Science.gov

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. 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.

  12. 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

  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

    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

  20. 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

  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. 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

  8. 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…

  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. 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...

  16. 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.

  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. 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

  4. 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

  5. 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)

  6. 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...

  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. 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.

  17. 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...

  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. 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...

  9. 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…

  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. 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

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

    ERIC Educational Resources Information Center

    Baker, Richard

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

  13. 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. 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

  17. 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

  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. 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

  5. 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…

  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. 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.

  11. 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

  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. 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

  15. 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.

  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

    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. 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.

  16. 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

  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. 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…

  20. 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...

  1. 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…

  2. 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…

  3. 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…

  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. 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…

  10. 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…

  11. 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.

  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. 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.

  1. 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

  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. 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.

  9. 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.

  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.