian conditions to salmonid abundance, and an economic model that incorporates both physical and biological models to estimate minimum cost allocations of conservation efforts. Our findings indicate that conservation alternatives such as passive and active riparian restoration, the width of riparian restoration zones, and the types of vegetation used in restoration activities should be selected based on the spatial distribution of riparian characteristics in the basin. The relative effectiveness of passive and active restoration plays an important role in determining the efficient allocations of conservation efforts. The time frame considered in the restoration efforts and the magnitude of desired temperature reductions also affect the efficient combinations of restoration activities. If the objective of conservation efforts is to maximize fish populations, then fishery benefits should be directly targeted. Targeting other criterion such as water temperatures would result in different allocations of conservation efforts, and therefore are not generally efficient. PMID:15763152

  1. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. 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

  4. Uncertainty estimation in integrated LiDAR- and radar-derived biomass maps at key national-level map scales

    NASA Astrophysics Data System (ADS)

    Joshi, N.; Fensholt, R.; Saatchi, S. S.; Mitchard, E. T.

    2013-12-01

    The international Reducing Emissions from Deforestation and Degradation (REDD) program requires accurate and cost-effective techniques of national-level mapping of above-ground biomass (AGB) and ground-sampling strategies. This paper explores a multi-sensor (radar and low-density airborne LiDAR) integration approach for country-wide AGB estimation and mapping in Denmark, selected as a test-country due to the unique availability of country-wide remote sensing and forest inventory data. We assess the potential use of ALOS PALSAR L-band radar and ENVISAT ASAR C-band radar in prediction and mapping of AGB with accuracies similar to LiDAR-derived AGB estimates at different map scales. We start by creating a LiDAR-based ';ground truth' map, using LiDAR-derived 95th Percentile of heights >1 m weighted by the Canopy Density ratio, together with 113 AGB plots to map AGB at a 0.25 ha resolution across the country. A leave-20%-out cross-validation indicates that the AGB estimates have a mean absolute error of 41 Mg ha-1 and a negative mean bias error of 1.7 Mg ha-1. Though the LiDAR model appears to have an overall species-specific bias for conifers and broadleaf (-5.2 Mg ha-1 and +12.3 Mg ha-1 respectively), these are found to be insignificant (p>0.05) when accounting for species sampling bias and the under-prediction of plots containing high-biomass (> 350 Mg ha-1). Using the LiDAR-derived biomass map as a ';truth-map', biomass-backscatter relations will be quantified at three map scales (0.25 ha, 1 ha and 100 ha) and using three spatial sampling frameworks (full-dataset, stratified random sampling equally representing low and high biomass pixels, clustered sampling). The approach aims to derive a minimal-sampling and mapping strategy for L- and C-band radar that achieves at least 20% accuracy in AGB estimation, along with quantified sources of error from ground-AGB estimates, scaling and sampling. It is expected that mapping techniques, uncertainty quantification and

  5. 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.

  6. 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

  7. 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. PMID:26520491

  8. 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.

  9. 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.

  10. Advances On Integration Between Stereo Sparse Data And Orientation Map

    NASA Astrophysics Data System (ADS)

    Caponetti, Laura; Chiaradia, Maria T.; Distante, Arcangelo; Mugnuolo, Raffaele; Stella, Ettore

    1990-03-01

    During last years, Computer Vision has developed algorithms for most of early vision processes. It is a common idea that each vision process seaparatly cannot supply a reliable descritpion of the scene. In fact, one of the keys in reliability and robustness of biological systems is their ability to integrate information from different early processes. The base concept of our vision system is to integrate information from stereo and shading (Fig.1). The results obtained from this scheme in previous works are very interesting and suggest us to continue on this methodology. In the first work 1.2 the base approach to integration scheme was presented. The work deals on general concepts and main evolutions on shading analysis, in terms of analysis simplifications and improved accuracy. The scheme was tested on both synthetical and real scenes.

  11. Neocartilage integration in temporomandibular joint discs: physical and enzymatic methods

    PubMed Central

    Murphy, Meghan K.; Arzi, Boaz; Prouty, Shannon M.; Hu, Jerry C.; Athanasiou, Kyriacos A.

    2015-01-01

    Integration of engineered musculoskeletal tissues with adjacent native tissues presents a significant challenge to the field. Specifically, the avascularity and low cellularity of cartilage elicit the need for additional efforts in improving integration of neocartilage within native cartilage. Self-assembled neocartilage holds significant potential in replacing degenerated cartilage, though its stabilization and integration in native cartilage require further efforts. Physical and enzymatic stabilization methods were investigated in an in vitro model for temporomandibular joint (TMJ) disc degeneration. First, in phase 1, suture, glue and press-fit constructs were compared in TMJ disc intermediate zone defects. In phase 1, suturing enhanced interfacial shear stiffness and strength immediately; after four weeks, a 15-fold increase in stiffness and a ninefold increase in strength persisted over press-fit. Neither suture nor glue significantly altered neocartilage properties. In phase 2, the effects of the enzymatic stabilization regimen composed of lysyl oxidase, CuSO4 and hydroxylysine were investigated. A full factorial design was employed, carrying forward the best physical method from phase 1, suturing. Enzymatic stabilization significantly increased interfacial shear stiffness after eight weeks. Combined enzymatic stabilization and suturing led to a fourfold increase in shear stiffness and threefold increase in strength over press-fit. Histological analysis confirmed the presence of a collagen-rich interface. Enzymatic treatment additionally enhanced neocartilage mechanical properties, yielding a tensile modulus over 6 MPa and compressive instantaneous modulus over 1200 kPa at eight weeks. Suturing enhances stabilization of neocartilage, and enzymatic treatment enhances functional properties and integration of neocartilage in the TMJ disc. Methods developed here are applicable to other orthopaedic soft tissues, including knee meniscus and hyaline articular

  12. 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

  13. 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...

  14. 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

  15. 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. PMID:26881782

  16. 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.

  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 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...

  18. 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...

  19. 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. PMID:24817334

  20. 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.

  1. 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.

  2. 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.

  3. Integrated map of new CA-repeats of human chromosome 21

    SciTech Connect

    Bosch, A.; Guimera, J.; Patterson, D.

    1994-09-01

    To contribute to the map of human chromosome 21 (HC21), 35 new CA-repeats isolated from an HC21 phage library (LA21NS01) have been characterized and localized on HC21 using somatic cell hybrids and the Genethon YAC panel. Their heterozygosities range between 0.10 and 0.90 with an average of 0.70. Twenty of them, with heterozygosities between 0.47 and 0.83, have been analyzed in the CEPH reference families. A linkage map was constructed using the CRI-MAP program with 46 markers. This linkage map contains 22 uniquely placed loci, ordered with odds of at least 1000:1, with an average size interval of 3.5 cM. 10 markers were approximately positioned on the map. The sex average length of the map is 73.4 cM, with male and female lengths being 64.2 and 83.5 cM, respectively. D21S1262 was placed in the same megalocus as the IFNAR and GART genes. D21S369 seems to be the most pericentromeric microsatellite marker on HC21 based on linkage analysis, with a heterozygosity of 0.60, and may be very useful for nondisjunction studies. Integration of the somatic cell hybrid, TAC and/or linkage maps have provided a more defined location for these 35 new CA-repeat markers which will contribute greatly to the integrated map of HC21.

  4. Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.

    PubMed Central

    Higgins, M J; Turmel, C; Noolandi, J; Neumann, P E; Lalande, M

    1990-01-01

    Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage of the two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a del13(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D13S10-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis. Images PMID:1970636

  5. High density physical mapping of chromosome 3p by hybridization of somatic cell hybrid derived Alu-PCR products

    SciTech Connect

    Shearman, A.M.; Andresen, J.M.; Aburatani, H.

    1994-09-01

    We have produced high density physical maps covering most of chromosome 3 using a hybridization-based approach to YAC isolation and contig assembly. The strategy has been to use a well characterized panel of somatic cell hybrids to generate probe sets distributed across the chromosome. From each of 50 somatic cell hybrids, a library of {approximately}100-600 cloned Alu-PCR products was isolated and Alu-PCR inserts from the full set of clones was spotted at high density on nylon membranes. Representative sets of unique clones from most of the hybrids were used to screen {approximately}16 genome equivalents of CEPH YACs by hybridization. These results, combined with our previous results and data from CEPH, produced contigs covering most of the chromosomes. The use of somatic cell hybrid-derived probe sets allowed easy integration of contigs with physical mapping boundaries defined by the somatic cell hybrids. We will describe various Alu-PCR strategies subsequently used to achieve closure, including successful identification of Alu-PCR products from the spotted set which lie in regions not previously covered by YAC contigs and use of Alu-PCR walking strategies to fill gaps and confirm tentative linkages. Our basic YAC screening methodology allows one individual to screen {approximately}16 genome equivalents of CEPH YACs with 96 probes/week at a material cost of less than $1 per locus. We have now mapped >2,200 loci on chromosome 3, with average interlocus distances of {approximately}50-100 kb over large regions. Alu-PCR-defined loci spaced along the chromosome at regular intervals are being converted to STSs. Our results indicate that use of a hybridization-based approach to physical mapping constitutes an efficient, accurate, high throughput method for isolating YACs and assembling YAC contigs.

  6. 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. PMID:24589632

  7. 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…

  8. 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

  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. 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…

  11. 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.

  12. 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.

  13. 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…

  14. Learning one-to-many mapping functions for audio-visual integrated perception

    NASA Astrophysics Data System (ADS)

    Lim, Jung-Hui; Oh, Do-Kwan; Lee, Soo-Young

    2010-04-01

    In noisy environment the human speech perception utilizes visual lip-reading as well as audio phonetic classification. This audio-visual integration may be done by combining the two sensory features at the early stage. Also, the top-down attention may integrate the two modalities. For the sensory feature fusion we introduce mapping functions between the audio and visual manifolds. Especially, we present an algorithm to provide one-to-many mapping function for the videoto- audio mapping. The top-down attention is also presented to integrate both the sensory features and classification results of both modalities, which is able to explain McGurk effect. Each classifier is separately implemented by the Hidden-Markov Model (HMM), but the two classifiers are combined at the top level and interact by the top-down attention.

  15. 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.

  16. 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.

  17. 'SPODOPTERA FRUGIPERDA' NUCLEAR POLYHEDROSIS VIRUS GENOME: PHYSICAL MAPS FOR RESTRICTION ENDONUCLEASES BAMHI AND HINDIII

    EPA Science Inventory

    The physical map for the genome of Spodoptera frugiperda nuclear polyhedrosis virus was constructed for restriction endonucleases BamHI and HindIII. The ordering of the restriction fragments was accomplished by cross-blot hybridization of BamHI, HindIII, and EcoRI fragments. The ...

  18. BACTERIAL ARTIFICIAL CHROMOSOME-BASED PHYSICAL MAP OF GIBBERELLA ZEAE (FUSARIUM GRAMINEARUM)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusarium graminearum is the primary causal pathogen of Fusarium head blight of wheat and barley, a major disease problem in the wheat and barley growing regions of the world. To accelerate genomic analysis of F. graminearum, we developed a bacterial artificial chromosome (BAC)-based physical map and...

  19. A First Generation BAC Physical Map of the Rainbow Trout Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. CHARACTERIZATION AND PHYSICAL MAPPING OF MAIZE BAC LIBRARIES USING HIGH DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A HindIII and an EcoRI maize BAC library have been constructed from maize inbred line B73. Use of both libraries to make a physical map should minimize the under representation of certain genomic regions caused by the use of a particular restriction enzyme. High-density filter sets from the two libr...

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Physical mapping of the congenital chloride diarrhea gene region in human chromosome 7

    SciTech Connect

    Kere, J.; Hoeglund, P.; Haila, S.

    1994-09-01

    The gene for congenital chloride diarrhea (CLD; MIM 214700) has been mapped to human chromosome 7 by a linkage study in Finnish families. The markers closest to the gene are D7S496 and D7S501, both with zero recombination fraction. In order to physically map the region and facilitate positional cloning, altogether 25 YAC clones have been isolated from the Washington University chromosome 7 collection of YACs. The clones form 2 contigs, 700 to 900 kb in size, around D7S496 and D7SS01. One YAC from the CEPH collection that bridges these contigs has been identified, but the link remains unconfirmed. Rare-cutter restriction mapping has identified as least 3 CpG islands within 50 to 200 kb of D7S496, supposed to map closest to CLD on the basis of linkage disequilibrium studies. Isolation of candidate cDNAs is in progress.

  6. 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. PMID:25219804

  7. Mental and Physical (MAP) Training: A Neurogenesis-Inspired Intervention that Enhances Health in Humans

    PubMed Central

    Shors, Tracey J.; Olson, Ryan L.; Bates, Marsha E.; Selby, Edward A.; Alderman, Brandon L.

    2015-01-01

    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 et al., 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 30 min of mental training with focused attention meditation (20 minutes sitting and 10 minutes 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 30 min 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 8 weeks) 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) as well as decreases 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. PMID:25219804

  8. Integration of the cytogenetic and genetic linkage maps of Brassica oleracea.

    PubMed Central

    Howell, Elaine C; Barker, Guy C; Jones, Gareth H; Kearsey, Michael J; King, Graham J; Kop, Erik P; Ryder, Carol D; Teakle, Graham R; Vicente, Joana G; Armstrong, Susan J

    2002-01-01

    We have assigned all nine linkage groups of a Brassica oleracea genetic map to each of the nine chromosomes of the karyotype derived from mitotic metaphase spreads of the B. oleracea var. alboglabra line A12DHd using FISH. The majority of probes were BACs, with A12DHd DNA inserts, which give clear, reliable FISH signals. We have added nine markers to the existing integrated linkage map, distributed over six linkage groups. BACs were definitively assigned to linkage map positions through development of locus-specific PCR assays. Integration of the cytogenetic and genetic linkage maps was achieved with 22 probes representing 19 loci. Four chromosomes (2, 4, 7, and 9) are in the same orientation as their respective linkage groups (O4, O7, O8, and O6) whereas four chromosomes (1, 3, 5, and 8) and linkage groups (O3, O9, O2, and O1) are in the opposite orientation. The remaining chromosome (6) is probably in the opposite orientation. The cytogenetic map is an important resource for locating probes with unknown genetic map positions and is also being used to analyze the relationships between genetic and cytogenetic maps. PMID:12136025

  9. Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4

    PubMed Central

    Li, Xia; Bachmanov, Alexander A.; Li, Shanru; Chen, Zhenyu; Tordoff, Michael G.; Beauchamp, Gary K.; de Jong, Pieter J.; Wu, Chenyan; Chen, Lianchun; West, David B.; Ross, David A.; Ohmen, Jeffery D.; Reed, Danielle R.

    2007-01-01

    The subtelomeric region of mouse chromosome (Chr) 4 harbors loci with effects on behavior, development, and disease susceptibility. Regions near the telomeres are more difficult to map and characterize than other areas because of the unique features of subtelomeric DNA. As a result of these problems, the available mapping information for this part of mouse Chr 4 was insufficient to pursue candidate gene evaluation. Therefore, we sought to characterize the area in greater detail by creating a comprehensive genetic, physical, and comparative map. We constructed a genetic map that contained 30 markers and covered 13.3 cM; then we created a 1.2-Mb sequence-ready BAC contig, representing a 5.1-cM area, and sequenced a 246-kb mouse BAC from this contig. The resulting sequence, as well as approximately 40 kb of previously deposited genomic sequence, yielded a total of 284 kb of sequence, which contained over 20 putative genes. These putative genes were confirmed by matching ESTs or cDNA in the public databases to the genomic sequence and/or by direct sequencing of cDNA. Comparative genome sequence analysis demonstrated conserved synteny between the mouse and the human genomes (1p36.3). DNA from two strains of mice (C57BL/6ByJ and 129P3/J) was sequenced to detect single nucleotide polymorphisms (SNPs). The frequency of SNPs in this region was more than threefold higher than the genome-wide average for comparable mouse strains (129/Sv and C57BL/6J). The resulting SNP map, in conjunction with the sequence annotation and with physical and genetic maps, provides a detailed description of this gene-rich region. These data will facilitate genetic and comparative mapping studies and identification of a large number of novel candidate genes for the trait loci mapped to this region. PMID:11773963

  10. Physical map of the genome of Treponema pallidum subsp. pallidum (Nichols).

    PubMed Central

    Walker, E M; Howell, J K; You, Y; Hoffmaster, A R; Heath, J D; Weinstock, G M; Norris, S J

    1995-01-01

    A physical map of the chromosome of Treponema pallidum subsp. pallidum (Nichols), the causative agent of syphilis, was constructed from restriction fragments produced by NotI, SfiI, and SrfI. These rare-cutting restriction endonucleases cleaved the T. pallidum genome into 16, 8, and 15 fragments, respectively. Summation of the physical lengths of the fragments indicates that the chromosome of T. pallidum subsp. pallidum is approximately 1,030 to 1,080 kbp in size. The physical map was constructed by hybridizing a variety of probes to Southern blots of single and double digests of T. pallidum genomic DNA separated by contour-clamped homogeneous electric field electrophoresis. Probes included cosmid clones constructed from T. pallidum subsp. pallidum genomic DNA, restriction fragments excised from gels, and selected genes. Physical mapping confirmed that the chromosome of T. pallidum subsp. pallidum is circular, as the SfiI and SrfI maps formed complete circles. A total of 13 genes, including those encoding five membrane lipoproteins (tpn47, tpn41, tpn29-35, tpn17, and tpn15), a putative outer membrane porin (tpn50), the flagellar sheath and hook proteins (flaA and flgE), the cytoplasmic filament protein (cfpA), 16S rRNA (rrnA), a major sigma factor (rpoD), and a homolog of cysteinyl-tRNA synthetase (cysS), have been localized in the physical map as a first step toward studying the genetic organization of this noncultivable pathogen. PMID:7896703

  11. Boundary integral equation Neumann-to-Dirichlet map method for gratings in conical diffraction.

    PubMed

    Wu, Yumao; Lu, Ya Yan

    2011-06-01

    Boundary integral equation methods for diffraction gratings are particularly suitable for gratings with complicated material interfaces but are difficult to implement due to the quasi-periodic Green's function and the singular integrals at the corners. In this paper, the boundary integral equation Neumann-to-Dirichlet map method for in-plane diffraction problems of gratings [Y. Wu and Y. Y. Lu, J. Opt. Soc. Am. A26, 2444 (2009)] is extended to conical diffraction problems. The method uses boundary integral equations to calculate the so-called Neumann-to-Dirichlet maps for homogeneous subdomains of the grating, so that the quasi-periodic Green's functions can be avoided. Since wave field components are coupled on material interfaces with the involvement of tangential derivatives, a least squares polynomial approximation technique is developed to evaluate tangential derivatives along these interfaces for conical diffraction problems. Numerical examples indicate that the method performs equally well for dielectric or metallic gratings. PMID:21643404

  12. 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

  13. 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. PMID:26499288

  14. Physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome.

    PubMed Central

    Cornillot, E; Croux, C; Soucaille, P

    1997-01-01

    A physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome was constructed. The macrorestriction map for CeuI, EagI, and SstII was created by ordering the 38 restriction sites by one- and two-dimensional pulsed-field gel electrophoresis (PFGE) and by using an original strategy based on the CeuI enzyme and indirect end labelling by hybridization on both sides of the CeuI sites with rrs (16S RNA) and 3' rrl (23S RNA) probes. The circular chromosome was estimated to be 4.15 Mb in size, and the average resolution of the physical map is 110 kb. The chromosome contains 11 rrn loci, which are localized on 44% of the chromosome in a divergent transcriptional orientation regarding the presumed location of the replication origin. In addition to these 11 rrn operons, a total of 40 identified genes were mapped by hybridization experiments with genes from C. acetobutylicum and from various other clostridia as probes. The genetic map of C. acetobutylicum was compared to that of the three other endospore-forming bacteria characterized so far: Bacillus subtilis, Clostridium beijerinckii, and Clostridium perfringens. Parodoxically, the chromosomal backbone of C. acetobutylicum showed more similarity to that of B. subtilis than to those of the clostridia. PMID:9393708

  15. Physical and genetic map of the Serpulina hyodysenteriae B78T chromosome.

    PubMed Central

    Zuerner, R L; Stanton, T B

    1994-01-01

    A combined physical and genetic map of the Serpulina hyodysenteriae B78T genome was constructed by using pulsed-field gel electrophoresis and DNA blot hybridizations. The S. hyodysenteriae genome is a single circular chromosome about 3.2 Mb in size. The physical map of the chromosome was constructed with the restriction enzymes BssHII, EclXI, NotI, SalI, and SmaI. The physical map was used to constructed a linkage map for genes encoding rRNA, flagellum subunit proteins, DNA gyrase, NADH oxidase, and three distinct hemolysins. Several flaB2-related loci, encoding core flagellum subunit proteins, were detected and are dispersed around the chromosome. The rRNA gene organization in S. hyodysenteriae is unusual. S. hyodysenteriae has one gene each for 5S (rrf), 16S (rrs), and 23S (rrl) rRNAs. The rrf and rrl genes are closely linked (within 5 kb), while the rrs gene is about 860 kb from the other two rRNA genes. Using a probe for the S. hyodysenteriae gyrA gene, we identified a possible location for the chromosomal replication origin. The size and genetic organization of the S. hyodysenteriae chromosome are different from those of previously characterized spirochetes. Images PMID:8106320

  16. A branch-and-cut approach to physical mapping with end-probes

    SciTech Connect

    Christof, T.; Reinelt, G.; Juenger, M.

    1997-12-01

    A fundamental problem in computational biology is the construction of physical maps of chromosomes from hybridization experiments between unique probes and clones of chromosome fragments in the presence of error. Alizadeh, Karp, Weisser and Zweig [AKWZ94] first considered a maximum-likelihood model of the problem that is equivalent to finding an ordering of the probes that minimizes a weighted sum of errors, and developed several effective heuristics. We show that by exploiting information about the end-probes of clones, this model can be formulated as a weighted Betweenness Problem. This affords the significant advantage of allowing the well-developed tools of integer linear-programming and branch-and-cut algorithms to be brought to bear on physical mapping, enabling us for the first time to solve small mapping instances to optimality even in the presence of high error. We also show that by combining the optimal solution of many small overlapping Betweenness Problems, one can effectively screen errors from larger instances, and solve the edited instance to optimality as a Hamming-Distance Traveling Salesman Problem. This suggests a new combined approach to physical map construction. 18 refs., 13 figs.

  17. GRAD-MAP: A Joint Physics and Astronomy Diversity Initiative at the University of Maryland

    NASA Astrophysics Data System (ADS)

    Wilkins, Ashlee N.; Jameson, Katherine; Taylor, Corbin James; Anderson, Neil; Megson, Peter; Roberg-Clark, Gareth; Sheppard, Kyle; Uher, Tim; Hammer, Donna; Vogel, Stuart N.

    2016-01-01

    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. Our poster describes the key elements of our program, and highlights successes and lessons learned; GRAD-MAP can serve as a model for other universities committed to diversity and inclusion.

  18. 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.

  19. Building an organized knowledge base: Concept mapping and achievement in secondary school physics

    NASA Astrophysics Data System (ADS)

    Pankratius, William J.

    Direct teaching of problem-solving methods to high school physics students met with little success. Expert problem solving depended upon an organized knowledge base. Concept mapping was found to be a key to organizing an effective knowledge base. The investigation of the effect of the degree of concept mapping on achievement was the purpose of this study. Six intact high school physics classes, taught by this investigator, took part in the study. Two classes were control groups and received standard instruction. Four classes received six weeks of concept-mapping instruction prior to the unit under study. Two of these four classes were the low-level treatment group and were required to submit concept maps at the conclusion of the instruction. The other two classes were the high-level treatment group and were required to submit concept maps at the beginning and at the conclusion of the unit under study. One class from each treatment group took a pretest prior to instruction. An analysis of the posttest results revealed no pretest sensitization. A one-way analysis of covariance indicated a significant main effect for the treatment level at the p < 0.05 level. A pair of single-df comparisons of the adjusted treatment means resulted in significant differences (p < 0.05) between the control group and the average of the treatment means as well as between the two experimental groups. It can be concluded that for this sample (upper-middle-class high school physics students) mapping concepts prior to, during, and subsequent to instruction led to greater achievement as measured by posttest scores.

  20. Physical map of the Clostridium beijerinckii (formerly Clostridium acetobutylicum) NCIMB 8052 chromosome.

    PubMed Central

    Wilkinson, S R; Young, M

    1995-01-01

    A combined physical and genetic map of the single, circular, 6.7-Mbp chromosome of the NCIMB 8052 strain of Clostridium beijerinckii (formerly Clostridium acetobutylicum) has been constructed by using a combination of cloned DNA fragments as hybridization probes and a bank of strains harboring insertions of the conjugative transposon Tn1545. The positions of 81 restriction endonuclease cleavage sites and 32 genes have been determined. Eight genes concerned with solventogenic fermentation are found at three different locations. The chromosome contains at least 13 rrn operons, 11 of which have been located on the map. Their transcriptional orientation diverges from the presumed location of the replication origin. PMID:7814334

  1. 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…

  2. 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.

  3. 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…

  4. 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…

  5. Tools for integrating women's health into medical education: clinical cases and concept mapping.

    PubMed

    Weiss, L B; Levison, S P

    2000-11-01

    The authors describe two teaching tools, case-based learning and concept mapping, and how they support cross-disciplinary, multidisciplinary, and interdisciplinary learning, use a biopsychosocial model, and promote the integration of sex- and gender-based science into the medical curriculum. The process of case development at MCP Hahnemann University (MCPHU) is outlined in detail for a specific case. That case, which integrates three different components of women's health, is then presented in full. The authors then provide an example of a concept map dealing with women and alcohol use; the map defines current knowledge and serves as a blueprint for developing curricular goals and learning objectives for the topic. Properly constructed concept maps and cases help teach patient-centered approaches to problem solving, address sex- and gender-based differences in disease as well as in pathophysiology and pharmacology, integrate psychosocial issues-such as family dynamics, environmental stressors, access to health care, effective gender-based communication between patient and provider, and cultural variations-along with biomedical ones, and encourage a multidisciplinary approach to patient care. The authors maintain that these tools might be used to transform medical education by making it more integrated and interdisciplinary. PMID:11078666

  6. 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. PMID:25956441

  7. Statewide Mapping of Aboveground Biomass by Integrating Airborne Lidar Data and National Forestry Inventory Plots

    NASA Astrophysics Data System (ADS)

    Chen, Q.; McRoberts, R. E.

    2015-12-01

    The freely available airborne lidar data at the sub-national level in the United States provide unprecedented opportunities for mapping large-area yet accurate information about vegetation structure, biomass, and carbon. However, the challenge of processing massive lidar data and extracting useful information is huge. This study is to conduct a statewide mapping study of aboveground biomass (AGB) by integrating airborne lidar data and FIA (Forest Inventory and Analysis) plot data for the whole state of Minnesota. We will share our experience and lessons in issues including 1) automatic generation of Digital Terrain Model from point cloud, 2) classification of vegetation returns, 3) calculation of AGB from FIA plots using different allometric models, 4) statistical modeling of AGB by integrating with FIA plots, and 5) assessing the uncertainty of mapped AGB.

  8. A high-resolution annotated physical map of the human chromosome 13q12-13 region containing the breast cancer susceptibility locus BRCA2.

    PubMed Central

    Fischer, S G; Cayanis, E; de Fatima Bonaldo, M; Bowcock, A M; Deaven, L L; Edelman, I S; Gallardo, T; Kalachikov, S; Lawton, L; Longmire, J L; Lovett, M; Osborne-Lawrence, S; Rothstein, R; Russo, J J; Soares, M B; Sunjevaric, I; Venkatraj, V S; Warburton, D; Zhang, P; Efstratiadis, A

    1996-01-01

    Various types of physical mapping data were assembled by developing a set of computer programs (Integrated Mapping Package) to derive a detailed, annotated map of a 4-Mb region of human chromosome 13 that includes the BRCA2 locus. The final assembly consists of a yeast artificial chromosome (YAC) contig with 42 members spanning the 13q12-13 region and aligned contigs of 399 cosmids established by cross-hybridization between the cosmids, which were selected from a chromosome 13-specific cosmid library using inter-Alu PCR probes from the YACs. The end sequences of 60 cosmids spaced nearly evenly across the map were used to generate sequence-tagged sites (STSs), which were mapped to the YACs by PCR. A contig framework was generated by STS content mapping, and the map was assembled on this scaffold. Additional annotation was provided by 72 expressed sequences and 10 genetic markers that were positioned on the map by hybridization to cosmids. Images Fig. 3 PMID:8570617

  9. 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. PMID:26235141

  10. Integrated multi-sensor fusion for mapping and localization in outdoor environments for mobile robots

    NASA Astrophysics Data System (ADS)

    Emter, Thomas; Petereit, Janko

    2014-05-01

    An integrated multi-sensor fusion framework for localization and mapping for autonomous navigation in unstructured outdoor environments based on extended Kalman filters (EKF) is presented. The sensors for localization include an inertial measurement unit, a GPS, a fiber optic gyroscope, and wheel odometry. Additionally a 3D LIDAR is used for simultaneous localization and mapping (SLAM). A 3D map is built while concurrently a localization in a so far established 2D map is estimated with the current scan of the LIDAR. Despite of longer run-time of the SLAM algorithm compared to the EKF update, a high update rate is still guaranteed by sophisticatedly joining and synchronizing two parallel localization estimators.

  11. 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,…

  12. Integrable maps from Galois differential algebras, Borel transforms and number sequences

    NASA Astrophysics Data System (ADS)

    Tempesta, Piergiulio

    A new class of integrable maps, obtained as lattice versions of polynomial dynamical systems is introduced. These systems are obtained by means of a discretization procedure that preserves several analytic and algebraic properties of a given differential equation, in particular symmetries and integrability (see Tempesta, 2010 [40]). Our approach is based on the properties of a suitable Galois differential algebra, that we shall call a Rota algebra. A formulation of the procedure in terms of category theory is proposed. In order to render the lattice dynamics confined, a Borel regularization is also adopted. As a byproduct of the theory, a connection between number sequences and integrability is discussed.

  13. Physical map of human Xq27-qter: localizing the region of the fragile X mutation.

    PubMed Central

    Poustka, A; Dietrich, A; Langenstein, G; Toniolo, D; Warren, S T; Lehrach, H

    1991-01-01

    We 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. Images PMID:1924290

  14. 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.

  15. Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf

    PubMed Central

    Sierro, Nicolas; van Oeveren, Jan; van Eijk, Michiel J T; Martin, Florian; Stormo, Keith E; Peitsch, Manuel C; Ivanov, Nikolai V

    2013-01-01

    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. PMID:23672264

  16. 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.

  17. Exclusion of epidermal growth factor and high-resolution physical mapping across the Rieger syndrome locus.

    PubMed Central

    Semina, E. V.; Datson, N. A.; Leysens, N. J.; Zabel, B. U.; Carey, J. C.; Bell, G. I.; Bitoun, P.; Lindgren, C.; Stevenson, T.; Frants, R. R.; van Ommen, G.; Murray, J. C.

    1996-01-01

    We have evaluated the 4q25-4q26 region where the autosomal dominant disorder Rieger syndrome has been previously mapped by linkage. We first excluded epidermal growth factor as a candidate gene by carrying out SSCP analysis of each of its 24 exons using a panel of seven unrelated individuals with Rieger syndrome. No evidence for etiologic mutations was detected in these individuals, although four polymorphic variants were identified, including three that resulted in amino acid changes. We next made use of two apparently balanced translocations, one familial and one sporadic, to identify a narrow physical localization likely to contain the gene or to be involved in regulation of gene function. Somatic cell hybrids were established from individuals with these balanced translocations, and these hybrids were used as a physical mapping resource for, first, preliminary mapping of the translocation breakpoints using known sequence tagged sites from chromosome 4 and then, after creating YAC and cosmids contigs encompassing the region, for fine mapping of those breakpoints. A cosmid contig spanning these breakpoints was identified and localized the gene to within approximately 150 kb of D4S193 on chromosome 4. The interval between the two independent translocations is approximately 50 kb in length and provides a powerful resource for gene identification. Images Figure 1 Figure 3 PMID:8940274

  18. 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

  19. 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.

  20. Toward a physical map of the genome of the nematode Caenorhabditis elegans

    SciTech Connect

    Coulson, A.; Sulston, J.; Brenner, S.; Karn, J.

    1986-10-01

    A technique for digital characterization and comparison of DNA fragments, using restriction enzymes, is described. The technique is being applied to fragments from the nematode Caenorhabditis elegans (i) to facilitate cross-indexing of clones emanating from different laboratories and (ii) to construct a physical map of the genome. Eight hundred sixty clusters of clones, from 35 to 350 kilobases long and totaling about 60% of the genome, have been characterized.

  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. 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.

  3. 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.

  4. 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.

  5. 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. PMID:25102957

  6. High-throughput physical mapping of chromosomes using automated in situ hybridization.

    PubMed

    George, Phillip; Sharakhova, Maria V; Sharakhov, Igor V

    2012-01-01

    Projects to obtain whole-genome sequences for 10,000 vertebrate species and for 5,000 insect and related arthropod species 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 platform. 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 assemblies. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented. 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 populations. 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 assemblies and

  7. 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)

  8. Physical approach to analytic simulation of Fresnel integrals

    NASA Astrophysics Data System (ADS)

    Anokhov, Sergey

    2007-01-01

    Fresnel integrals continue to find new applications in various areas of human activity, including technology and music. However, performing calculations with them is often hindered by a mathematical peculiarity of these integrals, which is the rapidly oscillating functions of the basic variable. This circumstance complicates the numerical calculations when these integrals need additional integral transformation: convolution, Fourier transform, etc. The suggested solution of the problem consists of replacement of the complex Fresnel integral by a single rational function that simulates this integral in the entire area of its existence with an accuracy up to 10-6. The advantages of the suggested approach are confirmed by the concrete example.

  9. Integrating field sampling, spatial statistics and remote sensing to map wetland vegetation in the Pantanal, Brazil

    NASA Astrophysics Data System (ADS)

    Arieira, J.; Karssenberg, D.; de Jong, S. M.; Addink, E. A.; Couto, E. G.; Nunes da Cunha, C.; Skøien, J. O.

    2010-09-01

    including new digital images as explanatory variables in the model. By comparing the resulting plant community map with a flood duration map, we verified that flooding duration is an important driver of vegetation zonation. We discuss our study in the context of developing a mapping approach that is able to integrate field point data and high-resolution remote sensing images, providing new basis to map wetland vegetation and allowing its future application in habitat management, conservation assessment and long-term ecological monitoring in wetland landscapes.

  10. Comparing Point Count System and physically-based approaches to map aquifer vulnerability

    NASA Astrophysics Data System (ADS)

    Lagomarsino, D.; Martina, M. L. V.; Todini, E.

    2009-04-01

    Pollution vulnerability maps of aquifers are an important instrument for land and water management. These maps are generally based on simplified Point Count System Models (PCSM), such as DRASTIC or SINTACS, without the use of physically based groundwater models, which may provide more accurate results. The present research aims at finding a trade-off between the accuracy provided by a physically-based model, which inevitably involves higher computational complexity and data requirements, and the coarser, albeit simpler and easy to implement, approach provided by an indicator based model such as one of the most important PCSM, the DRASTIC model (Aller et al., 1987). The alluvial aquifer of the conoid of the Reno River, extending from pedemountain hills of the Apennines chain towards Po plain, is one of the main sources of drinking water for the city of Bologna. The parameters considered by DRASTIC (Depth of water, net Recharge, Aquifer media, Soil media, Topography, Impact of vadose zone and hydraulic Conductivity) represent the main hydrogeological and environmental parameters that influence the pollution transport from the surface towards the groundwater. The real flow of the Reno aquifer, was then simulated by means of a finite element model (FEFLOW) that takes into account the physical processes of water movement and the associated transport of contaminant in the environment. The results obtained by the model have been compared with the DRASTIC vulnerability map. A preliminary analysis of the vulnerability map, based on chemical analyses of water, reveals that the concentration of Nitrates is actually higher in those zones where higher vulnerability values were found.

  11. 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

  12. 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.

  13. 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.

  14. Contribution of physical modelling to climate-driven landslide hazard mapping: an alpine test site

    NASA Astrophysics Data System (ADS)

    Vandromme, R.; Desramaut, N.; Baills, A.; Hohmann, A.; Grandjean, G.; Sedan, O.; Mallet, J. P.

    2012-04-01

    The aim of this work is to develop a methodology for integrating climate change scenarios into quantitative hazard assessment and especially their precipitation component. The effects of climate change will be different depending on both the location of the site and the type of landslide considered. Indeed, mass movements can be triggered by different factors. This paper describes a methodology to address this issue and shows an application on an alpine test site. Mechanical approaches represent a solution for quantitative landslide susceptibility and hazard modeling. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account the uncertainty in the analysis. In this perspective, a new hazard modeling method is developed and integrated in a program named ALICE. This program integrates mechanical stability analysis through a GIS software taking into account data uncertainty. This method proposes a quantitative classification of landslide hazard and offers a useful tool to gain time and efficiency in hazard mapping. However, an expertise approach is still necessary to finalize the maps. Indeed it is the only way to take into account some influent factors in slope stability such as heterogeneity of the geological formations or effects of anthropic interventions. To go further, the alpine test site (Barcelonnette area, France) is being used to integrate climate change scenarios into ALICE program, and especially their precipitation component with the help of a hydrological model (GARDENIA) and the regional climate model REMO (Jacob, 2001). From a DEM, land-cover map, geology, geotechnical data and so forth the program classifies hazard zones depending on geotechnics and different hydrological contexts varying in time. This communication, realized within the framework of Safeland project, is supported by the European Commission under the 7th Framework Programme for Research and Technological

  15. 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.

  16. Integrating Global Games in the Elementary Physical Education Curriculum

    ERIC Educational Resources Information Center

    Gross, Michael K.; Buchanan, Alice M.

    2011-01-01

    Global education units are great motivators for activity in elementary physical education because they can bring freshness and excitement to a physical education program. Additionally, children are provided with the opportunity to learn just how much physical education interacts with the other academic subjects that they study. This article…

  17. 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

  18. Multi-Sensor Integration to Map Odor Distribution for the Detection of Chemical Sources.

    PubMed

    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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. A YAC-, P1, and cosmid-based physical map of the BRCA1 region on chromosome 17q21

    SciTech Connect

    Couch, F.J.; Castilla, L.H.; Brody, L.C.

    1995-01-01

    A familial early-onset breast cancer gene (BRCA1) has been localized to chromosome 17q21. To characterize this region and to aid in the identification of the BRCA1 gene, a physical map of a region of 1.0-1.5 Mb between the EDH17B1 and the PPY loci on chromosome 17q21 was generated. The physical map is composed of a yeast artificial chromosome (YAC) and P1 phage contig with one gap. The majority of the interval has also been converted to a cosmid contig. Twenty-three PCR-based sequence-tagged sites (STSs) were mapped to these contigs, thereby confirming the order and overlap of individual clones. This complex physical map of the BRCA1 region was used to isolate genes by a number of gene identification techniques and to generate transcript maps of the region. 32 refs., 4 figs.

  5. 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

  6. Unveiling Accretion Disks - Physical Parameter Eclipse Mapping of Accretion Disks in Dwarf Novae

    NASA Astrophysics Data System (ADS)

    Vrielmann, S.

    1997-06-01

    This work presents a new tomography algorithm, the Physical Parameter Eclipse Mapping method. It has been designed to reconstruct the structure of accretion disks in cataclysmic variables in terms of the basic physical parameters. Cataclysmic variables are close interacting binaries, in which mass transfer from one of the stars, typically a main sequence star, to the other star, a white dwarf, proceeds via an accretion disk around the white dwarf. Accretion disks are of general importance in astrophysics, since they occur in a number of objects with mass accretion, like active galactic nuclei and young stellar objects. The eclipsing cataclysmic variables are ideal systems to study such accretion process, since with the varying orbital phase different parts of the accretion disk can be viewed. The tomography method is based on the classical Eclipse Mapping algorithm which yields intensity distributions in the accretion disk by fitting the observed eclipse light curve. In order to avoid ambiguities this back-projection is using a maximum entropy algorithm, with selects the smoothest solution still compatible with the data. In my new method the intensity distributions are replaced by distributions of physical parameters, using a specific theoretical model spectrum to fit a set of eclipse light curves at various wavelengths. The spectrum is chosen according to the type of cataclysmic variable under investigation and its state at the time of observation. This work shows through application to synthetic data that with such an approach given distributions in physical parameters can be reproduced, as long as the parameters assume values in the parameter space outside of regions where ambiguities arise. Versions with two simple models are tested, but in principle this method can cope with any given model spectrum. The Physical Parameter Eclipse Mapping method is applied to two sets of real data of the dwarf nova IP Pegasi on decline from outburst and HT Cassiopeiae in

  7. Integrating geology, rock physics, and seismology for reservoir-quality prediction

    NASA Astrophysics Data System (ADS)

    Florez-Nino, Juan-Mauricio

    This research focuses on the prediction of reservoir quality from seismic and well-log data, integrating concepts from geology and geophysics. The purpose has been to understand the geologic processes that control lateral variations in acoustic impedance and porosity. The work concentrates on the effect of rock texture and fractures on the elastic properties of sedimentary rocks. This work improves the understanding of the rock-physics depositional and diagenetic trends. The modified Hashin-Shtrikman lower bound can be used to distinguish between sorting and packing effects. It constitutes an upper bound for the sorting effect and a lower bound for the packing effect. Pressure solution is an alternative mechanism to reproduce the rock-physics diagenetic trend for high-porosity quartzose sands, using the Digby-Rutter model proposed here. The patterns that clastic sedimentary sequences present, in the rock-physics planes, agree with predictions from rock-physics models. Dispersed sand-clay mixtures predominate in fluvial deposits, whereas laminar mixtures predominate in mud-rich deep-water deposits. Scarcity of mixed lithofacies characterizes sand-rich deep-water deposits, whereas abundance of these lithofacies occurs in low-energy shallow marine deposits. The results demonstrate that the elastic properties of clastic mixed lithofacies strongly vary depending on the mixture's proportion and fabric, and rock-physics models can be used to predict these variations. The second part of this research deals with the use of outcrop information and seismic data to predict fracture distribution in the subsurface. This work documents a fundamental link between fracture hierarchies and sequence stratigraphy. Fracture spacing and dimensions of different fracture hierarchies are constrained by the thickness of the confining stratigraphic interval. It also documents examples of hierarchical shearing and progressive deformation, a concept that explains the evolution of faults and

  8. 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.

  9. A physical map of the 85 kb virulence plasmid of Rhodococcus equi 103.

    PubMed Central

    de la Peña-Moctezuma, A; Prescott, J F

    1995-01-01

    A physical map of the 85 kb virulence plasmid pOTS from Rhodococcus equi 103 was constructed. The restriction map contains 2 AsnI, 5 BglII, 9 EcoRI, 4 HindIII, and 3 XbaI sites. The positions of the EcoRI and HindIII of pOTS are identical to that of the 85 kb virulence plasmid of R. equi ATCC 33701 reported recently by others. EcoRI restriction fragment sizes were similar in the 85 kb plasmids isolated from 4 horse derived R. equi but, except apparently for the 28.3 and possibly 2.0 and 1.5 kb fragments, were different in an 80.1 kb plasmid isolated from a pig source R. equi. PMID:8521357

  10. A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map

    PubMed Central

    Solignac, Michel; Mougel, Florence; Vautrin, Dominique; Monnerot, Monique; Cornuet, Jean-Marie

    2007-01-01

    Background: 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. Results: 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. Conclusion: 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. PMID:17459148

  11. Physical and genetic map of the Clostridium saccharobutylicum (formerly Clostridium acetobutylicum) NCP 262 chromosome.

    PubMed

    Keis, S; Sullivan, J T; Jones, D T

    2001-07-01

    A physical and genetic map of the Clostridium saccharobutylicum NCP 262 chromosome was constructed. The order of macrorestriction fragments was determined by analysing fragments generated after single and double digestion with the restriction enzymes BssHII, I-CeuI, Sse8387I, RsrII and SfiI and separation by PFGE. The I-CeuI backbone of C. saccharobutylicum was constructed by indirect end-labelling with rrs- and 3' rrl-specific probes located on either side of the I-CeuI site in the rrn operon, and reciprocal separation of BssHII and I-CeuI digestion products by two-dimensional PFGE. The positions of BssHII fragments on the physical map were determined using a library of linking clones containing BssHII cleavage sites. The size of the circular genome was estimated to be 5.3 Mb with a mean resolution of approximately 140 kb. The chromosome of C. saccharobutylicum contains 12 rrn operons, located on 46% of the chromosome, which are transcribed divergently from the deduced origin of replication. The genetic map was constructed by determining the location of 28 genes involved in house-keeping, heat-shock response, sporulation, electron transfer and acid- and solvent-formation. Comparison of the C. saccharobutylicum genetic map with those of the spore-forming bacteria Bacillus subtilis, Clostridium acetobutylicum, Clostridium perfringens and Clostridium beijerinckii indicated C. saccharobutylicum to be most similar to the latter two Clostridium species, with the order of the genes within the gyrAB and recA loci being conserved. PMID:11429467

  12. 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

  13. 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.

  14. TRANSVERSE MERCATOR MAP PROJECTION OF THE SPHEROID USING TRANSFORMATION OF THE ELLIPTIC INTEGRAL

    NASA Technical Reports Server (NTRS)

    Wallis, D. E.

    1994-01-01

    This program produces the Gauss-Kruger (constant meridional scale) Transverse Mercator Projection which is used to construct the U.S. Army's Universal Transverse Mercator (UTM) Grid System. The method is capable of mapping the entire northern hemisphere of the earth (and, by symmetry of the projection, the entire earth) accurately with respect to a single principal meridian, and is therefore mathematically insensitive to proximity either to the pole or the equator, or to the departure of the meridian from the central meridian. This program could be useful to any map-making agency. The program overcomes the limitations of the "series" method (Thomas, 1952) presently used to compute the UTM Grid, specifically its complicated derivation, non-convergence near the pole, lack of rigorous error analysis, and difficulty of obtaining increased accuracy. The method is based on the principle that the parametric colatitude of a point is the amplitude of the Elliptic Integral of the 2nd Kind, and this (irreducible) integral is the desired projection. Thus, a specification of the colatitude leads, most directly (and with strongest motivation) to a formulation in terms of amplitude. The most difficult problem to be solved was setting up the method so that the Elliptic Integral of the 2nd Kind could be used elsewhere than on the principal meridian. The point to be mapped is specified in conventional geographic coordinates (geodetic latitude and longitudinal departure from the principal meridian). Using the colatitude (complement of latitude) and the longitude (departure), the initial step is to map the point to the North Polar Stereographic Projection. The closed-form, analytic function that coincides with the North Polar Stereographic Projection of the spheroid along the principal meridian is put into a Newton-Raphson iteration that solves for the tangent of one half the parametric colatitude, generalized to the complex plane. Because the parametric colatitude is the amplitude of

  15. Positional Accuracy of Airborne Integrated Global Positioning and Inertial Navigation Systems for Mapping in Glen Canyon, Arizona

    USGS Publications Warehouse

    Sanchez, Richard D.; Hothem, Larry D.

    2002-01-01

    High-resolution airborne and satellite image sensor systems integrated with onboard data collection based on the Global Positioning System (GPS) and inertial navigation systems (INS) may offer a quick and cost-effective way to gather accurate topographic map information without ground control or aerial triangulation. The Applanix Corporation?s Position and Orientation Solutions for Direct Georeferencing of aerial photography was used in this project to examine the positional accuracy of integrated GPS/INS for terrain mapping in Glen Canyon, Arizona. The research application in this study yielded important information on the usefulness and limits of airborne integrated GPS/INS data-capture systems for mapping.

  16. Physical map of the 850 kb Van der Woude critical region

    SciTech Connect

    Sander, A.; Schmelzle, R.; Schute, B.C.

    1994-09-01

    The VWS gene was recently localized for fine structure mapping within a 2 cM region of 1q32 between D1S245 and D1S205. D1S205 detected an allelic loss in one family where a developmental delay was cosegregating with typical features of VWS consistent with a submicroscopic deletion. D1S491 was mapped to the critical interval and proved to be heterozygous in at least one affected member of that family which narrows the critical interval to 1.6 cM. A YAC contig was constructed across this interval by screening the CEPH YAC {open_quote}A{close_quote} and {open_quote}B{close_quote} libraries with marker STSs and YAC end-clone STSs. A total of 16 YACs were identified and of these, 10 retested positive (5 from {open_quotes}A{close_quotes} and 5 from {open_quotes}B{close_quotes}). In addition, 2 other YACs were identified using data from the CEPH-Genethon Human Physical Map. The relative order of each YAC was deduced from the order of the genetic markers. The 12 YACs could be assembled into a single contig of about 4 Mb which includes the critical region. The maximum distance of the critical region is 850 kb based on the size of a single YAC which contains both flanking markers. We also mapped the microdeletion to this YAC by PCR using a human-hamster somatic cell hybrid whose human chromosome 1 component only contains the microdeletion. In addition, we mapped D1S70 to the critical interval and are testing a recently identified STRP from this clone in families with critical recombinants. Using the YAC clones and the microdeletion hybrid cell line, we excluded TAX1 and fibromodulin as candidate genes for VWS.

  17. Physical mapping, cloning, and identification of genes within a 500-kb region containing BRCA1.

    PubMed Central

    Brown, M A; Jones, K A; Nicolai, H; Bonjardim, M; Black, D; McFarlane, R; de Jong, P; Quirk, J P; Lehrach, H; Solomon, E

    1995-01-01

    BRCA1 is a breast/ovarian cancer susceptibility gene on human chromosome 17q21. We describe a complete and detailed physical map of a 500-kb region of genomic DNA containing the BRCA1 gene and the partial cloning in phage P1 artificial chromosomes. Approximately 70 exons were isolated from this region, 11 of which were components of the BRCA1 gene. Analysis of the other exons revealed a rho-related G protein and the interferon-induced leucine-zipper protein IFP-35. Images Fig. 1 Fig. 2 Fig. 4 PMID:7753812

  18. New generation of integrated geological-geomorphological reconstruction maps in the Rhine-Meuse delta, The Netherlands

    NASA Astrophysics Data System (ADS)

    Pierik, Harm Jan; Cohen, Kim; Stouthamer, Esther

    2016-04-01

    Geological-geomorphological reconstructions are important for integrating diverse types of data and improving understanding of landscape formation processes. This works especially well in densely populated Holocene landscapes, where large quantities of raw data are produced by geotechnical, archaeological, soil science and hydrological communities as well as in academic research. The Rhine-Meuse delta, The Netherlands, has a long tradition of integrated digital reconstruction maps and databases. This contributed to improve understanding of delta evolution, especially regarding the channel belt network evolution. In this contribution, we present a new generation of digital map products for the Holocene Rhine-Meuse delta. Our reconstructions expand existing channel belt network maps, with new map layers containing natural levee extent and relative elevation. The maps we present have been based on hundreds of thousands of lithological borehole descriptions, >1000 radiocarbon dates, and further integrate LIDAR data, soil maps and archaeological information. For selected time slices through the Late Holocene, the map products describe the patterns of levee distribution. Additionally, we mapped the palaeo-topography of the levees through the delta, aiming to resolve what parts of the overbank river landscape were the relatively low and high positioned areas in the past landscape. The resulting palaeogeographical maps are integrative products created for a very data-rich research area. They will allow for delta-wide analysis in studying changes in the Late Holocene landscape and the interaction with past habitation.

  19. Integrating Children's Books and Literacy into the Physical Education Curriculum

    ERIC Educational Resources Information Center

    Fingon, Joan C.

    2011-01-01

    Since the onset of No Child Left Behind (NCLB, 2002) schools have been focusing on raising test scores in reading and mathematics, while at the same time feeling pressured to reduce subjects such as physical education and health. It seems for many educators finding time in the school day for students' physical activity has become increasingly…

  20. The Relative Effectiveness of Integrated Reading Study Strategy and Conceptual Physics Approach

    ERIC Educational Resources Information Center

    Taslidere, Erdal; Eryilmaz, Ali

    2012-01-01

    The primary purpose of this study was to investigate the combined and partial effects of the Integrated Reading/Study Strategy and Conceptual Physics Approach on ninth grade private high school students' achievement in and attitudes toward optics. The Integrated Reading/Study Strategy is a new strategy which was developed by integrating previously…

  1. Volumetric ellipsoid zone mapping for enhanced visualisation of outer retinal integrity with optical coherence tomography.

    PubMed

    Itoh, Yuji; Vasanji, Amit; Ehlers, Justis P

    2016-03-01

    Objective assessment of retinal layer integrity with optical coherence tomography (OCT) is currently limited. The ellipsoid zone (EZ) has been identified as an important feature on OCT that has critical prognostic value in macular disorders. In this report, we describe a novel assessment tool for EZ integrity that provides visual and quantitative assessment across an OCT data set. Using this algorithm, we describe the findings in multiple clinical examples, including normal controls, age-related macular degeneration, drug effects (eg, ocriplasmin, hydroxychloroquine) and effects of surgical manipulation (eg, following membrane peeling using intraoperative OCT). EZ mapping provides both en face visualisation of EZ integrity and EZ-retinal pigment epithelium height. Additionally, volumetric, area and linear measurements are feasible using this assessment tool. PMID:26201354

  2. Parents' Perceptions of the Factors Essential for Integrated Physical Education Programs.

    ERIC Educational Resources Information Center

    Downing, John H.; Rebollo, Joanne

    1999-01-01

    A survey of 75 parents of elementary students with physical disabilities investigated their perspectives regarding the factors essential for placement into integrated physical-education programs. Results found they believed that class size, program support, physical and communicative skills, health status, and motivation were prerequisites of an…

  3. Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites.

    PubMed

    Serrao, Erik; Cherepanov, Peter; Engelman, Alan N

    2016-01-01

    Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients. PMID:27023428

  4. A 1. 8-Mb YAC contig in Xp11. 23: Identification of Cpg islands and physical mapping of CA repeats in a region of high gene density

    SciTech Connect

    Coleman, M.P.; Nemeth, A.H.; Campbell, L.; Raut, C.P.; Davies, K.E. ); Weissenbach, J. )

    1994-05-15

    The genes ARAF1, SYN1, TIMP, and PFC are clustered within 70 kb of one another, and, as reported in the accompanying paper, at least four more genes map within 400 kb: a cluster of Krueppel-type zinc finger genes (including ZNF21, ZNF41, and ZNF81) and ELK-1, a member of the ets oncogene superfamily. This gene-rich region is of particular interest because of the large number of disease genes mapping to Xp11.23: At least three eye diseases (retinitis pigmentosa type 2, congenital stationary night blindness CSNB1, and Aland Island eye disease), Wiskott-Aldrich syndrome, X-linked nephrolithiasis, and a translocation breakpoint associated with synovial sarcoma. The authors have constructed a 1.8-Mb YAC contig in this region, confirming the link between TIMP and OATL1 reported by Knight et al. (1994) and extending the map in the distal direction. To investigate the likelihood that more genes are located within this region, they have carried out detailed mapping of rare-cutter restriction sites in these YACs and identified seven CpG islands. At least six of these islands are located over 50 kb from any known gene locations, suggesting that the region contains at least this many as yet unidentified genes. They have also mapped the physical locations of six highly polymorphic CA repeats within the contig, thus integrating the physical, genetic, and transcriptional maps of the region and facilitating the mapping and identification of disease genes. Together with the report by Knight et al., these data indicate the following order of loci: Xpter-DXS1264-DXS1055-DXS1003-DXS1146-DXS1266-(ZNF41, ARAF1)-SYN1 CA repeat-SYN1 (3[prime] end)-TIMP-SYN1 (5[prime] end)-PFC CA repeat-PFC-(DXS426, ELK1)-(DXS1265, ZNF81)-ZNF21-DXS1267-OATL1-Xcen. 40 refs., 4 figs., 3 tabs.

  5. MAPS (My Atlas and Plot Service) for Integrated Earth Observation Data

    NASA Astrophysics Data System (ADS)

    Ichino, M.; Fukuda, K.; Sugiura, N.; Funakoshi, R.

    2010-12-01

    DIAS (Data integration and Analysis System) is one of the activities of GEOSS, and also one of Japanese National Key Technology activities. JAMSTEC collaborates with the University of Tokyo, the main contractor of the project. It is a five-year project until March 2011. We at JAMSTEC also have developed a data distribution system toward long-term sustainable services as part of DIAS. We launched the early website at 2007. It provided six integration and analysis datasets in the fields of “Ocean & Fishery Resources”, “Water Cycle” and “Land Ecosystem”. We also investigated users’ needs through an online questionnaire and through interviews regarding the types and quality of required data, data formats, website functions and so on. Accordingly, our new website, MAPS, which is short for My Atlas and Plot Service has been remodeled with four new datasets and new functions to meet users’ needs since the fall in 2010. We have provided online mapping and plotting services with MapServer, and download services with functions of extracting digital data by selected attribute and of converting into another file type. These services provide a powerful visualization and analysis capabilities for the data products. The input items and forms in online questionnaire and Contact-Us page in our website have been refined to collect feedbacks and comments about the new website functions. We are continuously researching the further future needs in order to promote the wider usage of the datasets.

  6. Fuzzy cognitive mapping in support of integrated ecosystem assessments: Developing a shared conceptual model among stakeholders.

    PubMed

    Vasslides, James M; Jensen, Olaf P

    2016-01-15

    Ecosystem-based approaches, including integrated ecosystem assessments, are a popular methodology being used to holistically address management issues in social-ecological systems worldwide. In this study we utilized fuzzy logic cognitive mapping to develop conceptual models of a complex estuarine system among four stakeholder groups. The average number of categories in an individual map was not significantly different among groups, and there were no significant differences between the groups in the average complexity or density indices of the individual maps. When ordered by their complexity scores, eight categories contributed to the top four rankings of the stakeholder groups, with six of the categories shared by at least half of the groups. While non-metric multidimensional scaling (nMDS) analysis displayed a high degree of overlap between the individual models across groups, there was also diversity within each stakeholder group. These findings suggest that while all of the stakeholders interviewed perceive the subject ecosystem as a complex series of social and ecological interconnections, there are a core set of components that are present in most of the groups' models that are crucial in managing the system towards some desired outcome. However, the variability in the connections between these core components and the rest of the categories influences the exact nature of these outcomes. Understanding the reasons behind these differences will be critical to developing a shared conceptual model that will be acceptable to all stakeholder groups and can serve as the basis for an integrated ecosystem assessment. PMID:26520042

  7. Localization of Jacobsen syndrome breakpoints on a 40-Mb physical map of distal chromosome 11q.

    PubMed

    Tunnacliffe, A; Jones, C; Le Paslier, D; Todd, R; Cherif, D; Birdsall, M; Devenish, L; Yousry, C; Cotter, F E; James, M R

    1999-01-01

    Jacobsen syndrome is a haploinsufficiency disorder caused, most frequently by terminal deletion of part of the long arm of chromosome 11, with breakpoints in 11q23.3-11q24.2. Inheritance of an expanded p(CCG)n trinucleotide repeat at the folate-sensitive fragile site FRA11B has been implicated in the generation of the chromosome breakpoint in several Jacobsen syndrome patients. The majority of such breakpoints, however, map distal to this fragile site and are not linked with its expression. To characterize these distal breakpoints and ultimately to further investigate the mechanisms of chromosome breakage, a 40-Mb YAC contig covering the distal long arm of chromosome 11 was assembled. The utility of the YAC contig was demonstrated in three ways: (1) by rapidly mapping the breakpoints from two new Jacobsen syndrome patients using FISH; (2) by demonstrating conversion to high resolution PAC contigs after direct screening of PAC library filters with a YAC clone containing a Jacobsen syndrome breakpoint; and (3) by placing 23 Jacobsen syndrome breakpoints on the physical map. This analysis has suggested the existence of at least two new Jacobsen syndrome breakpoint cluster regions in distal chromosome 11. PMID:9927483

  8. Physical map of the region containing the gene for Batten disease (CLN3)

    SciTech Connect

    Jaervelae, I.E.; Mitchinson, H.M.; Gardiner, R.M.

    1995-06-05

    CLN3 has been mapped genetically to 16p12, to the interval between D16S288 and D16S383, a sex-averaged genetic distance of 2.1 cM. Analysis of disease haplotypes for four microsatellite markers in this interval, D16S288, D16S299, D16S298, and SPN, has shown significant allelic association between one allele at each of these loci and CLN3. All four of the associated markers were used as nucleation sites in the isolation of genomic clones (YACs). A contig was assembled which contains 3 of the 4 associated markers and which confirmed the relative order of these markers. Marker D16S272 has been located on the physical map between D16S288 and D16S299. Restriction mapping has demonstrated the location of possible CpG islands. One gene, STP, has been localized on the YAC contig proximal to D16S298 and is therefore a candidate for CLN3. Other genes, including IL4R, SGLT2, and UQCRC2, have been excluded from this region. 12 refs., 2 figs.

  9. Characterizing physical habitats in rivers using map-derived drivers of fluvial geomorphic processes

    NASA Astrophysics Data System (ADS)

    Bizzi, Simone; Lerner, David N.

    2012-10-01

    New understanding of fluvial geomorphological processes has successfully informed flood mitigation strategies and rehabilitation schemes in recent years. However well established geomorphological assessments are location-specific and demanding in terms of resource and expertise required, and their routine application for regional or national river characterization, although desirable, is unlikely at present. This paper proposes a framework based on GIS procedures, empirical relationships and the self organized map for the analysis and classification of map-derived drivers of fluvial morphological processes. The geomorphic controls analysed are: channel gradient and hydrology, specific stream power, river order and floodplain extent. The case study is a gravel bed river in England. Using the self organized map, we analyse patterns of these controls along the river longitudinal profile and identify clusters of similar configuration. The reciprocal relationships that emerge amongst the geomorphic controls reflect the hierarchical nature of fluvial systems and are consistent with the current theoretical understanding of fluvial processes. Field observations from the River Habitat Survey are used to prove the influence of geomorphic drivers on reach-scale morphological forms. Six clusters are identified which describe six distinctive channel types. These proved to be characterized by distinctive configurations of geomorphic drivers and specific sets of physical habitat features. The method successfully characterizes the notable transitions in channel character along the river course. The framework is suitable for regional or national scale assessments through automatic GIS and statistical procedures with moderate effort.

  10. Genetic analysis of 12 unrelated CADASIL families: Demonstration of genetic homogeneity: Physical mapping of the gene

    SciTech Connect

    Tournier-Lasserve, E.; Nibbio, A.; Vahedi, K.

    1994-09-01

    CADASIL is the acronym (Cerebral Autosomal Dominant Arteriopathy with Subcortical Ischemic Strokes and Leukoencephalopathy) designating a recently identified mendelian cerebral arteriopathy characterized by the recurrence of ischemic sensory and motor deficits leading to a progressive subcortical dementia. Magnetic resonance imaging of the brain shows extensive areas of increased signal in the hemispheric white matter. We recently mapped the CADASIL locus in 2 large families on chromosome 19 in a 14 cM interval bracketed by D19S221 and D19S215{sup *}. Forty additional families have been collected. Twelve of them including more than 200 members have already been genotyped with a set of 10 highly polymorphic markers located between D19S221 and D19S215. All families are significantly linked to chromosome 19 demonstrating genetic homogeneity. Combined lod scores for several of these markers are above 30. The size of the mapping interval has been reduced to 2 cM. Genetic testing for presymptomatic individuals is now possible with respect to all ethical rules in this severe condition. Lastly, physical mapping of the affected gene has been started and data will be presented at the meeting.

  11. Genetic and Physical Mapping of Telomeres in the Rice Blast Fungus, Magnaporthe Grisea

    PubMed Central

    Farman, M. L.; Leong, S. A.

    1995-01-01

    Telomeric restriction fragments were genetically mapped to a previously described linkage map of Magnaporthe grisea, using RFLPs identified by a synthetic probe, (TTAGGG)(3). Frequent rearrangement of telomeric sequences was observed in progeny isolates creating a potential for misinterpretation of data. Therefore a consensus segregation data set was used to minimize mapping errors. Twelve of the 14 telomeres were found to be genetically linked to existing RFLP markers. Second-dimensional electrophoresis of restricted chromosomes confirmed these linkage assignments and revealed the chromosomal location of the two unlinked telomeres. We were thus able to assign all 14 M. grisea telomeres to their respective chromosome ends. The Achilles' cleavage (AC) technique was employed to determine that chromosome 1 markers 11 and CH5-120H were ~1.8 Mb and 1.28 Mb, respectively, from their nearest telomeres. RecA-AC was also used to determine that unlinked telomere 6 was ~530 kb from marker CH5-176H in strain 2539 and 580 kb in Guy11. These experiments indicated that large portions of some chromosome ends are unrepresented by genetic markers and provided estimates of the relationship of genetic to physical distance in these regions of the genome. PMID:7498730

  12. An Integrated Genetic Map of the African Human Malaria Vector Mosquito, Anopheles Gambiae

    PubMed Central

    Zheng, L.; Benedict, M. Q.; Cornel, A. J.; Collins, F. H.; Kafatos, F. C.

    1996-01-01

    We present a genetic map based on microsatellite polymorphisms for the African human malaria vector, Anopheles gambiae. Polymorphisms in laboratory strains were detected for 89% of the tested microsatellite markers. Genotyping was performed for individual mosquitoes from 13 backcross families that included 679 progeny. Three linkage groups were identified, corresponding to the three chromosomes. We added 22 new markers to the existing X chromosome map, for a total of 46 microsatellite markers spanning a distance of 48.9 cM. The second chromosome has 57 and the third 28 microsatellite markers spanning a distance of 72.4 and 93.7 cM, respectively. The overall average distance between markers is 1.6 cM (or 1.1, 1.2, and 3.2 cM for the X, second, and third chromosomes, respectively). In addition to the 131 microsatellite markers, the current map also includes a biochemical selectable marker, Dieldrin resistance (Dl), on the second chromosome and five visible markers, pink-eye (p) and white (w) on the X, collarless (c) and lunate (lu) on the second, and red-eye (r) on the third. The cytogenetic locations on the nurse cell polytene chromosomes have been determined for 47 markers, making this map an integrated tool for cytogenetic, genetic, and molecular analysis. PMID:8725240

  13. New generation of electro-anatomic mapping: full intracardiac ultrasound image integration.

    PubMed

    Packer, Douglas L; Johnson, Susan B; Kolasa, Mark W; Bunch, Thomas J; Henz, Benhur D; Okumura, Yasuo

    2008-11-01

    Surrogate electro-anatomic-derived geometries are used as the three-dimensional (3D) basis for mapping of cardiac arrhythmias. While merged computed tomography (CT) imaging may provide stellar pulmonary vein (PV) and left atrial (LA) anatomy, the applied scans must be obtained prior to ablation, and may not reflect physiologic conditions at the time of intervention. Patient-specific, ultrasound-derived 3D imaging has been developed as an alternative basis for new generation electro-anatomic mapping. An electro-anatomic sensor positioned at the tip of the phased-array intracardiac ultrasound catheter, provides the means to specify both location and orientation of each image as the 'context' for creating the 3D volumes for co-registration with electro-anatomic mapping. Specific anatomic details such as the pulmonary veins, membranous fossa, papillary muscles, or valve structures derived from real-time imaging can also be integrated into each segmented volume. This presentation reviews the basis and methods for this novel multi-modality image fusion for the creation of robust, nearly real-time anatomic images for guiding electro-anatomic mapping and ablation without requiring pre-acquired CT image sets, with accompanying limitations. PMID:18955397

  14. A BAC-based physical map of the Drosophila buzzatii genome

    SciTech Connect

    Gonzalez, Josefa; Nefedov, Michael; Bosdet, Ian; Casals, Ferran; Calvete, Oriol; Delprat, Alejandra; Shin, Heesun; Chiu, Readman; Mathewson, Carrie; Wye, Natasja; Hoskins, Roger A.; Schein, JacquelineE.; de Jong, Pieter; Ruiz, Alfredo

    2005-03-18

    Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophilabuzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and a {approx}18X expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

  15. The articulation of integration of clinical and basic sciences in concept maps: differences between experienced and resident groups.

    PubMed

    Vink, Sylvia; van Tartwijk, Jan; Verloop, Nico; Gosselink, Manon; Driessen, Erik; Bolk, Jan

    2016-08-01

    To determine the content of integrated curricula, clinical concepts and the underlying basic science concepts need to be made explicit. Preconstructed concept maps are recommended for this purpose. They are mainly constructed by experts. However, concept maps constructed by residents are hypothesized to be less complex, to reveal more tacit basic science concepts and these basic science concepts are expected to be used for the organization of the maps. These hypotheses are derived from studies about knowledge development of individuals. However, integrated curricula require a high degree of cooperation between clinicians and basic scientists. This study examined whether there are consistent variations regarding the articulation of integration when groups of experienced clinicians and basic scientists and groups of residents and basic scientists-in-training construct concept maps. Seven groups of three clinicians and basic scientists on experienced level and seven such groups on resident level constructed concept maps illuminating clinical problems. They were guided by instructions that focused them on articulation of integration. The concept maps were analysed by features that described integration. Descriptive statistics showed consistent variations between the two expertise levels. The concept maps of the resident groups exceeded those of the experienced groups in articulated integration. First, they used significantly more links between clinical and basic science concepts. Second, these links connected basic science concepts with a greater variety of clinical concepts than the experienced groups. Third, although residents did not use significantly more basic science concepts, they used them significantly more frequent to organize the clinical concepts. The conclusion was drawn that not all hypotheses could be confirmed and that the resident concept maps were more elaborate than expected. This article discusses the implications for the role that residents and

  16. Characterization and Physical Mapping of Ribosomal RNA Gene Families in Plantago

    PubMed Central

    DHAR, MANOJ K.; FRIEBE, BERND; KAUL, SANJANA; GILL, BIKRAM S.

    2006-01-01

    • Background and Aims The organization of rRNA genes in cultivated Plantago ovata Forsk. and several of its wild allies was analysed to gain insight into the phylogenetic relationships of these species in the genus which includes some 200 species. • Methods Specific primers were designed to amplify the internal transcribed spacer (ITS1 and ITS2) regions from seven Plantago species and the resulting fragments were cloned and sequenced. Similarly, using specific primers, the 5S rRNA genes from these species were amplified and subsequently cloned. Fluorescence in-situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal RNA genes. • Results The ITS1 region is 19–29 bp longer than the ITS2 in different Plantago species. The 5S rRNA gene-repeating unit varies in length from 289 to 581 bp. Coding regions are highly conserved across species, but the non-transcribed spacers (NTS) do not match any database sequences. The clone from the cultivated species P. ovata was used for physical mapping of these genes by FISH. Four species have one FISH site while three have two FISH sites. In P. lanceolata and P. rhodosperma, the 5S and 45S (18S-5·8S-25S) sites are coupled. • Conclusions Characterization of 5S and 45S rRNA genes has indicated a possible origin of P. ovata, the only cultivated species of the genus and also the only species with x = 4, from a species belonging to subgenus Psyllium. Based on the studies reported here, P. ovata is closest to P. arenaria, although on the basis of other data the two species have been placed in different subgenera. FISH mapping can be used as an efficient tool to help determine phylogenetic relationships in the genus Plantago and show the interrelationship between P. lanceolata and P. lagopus. PMID:16481363

  17. A Concept-Map Integrated Dynamic Assessment System for Improving Ecology Observation Competences in Mobile Learning Activities

    ERIC Educational Resources Information Center

    Hung, Pi-Hsia; Hwang, Gwo-Jen; Su, I-Hsiang; Lin, I-Hua

    2012-01-01

    Observation competence plays a fundamental role in outdoor scientific investigation. The computerized concept mapping technique as a Mindtool has shown the potential for enhancing meaningful learning in science education. The purposes of the present study are to develop a concept map integrated mobile learning design for ecology observation and to…

  18. The Articulation of Integration of Clinical and Basic Sciences in Concept Maps: Differences between Experienced and Resident Groups

    ERIC Educational Resources Information Center

    Vink, Sylvia; van Tartwijk, Jan; Verloop, Nico; Gosselink, Manon; Driessen, Erik; Bolk, Jan

    2016-01-01

    To determine the content of integrated curricula, clinical concepts and the underlying basic science concepts need to be made explicit. Preconstructed concept maps are recommended for this purpose. They are mainly constructed by experts. However, concept maps constructed by residents are hypothesized to be less complex, to reveal more tacit basic…

  19. The GDB Human Genome Data Base: a source of integrated genetic mapping and disease data.

    PubMed Central

    Brandt, K A

    1993-01-01

    The GDB Human Genome Data Base refers collectively to GDB and OMIM, Online Mendelian Inheritance in Man. GDB and OMIM are linked databases that provide an international repository for information generated by the Human Genome Initiative. GDB contains human gene mapping data, while OMIM offers the text of Dr. Victor A. McKusick's catalog of genetic disease and phenotype descriptions. These databases, updated and edited continuously, integrate bibliographic and full-text information with several types of mapping data. They are accessible through a flexible interface and are available through SprintNet and the Internet to the scientific community without cost. This paper provides an overview of the context, development, structure, content, and use of these databases. PMID:8374584

  20. A MAP OF THE INTEGRATED SACHS-WOLFE SIGNAL FROM LUMINOUS RED GALAXIES

    SciTech Connect

    Granett, Benjamin R.; Neyrinck, Mark C.; Szapudi, Istvan

    2009-08-10

    We construct a map of the time derivative of the gravitational potential traced by Sloan Digital Sky Survey luminous red galaxies (LRGs). The potential decays on large scales due to cosmic acceleration, leaving an imprint on cosmic microwave background (CMB) radiation through the integrated Sachs-Wolfe (ISW) effect. With a template fit, we directly measure this signature on the CMB at a 2{sigma} confidence level. The measurement is consistent with the cross-correlation statistic, strengthening the claim that dark energy is indeed the cause of the correlation. This new approach potentially simplifies the cosmological interpretation. Our constructed linear ISW map shows no evidence for degree-scale cold and hot spots associated with supervoid and supercluster structures. This suggests that the linear ISW effect in a concordance {lambda}CDM cosmology is insufficient to explain the strong CMB imprints from these structures that we previously reported.

  1. Integrating Multibeam Backscatter Angular Response, Mosaic and Bathymetry Data for Benthic Habitat Mapping

    PubMed Central

    Che Hasan, Rozaimi; Ierodiaconou, Daniel; Laurenson, Laurie; Schimel, Alexandre

    2014-01-01

    Multibeam echosounders (MBES) are increasingly becoming the tool of choice for marine habitat mapping applications. In turn, the rapid expansion of habitat mapping studies has resulted in a need for automated classification techniques to efficiently map benthic habitats, assess confidence in model outputs, and evaluate the importance of variables driving the patterns observed. The benthic habitat characterisation process often involves the analysis of MBES bathymetry, backscatter mosaic or angular response with observation data providing ground truth. However, studies that make use of the full range of MBES outputs within a single classification process are limited. We present an approach that integrates backscatter angular response with MBES bathymetry, backscatter mosaic and their derivatives in a classification process using a Random Forests (RF) machine-learning algorithm to predict the distribution of benthic biological habitats. This approach includes a method of deriving statistical features from backscatter angular response curves created from MBES data collated within homogeneous regions of a backscatter mosaic. Using the RF algorithm we assess the relative importance of each variable in order to optimise the classification process and simplify models applied. The results showed that the inclusion of the angular response features in the classification process improved the accuracy of the final habitat maps from 88.5% to 93.6%. The RF algorithm identified bathymetry and the angular response mean as the two most important predictors. However, the highest classification rates were only obtained after incorporating additional features derived from bathymetry and the backscatter mosaic. The angular response features were found to be more important to the classification process compared to the backscatter mosaic features. This analysis indicates that integrating angular response information with bathymetry and the backscatter mosaic, along with their derivatives

  2. Integration of Google Maps/Earth with microscale meteorology models and data visualization

    NASA Astrophysics Data System (ADS)

    Wang, Yansen; Huynh, Giap; Williamson, Chatt

    2013-12-01

    The Google Maps/Earth GIS has been integrated with a microscale meteorological model to improve the system's functionality and ease of use. Almost all the components of the model system, including the terrain data processing, morphological data generation, meteorological data gathering and initialization, and displaying/visualizing the model results, have been improved by using this approach. Different from the traditional stand-along model system, this novel system takes advantages of enormous resources in map and image data retrieving/handling, four-dimensional (space and time) data visualization, overlaying, and many other advanced GIS features that the Google Maps/Earth platform has to offer. We have developed modular components for all of the model system controls and data processing programs which are glued together with the JavaScript language and KML/XML data. We have also developed small modular software using the Google application program interface to convert the model results and intermediate data for visualizations and animations. Capabilities such as high-resolution image, street view, and 3D buildings in the Google Earth/Map are also used to quickly generate small-scale vegetation and building morphology data that are required for the microscale meteorological models. This system has also been applied to visualize the data from other instruments such as Doppler wind lidars. Because of the tight integration of the internet based GIS and a microscale meteorology model, the model system is more versatile, intuitive, and user-friendly than a stand-along system we had developed before. This kind of system will enhance the user experience and also help researchers to explore new phenomena in fine-scale meteorology.

  3. Rockfall hazard assessment integrating probabilistic physically based rockfall source detection (Norddal municipality, Norway).

    NASA Astrophysics Data System (ADS)

    Yugsi Molina, F. X.; Oppikofer, T.; Fischer, L.; Hermanns, R. L.; Taurisano, A.

    2012-04-01

    Traditional techniques to assess rockfall hazard are partially based on probabilistic analysis. Stochastic methods has been used for run-out analysis of rock blocks to estimate the trajectories that a detached block will follow during its fall until it stops due to kinetic energy loss. However, the selection of rockfall source areas is usually defined either by multivariate analysis or by field observations. For either case, a physically based approach is not used for the source area detection. We present an example of rockfall hazard assessment that integrates a probabilistic rockfall run-out analysis with a stochastic assessment of the rockfall source areas using kinematic stability analysis in a GIS environment. The method has been tested for a steep more than 200 m high rock wall, located in the municipality of Norddal (Møre og Romsdal county, Norway), where a large number of people are either exposed to snow avalanches, rockfalls, or debris flows. The area was selected following the recently published hazard mapping plan of Norway. The cliff is formed by medium to coarse-grained quartz-dioritic to granitic gneisses of Proterozoic age. Scree deposits product of recent rockfall activity are found at the bottom of the rock wall. Large blocks can be found several tens of meters away from the cliff in Sylte, the main locality in the Norddal municipality. Structural characterization of the rock wall was done using terrestrial laser scanning (TLS) point clouds in the software Coltop3D (www.terranum.ch), and results were validated with field data. Orientation data sets from the structural characterization were analyzed separately to assess best-fit probability density functions (PDF) for both dip angle and dip direction angle of each discontinuity set. A GIS-based stochastic kinematic analysis was then carried out using the discontinuity set orientations and the friction angle as random variables. An airborne laser scanning digital elevation model (ALS-DEM) with 1 m

  4. National Oceanic and Atmospheric Administration's Cetacean and Sound Mapping Effort: Continuing Forward with an Integrated Ocean Noise Strategy.

    PubMed

    Harrison, Jolie; Ferguson, Megan; Gedamke, Jason; Hatch, Leila; Southall, Brandon; Van Parijs, Sofie

    2016-01-01

    To help manage chronic and cumulative impacts of human activities on marine mammals, the National Oceanic and Atmospheric Administration (NOAA) convened two working groups, the Underwater Sound Field Mapping Working Group (SoundMap) and the Cetacean Density and Distribution Mapping Working Group (CetMap), with overarching effort of both groups referred to as CetSound, which (1) mapped the predicted contribution of human sound sources to ocean noise and (2) provided region/time/species-specific cetacean density and distribution maps. Mapping products were presented at a symposium where future priorities were identified, including institutionalization/integration of the CetSound effort within NOAA-wide goals and programs, creation of forums and mechanisms for external input and funding, and expanded outreach/education. NOAA is subsequently developing an ocean noise strategy to articulate noise conservation goals and further identify science and management actions needed to support them. PMID:26610985

  5. An integrated approach for updating cadastral maps in Pakistan using satellite remote sensing data

    NASA Astrophysics Data System (ADS)

    Ali, Zahir; Tuladhar, Arbind; Zevenbergen, Jaap

    2012-08-01

    Updating cadastral information is crucial for recording land ownership and property division changes in a timely fashioned manner. In most cases, the existing cadastral maps do not provide up-to-date information on land parcel boundaries. Such a situation demands that all the cadastral data and parcel boundaries information in these maps to be updated in a timely fashion. The existing techniques for acquiring cadastral information are discipline-oriented based on different disciplines such as geodesy, surveying, and photogrammetry. All these techniques require a large number of manpower, time, and cost when they are carried out separately. There is a need to integrate these techniques for acquiring cadastral information to update the existing cadastral data and (re)produce cadastral maps in an efficient manner. To reduce the time and cost involved in cadastral data acquisition, this study develops an integrated approach by integrating global position system (GPS) data, remote sensing (RS) imagery, and existing cadastral maps. For this purpose, the panchromatic image with 0.6 m spatial resolution and the corresponding multi-spectral image with 2.4 m spatial resolution and 3 spectral bands from QuickBird satellite were used. A digital elevation model (DEM) was extracted from SPOT-5 stereopairs and some ground control points (GCPs) were also used for ortho-rectifying the QuickBird images. After ortho-rectifying these images and registering the multi-spectral image to the panchromatic image, fusion between them was attained to get good quality multi-spectral images of these two study areas with 0.6 m spatial resolution. Cadastral parcel boundaries were then identified on QuickBird images of the two study areas via visual interpretation using participatory-GIS (PGIS) technique. The regions of study are the urban and rural areas of Peshawar and Swabi districts in the Khyber Pakhtunkhwa province of Pakistan. The results are the creation of updated cadastral maps with a

  6. Resolution enhancement in integral microscopy by physical interpolation

    PubMed Central

    Llavador, Anabel; Sánchez-Ortiga, Emilio; Barreiro, Juan Carlos; Saavedra, Genaro; Martínez-Corral, Manuel

    2015-01-01

    Integral-imaging technology has demonstrated its capability for computing depth images from the microimages recorded after a single shot. This capability has been shown in macroscopic imaging and also in microscopy. Despite the possibility of refocusing different planes from one snap-shot is crucial for the study of some biological processes, the main drawback in integral imaging is the substantial reduction of the spatial resolution. In this contribution we report a technique, which permits to increase the two-dimensional spatial resolution of the computed depth images in integral microscopy by a factor of √2. This is made by a double-shot approach, carried out by means of a rotating glass plate, which shifts the microimages in the sensor plane. We experimentally validate the resolution enhancement as well as we show the benefit of applying the technique to biological specimens. PMID:26309749

  7. An informative panel of somatic cell hybrids for physical mapping on human chromosome 19q.

    PubMed Central

    Bachinski, L L; Krahe, R; White, B F; Wieringa, B; Shaw, D; Korneluk, R; Thompson, L H; Johnson, K; Siciliano, M J

    1993-01-01

    A panel of 22 somatic cell hybrids divides the q arm of human chromosome 19 into 22 ordered subregions. The panel was characterized with respect to 41 genetic markers. In most cases, a single fragment of chromosome 19 was present in each hybrid. In two cell lines the presence of multiple fragments of the chromosome was demonstrated by segregation of these fragments in subclones. On the basis of the results of marker analysis in this panel, the most likely order of the markers tested is MANB-D19S7-PEPD-D19S9-GPI-C/EBP-TGFB1++ +-(CYP2A,BCKDHA,CGM2,NCA)-PSG1-(D19S8, XRCC1)-(ATP1A3,D19S19)-(D19S37,APOC2)-C KM-ERCC2-ERCC1-(D19S116,D19S117)- (D19S118,D19S119, D19S63,p36.1,D19S112,D19S62,D19S51,D19S54, D19S55)-pW39-D19S6-(D19S50,TNNT1)-D19S2 2-(HRC,CGB,FTL,PRKCG)-qter. This gene order is generally consistent with published physical and genetic mapping orders, although some discrepancies exist. By means of a mapping function that relates the frequency of cosegregation of markers to the distance between them, estimates were made of the sizes, in megabases, of the 19q subregions. The relative physical distances between reference markers were compared with published genetic distances for 19q. Excellent correlation was observed, suggesting that the physical distances calculated by this method are predictive of genetic distances in this region of the genome and, therefore, are just as useful in estimating relative positions of markers. Images Figure 1 PMID:8430698

  8. Organic–Inorganic Eu3+/Tb3+ codoped hybrid films for temperature mapping in integrated circuits

    PubMed Central

    Brites, Carlos D. S.; Lima, Patrícia P.; Silva, Nuno J. O.; Millán, Angel; Amaral, Vitor S.; Palacio, Fernando; Carlos, Luís D.

    2013-01-01

    The continuous decrease on the geometric size of electronic devices and integrated circuits generates higher local power densities and localized heating problems that cannot be characterized by conventional thermographic techniques. Here, a self-referencing intensity-based molecular thermometer involving a di-ureasil organic-inorganic hybrid thin film co-doped with Eu3+ and Tb3+ tris (β-diketonate) chelates is used to obtain the temperature map of a FR4 printed wiring board with spatio-temporal resolutions of 0.42 μm/4.8 ms. PMID:24790938

  9. Coupling ocean colour remote sensing data into physical-ecosystem models: mapping uncertainty distributions from space.

    NASA Astrophysics Data System (ADS)

    McKee, David; Twardowski, Mike; Trees, Chuck; Sanjuan-Calzado, Violeta

    2013-04-01

    Ocean colour remote sensing (OCRS) has transformed our understanding of complex feedback processes linking physical forcing events to biogeochemical responses. With continuous daily global coverage extending beyond the last decade, OCRS has become established as an essential global climate variable with potential use as a sensitive indicator of regional and global response to changing climate. There is increasing focus on use of OCRS data for validation and assimilation into coupled physical-ecosystem models for both environmental and operational applications. It is therefore essential that OCRS data products are not only optimised for maximum accuracy, but are also provided to end users with appropriate uncertainties. A simple spectral deconvolution model will be presented along with a new bootstrap approach for estimating product uncertainties. This approach can be adapted for both remote sensing and in situ data, opening up the possibility of mapping uncertainty distributions in 3-D for the first time, and can be applied to other established OCRS data products, including the existent historic data set. Ecosystem models seek to reproduce and predict ocean biogeochemical processes, where the models are constrained by physical parameters such as: wind, currents, density and light. The hydrographic aspects of marine ecosystems can generally be defined through ocean circulation models, which are largely independent of the ecosystem itself. The physical optics determining the light environment, on the other hand, are two-way coupled with ecosystem models since light interacts with seawater and suspended constituents. The Optical Physical and Ecosystem Regional Assessment (OPERA) model proposes a more comprehensive and challenging approach, where all optical interactions occurring within the volume of water are taken into account, thus providing a more accurate definition of light dependent processes.

  10. Coupling ocean colour remote sensing data into physical-ecosystem models: mapping uncertainty distributions from space.

    NASA Astrophysics Data System (ADS)

    McKee, David; Twardowski, Mike; Trees, Chuck; Sanjuan Calzado, Violeta

    2014-05-01

    Ocean colour remote sensing (OCRS) has transformed our understanding of complex feedback processes linking physical forcing events to biogeochemical responses. With continuous daily global coverage extending beyond the last decade, OCRS has become established as an essential global climate variable with potential use as a sensitive indicator of regional and global response to changing climate. There is increasing focus on use of OCRS data for validation and assimilation into coupled physical-ecosystem models for both environmental and operational applications. It is therefore essential that OCRS data products are not only optimised for maximum accuracy, but are also provided to end users with appropriate uncertainties. A simple spectral deconvolution model will be presented along with a new bootstrap approach for estimating product uncertainties. This approach can be adapted for both remote sensing and in situ data, opening up the possibility of mapping uncertainty distributions in 3-D for the first time, and can be applied to other established OCRS data products, including the existent historic data set. Ecosystem models seek to reproduce and predict ocean biogeochemical processes, where the models are constrained by physical parameters such as: wind, currents, density and light. The hydrographic aspects of marine ecosystems can generally be defined through ocean circulation models, which are largely independent of the ecosystem itself. The physical optics determining the light environment, on the other hand, are two-way coupled with ecosystem models since light interacts with seawater and suspended constituents. The Optical Physical and Ecosystem Regional Assessment (OPERA) model proposes a more comprehensive and challenging approach, where all optical interactions occurring within the volume of water are taken into account, thus providing a more accurate definition of light dependent processes.

  11. Integrating Animations, Narratives and Textual Information for Improving Physics Learning

    ERIC Educational Resources Information Center

    Adegoke, Benson Adesina

    2010-01-01

    Introduction: This article examined the effect of multimedia instruction on students' learning outcomes (achievement and interest) in secondary school physics. Method: The sample comprised of 517 (294 boys and 223 girls) students who came from 12 senior secondary schools in Ibadan Educational Zone 1, Oyo State, Nigeria. Their ages ranged between…

  12. How to Integrate Tai Ji Quan into Physical Education Programs

    ERIC Educational Resources Information Center

    Lu, Chunlei

    2008-01-01

    Tai ji quan, also known as "tai chi," is an ancient Chinese exercise characterized by soft, slow, and meditative movements. It consists of a set of continuous, evenly paced, carefully choreographed, but natural, body shifts. "Tai ji" is an ancient Chinese philosophy, while "tai ji quan" refers to a type of physical activity based on tai ji…

  13. An Integrated, Statistical Molecular Approach to the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Cartier, Stephen F.

    2009-01-01

    As an alternative to the "thermodynamics first" or "quantum first" approaches to the physical chemistry curriculum, the statistical definition of entropy and the Boltzmann distribution are introduced in the first days of the course and the entire two-semester curriculum is then developed from these concepts. Once the tools of statistical mechanics…

  14. Integrated Hydrologic Validation to Improve Physical Precipitation Retrievals for GPM

    NASA Astrophysics Data System (ADS)

    Peters-Lidard, C. D.; Harrison, K. W.; Tian, Y.; Kumar, S.

    2011-12-01

    One of the five scientific objectives for GPM is to "Improve hydrological modeling and prediction", including advancing prediction skill for high-impact hazards such as floods, droughts, landslides and landfalling hurricanes. Given the focus on land hydrology, and the range of hydrologic regimes targeted by GPM, it follows that a hydrologically-oriented ground validation program that covers these regimes from both the physical retrieval and the hydrological prediction perspectives is required for the successful application of GPM to land hydrology. In order to investigate the robustness of both hydrologic model predictions and physical precipitation retrievals, this talk will present recent evaluations of skill in land surface hydrologic models forced with TRMM-era multisensor products, with and without land data assimilation. In addition to LSM skill, we will also demonstrate how physical precipitation retrievals can be supported by land surface emissivity and temperature estimates obtained by coupling microwave emission models (e.g., the Joint Center for Satellite Data Assimilation Community Radiative Transfer Model CRTM and the European Center for Medium-Range Weather Forecasting's Community Microwave Emission Model CMEM) to the land surface models in the Land Information System (LIS; http://lis.gsfc.nasa.gov). Evaluation at multiple frequencies, with and without land data assimilation, demonstrates the critical impact of certain real-time ancillary data (e.g., snow cover) on the microwave background states required for physical retrievals.

  15. Integrating Microcomputers and Microelectronics into the Physics Curriculum.

    ERIC Educational Resources Information Center

    Gale, Douglas S.

    1980-01-01

    Describes an interdisciplinary microcomputer and microelectronics program offered jointly by the Physics and Computer Science Departments of East Texas State University. The program operates on both the graduate and undergraduate level. Content as well as structure of the program are discussed. (Author/DS)

  16. Rainsticks: Integrating Culture, Folklore, and the Physics of Sound

    ERIC Educational Resources Information Center

    Moseley, Christine; Fies, Carmen

    2007-01-01

    The purpose of this activity is for students to build a rainstick out of materials in their own environment and imitate the sound of rain while investigating the physical principles of sound. Students will be able to relate the sound produced by an instrument to the type and quantity of materials used in its construction.

  17. The Physics Tutor: Integrating Hypertext and Expert Systems.

    ERIC Educational Resources Information Center

    Jonassen, David H.; Wang, Sherwood

    1994-01-01

    Discussion of the development of intelligent tutoring systems (ITS) using expert systems and hypertext focuses on the Physics Tutor, a prototype ITS built with off-the-shelf software to test the utility, practicality, and generalizability of the ITS concept. Expert models and student models are explained. (Contains 27 references.) (LRW)

  18. Mapping the development of research on physical activity and the built environment

    PubMed Central

    Harris, Jenine K.; Lecy, Jesse; Parra, Diana C.; Hipp, Aaron; Brownson, Ross C.

    2014-01-01

    Objective The importance of the built environment for physical activity has been recognized in recent decades, resulting in new research. This study aims to understand the current structure of physical activity and built environment (PABE) research and identify gaps to address as the field continues to rapidly develop. Methods Key PABE articles were nominated by top scholars and a snowball sample of 2,764 articles was collected in 2013 using citation network links. Article abstracts were examined to determine research focus and network analysis was used to examine the evolution of scholarship. Results The network included 318 PABE articles. Of these, 191 were discovery-focused, examining the relationship between physical activity and built environment; 79 were reviews summarizing previous PABE work; 38 focused on theory and methods for studying PABE; six were delivery-focused, examining PABE interventions; and four addressed other topics. Conclusions Network composition suggested PABE is in the discovery phase, although may be transitioning given the large number and central position of review documents that summarize existing literature. The small amount of delivery research was not well integrated into the field. PABE delivery researchers may wish to make explicit connections to the discovery literature in order to better integrate the field. PMID:23859932

  19. Integrated Modeling, Mapping, and Simulation (IMMS) Framework for Exercise and Response Planning

    NASA Technical Reports Server (NTRS)

    Mapar, Jalal; Hoette, Trisha; Mahrous, Karim; Pancerella, Carmen M.; Plantenga, Todd; Yang, Christine; Yang, Lynn; Hopmeier, Michael

    2011-01-01

    EmergenCy management personnel at federal, stale, and local levels can benefit from the increased situational awareness and operational efficiency afforded by simulation and modeling for emergency preparedness, including planning, training and exercises. To support this goal, the Department of Homeland Security's Science & Technology Directorate is funding the Integrated Modeling, Mapping, and Simulation (IMMS) program to create an integrating framework that brings together diverse models for use by the emergency response community. SUMMIT, one piece of the IMMS program, is the initial software framework that connects users such as emergency planners and exercise developers with modeling resources, bridging the gap in expertise and technical skills between these two communities. SUMMIT was recently deployed to support exercise planning for National Level Exercise 2010. Threat, casualty. infrastructure, and medical surge models were combined within SUMMIT to estimate health care resource requirements for the exercise ground truth.

  20. A terracing operator for physical property mapping with potential field data

    USGS Publications Warehouse

    Cordell, L.; McCafferty, A.E.

    1989-01-01

    The terracing operator works iteratively on gravity or magnetic data, using the sense of the measured field's local curvature, to produce a field comprised of uniform domains separated by abrupt domain boundaries. The result is crudely proportional to a physical-property function defined in one (profile case) or two (map case) horizontal dimensions. This result can be extended to a physical-property model if its behavior in the third (vertical) dimension is defined, either arbitrarily or on the basis of the local geologic situation. The terracing algorithm is computationally fast and appropriate to use with very large digital data sets. The terracing operator was applied separately to aeromagnetic and gravity data from a 136km x 123km area in eastern Kansas. Results provide a reasonable good physical representation of both the gravity and the aeromagnetic data. Superposition of the results from the two data sets shows many areas of agreement that can be referenced to geologic features within the buried Precambrian crystalline basement. -from Authors

  1. Intensity Maps Production Using Real-Time Joint Streaming Data Processing From Social and Physical Sensors

    NASA Astrophysics Data System (ADS)

    Kropivnitskaya, Y. Y.; Tiampo, K. F.; Qin, J.; Bauer, M.

    2015-12-01

    Intensity is one of the most useful measures of earthquake hazard, as it quantifies the strength of shaking produced at a given distance from the epicenter. Today, there are several data sources that could be used to determine intensity level which can be divided into two main categories. The first category is represented by social data sources, in which the intensity values are collected by interviewing people who experienced the earthquake-induced shaking. In this case, specially developed questionnaires can be used in addition to personal observations published on social networks such as Twitter. These observations are assigned to the appropriate intensity level by correlating specific details and descriptions to the Modified Mercalli Scale. The second category of data sources is represented by observations from different physical sensors installed with the specific purpose of obtaining an instrumentally-derived intensity level. These are usually based on a regression of recorded peak acceleration and/or velocity amplitudes. This approach relates the recorded ground motions to the expected felt and damage distribution through empirical relationships. The goal of this work is to implement and evaluate streaming data processing separately and jointly from both social and physical sensors in order to produce near real-time intensity maps and compare and analyze their quality and evolution through 10-minute time intervals immediately following an earthquake. Results are shown for the case study of the M6.0 2014 South Napa, CA earthquake that occurred on August 24, 2014. The using of innovative streaming and pipelining computing paradigms through IBM InfoSphere Streams platform made it possible to read input data in real-time for low-latency computing of combined intensity level and production of combined intensity maps in near-real time. The results compare three types of intensity maps created based on physical, social and combined data sources. Here we correlate

  2. Optical-radar-DEM remote sensing data integration for geological mapping in the Afar Depression, Ethiopia

    NASA Astrophysics Data System (ADS)

    Thurmond, Allison K.; Abdelsalam, Mohamed G.; Thurmond, John B.

    2006-02-01

    The advantages of integrating optical (Landsat Enhanced Thematic Mapper Plus (ETM+) and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER)) and radar (Shuttle Imaging Radar (SIR) - C, X-band Synthetic Aperture Radar (SAR) and RADARSAT-1) remote sensing data, and digital elevation models (DEMs) (Shuttle Radar Topography Mission (SRTM)) for geological mapping in arid regions such as the Afar Depression in Ethiopia are demonstrated. The Afar Depression in NE Africa is a natural laboratory for studying processes of sea-floor spreading and the transition from rifting to true sea-floor spreading. It is ideal for geological remote sensing because of its vastness, remoteness and inaccessibility together with almost continuous exposure, and lack of vegetation and soil cover. Optical-radar-DEM remote sensing data integration is used for: (1) Distinguishing spatial and temporal distribution of individual lava flows in the Quaternary Erta 'Ale Volcanic Range in the northern part of the Afar Depression, by integrating band-ratios of ASTER thermal infrared (TIR) data with Landsat ETM+ visible and near infrared (VNIR) and SIR-C/X-SAR L-band ( λ = 24 cm) data with horizontally transmitted and horizontally received (HH) polarization. (2) Visualizing and interpreting extensional imbrication fans that constitute part of the Dobe Graben in the central part of the Afar Depression by integrating Landsat ETM+ VNIR data with RADARSAT C-band ( λ = 6 cm) data with HH polarization and SRTM DEMs. These imbrication fans were developed as layer-parallel gravitational slip of the border fault hanging-wall towards the graben center. (3) Mapping morphologically defined structures in rhyolite flows exposed on the flanks of the Tendaho Rift by merging ASTER VNIR and short wave infrared (SWIR) with RADARSAT C-band data with HH polarization. The Tendaho Rift constitutes part of the Tendaho-Gobaad Discontinuity that separates the southern and the central eastern parts of the Afar

  3. A physically based model for dielectric charging in an integrated optical MEMS wavelength selective switch.

    SciTech Connect

    Nielson, Gregory N.; Barbastathis, George

    2005-07-01

    A physical parameter based model for dielectric charge accumulation is proposed and used to predict the displacement versus applied voltage and pull-in response of an electrostatic MEMS wavelength selective integrated optical switch.

  4. Mixed signal custom integrated circuit development for physics instrumentation

    SciTech Connect

    Britton, C.L. Jr.; Bryan, W.L.; Emery, M.S.

    1998-10-01

    The Monolithic Systems Development Group at the Oak Ridge National Laboratory has been greatly involved in custom mixed-mode integrated circuit development for the PHENIX detector at the Relativistic Heavy Ion collider (RHIC) at Brookhaven National Laboratory and position-sensitive germanium spectrometer front-ends for the Naval Research Laboratory (NRL). This paper will outline the work done for both PHENIX and the Naval Research Laboratory in the area of full-custom, mixed-signal CMOS integrated electronics. This paper presents the architectures chosen for the various PHENIX detectors which include position-sensitive silicon, capacitive pixel, and phototube detectors, and performance results for the subsystems as well as a system description of the NRL germanium strip system and its performance. The performance of the custom preamplifiers, discriminators, analog memories, analog-digital converters, and control circuitry for all systems will be presented.

  5. Delivering integrated HAZUS-MH flood loss analyses and flood inundation maps over the Web

    USGS Publications Warehouse

    Hearn,, Paul P., Jr.; Longenecker, Herbert E., III; Aguinaldo, John J.; Rahav, Ami N.

    2013-01-01

    Catastrophic flooding is responsible for more loss of life and damages to property than any other natural hazard. Recently developed flood inundation mapping technologies make it possible to view the extent and depth of flooding on the land surface over the Internet; however, by themselves these technologies are unable to provide estimates of losses to property and infrastructure. The Federal Emergency Management Agency’s (FEMA's) HAZUS-MH software is extensively used to conduct flood loss analyses in the United States, providing a nationwide database of population and infrastructure at risk. Unfortunately, HAZUS-MH requires a dedicated Geographic Information System (GIS) workstation and a trained operator, and analyses are not adapted for convenient delivery over the Web. This article describes a cooperative effort by the US Geological Survey (USGS) and FEMA to make HAZUS-MH output GIS and Web compatible and to integrate these data with digital flood inundation maps in USGS’s newly developed Inundation Mapping Web Portal. By running the computationally intensive HAZUS-MH flood analyses offline and converting the output to a Web-GIS compatible format, detailed estimates of flood losses can now be delivered to anyone with Internet access, thus dramatically increasing the availability of these forecasts to local emergency planners and first responders.

  6. Delivering integrated HAZUS-MH flood loss analyses and flood inundation maps over the Web.

    PubMed

    Hearn, Paul P; Longenecker, Herbert E; Aguinaldo, John J; Rahav, Ami N

    2013-01-01

    Catastrophic flooding is responsible for more loss of life and damages to property than any other natural hazard. Recently developed flood inundation mapping technologies make it possible to view the extent and depth of flooding on the land surface over the Internet; however, by themselves these technologies are unable to provide estimates of losses to property and infrastructure. The Federal Emergency Management Agency's (FEMA's) HAZUS-MH software is extensively used to conduct flood loss analyses in the United States, providing a nationwide database of population and infrastructure at risk. Unfortunately, HAZUS-MH requires a dedicated Geographic Information System (GIS) workstation and a trained operator, and analyses are not adapted for convenient delivery over the Web. This article describes a cooperative effort by the US Geological Survey (USGS) and FEMA to make HAZUS-MH output GIS and Web compatible and to integrate these data with digital flood inundation maps in USGS's newly developed Inundation Mapping Web Portal. By running the computationally intensive HAZUS-MH flood analyses offline and converting the output to a Web-GIS compatible format, detailed estimates of flood losses can now be delivered to anyone with Internet access, thus dramatically increasing the availability of these forecasts to local emergency planners and first responders. PMID:24303773

  7. Encrypting three-dimensional information system based on integral imaging and multiple chaotic maps

    NASA Astrophysics Data System (ADS)

    Xing, Yan; Wang, Qiong-Hua; Xiong, Zhao-Long; Deng, Huan

    2016-02-01

    An encrypting three-dimensional (3-D) information system based on integral imaging (II) and multiple chaotic maps is proposed. In the encrypting process, the elemental image array (EIA) which represents spatial and angular information of the real 3-D scene is picked up by a microlens array. Subsequently, R, G, and B color components decomposed by the EIA are encrypted using multiple chaotic maps. Finally, these three encrypted components are interwoven to obtain the cipher information. The decryption process implements the reverse operation of the encryption process for retrieving the high-quality 3-D images. Since the encrypted EIA has the data redundancy property due to II, and all parameters of the pickup part are the secret keys of the encrypting system, the system sensitivity on the changes of the plaintext and secret keys can be significantly improved. Moreover, the algorithm based on multiple chaotic maps can effectively enhance the security. A preliminary experiment is carried out, and the experimental results verify the effectiveness, robustness, and security of the proposed system.

  8. Integration between ground based and satellite SAR data in landslide mapping: The San Fratello case study

    NASA Astrophysics Data System (ADS)

    Bardi, Federica; Frodella, William; Ciampalini, Andrea; Bianchini, Silvia; Del Ventisette, Chiara; Gigli, Giovanni; Fanti, Riccardo; Moretti, Sandro; Basile, Giuseppe; Casagli, Nicola

    2014-10-01

    The potential use of the integration of PSI (Persistent Scatterer Interferometry) and GB-InSAR (Ground-based Synthetic Aperture Radar Interferometry) for landslide hazard mitigation was evaluated for mapping and monitoring activities of the San Fratello landslide (Sicily, Italy). Intense and exceptional rainfall events are the main factors that triggered several slope movements in the study area, which is susceptible to landslides, because of its steep slopes and silty-clayey sedimentary cover. In the last three centuries, the town of San Fratello was affected by three large landslides, developed in different periods: the oldest one occurred in 1754, damaging the northeastern sector of the town; in 1922 a large landslide completely destroyed a wide area in the western hillside of the town. In this paper, the attention is focussed on the most recent landslide that occurred on 14 February 2010: in this case, the phenomenon produced the failure of a large sector of the eastern hillside, causing severe damages to buildings and infrastructures. In particular, several slow-moving rotational and translational slides occurred in the area, making it suitable to monitor ground instability through different InSAR techniques. PS-InSAR™ (permanent scatterers SAR interferometry) techniques, using ERS-1/ERS-2, ENVISAT, RADARSAT-1, and COSMO-SkyMed SAR images, were applied to analyze ground displacements during pre- and post-event phases. Moreover, during the post-event phase in March 2010, a GB-InSAR system, able to acquire data continuously every 14 min, was installed collecting ground displacement maps for a period of about three years, until March 2013. Through the integration of space-borne and ground-based data sets, ground deformation velocity maps were obtained, providing a more accurate delimitation of the February 2010 landslide boundary, with respect to the carried out traditional geomorphological field survey. The integration of GB-InSAR and PSI techniques proved to

  9. Mapping fluid distribution in a pinch-out reservoir model: A physical modeling study

    NASA Astrophysics Data System (ADS)

    Assis, Carlos A. M.; Ceia, Marco A. R.; Misságia, Roseane M.; Lupinacci, Wagner M.

    2014-10-01

    This work shows the results obtained from seismic physical modeling experiments that image the non-homogeneous, two-phase distribution of immiscible fluids inside a cavity in a pinch-out model. The main goal of this study was to verify how the seismic sections can be used to observe the fluid distribution in this type of reservoir. A high-resolution deconvolution method was applied to improve the image resolution and depth migration correctly positioned the events. Instantaneous attributes were used to assist data interpretation. The results provided an image of the oil-water interface and revealed a complex fluid compartmentalization pattern that was confirmed by numerical modeling simulations. The results of this study should improve the understanding of mapping fluid distributions from seismic sections in pinch-out reservoirs.

  10. Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies.

    PubMed

    Sharakhov, Igor V; Artemov, Gleb N; Sharakhova, Maria V

    2016-04-01

    Polymorphic inversions in mosquitoes are distributed nonrandomly among chromosomes and are associated with ecological, behavioral, and physiological adaptations related to pathogen transmission. Despite their significance, the patterns and mechanism of genome rearrangements are not well understood. Recent sequencing and physical mapping of the genomes for 16 Anopheles mosquito species provided an opportunity to study chromosome evolution at the highest resolution. New studies revealed that fixed rearrangement accumulated [Formula: see text]3 times faster on the X chromosome than on autosomes. The highest densities of transposable elements (TEs) and satellites of different sizes have also been found on the X chromosome, suggesting a mechanism for the inversion generation. The high rate of X chromosome rearrangements is in sharp contrast with the paucity of polymorphic inversions on the X in the majority of anopheline species. This paper highlights the advances in understanding chromosome evolution in malaria vectors and discusses possible future directions in studying mechanisms and biological roles of genome rearrangements. PMID:27021248

  11. Fingerprinting: Modelling and mapping physical top soil properties with the Mole

    NASA Astrophysics Data System (ADS)

    Loonstra, Eddie; van Egmond, Fenny

    2010-05-01

    The Mole is a passive gamma ray soil sensor system. It is designed for the mobile collection of radioactive energy stemming from soil. As the system is passive, it only measures energy that reaches the surface of soil. In general, this energy comes from upto 30 to 40 cm deep, which can be considered topsoil. The gathered energy spectra are logged every second, are processed with the method of Full Spectrum Analysis. This method uses all available spectral data and processes it with a Chi square optimalisation using a set of standard spectra into individual nuclide point data. A standard spectrum is the measured full spectrum of a specific detector derived when exposed to 1 Bq/kg of a nuclide. With this method the outcome of the surveys become quantitative.The outcome of a field survey with the Mole results in a data file containing point information of position, Total Counts and the decay products of 232Th, 238U, 40K and 137Cs. Five elements are therefor available for the modelling of soil properties. There are several ways for the modelling of soil properties with sensor derived gamma ray data. The Mole generates ratio scale output. For modelling a quantitative deterministic approach is used based on sample locations. This process is called fingerprinting. Fingerprinting is a comparison of the concentration of the radioactive trace elements and the lab results (pH, clay content, etc.) by regression analysis. This results in a mathematical formula describing the relationship between a dependent and independent property. The results of the sensor readings are interpolated into a nuclide map with GIS software. With the derived formula a soil property map is composed. The principle of fingerprinting can be applied on large geographical areas for physical soil properties such as clay, loam or sand (50 micron), grain size and organic matter. Collected sample data of previous field surveys within the same region can be used for the prediction of soil properties elsewhere

  12. Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes.

    PubMed

    Qiu, Dongru; Fujita, Kyoko; Sakuma, Yuko; Tanaka, Teruo; Ohashi, Yoshiaki; Ohshima, Hideyuki; Tomita, Masaru; Itaya, Mitsuhiro

    2004-10-01

    The complete SfiI and I-CeuI physical maps of four Bacillus subtilis (natto) strains, which were previously isolated as natto (fermented soybean) starters, were constructed to elucidate the genome structure. Not only the similarity in genome size and organization but also the microheterogeneity of the gene context was revealed. No large-scale genome rearrangements among the four strains were indicated by mapping of the genes, including 10 rRNA operons (rrn) and relevant genes required for natto production, to the loci corresponding to those of the B. subtilis strain Marburg 168. However, restriction fragment length polymorphism and the presence or absence of strain-specific DNA sequences, such as the prophages SP beta, skin element, and PBSX, as well as the insertion element IS4Bsu1, could be used to identify one of these strains as a Marburg type and the other three strains as natto types. The genome structure and gene heterogeneity were also consistent with the type of indigenous plasmids harbored by the strains. PMID:15466572

  13. Structural analysis and physical mapping of a pericentromeric region of chromosome 5 of Arabidopsis thaliana.

    PubMed

    Tutois, S; Cloix, C; Cuvillier, C; Espagnol, M C; Lafleuriel, J; Picard, G; Tourmente, S

    1999-01-01

    The Arabidopsis thaliana CIC YAC 2D2, 510 kb long and containing a small block of 180 bp satellite units was subcloned after EcoR1 digestion in the pBluescript plasmid. One of these clones was mapped genetically in the pericentromeric region of chromosome 5. The analysis of 40 subclones of this YAC showed that they all contain repeated sequences with a high proportion of transposable elements. Three new retrotransposons, two Ty-3 Gypsy-like and one Ty-1 Copia, were identified in addition to two new tandem-repeat families. A physical map of the chromosome 5 pericentromeric region was established using CIC YAC clones, spanning around 1000 kb. This contig extends from the CIC YAC 9F5 and 7A2 positioned on the left arm of chromosome 5 to a 5S rDNA genes block localized by in-situ hybridization in the pericentromeric region. Hybridization of the subclones on the CIC YAC library showed that some of them are restricted to the pericentromeric region of chromosome 5 and represent specific markers of this region. PMID:10328626

  14. Physical mapping and genomic structure of the human TNFR2 gene

    SciTech Connect

    Beltinger, C.P.; White, P.S.; Maris, J.M.

    1996-07-01

    The tumor necrosis factor receptor 2 (TNFR2) gene localizes to 1p36.2, a genomic region characteristically deleted in neuroblastomas and other malignancies. In addition, TNFR2 is the principal mediator of the effects of TNF on cellular immunity, and it may cooperate with TNFR1 in the killing of nonlymphoid cells. Therefore, we undertook an analysis of the genomic structure and precise physical mapping of this gene. The TNFR2 gene is contained on 10 exons that span 26 kb. Most of the functional domains of TNFR2 are encoded by separate exons, and each of the repeats of the extracellular cysteine-rich domain is interrupted by an intron. The genomic structure reveals a close relationship to TNFR1, another member of the TNFR superfamily. Based on electrophoretic analysis of yeast artificial chromosomes, TNFR2 maps within 400 kb of the genetic marker D1S434. In addition, we have identified a new polymorphic dinucleotide repeat within intron 4 of TNFR2. The genetic sequence information and exon-intron boundaries we have determined will facilitate mutational analysis of this gene to determine its potential role in neuroblastoma, as well as in other cancers with characteristic deletions or rearrangements of 1p36. 52 refs., 3 figs., 1 tab.

  15. Driven by Beliefs: Understanding Challenges Physical Science Teachers Face When Integrating Engineering and Physics

    ERIC Educational Resources Information Center

    Dare, Emily A.; Ellis, Joshua A.; Roehrig, Gillian H.

    2014-01-01

    It is difficult to ignore the increased use of technological innovations in today's world, which has led to various calls for the integration of engineering into K-12 science standards. The need to understand how engineering is currently being brought to science classrooms is apparent and necessary in order to address these calls for integration.…

  16. Becoming Physics People: Development of Integrated Physics Identity through the Learning Assistant Experience

    ERIC Educational Resources Information Center

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

    2016-01-01

    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.…

  17. Physical mapping of the pink-eyed dilution complex in mouse chromosome 7 shows that Atp10c is the only transcript between Gabrb3 and Ube3a.

    PubMed

    Dhar, Madhu S; Hauser, Loren J; Nicholls, Robert D; Johnson, Dabney K

    2004-08-01

    Phenotypic analyses of a set of homozygous-lethal deletion mutants at the pink-eyed dilution (p) locus has resulted in the identification of p-linked obesity locus 1 (plo 1), distal to the p locus, as a locus involved in the modulation of body fat and/or affecting lipid metabolism in these mice. The plo 1 region maps to mouse chromosome 7 (MMU 7) between two genes, Gabrb3 and Ube3a, which have been used as anchor points to generate an integrated deletion and physical map of plo 1 that encompasses about 1.2-1.3 Mb. A deletion/physical map was constructed and the genomic DNA between the two loci was sequenced to identify genes mapping to this region. Data show that Atp10c, a novel type IV ATPase a putative phospholipid transporter, is the only coding unit in this region of the chromosome. PMID:15620220

  18. Integrating Data from Several Remotely Sensed Platforms to Accurately Map Wetlands

    NASA Astrophysics Data System (ADS)

    Corcoran, Jennifer Marie

    Traditional wetland mapping methods are in need of modernization. They typically depend solely on few dates of optical imagery, cloud-free data acquisition, and therefore surface features of interest are often obstructed, inaccurately mapped, or not present during data acquisition. Despite the limitations of data acquisition during cloud-free daylight only, multi-temporal multi-spectral optical data are still highly valuable for mapping wetlands and classifying wetland type. However, radar sensors are unique in that they are insensitive to atmospheric and low light conditions, and thus can offer more consistent multi-temporal image acquisition. Unique characteristics about surface scattering mechanisms, such as saturated extent of wetlands, can be found by utilizing both the intensity and phase information from multiple polarizations and multiple wavelengths of radar data. In addition, information from lidar can reveal important details about the variability and structure of surface features, and the potentiality of water to collect in certain areas. The research presented in this dissertation will show important developments in wetland mapping by integrating several platforms of remotely sensed data, including: two sources of radar data including fully polarimetric RADARSAT-2 data (C-band) and dual-pol PALSAR data (L-band); two sources of optical data including Landsat TM imagery and aerial orthophotos, lidar point cloud data with intensity and derived topographic indices. Decision tree classification using the random forest model will be utilized to take advantage of the unique differences in these data. Assessments of outputs from random forest will be used to identify the most significant data sources for two levels of land cover classification: discriminating between water, wetland and upland areas, and sub-classifying wetland type. It is expected that results from this research will deliver a valuable, affordable, and practical wetland probability tool to aid

  19. Physical Maps of the Six Smallest Chromosomes of Saccharomyces Cerevisiae at a Resolution of 2.6 Kilobase Pairs

    PubMed Central

    Riles, L.; Dutchik, J. E.; Baktha, A.; McCauley, B. K.; Thayer, E. C.; Leckie, M. P.; Braden, V. V.; Depke, J. E.; Olson, M. V.

    1993-01-01

    Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae are presented. In order of increasing size, they are chromosomes I, VI, III, IX, V and VIII, comprising 2.49 megabase pairs of DNA. The maps are based on the analysis of an overlapping set of lambda and cosmid clones. Overlaps between adjacent clones were recognized by shared restriction fragments produced by the combined action of EcoRI and HindIII. The average spacing between mapped cleavage sites is 2.6 kb. Five of the six chromosomes were mapped from end to end without discontinuities; a single internal gap remains in the map of chromosome IX. The reported maps span an estimated 97% of the DNA on the six chromosomes; nearly all the missing segments are telomeric. The maps are fully cross-correlated with the previously published SfiI/NotI map of the yeast genome by A. J. Link and M. V. Olson. They have also been cross-correlated with the yeast genetic map at 51 loci. PMID:8514151

  20. Vertically integrated pixel readout chip for high energy physics

    SciTech Connect

    Deptuch, Grzegorz; Demarteau, Marcel; Hoff, James; Khalid, Farah; Lipton, Ronald; Shenai, Alpana; Trimpl, Marcel; Yarema, Raymond; Zimmerman, Tom; /Fermilab

    2011-01-01

    We report on the development of the vertex detector pixel readout chips based on multi-tier vertically integrated electronics for the International Linear Collider. Some testing results of the VIP2a prototype are presented. The chip is the second iteration of the silicon implementation of the prototype, data-pushed concept of the readout developed at Fermilab. The device was fabricated in the 3D MIT-LL 0.15 {micro}m fully depleted SOI process. The prototype is a three-tier design, featuring 30 x 30 {micro}m{sup 2} pixels, laid out in an array of 48 x 48 pixels.

  1. "Riding the Rip": An Experiential and Integrated Human-Physical Geography Curriculum in Costa Rica

    ERIC Educational Resources Information Center

    Brannstrom, Christian; Houser, Chris

    2015-01-01

    Integrating research into short-term study abroad programs is challenging because of language, fieldwork logistics, and traditional learning models based on passive classroom experiences. Experiential learning often makes use of research as experience, but relatively few examples integrate human and physical geography. Here, we describe an…

  2. Ego Integrity of Older People with Physical Disability and Therapeutic Recreation

    ERIC Educational Resources Information Center

    de Guzman, Allan B.; Shim, Hye-Eun; Sia, Charmin Kathleen M.; Siazon, Wilbart Harvey S.; Sibal, Mary Joyce Ann P.; Siglos, Joanna Brigitte Lorraine C.; Simeon, Francis Marlo C.

    2011-01-01

    Ego integrity, the last developmental task in Erikson's psychological theory, develops naturally among older people. However, the presence of loss-like physical disability-can considerably affect the quality of life, interactions, and well being of older adults. Hence, older people with physical disabilities need more assistance in accomplishing…

  3. Integrating Video-Capture Virtual Reality Technology into a Physically Interactive Learning Environment for English Learning

    ERIC Educational Resources Information Center

    Yang, Jie Chi; Chen, Chih Hung; Jeng, Ming Chang

    2010-01-01

    The aim of this study is to design and develop a Physically Interactive Learning Environment, the PILE system, by integrating video-capture virtual reality technology into a classroom. The system is designed for elementary school level English classes where students can interact with the system through physical movements. The system is designed to…

  4. The Impact of the Physical Environment on the Social Integration of Individuals with Disabilities in Community

    ERIC Educational Resources Information Center

    Christensen, Keith M.

    2010-01-01

    Social integration in community is especially important for individuals with disabilities well-being. Although individuals with disabilities reside within the community's physical environment, they are often marginalized in the social environment. This may be the result of individuals with disabilities residing in physical environments that…

  5. Understanding Introductory Students' Application of Integrals in Physics from Multiple Perspectives

    ERIC Educational Resources Information Center

    Hu, Dehui

    2013-01-01

    Calculus is used across many physics topics from introductory to upper-division level college courses. The concepts of differentiation and integration are important tools for solving real world problems. Using calculus or any mathematical tool in physics is much more complex than the straightforward application of the equations and algorithms that…

  6. The Effects of Role Modeling on Technology Integration within Physical Education Teacher Education

    ERIC Educational Resources Information Center

    Baert, Helena

    2014-01-01

    The national standards for physical education teacher education (PETE) in the US state that teacher candidates should be able to plan and implement technology infused lessons that meet lesson objectives and enhance learning in physical education (standard 3.7). Research shows that role modeling of technology integration can have a positive impact…

  7. Integrating Geology and Physics To Enhance Science Learning Experience of Students and Serve the Community.

    ERIC Educational Resources Information Center

    Revetta, Frank A.; Das, Biman

    2002-01-01

    Suggests an integrated approach to make science teaching and learning more effective, interesting and motivating to students. Argues that team teaching by physics and geology departments enables students to learn concepts and principles of physics and apply them to solve geological problems facing the local community. Reports that a typical…

  8. Models for Integrating Technology in Higher Education: The Physics of Sound

    ERIC Educational Resources Information Center

    MacKinnon, Gregory; Williams, Peter

    2006-01-01

    Institutions that place laptops in the hands of every student offer unique opportunities to integrate technology into instruction. The following is a description of how various technologies have been introduced into a new undergraduate physics course called Physics of Sound at a so-called laptop institution. This article presents classroom…

  9. Intuitive Physics of Free Fall: An Information Integration Approach to the Mass-Speed Belief

    ERIC Educational Resources Information Center

    Vicovaro, Michele

    2014-01-01

    In this study, the intuitive physics of free fall was explored using Information Integration Theory and Functional Measurement. The participants had to rate the speed of objects differing in mass and height of release at the end of an imagined free fall. According to physics, falling speed increases with height of release but it is substantially…

  10. Innovation Diffusion: A Deterministic Model of Space-Time Integration with Physical Analog

    ERIC Educational Resources Information Center

    Haynes, Kingsley E.; And Others

    1977-01-01

    Extends a fundamental temporal diffusion model to integrate space and time dimensions of innovation diffusion. Compares analogous developments in the physical sciences and argues that the proposed model may help link the concepts of catalysts in physical science diffusion processes to the role of change agents in social science systems. (Author/JG)

  11. Utility of Acculturation in Physical Activity Research in Latina Adults: An Integrative Review of Literature

    ERIC Educational Resources Information Center

    Benitez, Tanya J.; Dodgson, Joan E.; Coe, Kathryn; Keller, Colleen

    2016-01-01

    Latina adults in the United States have a disproportionately higher prevalence of chronic diseases related to low physical activity levels than non-Hispanic women. Literature indicates that acculturation may be a contributing factor to being physically active, but the extent of this association remains unclear. An integrative review of literature…

  12. Integrative Review of Nurse-Delivered Physical Activity Interventions in Primary Care.

    PubMed

    Richards, Elizabeth A; Cai, Yun

    2016-04-01

    Promotion of physical activity has been a public health priority for decades. The purpose of this integrative review is to examine the effectiveness of nurse-delivered physical activity interventions conducted in primary care settings. Computerized database and ancestry search strategies located distinct intervention trials between 1990 and 2014. Nineteen national and international studies with 7,350 participants were reviewed. The most common intervention was physical activity counseling with supportive or motivational contacts. Few studies utilized exercise training, device-based exercise monitoring, or exercise prescriptions. The most common follow-up durations were 3 to 12 months. Half the studies integrated health behavior theoretical frameworks into the intervention. Almost 80% of the studies reported significant increases in walking, moderate or vigorous physical activity, or overall physical activity in the intervention groups. Interventions successful in increasing physical activity most often utilized tailored techniques such as providing "stage of change"-specific strategies or helping patients set individualized goals. PMID:25903812

  13. Integrating the markers Pan I and haemoglobin with the genetic linkage map of Atlantic cod (Gadus morhua)

    PubMed Central

    2010-01-01

    Background Haemoglobin (Hb) and pantophysin (Pan I) markers have been used intensively in population studies of Atlantic cod (Gadus morhua) and in the analysis of traits such as temperature tolerance, growth characteristics and sexual maturation. We used an Illumina GoldenGate panel and the KASPar SNP genotyping system to analyse SNPs in three Atlantic cod families, one of which was polymorphic at the Hb β1 locus, and to generate a genetic linkage map integrating Pan I and multiple Hb loci. Findings Data generated allowed the mapping of nine Hb loci, the Pan I locus, and other 122 SNPs onto an existing linkage genetic map for Atlantic cod. Four Hb genes (i.e. α1, α4, β1 and β5) have been mapped on linkage group (LG) 2 while the other five (i.e. α2, α3, β2, β3 and β4) were placed on LG18. Pan I was mapped on LG 1 using a newly developed KASPar assay for a SNP variable only in Pan IA allelic variants. The new linkage genetic map presented here comprises 1046 SNPs distributed between 23 linkage groups, with a length of 1145.6 cM. A map produced by forcing additional loci, resulting in a reduced goodness-of-fit for mapped markers, allowed the mapping of a total of 1300 SNPs. Finally, we compared our genetic linkage map data with the genetic linkage map data produced by a different group and identified 29 shared SNPs distributed on 10 different linkage groups. Conclusions The genetic linkage map presented here incorporates the marker Pan I, together with multiple Hb loci, and integrates genetic linkage data produced by two different research groups. This represents a useful resource to further explore if Pan I and Hbs or other genes underlie quantitative trait loci (QTL) for temperature sensitivity/tolerance or other phenotypes. PMID:20946683

  14. Integrated visible and near-infrared, shortwave infrared, and longwave infrared full-range hyperspectral data analysis for geologic mapping

    NASA Astrophysics Data System (ADS)

    Kruse, Fred A.

    2015-01-01

    Airborne visible/infrared imaging spectrometer (AVIRIS) and spatially coincident hyperspectral thermal emission spectrometer (HyTES) data were used to map geology and alteration for a site in northern Death Valley, California and Nevada. AVIRIS with 224 bands from 0.4 to 2.5 μm were converted to reflectance. HyTES data with 256 bands covering 8 to 12 μm were converted to emissivity. Two approaches were investigated for integration of the datasets for full spectrum analysis. A combined (integrated) bands method utilized 332 spectral bands spanning both datasets. Spectral endmembers were extracted, and the predominant material at each pixel was mapped for the full spectral range using partial unmixing. This approach separated a variety of materials, but it was difficult to directly relate mapping results to surface properties. The second method used visible to near-infrared, shortwave infrared, and longwave infrared data independently to determine and map key endmembers in each spectral range. AVIRIS directly mapped a variety of specific minerals, while HyTES separated and mapped several igneous rock phases. Individual mapping results were then combined using geologically directed logical operators. The full-range results illustrate that integrated analysis provides advantages over use of just one spectral range, leading to improved understanding of the distribution of geologic units and alteration.

  15. Integrating fuel cell power systems into building physical plants

    SciTech Connect

    Carson, J.

    1996-12-31

    This paper discusses the integration of fuel cell power plants and absorption chillers to cogenerate chilled water or hot water/steam for all weather air conditioning as one possible approach to building system applications. Absorption chillers utilize thermal energy in an absorption based cycle to chill water. It is feasible to use waste heat from fuel cells to provide hydronic heating and cooling. Performance regimes will vary as a function of the supply and quality of waste heat. Respective performance characteristics of fuel cells, absorption chillers and air conditioning systems will define relationships between thermal and electrical load capacities for the combined systems. Specifically, this paper develops thermodynamic relationships between bulk electrical power and cooling/heating capacities for combined fuel cell and absorption chiller system in building applications.

  16. Integration of remote sensing and morphological data for an optimal mapping of badland areas

    NASA Astrophysics Data System (ADS)

    Simoniello, T.; Liberti, M.; Carone, M. T.; Coppola, R.; D'Emilio, M.; Macchiato, M.

    2009-04-01

    Badlands are complex and peculiar types of erosional formations deriving from the action of geological, geomorphological and denudation processes. For soil erosion assessment such as temporal monitoring of badland areas, digital soil mapping from remote sensing images can be a valuable tool. It can allow for exploring both the role of climate effects on landform development and changes of erosion rate due to human influence. However, in order to effectively use multispectral satellite data, which are still a main source of information for multitemporal analyses, many attempts are required to solve the problems linked to low spectral separability of land features. In particular, data from the Landsat TM/ETM series, recognized particularly appropriate for supporting both research and land conservation planning, showed their limit in accurately detecting eroded materials influenced by run-off processes. These surface processes, indeed, are responsible for the increase in spectral confusion by spreading materials from badlands to the surrounding areas. To overcome this problem, we proposed the integration of spectral data with morphological information deriving from a Digital Elevation Model. We used slope and hillslope aspect as key parameters in identifying eroded formations. Therefore, our protocol was developed by testing all possible combinations of classification algorithm (Maximum likelihood Classifier and Parallelepiped) and input layers (spectral and morphological). Results obtained in a badlands sites located in Basilicata region (Southern Italy) showed a progressive reduction of misclassified badlands-pixels in the surrounding deposition areas by adding the terrain predictors. Our methodology allowed the improvement of badlands mapping: the best performance was obtained by applying MLC on all TM seven bands together with slope and aspect maps. Here, we show results from validation tests carried out on an other badland areas with similar heterogeneity which

  17. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids

    PubMed Central

    Tangprasertchai, Narin S.; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S.; Qin, Peter Z.

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve “correct” all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260

  18. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.

    PubMed

    Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S; Qin, Peter Z

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260

  19. Preliminary integrated geologic map databases for the United States: Digital data for the geology of southeast Alaska

    USGS Publications Warehouse

    Gehrels, George E.; Berg, Henry C.

    2006-01-01

    The growth in the use of Geographic Information Systems (GIS) has highlighted the need for digital geologic maps that have been attributed with information about age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. This report is part of a series of integrated geologic map databases that cover the entire United States. Three national-scale geologic maps that portray most or all of the United States already exist; for the conterminous U.S., King and Beikman (1974a,b) compiled a map at a scale of 1:2,500,000, Beikman (1980) compiled a map for Alaska at 1:2,500,000 scale, and for the entire U.S., Reed and others (2005a,b) compiled a map at a scale of 1:5,000,000. A digital version of the King and Beikman map was published by Schruben and others (1994). Reed and Bush (2004) produced a digital version of the Reed and others (2005a) map for the conterminous U.S. The present series of maps is intended to provide the next step in increased detail. State geologic maps that range in scale from 1:100,000 to 1:1,000,000 are available for most of the country, and digital versions of these state maps are the basis of this product. The digital geologic maps presented here are in a standardized format as ARC/INFO export files and as ArcView shape files. Data tables that relate the map units to detailed lithologic and age information accompany these GIS files. The map is delivered as a set of 1:250,000-scale quadrangle files. To the best of our ability, these quadrangle files are edge-matched with respect to geology. When the maps are merged, the combined attribute tables can be used directly with the merged maps to make derivative maps.

  20. Calibrating the FloodMap model based on geomorphological fieldwork and terrain analysis to improve the integrated HydroProg-FloodMap system for forecasting inundation

    NASA Astrophysics Data System (ADS)

    Witek, Matylda; Remisz, Joanna; Swierczynska, Malgorzata; Borowicz, Dorota; Parzoch, Krzysztof; Yu, Dapeng

    2016-04-01

    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 high flows. The system has been experimentally implemented for the upper Nysa Klodzka river basin (SW Poland). HydroProg is also integrated with the well-established hydrodynamic model known as FloodMap. The aim of this integration is to forecast flood inundation (HydroProg is used for computing hydrograph prediction, while FloodMap is utilized for mapping the hydrograph prognosis into spatial domain). The HydroProg-FloodMap solution currently works at four sites (Szalejow Dolny, Zelazno, Gorzuchow and Krosnowice) situated within the Nysa Klodzka river basin in the Southwestern Poland. The FloodMap model has been already calibrated for Zelazno (the Biala Ladecka river), and now we want to obtain model parameters for Gorzuchow (the Scinawka river). We carry out several simulations from the FloodMap model at this site, based on historical and recent flow records, to check where potential inundation may take place. Using the 1-metre LIDAR (Light Detection and Ranging) data we identify old channels of the Scinawka river in this area. In addition, we carried out several field campaigns with the unmanned aerial vehicle (UAV) to produce digital surface model (DSM) which can show morphological changes within an alluvial river valley. This can be perceived as an evidence of past inundations. Both the LIDAR mode and DSM obtained using UAV appeared to be not accurate enough to fully reconstruct the pattern of paleo-fluvial relief. Hence, we additionally performed geodetic survey using a self-reducting theodolite Dhalta 010A. Moreover, to confirm the pattern of the paleochannel of the Scinawka river, paleohydraulic analysis is performed. Finally, calibration of the FloodMap model for the Gorzuchow site becomes possible due to access to newly-acquired data on past inundation episodes.

  1. Physical map of a conditionally dispensable chromosome in Nectria haematococca mating population VI and location of chromosome breakpoints.

    PubMed Central

    Enkerli, J; Reed, H; Briley, A; Bhatt, G; Covert, S F

    2000-01-01

    Certain isolates of the plant pathogenic fungus Nectria haematococca mating population (MP) VI contain a 1.6-Mb conditionally dispensable (CD) chromosome carrying the phytoalexin detoxification genes MAK1 and PDA6-1. This chromosome is structurally unstable during sexual reproduction. As a first step in our analysis of the mechanisms underlying this chromosomal instability, hybridization between overlapping cosmid clones was used to construct a map of the MAK1 PDA6-1 chromosome. The map consists of 33 probes that are linked by 199 cosmid clones. The polymerase chain reaction and Southern analysis of N. haematococca MP VI DNA digested with infrequently cutting restriction enzymes were used to close gaps and order the hybridization-derived contigs. Hybridization to a probe extended from telomeric repeats was used to anchor the ends of the map to the actual chromosome ends. The resulting map is estimated to cover 95% of the MAK1 PDA6-1 chromosome and is composed of two ordered contigs. Thirty-eight percent of the clones in the minimal map are known to contain repeated DNA sequences. Three dispersed repeats were cloned during map construction; each is present in five to seven copies on the chromosome. The cosmid clones representing the map were probed with deleted forms of the CD chromosome and the results were integrated into the map. This allowed the identification of chromosome breakpoints and deletions. PMID:10880471

  2. Using WordNet to improve the mapping of data elements to UMLS for data sources integration.

    PubMed

    Mougin, Fleur; Burgun, Anita; Bodenreider, Olivier

    2006-01-01

    Each biomedical system has its own way of naming the pieces of information it contains, i.e., of defining its data elements (DEs). Integrating DEs facilitates the integration of biomedical resources. However, the mapping of DEs to the UMLS is ambiguous in many cases, when any correspondence is found at all. We propose to evaluate the potential contribution of a more general terminology: WordNet. Our method is based on synonyms, definitions, and structural properties of the terminologies. We applied it to a set of 474 DEs extracted from eleven biomedical sources. We show that WordNet can improve the direct mapping of DEs to UMLS when used to validate and disambiguate UMLS direct mappings. WordNet can also help identify indirect mappings of DEs to the UMLS. PMID:17238406

  3. A Foundation for the Integration of Mathcad into the Undergraduate Physics Curriculum

    NASA Astrophysics Data System (ADS)

    Riffe, D. M.; Dennison, J. R.; Nickles, Neal

    1998-04-01

    The Utah State University Physics Department has undertaken a curriculum-wide integration of Mathcad into the undergraduate physics program. The foundation for this integration is a 1-credit computer-laboratory experience in which the students work through a Mathcad handbook, developed by the authors, that teaches the students to use Mathcad in the context of solving physics problems. By working through the handbook the students gain familarity with the functions of Mathcad that are most useful for solving undergraduate physics problems. Those functions include the automatic handling of units, solving simultaneous equations, two and three dimensional graphs, symbolic processing, linear regression, and nonlinear curve fitting. A final project utilizing all aspects of the material in the handbook is included in the curriculum. To date, this courseware has enabled Mathcad to be utilized in at least 10 upper-division physics courses at USU.

  4. Integrating Physics and Literacy Learning in a Physics Course for Prospective Elementary and Middle School Teachers

    NASA Astrophysics Data System (ADS)

    van Zee, Emily H.; Jansen, Henri; Winograd, Kenneth; Crowl, Michele; Devitt, Adam

    2013-06-01

    The ability to listen closely, speak clearly, write coherently, read with comprehension, and to create and critique media offerings in science contexts is essential for effective science teaching. How might instructors develop such abilities in a physics course for prospective elementary and middle school teachers? We describe here such a course, involving collaboration among physics, science education, and literacy faculty members and two graduate assistants. Meeting twice a week for 10 weeks, the course emphasized questioning, predicting, exploring, observing, discussing, writing, and reading in physical science contexts. We report common themes about aspects that fostered or hindered science and literacy learning, changes in views about science teaching and learning, and positive shifts in interest in science and intended teaching practices.

  5. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea

    PubMed Central

    Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K.; Bhatia, Sabhyata

    2015-01-01

    The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7–23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest

  6. [Unequal crossing over in Escherichia coli: genetic and physical mapping of duplications isolated in conjugational matings].

    PubMed

    Sukhodolets, V V; Dukhiĭ, D E

    1996-01-01

    We previously demonstrated that stable heterozygous duplications deoA deoB :: Tn5/deoC deoD can be isolated among Deo+ recombinants obtained in conjugational matings between Escherichia coli strains HfrH deoA deoB :: Tn5 and HfrH deoC deoD. In this work, 30 duplications were tested by transduction for the inclusion of a set of genetic markers adjoining the deo operon (99.5 min) at the genetic map of E. coli: cycA :: Tn10 (96 min), zji :: Tn10 (98.2 min), thr :: Tn9 (100/0 min), car :: Tn10 (1 min), leu :: Tn9 (2 min), and proAB :: Tn10 (6 min). The results obtained indicate that only three out of 30 duplications could have originated from unequal crossing over between the rrn operons. In eight strains, duplications were chosen for physical mapping by the use of Not I restriction, pulsed-field electrophoresis, and Southern blot hybridization with DNA of the deo operon. In all these strains, the presence of duplications (once a triplication) was confirmed by corresponding changes in the set of Not I digests, although some strains had additional genetic rearrangements. The order of operon copies in a tandem was determined, and the length of a duplicated chromosomal segment was calculated as equal to 25, 46, 80, 150.5, and 175 kb in duplication D49, D4, D5, D9, and D18, respectively. Thus, the use of the conjugational Hfr x Hfr system allows the generation of unique rearrangements of the E. coli genetic material. PMID:8647423

  7. Mapping a near surface variable geologic regime using an integrated geophysical approach

    SciTech Connect

    Rogers, N.T.; Sandberg, S.K.; Miller, P.; Powell, G.

    1997-10-01

    An integrated geophysical approach involving seismic, electromagnetic, and electrical methods was employed to map fluvial, colluvial and bedrock geology, to delineate bedrock channels, and to determine fracture and joint orientations that may influence migration of petroleum hydrocarbons at the Glenrock Oil Seep. Both P (primary)-wave and S (shear)-wave seismic refraction techniques were used to map the bedrock surface topography, bedrock minima, stratigraphic boundaries, and possible structure. S-wave data were preferred because of better vertical resolution due to the combination of slower velocities and lower frequency wave train. Azimuthal resistivity/EP (induced polarization) and azimuthal electromagnetics were used to determine fracture orientations and groundwater flow directions. Terrain conductivity was used to map the fluvial sedimentary sequences (e.g., paleochannel and overbank deposits) in the North Platte River floodplain. Conductivity measurements were also used to estimate bedrock depth and to assist in the placement and recording parameters of the azimuthal soundings. The geophysical investigation indicated that groundwater flow pathways were controlled by the fluvial paleochannels and bedrock erosional features. Primary groundwater flow direction in the bedrock and colluvial sediments was determined from the azimuthal measurements and confirmed by drilling to be N20-40W along the measured strike of the bedrock and joint orientations. Joint/fracture orientations were measured at N20-40W and N10-30E from the azimuthal data and confirmed from measurements at a bedrock outcrop south of the site. The bedrock has an apparent N10E anisotropy in the seismic velocity profiles on the old refinery property that closely match that of measured joint/fracture orientations and may have a minor effect on groundwater flow.

  8. Vertical integration of cosmid and YAC resources for interval mapping on the X-chromosome

    SciTech Connect

    Holland, J.; Coffey, A.J.; Giannelli, F.; Bentley, D.R. )

    1993-02-01

    The vertical integration of cosmid and yeast artificial chromosome (YAC) resources is of particular importance in the development of high-resolution maps of selected regions of the human genome. A resource of approximately 95,000 cosmids constructed using DNA from primary fibroblasts of karyotype 49,XXXXX was validated by detailed characterization of a 200-kb cosmid contig spanning exons 8-20 of the dystrophin gene. This resource was used to construct contigs in 0.65 Mb of Xq26 by hybridization of gel-purified YAC DNA to high-density gridded arrays of the cosmid library; positive cosmids were overlapped by fingerprinting. Contigs were oriented and ordered relative to existing YACs in the region using cross-hybridization. The overlaps between a representative set of cosmids define 54 intervals of 5-20 kb and were used to construct a high-resolution cosmid interval map of the region, locating markers, dinucleotide repeats, and candidate CpG islands. This approach can be applied rapidly to large regions of the genome and without recourse to subcloning of individual YACs. 49 refs., 5 figs.

  9. Multiloop Integral System Test (MIST): Final report: Test group 30, mapping tests

    SciTech Connect

    Geissler, G.O. . Nuclear Power Div.)

    1989-12-01

    The Multiloop Integral System Test (MIST) is part of a multiphase program started in 1983 to address small-break loss-of-coolant accidents (SBLOCAs) specific to Babcock and Wilcox designed plants. MIST is sponsored by the US Nuclear Regulatory Commission, the Babcock Wilcox Owners Group, the Electric Power Research Institute, and Babcock and Wilcox. The unique features of the Babcock and Wilcox design, specifically the hot leg U-bends and steam generators, prevented the use of existing integral system data or existing integral facilities to address the thermal-hydraulic SBLOCA questions. MIST and two other supporting facilities were specifically designed and constructed for this program, and an existing facility -- the Once Through Integral System (OTIS) -- was also used. Data from MIST and the other facilities will be used to benchmark the adequacy of system codes, such as RELAP5 and TRAC, for predicting abnormal plant transients. The MIST program is reported in 11 volumes. The program is summarized in Volume 1; Volumes 2 through 8 describe groups of tests by test type; Volume 9 presents inter-group comparisons; Volume 10 provides comparisons between the calculations of RELAP5/MOD2 and MIST observations, and Volume 11 presents the later Phase 4 tests. This Volume 2 pertains to MIST mapping tests performed to traverse the early post-SBLOCA events slowly. The tests investigated the effect of test-to-test variations in boundary system controls, and only the primary fluid mass varied during a specific test in this test group. 5 refs., 415 figs., 12 tabs.

  10. Integration of Self-Organizing Map (SOM) and Kernel Density Estimation (KDE) for network intrusion detection

    NASA Astrophysics Data System (ADS)

    Cao, Yuan; He, Haibo; Man, Hong; Shen, Xiaoping

    2009-09-01

    This paper proposes an approach to integrate the self-organizing map (SOM) and kernel density estimation (KDE) techniques for the anomaly-based network intrusion detection (ABNID) system to monitor the network traffic and capture potential abnormal behaviors. With the continuous development of network technology, information security has become a major concern for the cyber system research. In the modern net-centric and tactical warfare networks, the situation is more critical to provide real-time protection for the availability, confidentiality, and integrity of the networked information. To this end, in this work we propose to explore the learning capabilities of SOM, and integrate it with KDE for the network intrusion detection. KDE is used to estimate the distributions of the observed random variables that describe the network system and determine whether the network traffic is normal or abnormal. Meanwhile, the learning and clustering capabilities of SOM are employed to obtain well-defined data clusters to reduce the computational cost of the KDE. The principle of learning in SOM is to self-organize the network of neurons to seek similar properties for certain input patterns. Therefore, SOM can form an approximation of the distribution of input space in a compact fashion, reduce the number of terms in a kernel density estimator, and thus improve the efficiency for the intrusion detection. We test the proposed algorithm over the real-world data sets obtained from the Integrated Network Based Ohio University's Network Detective Service (INBOUNDS) system to show the effectiveness and efficiency of this method.

  11. Physical mapping of the human T-cell antigen receptor (TCR) {beta}-chain gene complex

    SciTech Connect

    Yashim, Y.; So, A.K.

    1994-09-01

    The genetic variation of the TCR loci and their contribution to autoimmune diseases is poorly defined, in direct contrast to the clear examples of disease association with the Class I and II alleles of the major histocompatibility complex. We have therefore started to determine the gene organization and polymorphism of the TCR {beta} locus. Yeast artificial chromosomes (YACs) were used to construct a physical map of the germline human TCR {beta}-chain gene complex. Variable gene (V{beta}) sequences for the 25 known V{beta} subfamilies were amplified by PCR and were used as probes to screen a YAC library. Five positive YACs were identified. YACs designated B3, E11 and H11 of sizes 820, 400 and 600 kbp, respectively, were analyzed for their V{beta} content by pulse-field gel electrophoresis (PFGE). YAC B3 was found to contain all 25 V{beta} subfamilies, E11 for 14 and H11 for 7. B3 was also positive for the constant region genes. Restriction enzyme mapping of B3 located V{beta} and C{beta} gene regions to four Sfi I fragments of 280, 110, 90 and 125 kbp, and was in accordance with published data. The data thus showed that YAC B3 encoded a complete and unrearranged TCR {beta}-gene locus. The map was further resolved by locating restriction sites for Sal I and Bssll II on B3. Fluorescent in situ hybridization to human metaphase chromosomes localized B3 to chromosome 7q35. However, two additional signals were obtained: one attributable to V{beta} orphon cluster on chromosome 9q21; the second to the long arm of chromosome 2. PCR amplification of a chromosome 2 somatic cell hybrid using primers for all 25 V{beta} gene families revealed the signal was not attributable to a second orphon cluster. It is suggested that B3 is a chimeric YAC with an intact TCR {beta} locus flanked by chromosome 2 sequences. The determination of the TCR genomic organization will help extend studies of the role T-cells play in autoimmune diseases.

  12. 3. 6-Mb genomic and YAC physical map of the Down syndrome chromosome region on chromosome 21

    SciTech Connect

    Dufresne-Zacharia, M.C.; Dahmane, N.; Theophile, D.; Orti, R.; Chettouh, Z.; Sinet, P.M.; Delabar, J.M. )

    1994-02-01

    The Down syndrome chromosome region (DCR) on chromosome 21 has been shown to contain a gene(s) important in the pathogenesis of Down syndrome. The authors constructed a long-range restriction map of the D21S55-D21S65 region covering the proximal part of the DCR. Pulsed-field gel electrophoresis of lymphocyte DNA digested with three rare cutting enzymes, NotI, NruI, and Mlu1, was used to establish two physical linkage groups of 5 and 7 markers, respectively, spanning 4.6 Mb on the NotI map. Mapping analysis of 40 YACs allowed the selection of 13 YACs covering 95% of the D21S55-D21S65 region and spanning 3.6 Mb. The restriction maps of these YACs and their positioning on the genomic map allowed 19 markers to be ordered, including 4 NotI linking clones, 9 polymorphic markers, the CBR gene, and the AML1 gene. The distances between markers could also be estimated. This physical map and the location of eight NotI sites between D21S55 and D21S17 should facilitate the isolation of previously unidentified genes in this region. 34 refs., 2 figs., 2 tabs.

  13. The Relative Effectiveness of Integrated Reading Study Strategy and Conceptual Physics Approach

    NASA Astrophysics Data System (ADS)

    Taslidere, Erdal; Eryilmaz, Ali

    2012-04-01

    The primary purpose of this study was to investigate the combined and partial effects of the Integrated Reading/Study Strategy and Conceptual Physics Approach on ninth grade private high school students' achievement in and attitudes toward optics. The Integrated Reading/Study Strategy is a new strategy which was developed by integrating previously existing reading strategies of the KWL and SQ3R with classroom lecturing. The Conceptual Physics Approach is an instructional strategy developed on the basis of Conceptual Physics suggested by Paul G. Hewitt. To investigate the partial and combined effects of methods, factorial design was used. The study was conducted with 124 students from two private high schools in the Çankaya district region of Ankara, Turkey. Various teaching/learning materials were developed and used for the study. Two measuring tools, Achievement Test about Optics and Attitude Scale about Optics were used as pre and post tests before and after instruction. The study continued for a two-month treatment period. The results of the study showed that the combined effect of the Integrated Reading/Study Strategy and Conceptual Physics Approach improved students' achievement significantly compared to the separate individual methods. Although the product of the Integrated Reading/Study Strategy and Conceptual Physics Approach increased students' attitudes more compared to the remaining methods, the result is not statistically significant.

  14. Integrating Physics and Literacy Learning in a Physics Course for Prospective Elementary and Middle School Teachers

    ERIC Educational Resources Information Center

    van Zee, Emily H.; Jansen, Henri; Winograd, Kenneth; Crowl, Michele; Devitt, Adam

    2013-01-01

    The ability to listen closely, speak clearly, write coherently, read with comprehension, and to create and critique media offerings in science contexts is essential for effective science teaching. How might instructors develop such abilities in a physics course for prospective elementary and middle school teachers? We describe here such a course,…

  15. Using conceptual blending to describe how students use mathematical integrals in physics

    NASA Astrophysics Data System (ADS)

    Hu, Dehui; Rebello, N. Sanjay

    2013-12-01

    Calculus is used across many physics topics from introductory to upper-division courses. The fundamental concepts of differentiation and integration are important tools for solving real-world problems involving nonuniformly distributed quantities. Research in physics education has reported students’ lack of ability to transfer their calculus knowledge to physics. In order to better understand students’ deficiencies, we collected data from group teaching or learning interviews as students solved physics problems requiring setting up integrals. We adapted the conceptual blending framework from cognitive science to make sense of the ways in which students combined their knowledge from calculus and physics to set up integrals. We found that many students were not able to blend their mathematics and physics knowledge in a productive way though they have the required mathematics knowledge. We discussed the productive and unproductive blends that students created when setting up integrals. The results of the study also suggested possible strategies to shifting students’ constructing of blends to more powerful ones.

  16. Progress towards the construction of a sequence-ready physical map of the 3AS chromosome arm of hexaploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large genome size (~17 Gb), polyploid nature, and repetitive sequence content (>90%) of hexaploid wheat (Triticum aestivum) present a challenge for constructing physical maps, which are fundamental resources to aid genomic sequencing and annotation, and gene cloning. One approach to reduce the c...

  17. Concept Maps as a Research and Evaluation Tool To Assess Conceptual Change in Quantum Physics.

    ERIC Educational Resources Information Center

    Sen, Ahmet Ilhan

    2002-01-01

    Informs teachers about using concept maps as a learning tool and alternative assessment tools in education. Presents research results of how students might use concept maps to communicate their cognitive structure. (Author/KHR)

  18. A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

    NASA Astrophysics Data System (ADS)

    Kazama, Yusuke; Ishii, Kotaro; Aonuma, Wataru; Ikeda, Tokihiro; Kawamoto, Hiroki; Koizumi, Ayako; Filatov, Dmitry A.; Chibalina, Margarita; Bergero, Roberta; Charlesworth, Deborah; Abe, Tomoko; Kawano, Shigeyuki

    2016-01-01

    Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving “the travelling salesman problem”, and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map.

  19. A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

    PubMed Central

    Kazama, Yusuke; Ishii, Kotaro; Aonuma, Wataru; Ikeda, Tokihiro; Kawamoto, Hiroki; Koizumi, Ayako; Filatov, Dmitry A.; Chibalina, Margarita; Bergero, Roberta; Charlesworth, Deborah; Abe, Tomoko; Kawano, Shigeyuki

    2016-01-01

    Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving “the travelling salesman problem”, and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map. PMID:26742857

  20. Physical mapping of the t(12;14) region in uterine leiomyomata: Identification of a YAC spanning the translocation breakpoint

    SciTech Connect

    Feizo, M.L.S.; Morton, C.C.; Montgomery, K.T.

    1994-09-01

    Uterine leiomyomata are the most common pelvic tumors in women and the major coded diagnosis for hysterectomy in the U.S. They are characterized by various chromosome rearrangements and four cytogenetic subgroups have been identified. One of these subgroups includes rearrangements of 12q14-q15, a hotspot for translocations in benign solid tumors including uterine leiomyoma, pleomorphic adenoma of the salivary gland, lipoma, and pulmonary chondroid hamartoma. We have focused on physical mapping of chromosome 12 in the t(12;14)(q14-q15;q24) breakpoint region found in uterine leiomyoma in an effort to clone the rearranged genes and further our understanding of the biology of these tumors. 38 YACs and 7 cosmids spanning 11 cM of 12q14-q15 have been mapped by FISH to tumor metaphases containing t(12;14). 12 YACs and 4 cosmids mapped proximal to and 25 YACs and 3 cosmids mapped distal to the breakpoint on chromosome 12. One YAC spanned the breakpoint with hybridization noted on the normal 12 and the derivative 12 and 14 chromosomes. 13 of 38 YACs were chimeric. Correlation between genetic and physical distances between YACs and cosmids indicates that the genetic distance exceeds the estimated physical distance in 12q14-q15. This region may be more susceptible to recombination events as well as chromosome rearrangement leading to an overestimate of genetic distance, or 12q14-q15 may be more condensed in interphase nuclei leading to underestimates of physical distance. Our efforts are now directed in search of the gene in this region involved in the pathobiology of uterine leiomyomata. The high density genetic map of this region determined by this effort will provide useful information for positional cloning of chromosome 12 breakpoints in other benign solid tumors as well as genes involved in other diseases that map to 12q14-q15.

  1. BESIII Physics Data Storing and Processing on HBase and MapReduce

    NASA Astrophysics Data System (ADS)

    LEI, Xiaofeng; Li, Qiang; Kan, Bowen; Sun, Gongxing; Sun, Zhenyu

    2015-12-01

    In the past years, we have successfully applied Hadoop to high-energy physics analysis. Although, it has not only improved the efficiency of data analysis, but also reduced the cost of cluster building so far, there are still some spaces to be optimized, like inflexible pre-selection, low-efficient random data reading and I/O bottleneck caused by Fuse that is used to access HDFS. In order to change this situation, this paper presents a new analysis platform for high-energy physics data storing and analysing. The data structure is changed from DST tree-like files to HBase according to the features of the data itself and analysis processes, since HBase is more suitable for processing random data reading than DST files and enable HDFS to be accessed directly. A few of optimization measures are taken for the purpose of getting a good performance. A customized protocol is defined for data serializing and desterilizing for the sake of decreasing the storage space in HBase. In order to make full use of locality of data storing in HBase, utilizing a new MapReduce model and a new split policy for HBase regions are proposed in the paper. In addition, a dynamic pluggable easy-to-use TAG (event metadata) based pre-selection subsystem is established. It can assist physicists even to filter out 999%o uninterested data, if the conditions are set properly. This means that a lot of I/O resources can be saved, the CPU usage can be improved and consuming time for data analysis can be reduced. Finally, several use cases are designed, the test results show that the new platform has an excellent performance with 3.4 times faster with pre-selection and 20% faster without preselection, and the new platform is stable and scalable as well.

  2. Chromosomal structure of Rhodobacter capsulatus strain SB1003: Cosmid encyclopedia and high-resolution physical and genetic map

    SciTech Connect

    Fonstein, M.; Haselkorn, R. )

    1993-03-15

    A combination of cosmid genome walking and pulsed-field gel electrophoresis was used to construct a high-resolution physical and genetic map of the 3.8-megabase (Mb) genome of Rhodobacter capsulatus SB1003. The mapping was done by hybridization of pulsed-field gel blots and by grouping and further mapping of the cosmids and bacteriophages from genomic libraries. Cosmid clones formed two uninterrupted and ordered groups, one corresponding to the chromosome of R. capsulatus, the other to its 134-kb plasmid. Cos site end-labeling and partial EcoRV digestion of cosmids were used to construct a high-resolution EvoRV map of the genome. Overlapping of the mosmids was confirmed by the resemblance of the cosmid restriction maps and by direct end-to-end hybridization with SP6- and T7-specific transcripts. Twenty-three previously cloned genes and eight groups of repeated sequences, revealed in this work, were located in the ordered gene library and mapped with an accuracy of 1-10 kb. Blots of a minimal set of 192 cosmids, covering the chromosome and the plasmid with the known map position of each cosmid, give to R. capsulatus the same advantages that the Kohara phage panel gives to E. coli. 15 refs., 4 figs.

  3. An integrative architecture for general intelligence and executive function revealed by lesion mapping

    PubMed Central

    Colom, Roberto; Solomon, Jeffrey; Krueger, Frank; Forbes, Chad; Grafman, Jordan

    2012-01-01

    Although cognitive neuroscience has made remarkable progress in understanding the involvement of the prefrontal cortex in executive control, the broader functional networks that support high-level cognition and give rise to general intelligence remain to be well characterized. Here, we investigated the neural substrates of the general factor of intelligence (g) and executive function in 182 patients with focal brain damage using voxel-based lesion–symptom mapping. The Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System were used to derive measures of g and executive function, respectively. Impaired performance on these measures was associated with damage to a distributed network of left lateralized brain areas, including regions of frontal and parietal cortex and white matter association tracts, which bind these areas into a coordinated system. The observed findings support an integrative framework for understanding the architecture of general intelligence and executive function, supporting their reliance upon a shared fronto-parietal network for the integration and control of cognitive representations and making specific recommendations for the application of the Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System to the study of high-level cognition in health and disease. PMID:22396393

  4. Kinect v2 and RGB Stereo Cameras Integration for Depth Map Enhancement

    NASA Astrophysics Data System (ADS)

    Ravanelli, R.; Nascetti, A.; Crespi, M.

    2016-06-01

    Today range cameras are widespread low-cost sensors based on two different principles of operation: we can distinguish between Structured Light (SL) range cameras (Kinect v1, Structure Sensor, ...) and Time Of Flight (ToF) range cameras (Kinect v2, ...). Both the types are easy to use 3D scanners, able to reconstruct dense point clouds at high frame rate. However the depth maps obtained are often noisy and not enough accurate, therefore it is generally essential to improve their quality. Standard RGB cameras can be a valuable solution to solve such issue. The aim of this paper is therefore to evaluate the integration feasibility of these two different 3D modelling techniques, characterized by complementary features and based on standard low-cost sensors. For this purpose, a 3D model of a DUPLOTM bricks construction was reconstructed both with the Kinect v2 range camera and by processing one stereo pair acquired with a Canon Eos 1200D DSLR camera. The scale of the photgrammetric model was retrieved from the coordinates measured by Kinect v2. The preliminary results are encouraging and show that the foreseen integration could lead to an higher metric accuracy and a major level of completeness with respect to that obtained by using only separated techniques.

  5. Comparing morphologies of drainage basins on Mars and Earth using integral-geometry and neural maps

    NASA Technical Reports Server (NTRS)

    Stepinski, T. F.; Coradetti, S.

    2004-01-01

    We compare morphologies of drainage basins on Mars and Earth in order to confine the formation process of Martian valley networks. Basins on both planets are computationally extracted from digital topography. Integral-geometry methods are used to represent each basin by a circularity function that encapsulates its internal structure. The shape of such a function is an indicator of the style of fluvial erosion. We use the self-organizing map technique to construct a similarity graph for all basins. The graph reveals systematic differences between morphologies of basins on the two planets. This dichotomy indicates that terrestrial and Martian surfaces were eroded differently. We argue that morphologies of Martian basins are incompatible with runoff from sustained, homogeneous rainfall. Fluvial environments compatible with observed morphologies are discussed. We also construct a similarity graph based on the comparison of basins hypsometric curves to demonstrate that hypsometry is incapable of discriminating between terrestrial and Martian basins. INDEX TERMS: 1824 Hydrology: Geomorphology (1625); 1886 Hydrology: Weathering (1625); 5415 Planetology: Solid Surface Planets: Erosion and weathering; 6225 Planetology: Solar System Objects Mars. Citation: Stepinski, T. F., and S. Coradetti (2004), Comparing morphologies of drainage basins on Mars and Earth using integral-ge

  6. Mapping of neural networks onto the memory-processor integrated architecture.

    PubMed

    Kim, Youngsik; Noh, Mi Jung; Han, Tack Don; Kim, Shin Dug

    1998-08-01

    In this paper, an effective memory-processor integrated architecture, called memory-based processor array for artificial neural networks (MPAA), is proposed. The MPAA can be easily integrated into any host system via memory interface. Specifically, the MPA system provides an efficient mechanism for its local memory accesses allowed by row and column bases, using hybrid row and column decoding, which is suitable for computation models of ANNs such as the accessing and alignment patterns given for matrix-by-vector operations. Mapping algorithms to implement the multilayer perceptron with backpropagation learning on the MPAA system are also provided. The proposed algorithms support both neuron and layer level parallelisms which allow the MPAA system to operate the learning phase as well as the recall phase in the pipelined fashion. Performance evaluation is provided by detailed comparison in terms of two metrics such as the cost and number of computation steps. The results show that the performance of the proposed architecture and algorithms is superior to those of the previous approaches, such as one-dimensional single-instruction multiple data (SIMD) arrays, two-dimensional SIMD arrays, systolic ring structures, and hypercube machines. PMID:12662777

  7. Feature Integration in the Mapping of Multi-Attribute Visual Stimuli to Responses

    PubMed Central

    Ishizaki, Takuya; Morita, Hiromi; Morita, Masahiko

    2015-01-01

    In the human visual system, different attributes of an object, such as shape and color, are separately processed in different modules and then integrated to elicit a specific response. In this process, different attributes are thought to be temporarily “bound” together by focusing attention on the object; however, how such binding contributes to stimulus-response mapping remains unclear. Here we report that learning and performance of stimulus-response tasks was more difficult when three attributes of the stimulus determined the correct response than when two attributes did. We also found that spatially separated presentations of attributes considerably complicated the task, although they did not markedly affect target detection. These results are consistent with a paired-attribute model in which bound feature pairs, rather than object representations, are associated with responses by learning. This suggests that attention does not bind three or more attributes into a unitary object representation, and long-term learning is required for their integration. PMID:25762010

  8. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    PubMed

    Oliver, Rebekah E; Tinker, Nicholas A; Lazo, Gerard R; Chao, Shiaoman; Jellen, Eric N; Carson, Martin L; Rines, Howard W; Obert, Donald E; Lutz, Joseph D; Shackelford, Irene; Korol, Abraham B; Wight, Charlene P; Gardner, Kyle M; Hattori, Jiro; Beattie, Aaron D; Bjørnstad, Åsmund; Bonman, J Michael; Jannink, Jean-Luc; Sorrells, Mark E; Brown-Guedira, Gina L; Mitchell Fetch, Jennifer W; Harrison, Stephen A; Howarth, Catherine J; Ibrahim, Amir; Kolb, Frederic L; McMullen, Michael S; Murphy, J Paul; Ohm, Herbert W; Rossnagel, Brian G; Yan, Weikai; Miclaus, Kelci J; Hiller, Jordan; Maughan, Peter J; Redman Hulse, Rachel R; Anderson, Joseph M; Islamovic, Emir; Jackson, Eric W

    2013-01-01

    A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources. PMID:23533580

  9. The concept map as a tool for the collaborative construction of knowledge: A microanalysis of high school physics students

    NASA Astrophysics Data System (ADS)

    Roth, Wolff-Michael; Roychoudhury, Anita

    Although concept mapping has been shown to help students in meaningful learning, particularly when done as a collaborative activity, little has been done to understand the microprocesses during the activity itself. However, in order to be able to improve the activity as a teaching and learning heuristic, we have to know more about the microprocesses that constitute concept mapping as process and as product. This study was designed to investigate concept mapping as a means of assessing the quality of student understanding from two perspectives: the analysis of the process of constructing meaning and the analysis of the products of this cognitive activity. An interpretive research methodology was adopted for the construction of meaning from the data. Twenty-nine students from two sections of a senior level high school physics course participated in the study. The data sources included videotapes, their transcripts, and all concept maps produced. Students worked in collaborative groups during all of the concept mapping sessions. Individual concept mapping was assessed twice, once delayed by a week, another time delayed by 6 weeks. To assess what happened to the cognitive achievement as the context of concept mapping changed from collaborative to individual activity, we used a tracer. A tracer is some bit of knowledge, procedure, or action that allows the researcher to follow a task through various settings. The concept maps as products differed in their hierarchical organization, the number of links, and the benefit to the individual students. Three major processes emerged, which students used to arrive at suitable propositions. Students mediated propositions verbally and nonverbally, they took adversarial positions and appealed to authority, and they formed temporary alliances based on presumed expertise. Both product and process hold promise but also show some limitations. On the positive side, concept mapping led to sustained discourse on the topic and improved the

  10. Integrated Analysis of EEG and fMRI Using Sparsity of Spatial Maps.

    PubMed

    Samadi, S; Soltanian-Zadeh, H; Jutten, C

    2016-09-01

    Integration of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) is an open problem, which has motivated many researches. The most important challenge in EEG-fMRI integration is the unknown relationship between these two modalities. In this paper, we extract the same features (spatial map of neural activity) from both modality. Therefore, the proposed integration method does not need any assumption about the relationship of EEG and fMRI. We present a source localization method from scalp EEG signal using jointly fMRI analysis results as prior spatial information and source separation for providing temporal courses of sources of interest. The performance of the proposed method is evaluated quantitatively along with multiple sparse priors method and sparse Bayesian learning with the fMRI results as prior information. Localization bias and source distribution index are used to measure the performance of different localization approaches with or without a variety of fMRI-EEG mismatches on simulated realistic data. The method is also applied to experimental data of face perception of 16 subjects. Simulation results show that the proposed method is significantly stable against the noise with low localization bias. Although the existence of an extra region in the fMRI data enlarges localization bias, the proposed method outperforms the other methods. Conversely, a missed region in the fMRI data does not affect the localization bias of the common sources in the EEG-fMRI data. Results on experimental data are congruent with previous studies and produce clusters in the fusiform and occipital face areas (FFA and OFA, respectively). Moreover, it shows high stability in source localization against variations in different subjects. PMID:27460558

  11. Mapping strategies: Chromosome 16 workshop. Final technical report

    SciTech Connect

    Not Available

    1989-12-31

    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.

  12. Implementing a global integrative rehabilitation medicine rotation: a physical medicine and rehabilitation residency program's experience.

    PubMed

    Kosasih, Judith B; Jurisic, Daniela H; Gandini, Cristiano; Sauter, Carley N; Braza, Diane W

    2013-06-01

    An innovative international rotation in integrative rehabilitation medicine was implemented as part of the physical medicine and rehabilitation residency program at the Medical College of Wisconsin. Rotation objectives were to introduce medical knowledge of integrative medicine treatments into physical medicine and rehabilitation practice and to initiate collaboration with international academic partners. Residents were approved based on their academic record, completion of prerequisites, and personal statement. During a 4-wk rotation located in Italy, residents developed an integrative treatment strategy for each patient using conventional medical care and other therapeutic options, including acupuncture, biofeedback, aquatic therapy, yoga, and others. Postrotation assessment included evaluations by Italian team and patients, residents' evidence-based presentations, and postrotation self-reflection. Participating residents reported high achievement in clinical performance, improved application of integrative medicine, broader appreciation of cultural diversity in patient care, and increased personal and professional development. This reciprocal program model serves as an example for other programs interested in implementing similar international rotations. PMID:23291603

  13. Health risk in the context of climate change and adaptation - Concept and mapping as an integrated approach

    NASA Astrophysics Data System (ADS)

    Kienberger, S.; Notenbaert, A.; Zeil, P.; Bett, B.; Hagenlocher, M.; Omolo, A.

    2012-04-01

    Climate change has been stated as being one of the greatest challenges to global health in the current century. Climate change impacts on human health and the socio-economic and related poverty consequences are however still poorly understood. While epidemiological issues are strongly coupled with environmental and climatic parameters, the social and economic circumstances of populations might be of equal or even greater importance when trying to identify vulnerable populations and design appropriate and well-targeted adaptation measures. The inter-linkage between climate change, human health risk and socio-economic impacts remains an important - but largely outstanding - research field. We present an overview on how risk is traditionally being conceptualised in the human health domain and reflect critically on integrated approaches as being currently used in the climate change context. The presentation will also review existing approaches, and how they can be integrated towards adaptation tools. Following this review, an integrated risk concept is being presented, which has been currently adapted under the EC FP7 research project (HEALTHY FUTURES; http://www.healthyfutures.eu/). In this approach, health risk is not only defined through the disease itself (as hazard) but also by the inherent vulnerability of the system, population or region under study. It is in fact the interaction of environment and society that leads to the development of diseases and the subsequent risk of being negatively affected by it. In this conceptual framework vulnerability is being attributed to domains of lack of resilience as well as underlying preconditions determining susceptibilities. To fulfil a holistic picture vulnerability can be associated to social, economic, environmental, institutional, cultural and physical dimensions. The proposed framework also establishes the important nexus to adaptation and how different measures can be related to avoid disease outbreaks, reduce

  14. 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

    NASA Astrophysics Data System (ADS)

    Martínez, Guadalupe; Pérez, Ángel Luis; Suero, María Isabel; Pardo, Pedro J.

    2013-04-01

    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 measuring instrument. The sample included 114 university students from the School of Industrial Engineering who were divided into two equivalent homogeneous groups of 57 students each. The amount of learning attained by the students in each group was compared, with the independent variable being the teaching method; the experimental group (E.G.) used concept maps, while the control group (C.G.) did not. We performed a crossover study with the two groups of students, with one group acting as the E.G. for the topic of optical fibers and as the C.G. for the topic of the fundamental particles of matter and vice versa for the other group. For each of the two topics studied, the evaluation instrument was a test of 100 dichotomous items. The resulting data were subjected to a comparative statistical analysis, which revealed a significant difference in the amount of learning attained by the E.G. students as compared with the C.G. students. The results allow us to state that for the use of concept maps, the average increment in the E.G. students' learning was greater than 19 percentage points.

  15. Flexible and Stretchable Physical Sensor Integrated Platforms for Wearable Human-Activity Monitoringand Personal Healthcare.

    PubMed

    Trung, Tran Quang; Lee, Nae-Eung

    2016-06-01

    Flexible and stretchable physical sensors that can measure and quantify electrical signals generated by human activities are attracting a great deal of attention as they have unique characteristics, such as ultrathinness, low modulus, light weight, high flexibility, and stretchability. These flexible and stretchable physical sensors conformally attached on the surface of organs or skin can provide a new opportunity for human-activity monitoring and personal healthcare. Consequently, in recent years there has been considerable research effort devoted to the development of flexible and stretchable physical sensors to fulfill the requirements of future technology, and much progress has been achieved. Here, the most recent developments of flexible and stretchable physical sensors are described, including temperature, pressure, and strain sensors, and flexible and stretchable sensor-integrated platforms. The latest successful examples of flexible and stretchable physical sensors for the detection of temperature, pressure, and strain, as well as their novel structures, technological innovations, and challenges, are reviewed first. In the next section, recent progress regarding sensor-integrated wearable platforms is overviewed in detail. Some of the latest achievements regarding self-powered sensor-integrated wearable platform technologies are also reviewed. Further research direction and challenges are also proposed to develop a fully sensor-integrated wearable platform for monitoring human activity and personal healthcare in the near future. PMID:26840387

  16. Toward a physical map of Drosophila buzzatii. Use of randomly amplified polymorphic dna polymorphisms and sequence-tagged site landmarks.

    PubMed Central

    Laayouni, H; Santos, M; Fontdevila, A

    2000-01-01

    We present a physical map based on RAPD polymorphic fragments and sequence-tagged sites (STSs) for the repleta group species Drosophila buzzatii. One hundred forty-four RAPD markers have been used as probes for in situ hybridization to the polytene chromosomes, and positive results allowing the precise localization of 108 RAPDs were obtained. Of these, 73 behave as effectively unique markers for physical map construction, and in 9 additional cases the probes gave two hybridization signals, each on a different chromosome. Most markers (68%) are located on chromosomes 2 and 4, which partially agree with previous estimates on the distribution of genetic variation over chromosomes. One RAPD maps close to the proximal breakpoint of inversion 2z(3) but is not included within the inverted fragment. However, it was possible to conclude from this RAPD that the distal breakpoint of 2z(3) had previously been wrongly assigned. A total of 39 cytologically mapped RAPDs were converted to STSs and yielded an aggregate sequence of 28,431 bp. Thirty-six RAPDs (25%) did not produce any detectable hybridization signal, and we obtained the DNA sequence from three of them. Further prospects toward obtaining a more developed genetic map than the one currently available for D. buzzatii are discussed. PMID:11102375

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

    PubMed Central

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

    2013-01-01

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

  18. Rapid mapping of schistosomiasis and other neglected tropical diseases in the context of integrated control programmes in Africa

    PubMed Central

    BROOKER, S.; KABATEREINE, N. B.; GYAPONG, J. O.; STOTHARD, J. R.; UTZINGER, J.

    2009-01-01

    SUMMARY There is growing interest and commitment to the control of schistosomiasis and other so-called neglected tropical diseases (NTDs). Resources for control are inevitably limited, necessitating assessment methods that can rapidly and accurately identify and map high-risk communities so that interventions can be targeted in a spatially-explicit and cost-effective manner. Here, we review progress made with (i) mapping schistosomiasis across Africa using available epidemiological data and more recently, climate-based risk prediction; (ii) the development and use of morbidity questionnaires for rapid identification of high-risk communities of urinary schistosomiasis; and (iii) innovative sampling-based approaches for intestinal schistosomiasis, using the lot quality assurance sampling technique. Experiences are also presented for the rapid mapping of other NTDs, including onchocerciasis, loiasis and lymphatic filariasis. Future directions for an integrated rapid mapping approach targeting multiple NTDs simultaneously are outlined, including potential challenges in developing an integrated survey tool. The lessons from the mapping of human helminth infections may also be relevant for the rapid mapping of malaria as its control efforts are intensified. PMID:19450373

  19. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,70...

  20. The Effect of Concept Mapping-Guided Discovery Integrated Teaching Approach on Chemistry Students' Achievement and Retention

    ERIC Educational Resources Information Center

    Fatokun, K. V. F.; Eniayeju, P. A.

    2014-01-01

    This study investigates the effects of Concept Mapping-Guided Discovery Integrated Teaching Approach on the achievement and retention of chemistry students. The sample comprised 162 Senior Secondary two (SS 2) students drawn from two Science Schools in Nasarawa State, Central Nigeria with equivalent mean scores of 9.68 and 9.49 in their pre-test.…

  1. Geoprocessing via google maps for assessing obesogenic built environments related to physical activity and chronic noncommunicable diseases: validity and reliability.

    PubMed

    Silva, Valter; Grande, Antonio Jose; Rech, Cassiano Ricardo; Peccin, Maria Stella

    2015-01-01

    This study analyzes the reliability and validity of obesogenic built environments related to physical activity and chronic noncommunicable diseases through Google Maps in a heterogeneous urban area (i.e., residential and commercial, very poor and very rich) in São Paulo (SP), Brazil. There are no important differences when comparing virtual measures with street audit. Based on Kappa statistic, respectively for validity and reliability, 78% and 80% of outcomes were classified as nearly perfect agreement or substantial agreement. Virtual measures of geoprocessing via Google Maps provided high validity and reliability for assessing built environments. PMID:25708376

  2. Mapping Depositional Facies on Great Bahama Bank: An Integration of Groundtruthing and Remote Sensing Methods

    NASA Astrophysics Data System (ADS)

    Hariss, M.; Purkis, S.; Ellis, J. M.; Swart, P. K.; Reijmer, J.

    2013-12-01

    Great Bahama Bank (GBB) has been used in many models to illustrate depositional facies variation across flat-topped, isolated carbonate platforms. Such models have served as subsurface analogs at a variety of scales. In this presentation we have integrated Landsat TM imagery, a refined bathymetric digital elevation model, and seafloor sample data compiled into ArcGIS and analyzed with eCognition to develop a depositional facies map that is more robust than previous versions. For the portion of the GBB lying to the west of Andros Island, the facies map was generated by pairing an extensive set of GPS-constrained field observations and samples (n=275) (Reijmer et al., 2009, IAS Spec Pub 41) with computer and manual interpretation of the Landsat imagery. For the remainder of the platform, which lacked such rigorous ground-control, the Landsat imagery was segmented into lithotopes - interpreted to be distinct bodies of uniform sediment - using a combination of edge detection, spectral and textural analysis, and manual editing. A map was then developed by assigning lithotopes to facies classes on the basis of lessons derived from the portion of the platform for which we had rigorous conditioning. The new analysis reveals that GBB is essentially a very grainy platform with muddier accumulations only in the lee of substantial island barriers; in this regard Andros Island, which is the largest island on GBB, exerts a direct control over the muddiest portion of GBB. Mudstones, wackestones, and mud-rich packstones cover 7%, 6%, and 15%, respectively, of the GBB platform top. By contrast, mud-poor packstones, grainstones, and rudstones account for 19%, 44%, and 3%, respectively. Of the 44% of the platform-top classified as grainstone, only 4% is composed of 'high-energy' deposits characterized by the development of sandbar complexes. The diversity and size of facies bodies is broadly the same on the eastern and western limb of the GBB platform, though the narrower eastern

  3. Integration of Landsat-based disturbance maps in the Landscape Change Monitoring System (LCMS)

    NASA Astrophysics Data System (ADS)

    Healey, S. P.; Cohen, W. B.; Eidenshink, J. C.; Hernandez, A. J.; Huang, C.; Kennedy, R. E.; Moisen, G. G.; Schroeder, T. A.; Stehman, S.; Steinwand, D.; Vogelmann, J. E.; Woodcock, C.; Yang, L.; Yang, Z.; Zhu, Z.

    2013-12-01

    Land cover change can have a profound effect upon an area's natural resources and its role in biogeochemical and hydrological cycles. Many land cover changes processes are sensitive to climate, including: fire; storm damage, and insect activity. Monitoring of both past and ongoing land cover change is critical, particularly as we try to understand the impact of a changing climate on the natural systems we manage. The Landsat series of satellites, which initially launched in 1972, has allowed land observation at spatial and spectral resolutions appropriate for identification of many types of land cover change. Over the years, and particularly since the opening of the Landsat archive in 2008, many approaches have been developed to meet individual monitoring needs. Algorithms vary by the cover type targeted, the rate of change sought, and the period between observations. The Landscape Change Monitoring System (LCMS) is envisioned as a sustained, inter-agency monitoring program that brings together and operationally provides the best available land cover change maps over the United States. Expanding upon the successful USGS/Forest Service Monitoring Trends in Burn Severity project, LCMS is designed to serve a variety of research and management communities. The LCMS Science Team is currently assessing the relative strengths of a variety of leading change detection approaches, primarily emphasizing Landsat observations. Using standardized image pre-processing methods, maps produced by these algorithms have been compared at intensive validation sites across the country. Additionally, LCMS has taken steps toward a data-mining framework, in which ensembles of algorithm outputs are used with non-parametric models to create integrated predictions of change across a variety of scenarios and change dynamics. We present initial findings from the LCMS Science Team, including validation results from individual algorithms and assessment of initial 'integrated' products from the

  4. Physical map of the chromosome of Neisseria gonorrhoeae FA1090 with locations of genetic markers, including opa and pil genes.

    PubMed Central

    Dempsey, J A; Litaker, W; Madhure, A; Snodgrass, T L; Cannon, J G

    1991-01-01

    A physical map of the chromosome of Neisseria gonorrhoeae FA1090 has been constructed. Digestion of strain FA1090 DNA with NheI, SpeI, BglII, or PacI resulted in a limited number of fragments that were resolved by contour-clamped homogeneous electric field electrophoresis. The estimated genome size was 2,219 kb. To construct the map, probes corresponding to single-copy chromosomal sequences were used in Southern blots of digested DNA separated on pulsed-field gels, to determine how the fragments from different digests overlapped. Some of the probes represented identified gonococcal genes, whereas others were anonymous cloned fragments of strain FA1090 DNA. By using this approach, a macrorestriction map of the strain FA1090 chromosome was assembled, and the locations of various genetic markers on the map were determined. Once the map was completed, the repeated gene families encoding Opa and pilin proteins were mapped. The 11 opa loci of strain FA1090 were distributed over approximately 60% of the chromosome. The pil loci were more clustered and were located in two regions separated by approximately one-fourth of the chromosome. Images PMID:1679431

  5. Toward an Integrated Linkage Map of Common Bean. III. Mapping Genetic Factors Controlling Host-Bacteria Interactions

    PubMed Central

    Nodari, R. O.; Tsai, S. M.; Guzman, P.; Gilbertson, R. L.; Gepts, P.

    1993-01-01

    Restriction fragment length polymorphism (RFLP)-based genetic linkage maps allow us to dissect the genetic control of quantitative traits (QT) by locating individual quantitative trait loci (QTLs) on the linkage map and determining their type of gene action and the magnitude of their contribution to the phenotype of the QT. We have performed such an analysis for two traits in common bean, involving interactions between the plant host and bacteria, namely Rhizobium nodule number (NN) and resistance to common bacterial blight (CBB) caused by Xanthomonas campestris pv. phaseoli. Analyses were conducted in the progeny of a cross between BAT93 (fewer nodules; moderately resistant to CBB) and Jalo EEP558 (more nodules; susceptible to CBB). An RFLP-based linkage map for common bean based on 152 markers had previously been derived in the F(2) of this cross. Seventy F(2)-derived F(3) families were inoculated in separate greenhouse experiments with Rhizobium tropici strain UMR1899 or X. c. pv. phaseoli isolate isolate W18. Regression and interval mapping analyses were used to identify genomic regions involved in the genetic control of these traits. These two methods identified the same genomic regions for each trait, with a few exceptions. For each trait, at least four putative QTLs were identified, which accounted for approximately 50% and 75% of the phenotypic variation in NN and CBB resistance, respectively. A chromosome region on linkage group D7 carried factor(s) influencing both traits. In all other cases, the putative QTLs affecting NN and CBB were located in different linkage groups or in the same linkage group, but far apart (more than 50 cM). Both BAT93 and Jalo EEP558 contributed alleles associated with higher NN, whereas CBB resistance was always associated with BAT93 alleles. Further investigations are needed to determine whether the QTLs for NN and CBB on linkage group D7 represent linked genes or the same gene with pleiotropic effects. Identification of the

  6. Using Computer-Assisted Argumentation Mapping to develop effective argumentation skills in high school advanced placement physics

    NASA Astrophysics Data System (ADS)

    Heglund, Brian

    Educators recognize the importance of reasoning ability for development of critical thinking skills, conceptual change, metacognition, and participation in 21st century society. There is a recognized need for students to improve their skills of argumentation, however, argumentation is not explicitly taught outside logic and philosophy---subjects that are not part of the K-12 curriculum. One potential way of supporting the development of argumentation skills in the K-12 context is through incorporating Computer-Assisted Argument Mapping to evaluate arguments. This quasi-experimental study tested the effects of such argument mapping software and was informed by the following two research questions: 1. To what extent does the collaborative use of Computer-Assisted Argumentation Mapping to evaluate competing theories influence the critical thinking skill of argument evaluation, metacognitive awareness, and conceptual knowledge acquisition in high school Advanced Placement physics, compared to the more traditional method of text tables that does not employ Computer-Assisted Argumentation Mapping? 2. What are the student perceptions of the pros and cons of argument evaluation in the high school Advanced Placement physics environment? This study examined changes in critical thinking skills, including argumentation evaluation skills, as well as metacognitive awareness and conceptual knowledge, in two groups: a treatment group using Computer-Assisted Argumentation Mapping to evaluate physics arguments, and a comparison group using text tables to evaluate physics arguments. Quantitative and qualitative methods for collecting and analyzing data were used to answer the research questions. Quantitative data indicated no significant difference between the experimental groups, and qualitative data suggested students perceived pros and cons of argument evaluation in the high school Advanced Placement physics environment, such as self-reported sense of improvement in argument

  7. Mapping wildland fuels for fire management across multiple scales: Integrating remote sensing, GIS, and biophysical modeling

    USGS Publications Warehouse

    Keane, R.E.; Burgan, R.; van Wagtendonk, J.

    2001-01-01

    Fuel maps are essential for computing spatial fire hazard and risk and simulating fire growth and intensity across a landscape. However, fuel mapping is an extremely difficult and complex process requiring expertise in remotely sensed image classification, fire behavior, fuels modeling, ecology, and geographical information systems (GIS). This paper first presents the challenges of mapping fuels: canopy concealment, fuelbed complexity, fuel type diversity, fuel variability, and fuel model generalization. Then, four approaches to mapping fuels are discussed with examples provided from the literature: (1) field reconnaissance; (2) direct mapping methods; (3) indirect mapping methods; and (4) gradient modeling. A fuel mapping method is proposed that uses current remote sensing and image processing technology. Future fuel mapping needs are also discussed which include better field data and fuel models, accurate GIS reference layers, improved satellite imagery, and comprehensive ecosystem models.

  8. Effects of Integrated Physical Exercises and Gestures on Preschool Children's Foreign Language Vocabulary Learning

    ERIC Educational Resources Information Center

    Mavilidi, Myrto-Foteini; Okely, Anthony D.; Chandler, Paul; Cliff, Dylan P.; Paas, Fred

    2015-01-01

    Research suggests that integrating human movement into a cognitive learning task can be effective for learning due to its cognitive and physiological effects. In this study, the learning effects of enacting words through whole-body movements (i.e., physical exercise) and part-body movements (i.e., gestures) were investigated in a foreign language…

  9. Retention of Differential and Integral Calculus: A Case Study of a University Student in Physical Chemistry

    ERIC Educational Resources Information Center

    Jukic Matic, Ljerka; Dahl, Bettina

    2014-01-01

    This paper reports a study on retention of differential and integral calculus concepts of a second-year student of physical chemistry at a Danish university. The focus was on what knowledge the student retained 14 months after the course and on what effect beliefs about mathematics had on the retention. We argue that if a student can quickly…

  10. Living Arrangements, Social Integration, and Loneliness in Later Life: The Case of Physical Disability

    ERIC Educational Resources Information Center

    Russell, David

    2009-01-01

    Despite the theoretical linkages between household composition and social integration, relatively limited research has considered how living arrangements affect risk for loneliness in later life. Prior work has also failed to consider whether physical disability moderates this potentially important relationship. Using data from a sample of older…

  11. Conceptual Integration of Hybridization by Algerian Students Intending to Teach Physical Sciences

    ERIC Educational Resources Information Center

    Salah, Hazzi; Dumon, Alain

    2011-01-01

    This work aims to assess the difficulties encountered by students of the Ecole Normale Superieure of Kouba (Algeria) intending to teach physical science in the integration of the hybridization of atomic orbitals. It is a concept that they should use in describing the formation of molecular orbitals ([sigma] and [pi]) in organic chemistry and gaps…

  12. Considerations for Integration of Physically Handicapped and Non-Handicapped Preschool Children.

    ERIC Educational Resources Information Center

    Cormack, Elizabeth O.

    Eight physically handicapped (blind, spina bifida, cerebral palsy, or genetic defect) preschool children and eight children with normal sensory motor abilities (mean age of both groups 3 1/2 years) participated in a preschool demonstration project designed to promote equal educational and social experiences in an integrated preschool through the…

  13. Abstract Applets: A Method for Integrating Numerical Problem Solving into the Undergraduate Physics Curriculum

    SciTech Connect

    Peskin, Michael E

    2003-02-13

    In upper-division undergraduate physics courses, it is desirable to give numerical problem-solving exercises integrated naturally into weekly problem sets. I explain a method for doing this that makes use of the built-in class structure of the Java programming language. I also supply a Java class library that can assist instructors in writing programs of this type.

  14. Integration of Information and Communication Technology and Pupils' Motivation in a Physical Education Setting

    ERIC Educational Resources Information Center

    Legrain, Pascal; Gillet, Nicolas; Gernigon, Christophe; Lafreniere, Marc-André

    2015-01-01

    The purpose of this study was to test an integrative model regarding the impact of information and communication technology (ICT) on achievement in physical education. Pupils' perceptions of autonomy-support from teacher, satisfaction of basic psychological needs, and self-determined motivation were considered to mediate the impact of ICT on…

  15. Lysozyme Thermal Denaturation and Self-Interaction: Four Integrated Thermodynamic Experiments for the Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Schwinefus, Jeffrey J.; Schaefle, Nathaniel J.; Muth, Gregory W.; Miessler, Gary L.; Clark, Christopher A.

    2008-01-01

    As part of an effort to infuse our physical chemistry laboratory with biologically relevant, investigative experiments, we detail four integrated thermodynamic experiments that characterize the denaturation (or unfolding) and self-interaction of hen egg white lysozyme as a function of pH and ionic strength. Students first use Protein Explorer to…

  16. Physical Integration and Social Segregation of Northern Negro College Students (1953, 1963 and 1965).

    ERIC Educational Resources Information Center

    Zimbardo, Philip G.

    Extensive observations of the pattern of seating by Negro and white college students in the cafeterias of Brooklyn College (1953) and City College of New York (1963 and 1965) revealed consistent isolation of the Negro students. This pattern of social (self) segregation existed within environments which have always been physically integrated and…

  17. Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions.

    PubMed

    Tuller, Tamir; Atar, Shimshi; Ruppin, Eytan; Gurevich, Michael; Achiron, Anat

    2011-09-15

    Multiple sclerosis (MS) is a central nervous system autoimmune inflammatory T-cell-mediated disease with a relapsing-remitting course in the majority of patients. In this study, we performed a high-resolution systems biology analysis of gene expression and physical interactions in MS relapse and remission. To this end, we integrated 164 large-scale measurements of gene expression in peripheral blood mononuclear cells of MS patients in relapse or remission and healthy subjects, with large-scale information about the physical interactions between these genes obtained from public databases. These data were analyzed with a variety of computational methods. We find that there is a clear and significant global network-level signal that is related to the changes in gene expression of MS patients in comparison to healthy subjects. However, despite the clear differences in the clinical symptoms of MS patients in relapse versus remission, the network level signal is weaker when comparing patients in these two stages of the disease. This result suggests that most of the genes have relatively similar expression levels in the two stages of the disease. In accordance with previous studies, we found that the pathways related to regulation of cell death, chemotaxis and inflammatory response are differentially expressed in the disease in comparison to healthy subjects, while pathways related to cell adhesion, cell migration and cell-cell signaling are activated in relapse in comparison to remission. However, the current study includes a detailed report of the exact set of genes involved in these pathways and the interactions between them. For example, we found that the genes TP53 and IL1 are 'network-hub' that interacts with many of the differentially expressed genes in MS patients versus healthy subjects, and the epidermal growth factor receptor is a 'network-hub' in the case of MS patients with relapse versus remission. The statistical approaches employed in this study enabled us

  18. Mapping the Properties of Blue Compact Dwarf Galaxies by Means of Integral Field Spectroscopy

    NASA Astrophysics Data System (ADS)

    Cairós, L. M.; Caon, N.; Weilbacher, P.; Papaderos, P.; García-Lorenzo, B.

    Blue Compact Dwarf (BCD) galaxies are metal-poor and gas-rich systems undergoing intense, spatially extended star-forming activity. These galaxies offer a unique opportunity to investigate dwarf galaxy formation and evolution, and probe violent star formation and its implications on the chemical, dynamical and structural properties of low-mass extragalactic systems near and far. Several fundamental questions in BCD research, such as their star formation histories and the mechanisms that control their cyclic starburst activity, are still far from well understood. In order to improve our understanding on BCD evolution, we are carrying out a comprehensive Integral Field Spectroscopic (IFS) survey of a large sample of BCDs. Integral Field Unit (IFU) spectroscopy provides simultaneously spectral and spatial information, allowing, in just one shot, to study the morphology and evolutionary status of the stellar component, and the physical properties of the warm interstellar medium (e.g., extinction, chemical abundances, kinematics). This ongoing IFS survey will supply much needed local templates that will ease the interpretation of IFS data for intermediate and high-redshift star-forming galaxies.

  19. An integrated map of genetic variation from 1,092 human genomes.

    PubMed

    Abecasis, Goncalo R; Auton, Adam; Brooks, Lisa D; DePristo, Mark A; Durbin, Richard M; Handsaker, Robert E; Kang, Hyun Min; Marth, Gabor T; McVean, Gil A

    2012-11-01

    By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. PMID:23128226

  20. An integrated map of genetic variation from 1,092 human genomes

    PubMed Central

    2012-01-01

    Summary Through characterising the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help understand the genetic contribution to disease. We describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methodologies to integrate information across multiple algorithms and diverse data sources we provide a validated haplotype map of 38 million SNPs, 1.4 million indels and over 14 thousand larger deletions. We show that individuals from different populations carry different profiles of rare and common variants and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways and that each individual harbours hundreds of rare non-coding variants at conserved sites, such as transcription-factor-motif disrupting changes. This resource, which captures up to 98% of accessible SNPs at a frequency of 1% in populations of medical genetics focus, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. PMID:23128226