WorldWideScience

Sample records for bac-based physical map

  1. Genomic tools development for Aquilegia: construction of a BAC-based physical map

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    Hodges Scott A

    2010-11-01

    Full Text Available Abstract Background The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance. Results BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5% across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs from the minimal tiling path (MTP allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes

  2. A dense genetic linkage map for common carp and its integration with a BAC-based physical map.

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    Lan Zhao

    Full Text Available BACKGROUND: Common carp (Cyprinus carpio is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps. RESULTS: The genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome. CONCLUSION: We integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for

  3. A BAC-based physical map of Zhikong scallop (Chlamys farreri Jones et Preston.

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    Xiaojun Zhang

    Full Text Available Zhikong scallop (Chlamys farreri is one of the most economically important aquaculture species in China. Physical maps are crucial tools for genome sequencing, gene mapping and cloning, genetic improvement and selective breeding. In this study, we have developed a genome-wide, BAC-based physical map for the species. A total of 81,408 clones from two BAC libraries of the scallop were fingerprinted using an ABI 3130xl Genetic Analyzer and a fingerprinting kit developed in our laboratory. After data processing, 63,641 (∼5.8× genome coverage fingerprints were validated and used in the physical map assembly. A total of 3,696 contigs were assembled for the physical map. Each contig contained an average of 10.0 clones, with an average physical size of 490 kb. The combined total physical size of all contigs was 1.81 Gb, equivalent to approximately 1.5 fold of the scallop haploid genome. A total of 10,587 BAC end sequences (BESs and 167 markers were integrated into the physical map. We evaluated the physical map by overgo hybridization, BAC-FISH (fluorescence in situ hybridization, contig BAC pool screening and source BAC library screening. The results have provided evidence of the high reliability of the contig physical map. This is the first physical map in mollusc; therefore, it provides an important platform for advanced research of genomics and genetics, and mapping of genes and QTL of economical importance, thus facilitating the genetic improvement and selective breeding of the scallop and other marine molluscs.

  4. Generation of a BAC-based physical map of the melon genome

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    Puigdomènech Pere

    2010-05-01

    Full Text Available Abstract Background Cucumis melo (melon belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high intra-specific genetic variation, morphologic diversity and a small genome size (450 Mb, which make this species suitable for a great variety of molecular and genetic studies that can lead to the development of tools for breeding varieties of the species. A number of genetic and genomic resources have already been developed, such as several genetic maps and BAC genomic libraries. These tools are essential for the construction of a physical map, a valuable resource for map-based cloning, comparative genomics and assembly of whole genome sequencing data. However, no physical map of any Cucurbitaceae has yet been developed. A project has recently been started to sequence the complete melon genome following a whole-genome shotgun strategy, which makes use of massive sequencing data. A BAC-based melon physical map will be a useful tool to help assemble and refine the draft genome data that is being produced. Results A melon physical map was constructed using a 5.7 × BAC library and a genetic map previously developed in our laboratories. High-information-content fingerprinting (HICF was carried out on 23,040 BAC clones, digesting with five restriction enzymes and SNaPshot labeling, followed by contig assembly with FPC software. The physical map has 1,355 contigs and 441 singletons, with an estimated physical length of 407 Mb (0.9 × coverage of the genome and the longest contig being 3.2 Mb. The anchoring of 845 BAC clones to 178 genetic markers (100 RFLPs, 76 SNPs and 2 SSRs also allowed the genetic positioning of 183 physical map contigs/singletons, representing 55 Mb (12% of the melon genome, to individual chromosomal loci. The melon FPC database is available for download at http://melonomics.upv.es/static/files/public/physical_map/. Conclusions Here we report the construction

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-03-18

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

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

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    Lee Soo

    2008-06-01

    Full Text Available Abstract 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.

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

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    Waldbieser Geoffrey C

    2007-02-01

    Full Text Available Abstract 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.

  8. Construction of BAC-based physical map and analysis of chromosome rearrangement in Chinese hamster ovary cell lines.

    Science.gov (United States)

    Cao, Yihua; Kimura, Shuichi; Itoi, Takayuki; Honda, Kohsuke; Ohtake, Hisao; Omasa, Takeshi

    2012-06-01

    Chinese hamster ovary (CHO) cells have frequently been used in biotechnology for many years as a mammalian host cell platform for cloning and expressing genes of interest. A detailed physical chromosomal map of the CHO DG44 cell line was constructed by fluorescence in situ hybridization (FISH) imaging using randomly selected 303 BAC clones as hybridization probes (BAC-FISH). The two longest chromosomes were completely paired chromosomes; other chromosomes were partly deleted or rearranged. The end sequences of 624 BAC clones, including 287 mapped BAC clones, were analyzed and 1,119 informative BAC end sequences were obtained. Among 303 mapped BAC clones, 185 clones were used for BAC-FISH analysis of CHO K1 chromosomes and 94 clones for primary Chinese hamster lung cells. Based on this constructed physical map and end sequences, the chromosome rearrangements between CHO DG44, CHO K1, and primary Chinese hamster cells were investigated. Among 20 CHO chromosomes, eight were conserved without large rearrangement in CHO DG44, CHO K1, and primary Chinese hamster cells. This result suggested that these chromosomes were stable and essential in CHO cells and supposedly conserved in other CHO cell lines.

  9. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

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    Gonser Rusty A

    2011-06-01

    Full Text Available Abstract Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis, which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.

  10. Map of physics

    Science.gov (United States)

    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.

  11. 棉花遗传锚定的基因组物理图谱%Toward a Genetically-anchored Physical Map of the Cotton Genomes

    Institute of Scientific and Technical Information of China (English)

    Andrew H. PATERSON; James C. ESTILL; Jun-kang RONG; Dawn T. WILLIAMS-COPLIN; Barry S. MARLER

    2002-01-01

    @@ We are using a high-density (1-cM) molecular map of the cotton genome based on RFLP, SSR,and EST markers as a foundation for development of a robust BAC based physical map. The 'overgo' approach is providing an efficient means by which to accomplish hybridization-based anchoring of geneticallymapped cotton sequences, and also heterologous sequences from other genomes that are useful for comparative biology.

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

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    Delany Mary E

    2011-09-01

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

  13. Physical Parameter Eclipse Mapping

    CERN Document Server

    Vrielmann, S

    2000-01-01

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

  14. Chicken genome mapping - Constructing part of a road map for mining this bird's DNA

    NARCIS (Netherlands)

    Aerts, J.

    2005-01-01

    The aim of the research presented in this thesis was to aid in the international chicken genome mapping effort. To this purpose, a significant contribution was made to the construction of the chicken whole-genome BAC-based physical map (presented in Chapter A). An important aspect of this constructi

  15. An Integrated Map of Soybean Physical Map and Genetic Map

    Institute of Scientific and Technical Information of China (English)

    QI Zhaoming; LI Hui; WU Qiong; SUN Yanan; LIU Chunyan; HU Guohua; CHEN Qingshan

    2009-01-01

    Soybean is a major crop in the world, and it is a main source of plant proteins and oil. A lot of soybean genetic maps and physical maps have been constructed, but there are no integrated map between soybean physical map and genetic map. In this study, soybean genome sequence data, released by JGI (US Department of Energy's Joint Genome Institute), had been downloaded. With the software Blast 2.2.16, a total of 161 super sequences were mapped on the soybean public genetic map to construct an integrated map. The length of these super sequences accounted for 73.08% of all the genome sequence. This integrated map could be used for gene cloning, gene mining, and comparative genome of legume.

  16. Statistical methods in physical mapping

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    Nelson, David O. [Univ. of California, Berkeley, CA (United States)

    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.

  17. Map of the Physical Sciences

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Evaluation of chronic lymphocytic leukemia by BAC-based microarray analysis

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    McDaniel Lisa D

    2011-02-01

    Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is a highly variable disease with life expectancies ranging from months to decades. Cytogenetic findings play an integral role in defining the prognostic significance and treatment for individual patients. Results We have evaluated 25 clinical cases from a tertiary cancer center that have an established diagnosis of CLL and for which there was prior cytogenetic and/or fluorescence in situ hybridization (FISH data. We performed microarray-based comparative genomic hybridization (aCGH using a bacterial artificial chromosome (BAC-based microarray designed for the detection of known constitutional genetic syndromes. In 15 of the 25 cases, aCGH detected all copy number imbalances identified by prior cytogenetic and/or FISH studies. For the majority of those not detected, the aberrations were present at low levels of mosaicism. Furthermore, for 15 of the 25 cases, additional abnormalities were detected. Four of those cases had deletions that mapped to intervals implicated in inherited predisposition to CLL. For most cases, aCGH was able to detect abnormalities present in as few as 10% of cells. Although changes in ploidy are not easily discernable by aCGH, results for two cases illustrate the detection of additional copy gains and losses present within a mosaic tetraploid cell population. Conclusions Our results illustrate the successful evaluation of CLL using a microarray optimized for the interrogation of inherited disorders and the identification of alterations with possible relevance to CLL susceptibility.

  19. A physical map of the mouse genome

    NARCIS (Netherlands)

    Gregory, SG; Sekhon, M; Schein, J; Zhao, SY; Osoegawa, K; Scott, CE; Evans, RS; Burridge, PW; Cox, TV; Fox, CA; Hutton, RD; Mullenger, IR; Phillips, KJ; Smith, J; Stalker, J; Threadgold, GJ; Birney, E; Wylie, K; Chinwalla, A; Wallis, J; Hillier, L; Carter, J; Gaige, T; Jaeger, S; Kremitzki, C; Layman, D; McGrane, R; Mead, K; Walker, R; Jones, S; Smith, M; Asano, J; Bosdet, I; Chan, S; Chittaranjan, S; Chiu, R; Fjell, C; Fuhrmann, D; Girn, N; Gray, C; Guin, R; Hsiao, L; Krzywinski, M; Kutsche, R; Lee, SS; Mathewson, C; McLeavy, C; Messervier, S; Ness, S; Pandoh, P; Prabhu, AL; Saeedi, P; Smailus, D; Spence, L; Stott, J; Taylor, S; Terpstra, W; Tsai, M; Vardy, J; Wye, N; Yang, G; Shatsman, S; Ayodeji, B; Geer, K; Tsegaye, G; Shvartsbeyn, A; Gebregeorgis, E; Krol, M; Russell, D; Overton, L; Malek, JA; Holmes, M; Heaney, M; Shetty, J; Feldblyum, T; Nierman, WC; Catanese, JJ; Hubbard, T; Waterston, RH; Rogers, J; de Jong, PJ; Fraser, CM; Marra, M; McPherson, JD; Bentley, DR

    2002-01-01

    A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs w

  20. Genome physical mapping of polyploids: a BIBAC physical map of cultivated tetraploid cotton, Gossypium hirsutum L.

    Science.gov (United States)

    Zhang, Meiping; Zhang, Yang; Huang, James J; Zhang, Xiaojun; Lee, Mi-Kyung; Stelly, David M; Zhang, Hong-Bin

    2012-01-01

    Polyploids account for approximately 70% of flowering plants, including many field, horticulture and forage crops. Cottons are a world-leading fiber and important oilseed crop, and a model species for study of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. This study has addressed the concerns of physical mapping of polyploids with BACs and/or BIBACs by constructing a physical map of the tetraploid cotton, Gossypium hirsutum L. The physical map consists of 3,450 BIBAC contigs with an N50 contig size of 863 kb, collectively spanning 2,244 Mb. We sorted the map contigs according to their origin of subgenome, showing that we assembled physical maps for the A- and D-subgenomes of the tetraploid cotton, separately. We also identified the BIBACs in the map minimal tilling path, which consists of 15,277 clones. Moreover, we have marked the physical map with nearly 10,000 BIBAC ends (BESs), making one BES in approximately 250 kb. This physical map provides a line of evidence and a strategy for physical mapping of polyploids, and a platform for advanced research of the tetraploid cotton genome, particularly fine mapping and cloning the cotton agronomic genes and QTLs, and sequencing and assembling the cotton genome using the modern next-generation sequencing technology.

  1. Statistical and computational challenges in physical mapping

    Energy Technology Data Exchange (ETDEWEB)

    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. Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

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    Doležel Jaroslav

    2010-02-01

    Full Text Available Abstract Background The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy. Results The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the

  3. Physical mapping and cloning of RAD56

    DEFF Research Database (Denmark)

    Mathiasen, David P; Gallina, Irene; Germann, Susanne Manuela

    2013-01-01

    Here we report the physical mapping of the rad56-1 mutation to the NAT3 gene, which encodes the catalytic subunit of the NatB N-terminal acetyltransferase in Saccharomyces cerevisiae. Mutation of RAD56 causes sensitivity to X-rays, methyl methanesulfonate, zeocin, camptothecin and hydroxyurea, bu...

  4. BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping.

    Science.gov (United States)

    Vu, Giang T H; Dear, Paul H; Caligari, Peter D S; Wilkinson, Mike J

    2010-02-08

    Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning approximately 10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual "BAC-HAPPY-mapping" to convert BAC landing data into BAC linkage contigs is possible.

  5. A BAC-based transgenic mouse specifically expresses an inducible Cre in the urothelium.

    Directory of Open Access Journals (Sweden)

    Tian Huai Shen

    Full Text Available Cre-loxp mediated conditional knockout strategy has played critical roles for revealing functions of many genes essential for development, as well as the causal relationships between gene mutations and diseases in the postnatal adult mice. One key factor of this strategy is the availability of mice with tissue- or cell type-specific Cre expression. However, the success of the traditional molecular cloning approach to generate mice with tissue specific Cre expression often depends on luck. Here we provide a better alternative by using bacterial artificial chromosome (BAC-based recombineering to insert iCreERT2 cDNA at the ATG start of the Upk2 gene. The BAC-based transgenic mice express the inducible Cre specifically in the urothelium as demonstrated by mRNA expression and staining for LacZ expression after crossing with a Rosa26 reporter mouse. Taking into consideration the size of the gene of interest and neighboring genes included in a BAC, this method should be widely applicable for generation of mice with tissue specific gene expression or deletions in a more specific manner than previously reported.

  6. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar

    Directory of Open Access Journals (Sweden)

    Jurman Irena

    2010-03-01

    Full Text Available Abstract Background Most of the grapevine (Vitis vinifera L. cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. Results We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. Conclusions We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.

  7. BAC-based sequencing of behaviorally-relevant genes in the prairie vole.

    Directory of Open Access Journals (Sweden)

    Lisa A McGraw

    Full Text Available The prairie vole (Microtus ochrogaster is an important model organism for the study of social behavior, yet our ability to correlate genes and behavior in this species has been limited due to a lack of genetic and genomic resources. Here we report the BAC-based targeted sequencing of behaviorally-relevant genes and flanking regions in the prairie vole. A total of 6.4 Mb of non-redundant or haplotype-specific sequence assemblies were generated that span the partial or complete sequence of 21 behaviorally-relevant genes as well as an additional 55 flanking genes. Estimates of nucleotide diversity from 13 loci based on alignments of 1.7 Mb of haplotype-specific assemblies revealed an average pair-wise heterozygosity (8.4×10(-3. Comparative analyses of the prairie vole proteins encoded by the behaviorally-relevant genes identified >100 substitutions specific to the prairie vole lineage. Finally, our sequencing data indicate that a duplication of the prairie vole AVPR1A locus likely originated from a recent segmental duplication spanning a minimum of 105 kb. In summary, the results of our study provide the genomic resources necessary for the molecular and genetic characterization of a high-priority set of candidate genes for regulating social behavior in the prairie vole.

  8. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

    2007-06-15

    Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

  9. A physical map of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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. Correlation of physical and genetic maps of human chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Construction of the Primary Physical Map of Rice Chromosome 12

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A primary physical map of rice chromosome 12 was constructed using marker-based chromosome landing and chromosome walking. A BAC library from IR64 was screened using 84 RFLP markers, 4 STS markers and 6 microsatellite markers on chromosome 12 by colony hybridization and polymerase chain reaction (PCR) amplification. A total of 59 contigs consisting of 419 BAC clones including 5 single-clones were physically aligned on rice chromosome 12 with the largest BAC contig covering 855 kb. The whole physical map had a size of ~16 Mb and covered about 52% of rice chromosome 12. This physical map will be certainly helpful for map-based gene cloning of agronomically and biological important genes and understanding the genome structure of the chromosome.

  13. Using Concept Maps with Trainee Physics Teachers.

    Science.gov (United States)

    Adamczyk, Peter; Willson, Mike

    1996-01-01

    Describes how the technique of concept mapping can be useful for identifying gaps in preservice teachers' knowledge. Validity of the technique was tested using blind interviews with a representative sample of eight trainees. Has potential as a valuable self-diagnostic tool for teachers teaching outside their area of specialization. (DDR)

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

    Science.gov (United States)

    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…

  15. [Physical mapping of DNA of cyanophage LPP-3].

    Science.gov (United States)

    Syrchin, S A; Mendzhul, M I

    2002-01-01

    Restrictases fit for the purposes of physical mapping of cyanophage LPP-3 DNA have been selected as a result of the restriction analysis. The use of the methods of mutual hydrolysis, restriction of the fragment isolated from gel and terminal labeling allowed formation a physical map of LPP-3 cyanophage DNA with the complete scheme of allocation of 14 sites for 8 restrictases: Alw44I, Bsp1191, BsuRI, Eco147I, EheI, NcoI, Kpn2I and PvuI as well as the position of certain sites for restrictases HindIII, KpnI and Sau3A.

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

    Science.gov (United States)

    Weier, H U

    2001-08-01

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

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

    Science.gov (United States)

    Mashhadi, Azam; Woolnough, Brian

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

  18. Numerical and physical magnitudes are mapped into time.

    Science.gov (United States)

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

    2012-01-01

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

  19. Physical accessibility of non-completely positive maps

    CERN Document Server

    Carteret, H; Zyczkowski, K; Carteret, Hilary; Terno, Daniel R.; Zyczkowski, Karol

    2005-01-01

    We study classes of generalized dynamical maps which are not completely positive. We show that some of these maps correspond to actual, physical systems described in the environmental representation by a unitary dynamics of an extended system and the partial trace. The non complete positivity is due to certain prior correlations of the principal system with the environment. These correlation may have classical nature and no entanglement is necessary to generate a non CP dynamics. We discuss its applications to the dynamical decoupling and quantum channels.

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

    Science.gov (United States)

    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

  1. A Novel Dynamic Physical Storage Model for Vehicle Navigation Maps

    Directory of Open Access Journals (Sweden)

    Shaohua Wang

    2016-04-01

    Full Text Available The physical storage model is one of the key technologies for vehicle navigation maps used in a navigation system. However, the performance of most traditional storage models is limited in dynamic navigation due to the static storage format they use. In this paper, we proposed a new physical storage model, China Navigation Data Format (CNDF, which helped access and update the navigation data. The CNDF model used the reach-based hierarchy method to build a road hierarchal network, which enhanced the efficiency of data compression. It also adopted the Linear Link Coding method, in which the start position was combined with the end position as the identification code for multi-level links, and each link traced up-level links consistently without recording the array of identifications. The navigation map of East China (including Beijing, Tianjin, Shandong, Hebei, and Jiangsu at 1:10,000, generated using the CNDF model, and the real time traffic information in Beijing were combined to test the performance of a navigation system using an embedded navigation device. Results showed that it cost less than 1 second each time to refresh the navigation map, and the accuracy of the hierarchal shortest-path algorithm was 99.9%. Our work implied that the CNDF model is efficient in vehicle navigation applications.

  2. Genetic and physical mapping of two centromere-proximal regions of chromosome IV in Aspergillus nidulans

    DEFF Research Database (Denmark)

    Aleksenko, Alexei Y.; Nielsen, Michael Lynge; Clutterbuck, A.J.

    2001-01-01

    The centromere-proximal portion of the chromosome was mapped physically using overlapping clones of a cosmid genomic library. Two contiguous segments of a physical map, based on restriction mapping of cosmid clones, were generated, together covering more than 0.4 Mb DNA. A reverse genetic mapping...... approach was used to establish a correlation between physical and genetic maps; i,e., marker genes were integrated into physically mapped segments and subsequently mapped by mitotic and meiotic recombination. The resulting data, together with additional classical genetic mapping, lead to a substantial...... revision of the genetic map of the chromosome, including the position of the centromere, Comparison of physical and genetic maps indicates that meiotic recombination is low in subcentromeric DNA, its frequency being reduced from 1 crossover per 0.8 Mb to approximately 1 crossover per 5 Mb per meiosis...

  3. Integration of the cytogenetic, genetic, and physical maps of the human genome by FISH mapping of CEPH YAC clones

    Energy Technology Data Exchange (ETDEWEB)

    Bray-Ward, P.; Menninger, J.; Lieman, J. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

    1996-02-15

    This article discusses the genetic mapping of over 950 yeast artificial chromosome (YAC) clones on human chromosomes. This integration of the cytogenetic, genetic and physical maps of the human genome was accomplished using fluorescence in situ hybridization (FISH) mapping and the CEPH library of YAC clones. 27 refs., 2 figs., 1 tab.

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

    Energy Technology Data Exchange (ETDEWEB)

    Chevillard, C.; Passage, E.; Cudrey, C. [INSERM Marseille (France)] [and others

    1994-09-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    Gourlay, H.

    2017-01-01

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

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

    Science.gov (United States)

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

    2003-12-01

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

  8. Connexin32 mutations and Xq13 physical map

    Energy Technology Data Exchange (ETDEWEB)

    Johanson, R.A.; Bone, L.J. [Univ. of Pennsylvania School of Medicine, Philadelphia (United States); Neystat, M. [Columbia Univ., New York, NY (United States)] [and others

    1994-09-01

    Mutations in the gap junction protein connexin32 (Cx32) are associated with X-linked Charcot-Marie-Tooth disease (CMTX). We and others have identified 24 separate mutations in 27 families. The third transmembrane domain of Cx32 has two mutations that occur in multiple families: three unrelated families have the same missense mutation at codon 139 (Val to Met), and two additional unrelated families have a single base change in codon 142 (Arg to Trp). In order to physically map the region surrounding the Cx32 gene and identify regulatory sequences that could be affected by additional mutations, we are developing a contiguous set of YAC clones for the region (Xq13.1-13.3). The YACs were identified primarily by PCR-based screening of total genomic YAC libraries from CEPH and Genethon. Additional YACs were obtained from collaborating investigators and a local library. A total of 41 overlapping YACs were identified with the STSs DXS106, DXS453, DXS348, IL2RG, GJB1(Cx32), CCG1, DXS559, DXS227, DXS986, DXS1197, and DXS128. Overlap between the YACs was determined by shared STS content and by appearance of identical segments in inter-Alu PCR. The set of overlapping YAC clones helps to define the relationship between CMTX/Cx32 and the nearby gene for severe combined immunodeficiency syndrome (SCIDX/IL2RG), and it is now being used in localization of the gene for dystonia-parkinsonism syndrome (lubag disease, DYT3), which also maps to this region.

  9. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

    Directory of Open Access Journals (Sweden)

    de Boer Jan M

    2011-12-01

    Full Text Available Abstract Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH. Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and

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

    Energy Technology Data Exchange (ETDEWEB)

    Reguigne-Arnould, I.; Mollicone, R.; Candelier, J.J. [INSERM, Villejuif (France)] [and others

    1996-03-05

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    Teixeira, Manuel; Bateira, Carlos; Soares, Laura

    2013-04-01

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

  14. Alignment Between Genetic and Physical Maps of Gibberella zeae

    Science.gov (United States)

    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...

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

    Science.gov (United States)

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

    1998-10-23

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

  16. An integrated physical map covering 25 cM of human chromosome 8

    Energy Technology Data Exchange (ETDEWEB)

    Chen, W.; Hou, J.; Wagner, M.J.; Wells, D.E. [Univ. of Houston, TX (United States)

    1996-02-15

    This article reports on an integrated physical map of human chromosome 8 using STS content analysis of somatic cell hybrids and YAC contigs. Such mapping efforts will help to localize genes linked to hereditary diseases. 17 refs., 1 fig., 1 tab.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

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

    2004-04-01

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

  2. Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding.

    Directory of Open Access Journals (Sweden)

    Yanliang Jiang

    Full Text Available Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge.

  3. Generation of Physical Map Contig-Specific Sequences Useful for Whole Genome Sequence Scaffolding

    Science.gov (United States)

    Jiang, Yanliang; Ninwichian, Parichart; Liu, Shikai; Zhang, Jiaren; Kucuktas, Huseyin; Sun, Fanyue; Kaltenboeck, Ludmilla; Sun, Luyang; Bao, Lisui; Liu, Zhanjiang

    2013-01-01

    Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly) were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge. PMID:24205335

  4. Mapping the Physical Properties of Cosmic Hot Gas with Hyper-spectral Imaging

    CERN Document Server

    O'Dwyer, M; Raychaudhuri, S; Dwyer, Mark O'; Ponman, Trevor; Raychaudhury, Ela Claridge & Somak

    2005-01-01

    A novel inversion technique is proposed to compute parametric maps showing the temperature, density and chemical composition of cosmic hot gas from X-ray hyper-spectral images. The parameters are recovered by constructing a unique non-linear mapping derived by combining a physics-based modelling of the X-ray spectrum with the selection of optimal bandpass filters. Preliminary results and analysis are presented.

  5. 3-D or median map? Earthquake scenario ground-motion maps from physics-based models versus maps from ground-motion prediction equations

    Science.gov (United States)

    Porter, K.

    2015-12-01

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

  6. Mitotic-chromosome-based physical mapping of the Culex quinquefasciatus genome.

    Science.gov (United States)

    Naumenko, Anastasia N; Timoshevskiy, Vladimir A; Kinney, Nicholas A; Kokhanenko, Alina A; deBruyn, Becky S; Lovin, Diane D; Stegniy, Vladimir N; Severson, David W; Sharakhov, Igor V; Sharakhova, Maria V

    2015-01-01

    The genome assembly of southern house mosquito Cx. quinquefasciatus is represented by a high number of supercontigs with no order or orientation on the chromosomes. Although cytogenetic maps for the polytene chromosomes of this mosquito have been developed, their utilization for the genome mapping remains difficult because of the low number of high-quality spreads in chromosome preparations. Therefore, a simple and robust mitotic-chromosome-based approach for the genome mapping of Cx. quinquefasciatus still needs to be developed. In this study, we performed physical mapping of 37 genomic supercontigs using fluorescent in situ hybridization on mitotic chromosomes from imaginal discs of 4th instar larvae. The genetic linkage map nomenclature was adopted for the chromosome numbering based on the direct positioning of 58 markers that were previously genetically mapped. The smallest, largest, and intermediate chromosomes were numbered as 1, 2, and 3, respectively. For idiogram development, we analyzed and described in detail the morphology and proportions of the mitotic chromosomes. Chromosomes were subdivided into 19 divisions and 72 bands of four different intensities. These idiograms were used for mapping the genomic supercontigs/genetic markers. We also determined the presence of length polymorphism in the q arm of sex-determining chromosome 1 in Cx. quinquefasciatus related to the size of ribosomal locus. Our physical mapping and previous genetic linkage mapping resulted in the chromosomal assignment of 13% of the total genome assembly to the chromosome bands. We provided the first detailed description, nomenclature, and idiograms for the mitotic chromosomes of Cx. quinquefasciatus. Further application of the approach developed in this study will help to improve the quality of the southern house mosquito genome.

  7. Physical Activity, Physical Fitness and Academic Achievement in Adolescents: A Self-Organizing Maps Approach

    Science.gov (United States)

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

    2015-01-01

    The relationship among physical activity, physical fitness and academic achievement in adolescents has been widely studied; however, controversy concerning this topic persists. The methods used thus far to analyse the relationship between these variables have included mostly traditional lineal analysis according to the available literature. The…

  8. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

    NARCIS (Netherlands)

    Boer, de J.M.; Borm, T.J.A.; Jesse, T.; Brugmans, B.W.; Tang, X.; Bryan, G.J.; Bakker, J.; Eck, van H.J.; Visser, R.G.F.

    2011-01-01

    Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so

  9. Mapping the physical location of Telecenter using the geospatial information systems: A requirement of spatial digital mapping

    Science.gov (United States)

    Bohari, Abdul Manaf; Hin, Cheng Wei; Fuad, Nurwahida

    2016-08-01

    Recently, a study of Telecenter lifetime value is vital to academician, government and non-profit organization where Telecenter has great contribute to the nation development of rural community. Telecenter as important location of enhance the relationship of socio-economic, where placed all non-profit activity into single location platform. Consistently, previous studies mentioned Telecenter have significance contribution toward the nation, however, research and knowledge still lacking regarding the location factors that affecting the Telecenter specifically on spatial aspects of physical location environment. This research aimed to understand the requirement of spatial digital mapping the physical location of Telecenter, according to location of user and it environment, by using the geospatial information systems references, as called grid coordinate systems. The suggestion and implications of this study are briefly explored where spatial location factor plays important role in determine the lifetime value of Telecenter.

  10. Mental and Physical (MAP) Training: a neurogenesis-inspired intervention that enhances health in humans.

    Science.gov (United States)

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

    2014-11-01

    New neurons are generated in the hippocampus each day and their survival is greatly enhanced through effortful learning (Shors, 2014). The numbers of cells produced can be increased by physical exercise (van Praag, Kempermann, & Gage, 1999). These findings inspired us to develop a clinical intervention for humans known as Mental and Physical Training, or MAP Training. Each session consists of 30min of mental training with focused attention meditation (20min sitting and 10min walking). Meditation is an effortful training practice that involves learning about the transient nature of thoughts and thought patterns, and acquiring skills to recognize them without necessarily attaching meaning and/or emotions to them. The mental training component is followed by physical training with 30min of aerobic exercise performed at moderate intensity. During this component, participants learn choreographed dance routines while engaging in aerobic exercise. In a pilot "proof-of-concept" study, we provided supervised MAP Training (2 sessions per week for 8weeks) to a group of young mothers in the local community who were recently homeless, most of them having previously suffered from physical and sexual abuse, addiction, and depression. Preliminary data suggest that MAP Training improves dependent measures of aerobic fitness (as assessed by maximal rate of oxygen consumed) while decreasing symptoms of depression and anxiety. Similar changes were not observed in a group of recently homeless women who did not participate in MAP Training. It is not currently possible to determine whether new neurons in the human brain increase in number as a result of MAP Training. Rather these preliminary results of MAP Training illustrate how neuroscientific research can be translated into novel clinical interventions that benefit human health and wellness.

  11. Construction of physical maps for the sex-specific regions of papaya sex chromosomes

    Directory of Open Access Journals (Sweden)

    Na Jong-Kuk

    2012-05-01

    Full Text Available Abstract Background Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male, XYh (hermaphrodite, and XX (female. The papaya hermaphrodite-specific Yh chromosome region (HSY is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement. Results A reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY-specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F2 individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89% DNA sequence expansion. Conclusion The 89% increase of DNA sequence in HSY indicates rapid expansion of the Yh chromosome after genetic recombination was suppressed 2–3 million years ago. The

  12. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Wu Cheng-Cang

    2011-05-01

    Full Text Available Background Although second generation sequencing (2GS technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result Five new BAC libraries were constructed for barley (Hordeum vulgare L. cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast, empty wells and off-scale clones (clones with 250 fragments. Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. Conclusion BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    Smith, Robyn; Rogoszinski, Zeeve; Sheppard, Kyle; Taylor, Corbin; Wilkins, Ashlee; Vogel, Stuart; Rolston, Steve; Hammer, Donna; Gezari, Suvi; Williams, Jimmy

    2017-01-01

    Graduate Resources for Advancing Diversity with Maryland's Astronomy and Physics (GRAD-MAP) builds connections with mid-Atlantic HBCUs, Minority-Serving Institutions (MSIs), and community colleges using seminars, forums, and workshops to foster a diverse community: undergraduates prepared to succeed in graduate school, inclusion-minded graduate student mentors, and faculty versed in the experiences of students at MSIs. In its fourth year, GRAD-MAP remains a graduate-student-powered initiative with a four-pronged approach: 1) Fall Collaborative Seminars, 2) Winter Workshop, 3) Spring Symposium, and 4) Summer Scholars Program. This coherent programming allows GRAD-MAP to do more than just increase the number of minority students or simply shuffle around students who already are, or would be, active in research. GRAD-MAP is committed to identifying students who are underserved or overlooked by the traditional academic pipeline. Our goal is not only to get them on the path to be successful undergraduate researchers and eventual graduate applicants, but also to make substantial, sustainable efforts toward a more inclusive climate in physics and astronomy. We will describe the key elements of our program, highlight successes and lessons learned, and describe formal evaluation currently underway with the intent that GRAD-MAP could serve as a model for other universities committed to diversity and inclusion.

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

    Science.gov (United States)

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

    2016-01-01

    Graduate Resources for Advancing Diversity with Maryland's Astronomy and Physics (GRAD-MAP), builds connections between UMD and mid-Atlantic HBCUs, Minority-Serving Institutions, and community colleges, and uses seminars, forums, and workshops to foster a diverse community of undergraduates prepared to succeed in graduate school, and is now in its third year. GRAD-MAP launched with a three-pronged approach: 1) Collaborative Seminars, 2) A Winter Workshop, and 3) A Spring Symposium. This program allows GRAD-MAP to do more than just increase the numbers of minority students participating in astronomy and physics research (or, worse, simply shuffle around students who already are or would be); it is committed to identifying students who are otherwise underserved or overlooked by the traditional academic pipeline, not only to get them on the path to be successful undergraduate researchers and eventual graduate applicants, but also to make the climate of academic physics and astronomy more inclusive to them and all other underrepresented minority students. Our poster describes the key elements of our program, and highlights successes and lessons learned; GRAD-MAP can serve as a model for other universities committed to diversity and inclusion.

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

    Energy Technology Data Exchange (ETDEWEB)

    Christof, T.; Reinelt, G. [Universitaet Heidelberg (Germany); Juenger, M. [Universitaet zu Koeln (Germany)] [and others

    1997-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Kudrna Dave

    2010-06-01

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

  18. A branch-and-cut approach to physical mapping of chromosomes by unique end-probes.

    Science.gov (United States)

    Christof, T; Jünger, M; Kececioglu, J; Mutzel, P; Reinelt, G

    1997-01-01

    A fundamental problem in computational biology is the construction of physical maps of chromosomes from hybridization experiments between unique probes and clones of chromosome fragments in the presence of error. Alizadeh, Karp, Weisser and Zweig (Algorithmica 13:1/2, 52-76, 1995) first considered a maximum-likelihood model of the problem that is equivalent to finding an ordering of the probes that minimizes a weighted sum of errors and developed several effective heuristics. We show that by exploiting information about the end-probes of clones, this model can be formulated as a Weighted Betweenness Problem. This affords the significant advantage of allowing the well-developed tools of integer linear-programming and branch-and-cut algorithms to be brought to bear on physical mapping, enabling us for the first time to solve small mapping instances to optimality even in the presence of high error. We also show that by combining the optimal solution of many small overlapping Betweenness Problems, one can effectively screen errors from larger instances and solve the edited instance to optimality as a Hamming-Distance Traveling Salesman Problem. This suggests a new approach, a Betweenness-Traveling Salesman hybrid, for constructing physical maps.

  19. Physical mapping and molecular cloning of mung bean yellow mosaic virus DNA.

    Science.gov (United States)

    Morinaga, T; Ikegami, M; Miura, K

    1990-01-01

    Viral single-stranded DNA of mung bean yellow mosaic virus (MYMV) was converted to the double-stranded state in vitro, and physical mapping was carried out. The genome of MYMV was found to consist of two major components (designated as DNA 1 and DNA 2). In addition, some minor components were detected. Molecular cloning of the major components was carried out, using in vitro double-stranded DNA and replicative intermediate DNAs. DNA 1 is about 2.72 and DNA 2 about 2.67 kilobase pairs. No similarities were observed when the two restriction maps of DNA 1 and 2 were compared.

  20. The Effectiveness of Concept Maps in Teaching Physics Concepts Applied to Engineering Education: Experimental Comparison of the Amount of Learning Achieved with and without Concept Maps

    Science.gov (United States)

    Martinez, Guadalupe; Perez, Angel Luis; Suero, Maria Isabel; Pardo, Pedro J.

    2013-01-01

    A study was conducted to quantify the effectiveness of concept maps in learning physics in engineering degrees. The following research question was posed: What was the difference in learning results from the use of concept maps to study a particular topic in an engineering course? The study design was quasi-experimental and used a post-test as a…

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Genetic and physical mapping of the genomic region spanning CMT4A

    Energy Technology Data Exchange (ETDEWEB)

    Othmane, K.B.; Loeb, D.; Roses, A.D. [Duke Univ. Medical Center, Durham, NC (United States)] [and others

    1994-09-01

    Autosomal recessive Charcot-Marie-Tooth disease (CMT4) is a severe childhood neuropathy classified into three types: A, B, and C. We previously mapped CMT4A to chromosome 8q13-q21 in four large Tunisian families. Analysis of recombination events suggested the order: cent.-D8S279-(D8S286,D8S164, CMT4A)-D8S84-tel. Families with types B and C were subsequently typed and linkage for these types was excluded for the CMT4A region and other known CMT loci. Recently, the gene for a major peripheral myelin protein (PMP2) was mapped by FISH to chromosome 8q21-q22 and therefore appeared to be a strong candidate gene for CMT4A. We used SSCP analysis, DNA sequencing, FISH and YAC mapping analysis, and demonstrated that PMP2 is not the defect in CMT4A. Using physical mapping data, we sublocalized a new genethon marker (D8S548) to the CMT4A region between D8S286 and D8S164. All affected CMT4A patients were homozygotes for this polymorphic microsatellite as expected from its physical localization. We screened the CEPH megabase YAC library using the closest markers; over 30 YACs were isolated and characterized by PFGE. FISH analysis revealed about 16% chimeras. The YACs span the 8 cM region between D8S279 and PMP2 (mapped distal to D8S84), with a current 1 cM gap between D8S164 and D8S84. We are currently using Alu-PCR and vectorette to develop end clones in order to identify new YACs in the region and further close this gap. Alu-PCR fragments have identified several new microsatellites in the region which can be used for additional mapping of the CMT4A gene.

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

    Science.gov (United States)

    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.

  4. The Riccati Equation Mapping Method for Solving Nonlinear Partial Differential Equations in Mathematical Physics

    Directory of Open Access Journals (Sweden)

    Elsayed Mohamed Elsayed ZAYED

    2014-07-01

    Full Text Available In this article, many new exact solutions of the (2+1-dimensional nonlinear Boussinesq-Kadomtsev-Petviashvili equation and the (1+1-dimensional nonlinear heat conduction equation are constructed using the Riccati equation mapping method. By means of this method, many new exact solutions are successfully obtained. This method can be applied to many other nonlinear evolution equations in mathematical physics.doi:10.14456/WJST.2014.14

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1986-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Giattina Emily

    2011-09-01

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

  7. ConMap: Investigating new computer-based approaches to assessing conceptual knowledge structure in physics

    Science.gov (United States)

    Beatty, Ian D.

    2000-06-01

    There is a growing consensus among educational researchers that traditional problem-based assessments are not effective tools for diagnosing a student's knowledge state and for guiding pedagogical intervention, and that new tools grounded in the results of cognitive science research are needed. The ConMap (``Conceptual Mapping'') project, described in this dissertation, proposed and investigated some novel methods for assessing the conceptual knowledge structure of physics students. A set of brief computer-administered tasks for eliciting students' conceptual associations was designed. The basic approach of the tasks was to elicit spontaneous term associations from subjects by presenting them with a prompt term, or problem, or topic area, and having them type a set of response terms. Each response was recorded along with the time spent thinking of and typing it. Several studies were conducted in which data was collected on introductory physics students' performance on the tasks. A detailed statistical description of the data was compiled. Phenomenological characterization of the data (description and statistical summary of observed patterns) provided insight into the way students respond to the tasks, and discovered some notable features to guide modeling efforts. Possible correlations were investigated, some among different aspects of the ConMap data, others between aspects of the data and students' in-course exam scores. Several correlations were found which suggest that the ConMap tasks can successfully reveal information about students' knowledge structuring and level of expertise. Similarity was observed between data from one of the tasks and results from a traditional concept map task. Two rudimentary quantitative models for the temporal aspects of student performance on one of the tasks were constructed, one based on random probability distributions and the other on a detailed deterministic representation of conceptual knowledge structure. Both models were

  8. Mapping virtual addresses to different physical addresses for value disambiguation for thread memory access requests

    Science.gov (United States)

    Gala, Alan; Ohmacht, Martin

    2014-09-02

    A multiprocessor system includes nodes. Each node includes a data path that includes a core, a TLB, and a first level cache implementing disambiguation. The system also includes at least one second level cache and a main memory. For thread memory access requests, the core uses an address associated with an instruction format of the core. The first level cache uses an address format related to the size of the main memory plus an offset corresponding to hardware thread meta data. The second level cache uses a physical main memory address plus software thread meta data to store the memory access request. The second level cache accesses the main memory using the physical address with neither the offset nor the thread meta data after resolving speculation. In short, this system includes mapping of a virtual address to a different physical addresses for value disambiguation for different threads.

  9. Physical and genetic mapping of the muscle phosphofructokinase gene (PFKM): Reassignment to human chromosome 12q

    Energy Technology Data Exchange (ETDEWEB)

    Howard, T.D.; Akots, G.; Bowden, D.W. [Bowman Gray School of Medicine of Wake Forest Univ., Winston-Salem, NC (United States)

    1996-05-15

    Phosphofructokinase (PFK) is a key rate-limiting enzyme in glycolysis and represents a major control point in the metabolism of glucose. There are at least three known isoforms of PFK in humans, referred to as the muscle, platelet, and liver forms, each of which is differentially expressed in various tissues. The gene for muscle phosphofructokinase, PFKM, is mutated in Tarui disease and conceivably contributes to non-insulin-dependent diabetes mellitus (NIDDM). Based on physical and genetic mapping, we have found that the gene for PFKM does not map to chromosome 1 as previously described, but instead maps to chromosome 12. PCR analysis with a somatic cell hybrid mapping panel using primers derived from intron 6 and exon 18 of the PFKM gene showed consistent amplification of cell lines containing chromosome 12 (concordance, 100%). Fluorescence in situ hybridization analysis with CEPH YAC 762G4, isolated with exon 18 primers, indicated that this clone maps to 12q13, centromeric to the diacylglycerol kinase gene (DAGK) at 12q13.3. A highly informative genetic marker isolated from YAC 762G4 was used to map PFKM genetically between the CHLC framework markers D12S1090 and D12S390. This placement for 762G4 was significantly proximal to the recently reported locus for a third gene for maturity onset diabetes of the young (MODY). The PFKM-associated microsatellite will be a valuable tool in the evaluation of PFKM in diabetic populations as well as in linkage analysis in families with Tarui disease. 23 refs., 3 figs., 2 tabs.

  10. Spectroscopic mapping of the physical properties of supernova remnant N\\,49

    CERN Document Server

    Pauletti, Diogo

    2016-01-01

    Physical conditions inside a supernova remnant can vary significantly between different positions. However, typical observational data are integrated data or contemplate specific portions of the remnant. We study the spatial variation in the physical properties of the N\\,49 supernova remnant based on a spectroscopic mapping of the whole nebula. Long-slit spectra were obtained with the slit ($\\sim4\\arcmin \\times 1.03\\arcsec$) aligned along the east-west direction from 29 different positions spaced by $2\\arcsec$ in declination. A total of 3248 1D spectra were extracted from sections of $2\\arcsec$ of the 2D spectra. More than 60 emission lines in the range 3550\\,\\AA{} to 8920\\,\\AA{} were measured in these spectra. Maps of the fluxes and of intensity ratios of these emission lines were built with a spatial resolution of $2\\arcsec \\times 2\\arcsec$. An electron density map has been obtained using the [S\\,{\\sc ii}]\\,$\\lambda6716/\\lambda6731$ line ratio. Values vary from $\\sim$500\\,cm$^{-3}$ at the northeast region t...

  11. An AHP-derived method for mapping the physical vulnerability of coastal areas at regional scales

    Directory of Open Access Journals (Sweden)

    G. Le Cozannet

    2013-05-01

    Full Text Available Assessing coastal vulnerability to climate change at regional scales is now mandatory in France since the adoption of recent laws to support adaptation to climate change. However, there is presently no commonly recognised method to assess accurately how sea level rise will modify coastal processes in the coming decades. Therefore, many assessments of the physical component of coastal vulnerability are presently based on a combined use of data (e.g. digital elevation models, historical shoreline and coastal geomorphology datasets, simple models and expert opinion. In this study, we assess the applicability and usefulness of a multi-criteria decision-mapping method (the analytical hierarchy process, AHP to map physical coastal vulnerability to erosion and flooding in a structured way. We apply the method in two regions of France: the coastal zones of Languedoc-Roussillon (north-western Mediterranean, France and the island of La Réunion (south-western Indian Ocean, notably using the regional geological maps. As expected, the results show not only the greater vulnerability of sand spits, estuaries and low-lying areas near to coastal lagoons in both regions, but also that of a thin strip of erodible cliffs exposed to waves in La Réunion. Despite gaps in knowledge and data, the method is found to provide a flexible and transportable framework to represent and aggregate existing knowledge and to support long-term coastal zone planning through the integration of such studies into existing adaptation schemes.

  12. Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus

    Directory of Open Access Journals (Sweden)

    Lindblad-Toh Kerstin

    2010-11-01

    Full Text Available Abstract Background The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species. Results We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies. Conclusions Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years. These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.

  13. Correlation of physical and genetic maps of human chromosome 16. Annual progress report, October 1, 1990--July 31, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, G.R.

    1991-12-31

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

  14. Physical and genetic mapping of the genomes of five Mycoplasma hominis strains by pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Ladefoged, Søren; Christiansen, Gunna

    1992-01-01

    -field gel electrophoresis. All the ApaI, SmaI, BamHI, XhoI, and SalI restriction sites (total of 21 to 33 sites in each strain) were placed on the physical map, yielding an average resolution of 26 kb. The maps were constructed using three different approaches: (i) size determination of DNA fragments...

  15. Evidence, Theory and Context: Using intervention mapping to develop a worksite physical activity intervention

    Directory of Open Access Journals (Sweden)

    Conner Mark

    2008-09-01

    Full Text Available Abstract Background The workplace is an ideal setting for health promotion. Helping employees to be more physically active can not only improve their physical and mental health, but can also have economic benefits such as reduced sickness absence. The current paper describes the development of a three month theory-based intervention that aims to increase levels of moderate intensity physical activity amongst employees in sedentary occupations. Methods The intervention was developed using an intervention mapping protocol. The intervention was also informed by previous literature, qualitative focus groups, an expert steering group, and feedback from key contacts within a range of organisations. Results The intervention was designed to target awareness (e.g. provision of information, motivation (e.g. goal setting, social support and environment (e.g. management support and to address behavioural (e.g. increasing moderate physical activity in work and interpersonal outcomes (e.g. encourage colleagues to be more physically active. The intervention can be implemented by local facilitators without the requirement for a large investment of resources. A facilitator manual was developed which listed step by step instructions on how to implement each component along with a suggested timetable. Conclusion Although time consuming, intervention mapping was found to be a useful tool for developing a theory based intervention. The length of this process has implications for the way in which funding bodies allow for the development of interventions as part of their funding policy. The intervention will be evaluated in a cluster randomised trial involving 1350 employees from 5 different organisations, results available September 2009.

  16. BAC Library Construction and Physical Mapping of Bacillus anthracis A16R

    Institute of Scientific and Technical Information of China (English)

    Zhang Da; Zhu Houchu; Huang Liuyu

    2013-01-01

    Bacillus anthracis is an endospore-forming bacterium that causes severe inhalational anthrax, and bacillus anthracis A16R is an attenuated strain derived from Bacillus anthracis A16. The development of bacterial artificial chromosome (BAC) system has allowed the construction of large insert-size DNA libraries, and the bacterial artificial chromosomes (BACs) have become the preferred large insert cloning system for genomic analysis because such libraries are characteristically stable, high in ifdelity and easy to handle. To facilitate genome studies of this bacterium, a bacterial artiifcial chromosome library (BAC) has been established from genome DNA of Bacillus anthracis A16R. This library consisted of 9 600 clones randomly selected from more than 15 000 recombinant clones carrying inserts in the plindigoBAC-5 vectors. The mean insert size was 56 kbp, representing an approximate 12-fold genome coverage, while end sequences were obtained from 700 randomly selected clones. Sequences were compared with Bacillus anthracis Ames and Bacillus cereus ATCC 14579 Genome Project databases using the NCBI BLASTN search project. And most BLASTN results showed high identities and that the sequences’ sites could be used as STSs. To construct this physical map, Excel was used for the array of STSs and some gaps of the map were iflled up by PCR walking. Artemis-V4 was used in the construction of a genome-wide physical map with 93%genome coverage. The A16R BAC library proved to be a vital tool for the generation of a map that would not only allow the subsequent sequencing of defined areas of genome, but also provide immediate access to clones that were stable and convenient for functional genomic researches.

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

    Science.gov (United States)

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

    2001-07-01

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

  18. BAC Library Construction and Physical Mapping of Bacillus anthracis A16R

    Directory of Open Access Journals (Sweden)

    Da Zhang

    2013-12-01

    Full Text Available Bacillus anthracis is an endospore-forming bacterium that causes severe inhalational anthrax, and bacillus anthracis A16R is an attenuated strain derived from Bacillus anthracis A16. The development of bacterial artificial chromosome (BAC system has allowed the construction of large insert-size DNA libraries, and the bacterial artificial chromosomes (BACs have become the preferred large insert cloning system for genomic analysis because such libraries are characteristically stable, high in fidelity and easy to handle. To facilitate genome studies of this bacterium, a bacterial artificial chromosome library (BAC has been established from genome DNA of Bacillus anthracis A16R. This library consisted of 9 600 clones randomly selected from more than 15 000 recombinant clones carrying inserts in the plindigoBAC-5 vectors. The mean insert size was 56 kbp, representing an approximate 12-fold genome coverage, while end sequences were obtained from 700 randomly selected clones. Sequences were compared with Bacillus anthracis Ames and Bacillus cereus ATCC 14579 Genome Project databases using the NCBI BLASTN search project. And most BLASTN results showed high identities and that the sequences’ sites could be used as STSs. To construct this physical map, Excel was used for the array of STSs and some gaps of the map were filled up by PCR walking. Artemis-V4 was used in the construction of a genome-wide physical map with 93% genome coverage. The A16R BAC library proved to be a vital tool for the generation of a map that would not only allow the subsequent sequencing of defined areas of genome, but also provide immediate access to clones that were stable and convenient for functional genomic researches.

  19. PHYSICAL VALUE MAPPING ALGORITHM OF MESH IN FINE CAE ANALYSIS OF AUTOMOBILE BODY STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    Hu Ping; Gong Kejia; Bao Yidong

    2005-01-01

    A physical value mapping (PVM) algorithm based on finite element mesh from the stamped part in stamping process to the product is presented. In order to improve the efficiency of the PVM algorithm, a search way from the mesh of the product to the mesh of the stamped part will be adopted. At the same time, the search process is divided into two steps: entire search (ES) and local search (LS), which improve the searching efficiency. The searching area is enlarged to avoid missing projection elements in ES process. An arc-length method is introduced in LS process. The validity is confirmed by the results of the complex industry-forming product.

  20. High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

    Directory of Open Access Journals (Sweden)

    Bonavita Gina

    2002-08-01

    Full Text Available Abstract Background The Blau syndrome (MIM 186580, an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order of microsatellite markers, hampered us from further refining the genetic locus for the Blau syndrome. To address this problem, we constructed our own high-resolution physical map for the Blau susceptibility region. Results We generated a high-resolution physical map that provides more than 90% coverage of a refined Blau susceptibility region. The map consists of four contigs of sequence tagged site-based bacterial artificial chromosomes with a total of 124 bacterial artificial chromosomes, and spans approximately 7.5 Mbp; however, three gaps still exist in this map with sizes of 425, 530 and 375 kbp, respectively, estimated from radiation hybrid mapping. Conclusions Our high-resolution map will assist genetic studies of loci in the interval from D16S3080, near D16S409, and D16S408 (16q12.1 to 16q13.

  1. Physical mapping of the retinoid X receptor B gene in mouse and human

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, T.; Kitagawa, K.; Taketo, M. [Banyu Tsukuba Research Institute, Tsukuba (Japan); Weiss, E.H. [Ludwig-Maximilians-Univ., Munich (Germany); Abe, K. [Kumamoto Univ. School of Medicine, Kumamoto (Japan); Ando, A.; Yara-Kikuti, Y.; Inoko, H. [Tokai Univ. School of Medicine, Isehara (Japan); Seldin, M.F. [Duke Univ. Medical Center, Durham, NC (United States); Ozato, K. [National Institutes of Health, Bethesda, MD (United States)

    1995-01-11

    Retinoid X receptors (RXRs) are zinc finger-containing nuclear transcription factors. They belong to the nuclear receptor superfamily that contains retinoid receptors, vitamin D receptors, thyroid hormone receptors, and steroid hormone receptors as well as the so-called orphan receptors. We previously mapped all three RXR genes on mouse chromosomes, using a panel of Mus spretus-Mus musculus interspecific backcross mice: namely, the RXRA-gene (Rxra) on Chr 2 near the centromere, the RXRB gene (Rxrb) on Chr 17 in the H2 region, and the RXRG gene (Rxrg) on distal Chr 1. Using cosmid clones that cover the major histocompatibility complex (MHC) region, we determined the precise physical map positions of the gene encoding mouse and human RXRB, respectively. The mouse gene (Rxrb) maps between H2-Ke4 and H2-Ke5: namely, immediately telomeric to H2-Ke4 which encodes a histidine-rich transmembrane protein, and 12 kilobases centromeric to H2-Ke5 which is expressed in lymphoid tissues, Rxrb and H2-Ke4 are transcribed into opposite directions from a CpG-rich promoter of about 250 base pairs. This gene organization is well conserved also in the human genome at the HLA-DP subregion of Chr 6p, underscoring the strong conservation of the gene organization in the MHC region between the two mammals. 54 refs., 4 figs.

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

    Science.gov (United States)

    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

  3. Optimization of the sampling scheme for maps of physical and chemical properties estimated by kriging

    Directory of Open Access Journals (Sweden)

    Gener Tadeu Pereira

    2013-10-01

    Full Text Available The sampling scheme is essential in the investigation of the spatial variability of soil properties in Soil Science studies. The high costs of sampling schemes optimized with additional sampling points for each physical and chemical soil property, prevent their use in precision agriculture. The purpose of this study was to obtain an optimal sampling scheme for physical and chemical property sets and investigate its effect on the quality of soil sampling. Soil was sampled on a 42-ha area, with 206 geo-referenced points arranged in a regular grid spaced 50 m from each other, in a depth range of 0.00-0.20 m. In order to obtain an optimal sampling scheme for every physical and chemical property, a sample grid, a medium-scale variogram and the extended Spatial Simulated Annealing (SSA method were used to minimize kriging variance. The optimization procedure was validated by constructing maps of relative improvement comparing the sample configuration before and after the process. A greater concentration of recommended points in specific areas (NW-SE direction was observed, which also reflects a greater estimate variance at these locations. The addition of optimal samples, for specific regions, increased the accuracy up to 2 % for chemical and 1 % for physical properties. The use of a sample grid and medium-scale variogram, as previous information for the conception of additional sampling schemes, was very promising to determine the locations of these additional points for all physical and chemical soil properties, enhancing the accuracy of kriging estimates of the physical-chemical properties.

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

    Science.gov (United States)

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

    2014-05-01

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

  5. Theory, evidence and Intervention Mapping to improve behavior nutrition and physical activity interventions

    Directory of Open Access Journals (Sweden)

    Ferreira Isabel

    2005-04-01

    Full Text Available Abstract Background The present paper intends to contribute to the debate on the usefulness and barriers in applying theories in diet and physical activity behavior-change interventions. Discussion Since behavior theory is a reflection of the compiled evidence of behavior research, theory is the only foothold we have for the development of behavioral nutrition and physical activity interventions. Application of theory should improve the effectiveness of interventions. However, some of the theories we use lack a strong empirical foundation, and the available theories are not always used in the most effective way. Furthermore, many of the commonly-used theories provide at best information on what needs to be changed to promote healthy behavior, but not on how changes can be induced. Finally, many theories explain behavioral intentions or motivation rather well, but are less well-suited to explaining or predicting actual behavior or behavior change. For more effective interventions, behavior change theory needs to be further developed in stronger research designs and such change-theory should especially focus on how to promote action rather than mere motivation. Since voluntary behavior change requires motivation, ability as well as the opportunity to change, further development of behavior change theory should incorporate environmental change strategies. Conclusion Intervention Mapping may help to further improve the application of theories in nutrition and physical activity behavior change.

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2016-10-01

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

  8. Phylogenetic conservation and physical mapping of members of the H6 homeobox gene family.

    Science.gov (United States)

    Stadler, H S; Murray, J C; Leysens, N J; Goodfellow, P J; Solursh, M

    1995-06-01

    Homeobox genes represent a class of transcription factors that play key roles in the regulation of embryogenesis and development. Here we report the identification of a homeobox-containing gene family that is highly conserved at both the nucleotide and amino acid levels in a diverse number of species. These species encompass both vertebrate and invertebrate phylogenies, ranging from Homo sapiens to Drosophila melanogaster. In humans, at least two homeobox sequences from this family were identified representing a previously reported member of this family as well as a novel homeobox sequence that we physically mapped to the 10q25.2-q26.3 region of human Chromosome (Chr) 10. Multiple members of this family were also detected in three additional vertebrate species including Equus caballus (horse), Gallus gallus (Chicken), and Mus musculus (mouse), whereas only single members were detected in Tripneustes gratilla (sea urchin), Petromyzon marinus (lamprey), Salmo salar (salmon), Ovis aries (sheep), and D. melanogaster (fruit fly).

  9. Analysis of Radiation Impact on White Mice through Radiation Dose Mapping in Medical Physics Laboratory

    Science.gov (United States)

    Sutikno, Madnasri; Susilo; Arya Wijayanti, Riza

    2016-08-01

    A study about X-ray radiation impact on the white mice through radiation dose mapping in Medical Physic Laboratory is already done. The purpose of this research is to determine the minimum distance of radiologist to X-ray instrument through treatment on the white mice. The radiation exposure doses are measured on the some points in the distance from radiation source between 30 cm up to 80 with interval of 30 cm. The impact of radiation exposure on the white mice and the effects of radiation measurement in different directions are investigated. It is founded that minimum distance of radiation worker to radiation source is 180 cm and X-ray has decreased leukocyte number and haemoglobin and has increased thrombocyte number in the blood of white mice.

  10. DIGITAL FLOOD INSURANCE RATE MAP DATABASE, DODGE COUNTY, WISCONSIN (AND INCORPORATED AREAS) - Fox Lake Physical Map Revision

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Digital Flood Insurance Rate Map (DFIRM) Database depicts flood risk information and supporting data used to develop the risk data. The primary risk;...

  11. Physical map and one-megabase sequencing of the human immunoglobulin lambda locus

    Directory of Open Access Journals (Sweden)

    Geraldo A.S. Passos Jr.

    1998-06-01

    Full Text Available The human immunoglobulin lambda (IGL locus is located on chromosome 22q11.1-q11.2 and contains the genes responsible for the immunoglobulin lambda light chains. This locus was recently mapped (physical map and its 1-Mb DNA totally sequenced. In this review we focus on the characterization of the v-lambda genes, its chromosomal location, genomics and sequencing of the IGL locus.O locus IGL humano está localizado no cromosomo 22q11.1-q11.2 e contém os genes responsáveis pelas cadeias leves de imunoglobulina tipo lambda. Este locus foi recentemente mapeado (mapa físico e seu 1 Mb DNA totalmente sequenciado. Nesta revisão focamos os principais resultados de caracterização dos genes v-lambda, sua localização cromossômica, a genômica e seqüenciamento do locus IGL.

  12. Physical mapping of Bph3, a brown planthopper resistance locus in rice

    Directory of Open Access Journals (Sweden)

    Jirapong Jairin

    2007-09-01

    Full Text Available Resistance to brown planthopper (BPH, a destructive phloem feeding insect pest, is an important objective in rice breeding programs in Thailand. The broad-spectrum resistance gene Bph3 is one of the major BPH resistance genes identified so far in cultivated rice and has been widely used in rice improvement programs. This resistance gene has been identified and mapped on the short arm of chromosome 6. In this study, physical mapping of Bph3 was performed using a BC3F3 population derived from a cross between Rathu Heenati and KDML105. Recombinant BC3F3 individuals with the Bph3 genotype were determined by phenotypic evaluation using modified mass tiller screening at the vegetative stage of rice plants. The recombination events surrounding the Bph3 locus were used to identify the co-segregate markers. According to the genome sequence of Nipponbare, the Bph3 locus was finally localized approximately in a 190 kb interval flanked by markers RM19291 and RM8072, which contain twenty-two putative genes. Additional phenotypic experiment revealed that the resistance in Rathu Heenati was decreased by increasing nitrogen content in rice plants through remobilization of nitrogen. This phenomenon should be helpful for identifying the Bph3 gene.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

    Sen, Ahmet Ilhan

    2002-01-01

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

  17. Real-time Deformation of Detailed Geometry Based on Mappings to a Less Detailed Physical Simulation on the GPU

    DEFF Research Database (Denmark)

    Mosegaard, Jesper; Sørensen, Thomas Sangild

    2005-01-01

    Modern graphics processing units (GPUs) can be effectively used to solve physical systems. To use the GPUoptimally, the discretization of the physical system is often restricted to a regular grid. When grid values representspatial positions, a direct visualization can result in a jagged appearance....... In this paper we propose todecouple computation and visualization of such systems. We define mappings that enable the deformation of ahigh-resolution surface based on a physical simulation on a lower resolution uniform grid. More specifically weinvestigate new approaches for the visualization of a GPU based...

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

    Directory of Open Access Journals (Sweden)

    Rebekah E Oliver

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

  19. SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

    Science.gov (United States)

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

    2013-01-01

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

  20. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

    Directory of Open Access Journals (Sweden)

    Kumar Ajay

    2012-11-01

    Full Text Available Abstract Background Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb, highly repetitive (>80% and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. Results Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB, to produce pentaploid RH1s (AABBD, which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (1 seeds. This panel showed a homogenous marker loss (2.1% after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker

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

    Science.gov (United States)

    Roth, Wolff-Michael; Roychoudhury, Anita

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

  2. Hierarchical Bayesian approach for estimating physical properties in spiral galaxies: Age Maps for M74

    CERN Document Server

    Gil, M Carmen Sánchez; Alfaro, Emilio J; Pérez, Enrique; Sarro, Luis M

    2015-01-01

    One of the fundamental goals of modern Astronomy is to estimate the physical parameters of galaxies from images in different spectral bands. We present a hierarchical Bayesian model for obtaining age maps from images in the \\Ha\\ line (taken with Taurus Tunable Filter (TTF)), ultraviolet band (far UV or FUV, from GALEX) and infrared bands (24, 70 and 160 microns ($\\mu$m), from Spitzer). As shown in S\\'anchez-Gil et al. (2011), we present the burst ages for young stellar populations in the nearby and nearly face on galaxy M74. As it is shown in the previous work, the \\Ha\\ to FUV flux ratio gives a good relative indicator of very recent star formation history (SFH). As a nascent star-forming region evolves, the \\Ha\\ line emission declines earlier than the UV continuum, leading to a decrease in the \\Ha\\/FUV ratio. Through a specific star-forming galaxy model (Starburst 99, SB99), we can obtain the corresponding theoretical ratio \\Ha\\ / FUV to compare with our observed flux ratios, and thus to estimate the ages of...

  3. To cut... or not to cut (applications of comparative physical maps in molecular evolution)

    Energy Technology Data Exchange (ETDEWEB)

    Hannenhalli, S. [Pennsylvania State Univ., Univeristy Park, PA (United States); Pevzner, P. [Univ. of Southern California, Los Angeles, CA (United States)

    1996-12-31

    Studies of genomes evolving by rearrangements lead to cornbinatorial problem of sorting permutation by reversals. Kececioglu and Sankoff conjectured that for every permutation there exists an optimal sorting by reversals which does not cut long strips in the permutation. We prove this conjecture and further study the problem of sorting by reversals for permutations without strips of size one, called singletons. We give a polynomial algorithm for sorting such permutations, thus demonstrating that singletons present the major obstacle on the way towards an efficient algorithm for sorting by reversals. Using this result, we prove the strong Kecedoglu-Sankoff conjecture: for every permutation there exists an optimal sorting by reversals that never increases the number of breakpoints. Finally we present a new algorithm for sorting by reversals based on the notion of the spin of a permutation. For permutations with O(log n) singletons the algorithm runs in polynomial time and suggests a desired trade-off of resolution for cross-hybridization physical mapping in molecular evolution studies. We describe applications of this algorithm to analyze rearrangements in maize and green algae, in particular we find a most parsimonious rearrangement scenario for Chlamydomonas moewusii versus Chlamydomonas reinhardtii representing the most complicated known case of rearrangements in organelles.

  4. The Effectiveness of Concept Maps in Teaching Physics Concepts Applied to Engineering Education: Experimental Comparison of the Amount of Learning Achieved With and Without Concept Maps

    Science.gov (United States)

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

    2013-04-01

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

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

    Science.gov (United States)

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

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

    Science.gov (United States)

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

    2015-01-01

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

  7. An Integrated Genetic,Physical and Transcript Map of Homoeologous Chromosomes 12 and 26 in Upland Cotton (Gossypium hirsutum L.)

    Institute of Scientific and Technical Information of China (English)

    XU Zhang-you; KOHEL Russell J; SONG Guo-li; CHO Jaemin; YU Jing; YU Shu-xun; TOMKINS Jeffrey; YU John Z

    2008-01-01

    @@ While Upland cotton (Gossypium hirsutum L.) represents 95% of the world production,its genetic improvement is hindered by the shortage of effective genomic tools and resources.The complex allotetraploid genome of the Upland cotton presents a unique challenge to such research efforts including integrated genome mapping and sequencing,which are considered highly experimental.Here,we report an integrated genetic,physical,and transcript map of homoeologous chromosomes 12 and 26 based on BAC/BIBAC clones,DNA markers,and EST unigenes.

  8. Construction of physical and genetic maps of Chlamydia trachomatis serovar L2 by pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Birkelund, Svend; Stephens, RS

    1992-01-01

    We constructed the physical map of Chlamydia trachomatis serovar L2 by using three restriction endonucleases, NotI (GC[GGCCGC), SgrAI (C(A/G)[CCGG(T/G)G), and Sse8387I (CCTGCA[GG), and we analyzed the fragments by pulsed-field gel electrophoresis. A total of 25 restriction endonuclease sites and 13...... genes and/or operons were located on the map. The genome size was determined to be 1,045 kb. Neither highly transcribed chlamydia genes nor developmental cycle-specific genes were clustered on the genome....

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

    Science.gov (United States)

    Heglund, Brian

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

  10. Hierarchical Bayesian approach for estimating physical properties in spiral galaxies: Age Maps for M74

    Science.gov (United States)

    Sánchez Gil, M. Carmen; Berihuete, Angel; Alfaro, Emilio J.; Pérez, Enrique; Sarro, Luis M.

    2015-09-01

    One of the fundamental goals of modern Astronomy is to estimate the physical parameters of galaxies from images in different spectral bands. We present a hierarchical Bayesian model for obtaining age maps from images in the Ha line (taken with Taurus Tunable Filter (TTF)), ultraviolet band (far UV or FUV, from GALEX) and infrared bands (24, 70 and 160 microns (μm), from Spitzer). As shown in [1], we present the burst ages for young stellar populations in the nearby and nearly face on galaxy M74. As it is shown in the previous work, the Hα to FUV flux ratio gives a good relative indicator of very recent star formation history (SFH). As a nascent star-forming region evolves, the Ha line emission declines earlier than the UV continuum, leading to a decrease in the HαFUV ratio. Through a specific star-forming galaxy model (Starburst 99, SB99), we can obtain the corresponding theoretical ratio Hα / FUV to compare with our observed flux ratios, and thus to estimate the ages of the observed regions. Due to the nature of the problem, it is necessary to propose a model of high complexity to take into account the mean uncertainties, and the interrelationship between parameters when the Hα / FUV flux ratio mentioned above is obtained. To address the complexity of the model, we propose a Bayesian hierarchical model, where a joint probability distribution is defined to determine the parameters (age, metallicity, IMF), from the observed data, in this case the observed flux ratios Hα / FUV. The joint distribution of the parameters is described through an i.i.d. (independent and identically distributed random variables), generated through MCMC (Markov Chain Monte Carlo) techniques.

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

    Science.gov (United States)

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

    2012-06-01

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

  12. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L. genome

    Directory of Open Access Journals (Sweden)

    Cloutier Sylvie

    2011-05-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb. The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%, followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable

  13. An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula

    NARCIS (Netherlands)

    Schnabel, E.; Kulikova, O.; Penmetsa, R.V.; Bisseling, T.; Cook, D.R.; Frugoli, J.

    2003-01-01

    The sunn mutation of Medicago truncatula is a single-gene mutation that confers a novel supernodulation phenotype in response to inoculation with Sinorhizobium meliloti. We took advantage of the publicly available codominant PCR markers, the high-density genetic map, and a linked cytogenetic map to

  14. Analysing Concept Maps as an Assessment Tool in Teaching Physics and Comparison with the Achievement Tests

    Science.gov (United States)

    Ingec, Sebnem Kandil

    2009-01-01

    Concept mapping is a technique that paves the way to represent knowledge schematically. In this research, concept mapping was used as an assessment method on the impulse-momentum topic. The purpose of this study was to determine teacher candidates' knowledge about understanding of the concepts of impulse and momentum by comparing and contrasting…

  15. Novel methods for physical mapping of the human genome applied to the long arm of chromosome 5. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McClelland, M.

    1991-12-01

    The object of our current grant is to develop novel methods for mapping of the human genome. The techniques to be assessed were: (1) three methods for the production of unique sequence clones from the region of interest; (2) novel methods for the production and separation of multi-megabase DNA fragments; (3) methods for the production of ``physical linking clones`` that contain rare restriction sites; (4) application of these methods and available resources to map the region of interest. Progress includes: In the first two years methods were developed for physical mapping and the production of arrayed clones; We have concentrated on developing rare- cleavage tools based or restriction endonucleases and methylases; We studied the effect of methylation on enzymes used for PFE mapping of the human genome; we characterized two new isoschizomers of rare cutting endonucleases; we developed a reliable way to produce partial digests of DNA in agarose plugs and applied it to the human genome; and we applied a method to double the apparent specificity of the ``rare-cutter`` endonucleases.

  16. Novel methods for physical mapping of the human genome applied to the long arm of chromosome 5

    Energy Technology Data Exchange (ETDEWEB)

    McClelland, M.

    1991-12-01

    The object of our current grant is to develop novel methods for mapping of the human genome. The techniques to be assessed were: (1) three methods for the production of unique sequence clones from the region of interest; (2) novel methods for the production and separation of multi-megabase DNA fragments; (3) methods for the production of physical linking clones'' that contain rare restriction sites; (4) application of these methods and available resources to map the region of interest. Progress includes: In the first two years methods were developed for physical mapping and the production of arrayed clones; We have concentrated on developing rare- cleavage tools based or restriction endonucleases and methylases; We studied the effect of methylation on enzymes used for PFE mapping of the human genome; we characterized two new isoschizomers of rare cutting endonucleases; we developed a reliable way to produce partial digests of DNA in agarose plugs and applied it to the human genome; and we applied a method to double the apparent specificity of the rare-cutter'' endonucleases.

  17. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza.

    Science.gov (United States)

    Kim, HyeRan; Hurwitz, Bonnie; Yu, Yeisoo; Collura, Kristi; Gill, Navdeep; SanMiguel, Phillip; Mullikin, James C; Maher, Christopher; Nelson, William; Wissotski, Marina; Braidotti, Michele; Kudrna, David; Goicoechea, José Luis; Stein, Lincoln; Ware, Doreen; Jackson, Scott A; Soderlund, Carol; Wing, Rod A

    2008-01-01

    We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

  18. A qualitative enquiry into learner experience of utilising concept maps as a learning method in physical science

    Directory of Open Access Journals (Sweden)

    Piet J Ankiewicz

    1998-03-01

    Full Text Available The aim of this study was to describe the experience of learners who utilise concept maps as a learning method in Physical Science.

    Opsomming
    Die doel met die studie was om die ervaring van leerders, wat begripskaarte as leermetode in Natuur- en Skeikunde gebruik, te beskryf. *Please note: This is a reduced version of the abstract. Please refer to PDF for full text.

  19. Concept maps representing knowledge of physics: Connecting structure and content in the context of electricity and magnetism

    Directory of Open Access Journals (Sweden)

    Maija Nousiainen

    2010-09-01

    Full Text Available Many assume that the quality of students’ content knowledge can be connected to certain structural characteristics of concept maps, such as the clustering of concepts around other concepts, cyclical paths between concepts and the hierarchical ordering of concepts. In order to study this relationship, we examine concept maps in electricity and magnetism drawn by physics teacher students and their instructors. The structural analysis of the maps is based on the operationalisation of important structural features (i.e. the features of interest are recognised and made measurable. A quantitative analysis of 43 concept maps was carried out on this basis. The results show that structure and content are closely connected; the structural features of clustering, cyclicity and hierarchy can serve as quantitative measures in characterising structural quality as well as the quality of content knowledge in concept maps. These findings have educational implications in regard to fostering the teacher student’s organisation of knowledge and in monitoring the process of such organisation.

  20. Mapping University Students' Epistemic Framing of Computational Physics Using Network Analysis

    Science.gov (United States)

    Bodin, Madelen

    2012-01-01

    Solving physics problem in university physics education using a computational approach requires knowledge and skills in several domains, for example, physics, mathematics, programming, and modeling. These competences are in turn related to students' beliefs about the domains as well as about learning. These knowledge and beliefs components are…

  1. A 1.6-Mb P1-based physical map of the Down syndrome region on chromosome 21

    Energy Technology Data Exchange (ETDEWEB)

    Ohira, Miki; Suzuki, Kazunobu [National Cancer Center Research Institute, Tokyo (Japan)]|[Kazusa DNA Research Institute, Chiba (Japan); Ichikawa, Hitoshi [National Cancer Center Research Institute, Tokyo (Japan)] [and others

    1996-04-01

    The Down Syndrome (DS) region on chromosome 21, which is responsible for the main features of DS such as characteristic facial features, a congenital heart defect, and mental retardation, has been defined by molecular analysis of DS patients with partial trisomy 21. The 2.5-Mb region around the marker D21S55 between D21S17 and ERG in 21q22 is thought to be important, although contributions of other regions cannot be excluded. In this region, we focused on a 1.6-Mb region between a NotI site, LA68 (D21S396, which is mapped distal to D21S17) and ERG, because analysis of a Japanese DS family with partial trisomy 21 revealed that the proximal border of its triplicated region was distal to LA68. We constructed P1 contigs with 46 P1 clones covering more than 95% of the 1.6-Mb region. A high-resolution restriction map using BamHI was also constructed for more details analysis. Our P1 contig map supplements other physical maps previously reported and provides useful materials for further analysis including isolation and sequencing of the DS region. 31 refs., 7 figs., 1 tab.

  2. NotI linking clones as a tool for joining physical and genetic maps of the human genome.

    Science.gov (United States)

    Allikmets, R L; Kashuba, V I; Pettersson, B; Gizatullin, R; Lebedeva, T; Kholodnyuk, I D; Bannikov, V M; Petrov, N; Zakharyev, V M; Winberg, G

    1994-01-15

    To study the connection among NotI linking clones, CpG islands, and genes, the sequence surrounding 143 NotI sites was determined. These NotI linking clones were isolated from human chromosome 3-specific libraries and contain an average C + G content of 65%. These clones represent sequence-tagged sites that can be positioned onto chromosome maps and used for generating a long-range NotI map of the human genome. A majority (about 90%) of these clones contain transcribed sequences, as detected by Northern blot hybridization, providing an efficient link between physical and functional (genetic) maps. The GenBank nucleotide database was searched with sequences from these NotI linking clones. For many clones, homology was found to human and other vertebrate genes. About 20 clones contained various repeats in their sequences and may represent microsatellite loci. Most of these NotI linking clones therefore represent evolutionarily conserved DNA fragments and also can be used for comparative genome mapping of other mammalian species. In addition, approximately 20% of all sequenced human CpG island-containing genes and more than 12% of all well-characterized human genes were found to possess NotI restriction sites. This is at least 2-5 times more than has been previously estimated and suggests that NotI sites have a much stronger association with genes.

  3. NotL linking clones as a tool for joining physical and genetic maps of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Allikmets, R.L.; Dean, M.; Modi, W. (DynCorp National Cancer Institute, Frederick, MD (United States)); Kholodnyuk, I.D.; Winberg, G.; Klein, G. (Karolinska Institutet, Stockholm (Sweden)); Pettersson, B.; Uhlen, M. (Royal Institute of Technology, Stockholm (Sweden)); Gizatullin, R.; Bannikov, V.M. (and others)

    1994-01-15

    To study the connection among NotI linking clones, CpG islands, and genes, the sequence surrounding 143 NotI sites was determined. These NotI linking clones were isolated from human chromosome 3-specific libraries and contain an average C + G content of 65%. These clones represent sequence-tagged sites that can be positioned onto chromosome maps and used for generating a long-range NotI map of the human genome. A majority (about 90%) of these clones contain transcribed sequences, as detected by Northern blot hybridization, providing an efficient link between physical and functional (genetic) maps. The GenBank nucleotide database was searched with sequences from these NotI linking clones. For many clones, homology was found to human and other vertebrate genes. About 20 clones contained various repeats in their sequences and may represent microsatellite loci. Most of these NotI linking clones therefore represent evolutionarily conserved DNA fragments and also can be used for comparative genome mapping of other mammalian species. In addition, approximately 20% of all sequenced human CpG island-containing genes and more than 12% of all well-characterized human genes were found to possess NotI restriction sites. This is at least 2-5 times more than has been previously estimated and suggests that NotI sites have a much stronger association with genes. 41 refs., 3 figs., 2 tabs.

  4. Mapping university students’ epistemic framing of computational physics using network analysis

    Directory of Open Access Journals (Sweden)

    Madelen Bodin*

    2012-04-01

    Full Text Available Solving physics problem in university physics education using a computational approach requires knowledge and skills in several domains, for example, physics, mathematics, programming, and modeling. These competences are in turn related to students’ beliefs about the domains as well as about learning. These knowledge and beliefs components are referred to here as epistemic elements, which together represent the students’ epistemic framing of the situation. The purpose of this study was to investigate university physics students’ epistemic framing when solving and visualizing a physics problem using a particle-spring model system. Students’ epistemic framings are analyzed before and after the task using a network analysis approach on interview transcripts, producing visual representations as epistemic networks. The results show that students change their epistemic framing from a modeling task, with expectancies about learning programming, to a physics task, in which they are challenged to use physics principles and conservation laws in order to troubleshoot and understand their simulations. This implies that the task, even though it is not introducing any new physics, helps the students to develop a more coherent view of the importance of using physics principles in problem solving. The network analysis method used in this study is shown to give intelligible representations of the students’ epistemic framing and is proposed as a useful method of analysis of textual data.

  5. Mapping university students' epistemic framing of computational physics using network analysis

    Science.gov (United States)

    Bodin, Madelen

    2012-06-01

    Solving physics problem in university physics education using a computational approach requires knowledge and skills in several domains, for example, physics, mathematics, programming, and modeling. These competences are in turn related to students’ beliefs about the domains as well as about learning. These knowledge and beliefs components are referred to here as epistemic elements, which together represent the students’ epistemic framing of the situation. The purpose of this study was to investigate university physics students’ epistemic framing when solving and visualizing a physics problem using a particle-spring model system. Students’ epistemic framings are analyzed before and after the task using a network analysis approach on interview transcripts, producing visual representations as epistemic networks. The results show that students change their epistemic framing from a modeling task, with expectancies about learning programming, to a physics task, in which they are challenged to use physics principles and conservation laws in order to troubleshoot and understand their simulations. This implies that the task, even though it is not introducing any new physics, helps the students to develop a more coherent view of the importance of using physics principles in problem solving. The network analysis method used in this study is shown to give intelligible representations of the students’ epistemic framing and is proposed as a useful method of analysis of textual data.

  6. Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

    Directory of Open Access Journals (Sweden)

    You Frank M

    2010-06-01

    Full Text Available Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum, Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete

  7. A candidate region for Nevoid Basal Cell Carcinoma Syndrome defined by genetic and physical mapping

    Energy Technology Data Exchange (ETDEWEB)

    Wainwright, B.; Negus, K.; Berkman, J. [Univ. of Queensland, Brisbane (Australia)] [and others

    1994-09-01

    Nevoid Basal Cell Carcinoma Syndrome (NBCCS, or Gorlin`s syndrome) is a cancer predisposition syndrome charcterized by multiple basal cell carcinomas (BCCs) and diverse developmental defects. The gene responsible for NBCCS, which is most likely to be a tumor suppressor gene, has previously been mapped to 9q22.3-q31 in a 12 cM interval between the microsatellite marker loci D9S12 and D9S109. Combined multipoint and haplotype analyses of Australian pedigrees has further refined the localization to a 2 cM interval between markers D9S196 and D9S180. Our loss of heterozygosity (LOH) studies from sporadic (n= 58) and familial (n=41) BCCs indicate that 50% have deletions within the NBCCS candidate region. All LOH is consistent with the genetic mapping of the NBCCS locus. Additionally, one sporadic tumor indicates that the smallest region of overlap in the deletions is within the interval D9S287 (proximal) and D9S180 (distal). A series of YAC clones from within this region has been mapped by FISH to examine chimerism. These clones, which have been mapped with respect to one another, form a contig which encompasses the candidate region from D9S196 to D9S180.

  8. Prevalence of Mind Mapping as a Teaching and Learning Strategy in Physical Therapy Curricula

    Science.gov (United States)

    Zipp, Genevieve; Maher, Catherine

    2013-01-01

    Background and Purpose: Regardless of our discipline educators seek to create environments that actively engage students in their learning journey. One teaching and learning strategy that has emerged in higher education is mind mapping (MM). The purpose of this exploratory study was to determine the prevalence of MM usage in a health science…

  9. Development of one set of chromosome-specific microsatellite-containing BACs and their physical mapping in Gossypium hirsutum L.

    Science.gov (United States)

    Wang, Kai; Guo, Wangzhen; Zhang, Tianzhen

    2007-09-01

    Fluorescence in situ hybridization (FISH), using bacterial artificial chromosome (BAC) clone as probe, is a reliable cytological technique for chromosome identification. It has been used in many plants, especially in those containing numerous small chromosomes. We previously developed eight chromosome-specific BAC clones from tetraploid cotton, which were used as excellent cytological markers for chromosomes identification. Here, we isolated the other chromosome-specific BAC clones to make a complete set for the identification of all 26 chromosome-pairs by this technology in tetraploid cotton (Gossypium hirsutum L.). This set of BAC markers was demonstrated to be useful to assign each chromosome to a genetic linkage group unambiguously. In addition, these BAC clones also served as convenient and reliable landmarks for establishing physical linkage with unknown targeted sequences. Moreover, one BAC containing an EST, with high sequence similarity to a G. hirsutum ethylene-responsive element-binding factor was located physically on the long arm of chromosome A7 with the help of a chromosome-A7-specific BAC FISH marker. Comparative analysis of physical marker positions in the chromosomes by BAC-FISH and genetic linkage maps demonstrated that most of the 26 BAC clones were localized close to or at the ends of their respective chromosomes, and indicated that the recombination active regions of cotton chromosomes are primarily located in the distal regions. This technology also enables us to make associations between chromosomes and their genetic linkage groups and re-assign each chromosome according to the corresponding genetic linkage group. This BAC clones and BAC-FISH technology will be useful for us to evaluate grossly the degree to which a linkage map provides adequate coverage for developing a saturated genetic map, and provides a powerful resource for cotton genomic researches.

  10. Physical and transcriptional mapping of the 17p13.3 region that is frequently deleted in human cancer

    DEFF Research Database (Denmark)

    Hoff, C; Seranski, P; Mollenhauer, J;

    2000-01-01

    suppressor gene that has also been suggested to play a role in the pathogenesis of Miller-Diecker syndrome (MDS). However, single-gene isolation efforts have retrieved additional genes from 17p13.3 that could play a role in tumorigenesis. This indicates that the full potential of this chromosomal region...... with respect to disease-related genes has not yet been exhausted and that there may exist still unknown genes that contribute to tumorigenesis or to the complex MDS phenotype. To provide a basis for the systematic isolation and evaluation of such genes, we established a physical map over 1.5 Mb of 17p13...

  11. A Bayesian and Physics-Based Ground Motion Parameters Map Generation System

    Science.gov (United States)

    Ramirez-Guzman, L.; Quiroz, A.; Sandoval, H.; Perez-Yanez, C.; Ruiz, A. L.; Delgado, R.; Macias, M. A.; Alcántara, L.

    2014-12-01

    We present the Ground Motion Parameters Map Generation (GMPMG) system developed by the Institute of Engineering at the National Autonomous University of Mexico (UNAM). The system delivers estimates of information associated with the social impact of earthquakes, engineering ground motion parameters (gmp), and macroseismic intensity maps. The gmp calculated are peak ground acceleration and velocity (pga and pgv) and response spectral acceleration (SA). The GMPMG relies on real-time data received from strong ground motion stations belonging to UNAM's networks throughout Mexico. Data are gathered via satellite and internet service providers, and managed with the data acquisition software Earthworm. The system is self-contained and can perform all calculations required for estimating gmp and intensity maps due to earthquakes, automatically or manually. An initial data processing, by baseline correcting and removing records containing glitches or low signal-to-noise ratio, is performed. The system then assigns a hypocentral location using first arrivals and a simplified 3D model, followed by a moment tensor inversion, which is performed using a pre-calculated Receiver Green's Tensors (RGT) database for a realistic 3D model of Mexico. A backup system to compute epicentral location and magnitude is in place. A Bayesian Kriging is employed to combine recorded values with grids of computed gmp. The latter are obtained by using appropriate ground motion prediction equations (for pgv, pga and SA with T=0.3, 0.5, 1 and 1.5 s ) and numerical simulations performed in real time, using the aforementioned RGT database (for SA with T=2, 2.5 and 3 s). Estimated intensity maps are then computed using SA(T=2S) to Modified Mercalli Intensity correlations derived for central Mexico. The maps are made available to the institutions in charge of the disaster prevention systems. In order to analyze the accuracy of the maps, we compare them against observations not considered in the

  12. Physical mapping of the human ELA1 gene between D12S361 and D12S347 on chromosome 12q13

    Energy Technology Data Exchange (ETDEWEB)

    Davies, R.L. [Sweet Briar College, VA (United States); Yoon, Sung Joo; Kucherlapati, R. [Albert Einstein College of Medicine, New York, NY (United States)] [and others

    1995-10-10

    ELA1, the pancreatic elastase 1 gene, is conserved in mammalian genomes. ELA1 was previously mapped to chromosome 12 using a panel of mouse-human somatic cell hybrids. We now report the physical and cytogenetic localization of the ELA1 gene. On the physical map, ELA1 is adjacent to the polymorphic marker AFMa283yg1 and between D12S361 and D12S347. Using fluorescence in situ hybridization, we determined that ELA1 maps to 12q13. 13 refs., 2 figs.

  13. A 4.5-megabase YAC contig and physical map over the hemochromatosis gene region

    Energy Technology Data Exchange (ETDEWEB)

    Burt, M.J.; Smit, D.J.; Pyper, W.R.; Powell, L.W.; Jazwinska, E.C. [Univ. of Queensland, Brisbane (Australia)

    1996-04-15

    We have constructed a yeast artificial chromosome (YAC) contig over the candidate hemochromatosis gene region. This contig comprises hemochromatosis gene region. This contig comprises 16 YACs from the CEPH, Washington University, and ICI YAC libraries and covers 4.5 Mb at 6p21.3-6p22. The complete contig has been restriction mapped, enabling the precise relationship between the YACs to be determined and the mapping of a total of 12 STSs. Nine of these are highly polymorphic STSs that are closely linked to hemochromatosis; this series includes D6S265 and D6S1260, which comprise the most proximal and distal markers linked to HC. This is the first YAC contig that spans the hemochromatosis candidate region, and it provides valuable resource material for the cloning of this and other genes in the region distal to the MHC class I complex. 33 refs., 1 fig., 1 tab.

  14. Physical Properties of the Magellanic Bridge Tidal Remnant through Mapped Hα, [SII], and [NII] Emission

    Science.gov (United States)

    Barger, Kathleen; Haffner, L. Matthew

    2016-01-01

    We present the first kinematically resolved [S II] λ6716 and [N II] λ6583 emission maps of the entire Magellanic Bridge that were observed with the Wisconsin Hα Mapper Telescope. Combining these maps with the complementary Hα maps of Barger et al. (2013), we explore the temperature, sulfur and nitrogen ionization state, and sources of the ionization of the warm-ionized gas in the Magellanic Bridge, the SMC-Tail, and the LMC-Bridge interface region. Within the Magellanic Bridge, we find that the low velocity (+100 to +200 km s-1 ) and the high velocity (+200 to +300 km s-1 ) gas have different properties, suggesting that it is composed of at least two separate and coherent filaments. Within the high-velocity filament, a high-velocity ridge of gas—with different properties from the high-velocity structure—extends along the high-latitude edge of the Hα SMC-Tail to low latitude edge LMC-Bridge interface. This ridge coincides with a strip of early-type stars, suggesting that these stars are influencing this gas. We further find that the properties of both the SMC-Tail and LMC-Bridge interface regions have similar properties and therefore are likely affected by similar ionization sources.

  15. Physical mapping of the Gorlin syndrome region on 9q22 by pulsed field gel electrophoresis (PFGE) and FISH

    Energy Technology Data Exchange (ETDEWEB)

    Levanat, S.; Gailani, M. [Yale Univ. School of Medicine, New Haven, CT (United States); Dean, M. [National Cancer Institute, Frederick, MD (United States)] [and others

    1994-09-01

    Gorlin syndrome is an autosomal dominant disorder characterized by basal cell carcinomas, medulloblastomas, and ovarian fibromas, as well as widespread developmental defects. Linkage and tumor deletion studies localized the gene for this syndrome to the 3 cM region on chromosome 9q22 between D9S196 and D9S180. Several groups have constructed YAC contigs of this region, but many of the YACs are known to contain rearrangements. Mapping by PGE and FISH is useful in further characterization of the relationship between physical distance and genetic distance. We isolated seven cosmids mapping to this region (D9S180, D9S196, D9S287, Col 15A1, XPA and two new anonymous cosmids). FISH gave a distance between D9S196 and D9S180 of at least 2 Mb and showed that Col15A1, previously considered as a candidate gene, mapped a few hundred kb distal to S180. For PFGE, DNA blocks from normal and 20 Gorlin syndrome patients were digested with 5 restriction enzymes and probed with single copy fragments of the seven cosmids. No aberrant bands have been identified in patients. Non-overlapping Not I fragments from these seven markers totalled 2.3 kb. Given an average gene density, a region of this size would contain 50-100 genes.

  16. Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes.

    Science.gov (United States)

    Thierry, A; Dujon, B

    1992-11-11

    We have developed a new method for the physical mapping of genomes and the rapid sorting of genomic libraries which is based on chromosome fragmentation by the meganuclease I-Sce I, the first available member of a new class of endonucleases with very long recognition sequences. I-Sce I allows complete cleavage at a single artificially inserted site in an entire genome. Sites can be inserted by homologous recombination using specific cassettes containing selectable markers or, at random, using transposons. This method has been applied to the physical mapping of chromosome XI (620 kb) of Saccharomyces cerevisi and to the sorting of a cosmid library. Our strategy has potential applications to various genome mapping projects. A set of transgenic yeast strains carrying the I-Sce I sites at various locations along a chromosome defines physical intervals against which new genes, DNA fragments or clones can be mapped directly by simple hybridizations.

  17. LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

    Directory of Open Access Journals (Sweden)

    Feuillet Catherine

    2010-11-01

    Full Text Available Abstract Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC software, which often results in short contig lengths (of 3-5 clones before merging as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs. Results To address these problems, we propose a novel approach that: (i reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly

  18. Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus.

    Science.gov (United States)

    Telgmann-Rauber, Alexa; Jamsari, Ari; Kinney, Michael S; Pires, J Chris; Jung, Christian

    2007-09-01

    Asparagus officinalis L. is a dioecious plant. A region called the M-locus located on a pair of homomorphic sex chromosomes controls the sexual dimorphism in asparagus. The aim of this work was to clone the region determining sex in asparagus from its position in the genome. The structure of the region encompassing M should be investigated and compared to the sex-determining regions in other dioecious model species. To establish an improved basis for physical mapping, a high-resolution genetic map was enriched with AFLP markers closely linked to the target locus by carrying out a bulked segregant analysis. By screening a BAC library with AFLP- and STS-markers followed by chromosome walking, a physical map with eight contigs could be established. However, the gaps between the contigs could not be closed due to a plethora of repetitive elements. Surprisingly, two of the contigs on one side of the M-locus did not overlap although they have been established with two markers, which mapped in a distance as low as 0.25 cM flanking the sex locus. Thus, the clustering of the markers indicates a reduced recombination frequency within the M-region. On the opposite side of the M-locus, a contig was mapped in a distance of 0.38 cM. Four closely linked BAC clones were partially sequenced and 64 putative ORFs were identified. Interestingly, only 25% of the ORFs showed sequence similarity to known proteins and ESTs. In addition, an accumulation of repetitive sequences and a low gene density was revealed in the sex-determining region of asparagus. Molecular cytogenetic and sequence analysis of BACs flanking the M-locus indicate that the BACs contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes, which hindered the localization of the M-locus to the single pair of sex chromosomes. We speculate that dioecious Silene, papaya and Asparagus species may represent three stages in the evolution of XX, XY sex

  19. Student facility with ratio and proportion: Mapping the reasoning space in introductory physics

    CERN Document Server

    Boudreaux, Andrew; Brahmia, Suzanne

    2015-01-01

    Six specific modes of reasoning about ratio and proportion have been delineated as a means of operationalizing expert practice. These modes stem from consideration of how physicists reason in context, are informed by prior work in physics and mathematics education, and have grain size matched to the steps in reasoning needed to solve problems commonly used in physics instruction. A suite of assessment questions has been developed and validated to probe student facility with the reasoning modes. Responses to open-ended and multiple-choice versions of the assessment questions have been collected from more than 3000 students at Western Washington University, Rutgers University, and New Mexico State University. Results have been used to identify specific reasoning difficulties, to document differences in performance between student populations, and to explore the effect of question context on student reasoning. We find that students enrolled in university physics courses have difficulty interpreting and applying ...

  20. Genetic and physical mapping of AvrPi7, a novel avirulence gene of Magnaporthe oryzae using physical position-ready markers

    Institute of Scientific and Technical Information of China (English)

    FENG ShuJie; WANG Ling; MA JunHong; LIN Fei; PAN QingHua

    2007-01-01

    Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating crop diseases worldwide. The avirulence gene corresponding to rice blast resistance gene Pi7 in field isolate CHL346 was inherited as a single gene, designated AvrPi7, in a segregating population consisting of 189 ascospore progenies derived from a cross between field isolates CHL346 and CHL42. In order to determine the chromosomal location of the AvrPi7 locus, a total of 121 simple sequence repeat (SSR) markers were developed based on the whole-genome sequence of reference isolate 70-15 of M. oryzae.Linkage analysis of the locus with these SSR markers showed that eight SSR markers on chromosome1 were linked to the locus, among which the closest flanking markers MS1-9 and MS1-15 were 3.2 and 16.4 cM from the locus, respectively. For fine mapping, additional PCR-based makers including eight SSR markers and three candidate avirulence gene (CAG) markers were developed in the region flanking both markers. The AvrPi7 locus was genetically delimited within a 1.6-cM region flanked by markers MS1-21 and MS1-22, and co-segregated with the marker CAG2. To construct a physical map of the AvrPi7 locus, molecular markers linked to the Avr gene were mapped on the supercontigs of the reference isolate 70-15 through bioinformation analysis (BIA). Consequently, the AvrPi7 locus was delimited to a 75-kb interval flanked by markers MS1-21 and MS1-22 based on the reference sequence.Merodiploids observed in this study are also discussed.

  1. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides.

    Directory of Open Access Journals (Sweden)

    Shuhong Ouyang

    Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90 via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.

  2. Theory, evidence and Intervention Mapping to improve behavior nutrition and physical activity interventions.

    NARCIS (Netherlands)

    J. Brug (Hans); A. Oenema (Anke); A. Ferreira (Isabel)

    2005-01-01

    textabstractBACKGROUND: The present paper intends to contribute to the debate on the usefulness and barriers in applying theories in diet and physical activity behavior-change interventions. DISCUSSION: Since behavior theory is a reflection of the compiled evidence of behavior research, theory is th

  3. What Do We Know about "How" to Promote Physical Activity to Adolescents? A Mapping Review

    Science.gov (United States)

    Bush, Paula Louise; García Bengoechea, Enrique

    2015-01-01

    To date, adolescent physical activity (PA) intervention research has focused on the school setting and suggests a need to extend interventions beyond this setting to influence teenagers' overall level of PA. But, the relative effectiveness of PA promotion strategies that can be part of such multi-setting interventions remains unknown. We completed…

  4. Physical Localization and Genetic Mapping of Fertility Restoration Gene Rfo in Canola (Brassica napus L.)

    Science.gov (United States)

    The Ogu cytoplasm for male fertility and its fertility restorer gene Rfo in canola (Brassica napus L.) were originally introgressed from radish (Raphanus sativus L.) and have been widely used for canola hybrid production and breeding. The objective of this study was to determine the physical locati...

  5. Physical mapping and YAC contig analysis of the region surrounding Xist on the mouse X chromosome.

    Science.gov (United States)

    Heard, E; Simmler, M C; Larin, Z; Rougeulle, C; Courtier, B; Lehrach, H; Avner, P

    1993-03-01

    The Xist sequence has been proposed as a potential candidate for the X-inactivation center based both on its localization within the candidate region for the X-inactivation center in man and mouse and on its unique pattern of expression from the inactive X chromosome. We have cloned 550 kb of DNA surrounding the mouse Xist sequence in contiguously overlapping YAC clones and have developed a long-range restriction map that spans almost 1 Mb of this region and includes this YAC contig. The detailed restriction map we have established provides a framework for the identification of expressed sequences other than Xist that may equally exhibit unusual expression characteristics associated with X inactivation. The presence of possible structural or methylation differences within this region between the active and inactive X chromosomes has been investigated through comparative analysis of male and female genomic DNA, and we report here the identification of certain CpG-containing restriction sites around Xist that have an interesting differential methylation status on the inactive and active X chromosomes.

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

    Science.gov (United States)

    2009-01-01

    ms. What is the value of I? (Problem 21-37, Giancoli 1991). This problem is represented by a case of 14 facts, defining the entities, events...domains. For example, Giancoli (1991) introduces rotational motion over an entire chapter, coming back to the analogy with linear motion repeatedly...retrieval? 6.1 Materials The problems were selected from a variety of physics resources, (Shearer et al. 1971; Giancoli 1991; Ogata 1997; Fogiel

  7. Physical mapping of probes within 14q32, a subtelomeric region showing a high recombination frequency.

    Science.gov (United States)

    Hofker, M H; Smith, S; Nakamura, Y; Teshima, I; White, R; Cox, D W

    1990-01-01

    The genetic linkage map of chromosome 14q32 contains 11 loci which span a distance of more than 60 cM. We have assigned 10 of these loci and the AKT1 proto-oncogene to segments of 14q32, using breakpoints derived from four independent chromosomal deletions or rearrangements. The most telomeric breakpoint was found in a proband (HSC 6) carrying a ring-14 chromosome. HSC 6 is monosomic for the distal part of 14q32, which contains the immunoglobulin heavy-chain locus (IGH), and random markers D14S20, D14S19, and D14S23. Two other chromosomal breakpoints, found in probands HSC 121 and HSC 981, could not be distinguished from each other using DNA probes, although the cytogenetic breakpoints appeared to be different at 14q32.32 and 14q32.31, respectively. The region between the breakpoints of HSC 6 and HSC 121 contains AKT1, D14S1, D14S17, and D14S16. The entire telomeric band 14q32 is assumed to contain about 10% of chromosome 14, or approximately 10 Mb. The 8 most telomeric loci, including D14S1, map to 14q32.32-qter, which measures only several megabases. However, these loci span a genetic distance of 23 cM. The high recombination frequency contrasts with the observation that two of the gamma genes in the IGH constant region show a high degree of linkage disequilibrium, though 180 kb apart. This finding suggests that a telomeric localization per se does not lead to a higher recombination frequency and favors the hypothesis that the higher recombination frequency at the telomeres may be due to specific "hot spots" for recombination.

  8. Comparative Mapping of Soil Physical-Chemical and Structural Parameters at Field Scale to Identify Zones of Enhanced Leaching Risk

    DEFF Research Database (Denmark)

    Nørgaard, Trine; Møldrup, Per; Olsen, Preben;

    2013-01-01

    , indicating that a few well-aligned and better connected macropores might change the hydraulic conductivity between the macropores and the soil matrix, triggering an on-set of preferential flow at lower rain intensities compared to less compacted soil. Overall, a comparison mapping of basic and structural......Preferential flow and particle-facilitated transport through macropores contributes significantly to the transport of strongly sorbing substances such as pesticides and phosphorus. The aim of this study was to perform a field-scale characterization of basic soil physical properties like clay...... and organic carbon content and investigate whether it was possible to relate these to derived structural parameters such as bulk density and conservative tracer parameters and to actual particle and phosphorus leaching patterns obtained from laboratory leaching experiments. Sixty-five cylindrical soil columns...

  9. 3-D mapping with ellipsometrically determined physical thickness/refractive index of spin coated sol–gel silica layer

    Indian Academy of Sciences (India)

    S Das; P Pal; S Roy; S Chakraboarty; P K Biswas

    2002-11-01

    Precursor sol for sol–gel silica layer was prepared from the starting material, tetraethylorthosilicate (TEOS). The sol was deposited onto borosilicate crown (BSC) glass by the spinning technique (rpm 2500). The gel layer thus formed transformed to oxide layer on heating to 450°C for ∼ 30 min. The physical thicknessand the refractive index of the layer were measured ellipsometrically (Rudolph Auto EL II) at 632.8 nm. About 10 × 10 mm surface area of the silica layer was chosen for evaluation of thickness and refractive index values at different points (121 nos.) with 1 mm gap between two points. Those data were utilized in the Autolisp programme for 3-D mapping. Radial distribution of the evaluated values was also displayed.

  10. Linkage analysis and physical mapping near the gene for x-linked agammaglobulinemia at Xq22

    Energy Technology Data Exchange (ETDEWEB)

    Parolini, O.; Lassiter, G.L.; Henry, M.J.; Conley, M.E. (Univ. of Tennessee College of Medicine, Memphis (United States) St. Jude Children' s Research Hospital, Memphis, TN (United States)); Hejtmancik, J.F. (National Inst. of Health, Bethesda, MD (United States)); Allen, R.C.; Belmont, J.W. (Baylor College of Medicine, Houston, TX (United States)); Barker, D.F. (Univ. of Utah, Salt Lake City (United States))

    1993-02-01

    The gene for x-linked agammaglobulinemia (XLA) has been mapped to Xq22. No recombinations have been reported between the gene and the prob p212 at DXS178; however, this probe is informative in only 30-40% of women and the reported flanking markers, DXS3 and DXS94, and 10-15 cM apart. To identify additional probes that might be useful in genetic counseling, we examined 11 polymorphisms that have been mapped to the Xq21.3-q22 region in 13 families with XLA. In addition, pulsed-field gel electrophoresis and yeast artificial chromosomes (YACs) were used to further characterize the segman of DNA within which the gene for SLA must lie. The results demonstrated that DXS366 and DXS442, which share a 430-kb pulsed-field fragment, could replace DXS3 as proximal flanking markers. Probes at DXS178 and DXS265 identified the same 145-kb pulsed-field fragment, and both loci were contained within a 200-kb YAC identified with the probe p212. A highly polymorphic CA repeat (DCS178CA) was isolated from one end of this YAC and used in linkage analysis. Probes at DXS101 and DXS328 shared several pulsed-field fragments, the smallest of which was 250 kb. No recombinations were seen between XLA and the DXS178-DXS265-DXS178CA complex, DXS101, DXS328, DXS87, or the gene for proteolipid protein (PLP). Key crossovers, when combined with the linkage data from families with Alport syndrome, suggested the following order of loci: cen-DXS3-DXS366-DXS442-(PLP, DXS101, DXS328, DXS178-DXS265-DXS178CA complex, XL)-(DXS87, DXS94)-DXS327-(DXS350, DXS362)-tel. Our studies also limit the segment of DNA within which the XLA gene must lie to the 3- to 4-cM distance between DCS442 and DXS94 and they identify and orient polymorphisms that can be used in genetic counseling not only for XLA but also for Pelizaeus-Merzbacher disease (PLP deficiency), Alport syndrome (COL4A5 deficiency), and Fabry disease ([alpha]-galactosidase A difficiency). 31 refs., 5 figs., 2 tabs.

  11. Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.

    Science.gov (United States)

    Delgado, Claudia Leticia Rodríguez; Waters, Paul D; Gilbert, Clément; Robinson, Terence J; Graves, Jennifer A Marshall

    2009-01-01

    All therian mammals (eutherians and marsupials) have an XX female/XY male sex chromosome system or some variant of it. The X and Y evolved from a homologous pair of autosomes over the 166 million years since therian mammals diverged from monotremes. Comparing the sex chromosomes of eutherians and marsupials defined an ancient X conserved region that is shared between species of these mammalian clades. However, the eutherian X (and the Y) was augmented by a recent addition (XAR) that is autosomal in marsupials. XAR is part of the X in primates, rodents, and artiodactyls (which belong to the eutherian clade Boreoeutheria), but it is uncertain whether XAR is part of the X chromosome in more distantly related eutherian mammals. Here we report on the gene content and order on the X of the elephant (Loxodonta africana)-a representative of Afrotheria, a basal endemic clade of African mammals-and compare these findings to those of other documented eutherian species. A total of 17 genes were mapped to the elephant X chromosome. Our results support the hypothesis that the eutherian X and Y chromosomes were augmented by the addition of autosomal material prior to eutherian radiation. Not only does the elephant X bear the same suite of genes as other eutherian X chromosomes, but gene order appears to have been maintained across 105 million years of evolution, perhaps reflecting strong constraints posed by the eutherian X inactivation system.

  12. Fractal Information by Means of Harmonic Mappings and Some Physical Implications

    Directory of Open Access Journals (Sweden)

    Maricel Agop

    2016-04-01

    Full Text Available Considering that the motions of the complex system structural units take place on continuous, but non-differentiable curves, in the frame of the extended scale relativity model (in its Schrödinger-type variant, it is proven that the imaginary part of a scalar potential of velocities can be correlated with the fractal information and, implicitly, with a tensor of “tensions”, which is fundamental in the construction of the constitutive laws of material. In this way, a specific differential geometry based on a Poincaré-type metric of the Lobachevsky plane (which is invariant to the homographic group of transformations and also a specific variational principle (whose field equations represent an harmonic map from the usual space into the Lobachevsky plane are generated. Moreover, fractal information (which is made explicit at any scale resolution is produced, so that the field variables define a gravitational field. This latter situation is specific to a variational principle in the sense of Matzner–Misner and to certain Ernst-type field equations, the fractal information being contained in the material structure and, thus, in its own space associated with it.

  13. Mapping the productive sands of Lower Goru Formation by using seismic stratigraphy and rock physical studies in Sawan area, southern Pakistan: A case study

    KAUST Repository

    Munir, K.

    2011-02-24

    This study has been conducted in the Sawan gas field located in southern Pakistan. The aim of the study is to map the productive sands of the Lower Goru Formation of the study area. Rock physics parameters (bulk modulus, Poisson\\'s ratio) are analysed after a detailed sequence stratigraphic study. Sequence stratigraphy helps to comprehend the depositional model of sand and shale. Conformity has been established between seismic stratigraphy and the pattern achieved from rock physics investigations, which further helped in the identification of gas saturation zones for the reservoir. Rheological studies have been done to map the shear strain occurring in the area. This involves the contouring of shear strain values throughout the area under consideration. Contour maps give a picture of shear strain over the Lower Goru Formation. The identified and the productive zones are described by sands, high reflection strengths, rock physical anomalous areas and low shear strain.

  14. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).

    Science.gov (United States)

    Dohm, Juliane C; Lange, Cornelia; Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Borchardt, Dietrich; Schulz, Britta; Lehrach, Hans; Weisshaar, Bernd; Himmelbauer, Heinz

    2012-05-01

    Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.

  15. The ionized gas in the central region of NGC 5253. 2D mapping of the physical and chemical properties

    Science.gov (United States)

    Monreal-Ibero, A.; Walsh, J. R.; Vílchez, J. M.

    2012-08-01

    Context. Blue compact dwarf (BCD) galaxies constitute the ideal laboratories to test the interplay between massive star formation and the surrounding gas. As one of the nearest BCD galaxies, NGC 5253 was previously studied with the aim to elucidate in detail the starburst interaction processes. Some open issues regarding the properties of its ionized gas still remain to be addressed. Aims: The 2D structure of the main physical and chemical properties of the ionized gas in the core of NGC 5253 has been studied. Methods: Optical integral field spectroscopy (IFS) data has been obtained with FLAMES Argus and lower resolution gratings of the Giraffe spectrograph. Results: We derived 2D maps for different tracers of electron density (ne), electron temperature (Te) and ionization degree. The maps for ne as traced by [O ii], [S ii], [Fe iii], and [Ar iv] line ratios are compatible with a 3D stratified view of the nebula with the highest ne in the innermost layers and a decrease of ne outwards. 2D maps of Te were measured from [O iii] and [S ii] line ratios; to our knowledge, this is the first time that a Te map based on [S ii] lines for an extragalactic object has been presented. The joint interpretation of the Te([S ii]) and Te([O iii]) maps is consistent with a Te structure in 3D with higher temperatures close to the main ionizing source surrounded by a colder and more diffuse component. The highest ionization degree is found at the peak of emission for the gas with relatively high ionization in the main Giant H ii Region and lower ionization degree delineating the more extended diffuse component. We derived abundances of oxygen, neon, argon, and nitrogen. Abundances for O, Ne and Ar are constant over the mapped area within ≲0.1 dex. The mean 12 + log (O/H) is 8.26 ± 0.04 while the relative abundances of log (N/O), log (Ne/O) and log (Ar/O) were ~-1.32 ± 0.05, -0.65 ± 0.03 and -2.33 ± 0.06, respectively. There are two locations with enhanced N/O. The first (log (N

  16. Academic skills, knowledge pedagogic tasks of the Physical Education Teacher: mapping links

    Directory of Open Access Journals (Sweden)

    Fernando Jaime González

    2015-05-01

    Full Text Available This research had to identify the knowledge mobilized by a physical education teacher in her teaching practice evidences of her initial formation. Therefore, we performed a study case consisted of seventeen lessons in observation of a teacher, in school in Ijuí/ RS. The results indicate most of the part of the knowledge manifested by the teacher in her professional practice, can be identified as original from the initial formation. Evidences of this can be found by looking the plurality of bodily practices developed and in the form of education and sports, based on the decision making in the invasion games, which coincides with the principles defended by course of initial formation the teacher.

  17. Whole-body energy mapping under physical exercise using positron emission tomography.

    Science.gov (United States)

    Iemitsu, M; Itoh, M; Fujimoto, T; Tashiro, M; Nagatomi, R; Ohmori, H; Ishii, K

    2000-12-01

    We attempted to visualize dynamic adjustment of glucose utilization in humans in the whole-body organs during physical exercise by using three-dimensional positron emission tomography (3D-PET) and [18F]-2-fluoro-deoxy-glucose (FDG). Twelve healthy male volunteers collaborated on the study; six subjects were assigned to the resting control group (C) and the other six to the running group (E). Group E subjects performed running on a flat road for 35 min. After 15 min of running, subjects injected FDG and kept on running thereafter for another 20 min. Group C subjects sat on a comfortable chair in a quiet room for 35 min after the injection of FDG. After scanning by PET, the regions of interest (ROIs) were manually set on brain, heart, thorax, abdomen, lower extremities, and the rest of the body on the corresponding transaxial images. The uptake of FDG in each region was evaluated as the % fraction of FDG accumulation relative to the total amount of whole-body accumulation. The results revealed increase of FDG uptake after running in the lower leg muscles from 24.6 +/- 9.5% to 43.1 +/- 4.7% and in the heart from 2.3 +/- 0.4% to 2.8 +/- 0.6%. The differences were significant (P body. FDG uptake in the abdominal region reduced from 37.3 +/- 7.2% to 19.7 +/- 4.9%. However, FDG uptake in the brain remained stable, i.e., 11.9 +/- 2.8% at rest and 10.3 +/- 2.5% after exercise. Thus, 3D-PET is a tool to visualize the dynamic adjustment of energy consumption during physical exercise in humans.

  18. Application of an efficient strategy with a phage lambda vector for constructing a physical map of the amyloplast genome of sycamore (Acer pseudoplatanus).

    Science.gov (United States)

    Ngernprasirtsiri, J; Kobayashi, H

    1990-01-01

    Amyloplasts were isolated from a heterotrophic culture cell line of a woody plant, sycamore (Acer pseudoplatanus), and their DNA was purified. Conventional procedures for making a physical map were not easily applicable to the amyloplast DNA, since the yield of DNA was too low and the presence of repeated sequences interfered with the analysis. Therefore, the pieces of amyloplast DNA starting with a few micrograms of DNA were cloned in the lambda Fix vector, which is a derivative of lambda EMBL vectors improved for efficient cloning and gene walking. Cloned DNA fragments were randomly picked, mapped for restriction endonuclease sites by a refined procedure, and combined by overlapping their physical maps. The DNA library was also subjected to screening by gene walking using promoters recognized by T3 and T7 RNA polymerases in the vector to fill the gaps between sequences determined by overlapping the physical maps. In this way, we constructed the entire DNA library and the complete physical map of the amyloplast DNA. The sycamore amyloplast genome was composed of 141.7-kbp nucleotides with the same gene arrangement as that of tobacco chloroplasts.

  19. [Developing a physical map of human chromosome 22 using Pace electrophoresis and large fragment cloning]. Annual report, October 1, 1991--July 1, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Simon, M.I.

    1994-12-31

    In the past two years, the authors have made a great deal of progress in establishing Fosmid and BAC libraries and in using large BAC libraries for gene mapping. In addition, they initiated work on the application of BAC clones to long range genome sequencing. They continue to increase the ability to rapidly generate large BAC libraries and to efficiently apply these libraries to genome mapping. The BACs provide a very effective means of developing physical maps. The current work suggests that BAC contigs will be extremely useful as source material for genome sequencing.

  20. Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii.

    Science.gov (United States)

    Jacobson, M R; Brigle, K E; Bennett, L T; Setterquist, R A; Wilson, M S; Cash, V L; Beynon, J; Newton, W E; Dean, D R

    1989-02-01

    Determination of a 28,793-base-pair DNA sequence of a region from the Azotobacter vinelandii genome that includes and flanks the nitrogenase structural gene region was completed. This information was used to revise the previously proposed organization of the major nif cluster. The major nif cluster from A. vinelandii encodes 15 nif-specific genes whose products bear significant structural identity to the corresponding nif-specific gene products from Klebsiella pneumoniae. These genes include nifH, nifD, nifK, nifT, nifY, nifE, nifN, nifX, nifU, nifS, nifV, nifW, nifZ, nifM, and nifF. Although there are significant spatial differences, the identified A. vinelandii nif-specific genes have the same sequential arrangement as the corresponding nif-specific genes from K. pneumoniae. Twelve other potential genes whose expression could be subject to nif-specific regulation were also found interspersed among the identified nif-specific genes. These potential genes do not encode products that are structurally related to the identified nif-specific gene products. Eleven potential nif-specific promoters were identified within the major nif cluster, and nine of these are preceded by an appropriate upstream activator sequence. A + T-rich regions were identified between 8 of the 11 proposed nif promoter sequences and their upstream activator sequences. Site-directed deletion-and-insertion mutagenesis was used to establish a genetic map of the major nif cluster.

  1. Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

    Indian Academy of Sciences (India)

    Irfan A Ghazi; Prem S Srivastava; Vivek Dalal; Kishor Gaikwad; Ashok K Singh; Tilak R Sharma; Nagendra K Singh; Trilochan Mohapatra

    2009-06-01

    Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

  2. PHYSICS

    CERN Multimedia

    P. Sphicas

    There have been three physics meetings since the last CMS week: “physics days” on March 27-29, the Physics/ Trigger week on April 23-27 and the most recent physics days on May 22-24. The main purpose of the March physics days was to finalize the list of “2007 analyses”, i.e. the few topics that the physics groups will concentrate on for the rest of this calendar year. The idea is to carry out a full physics exercise, with CMSSW, for select physics channels which test key features of the physics objects, or represent potential “day 1” physics topics that need to be addressed in advance. The list of these analyses was indeed completed and presented in the plenary meetings. As always, a significant amount of time was also spent in reviewing the status of the physics objects (reconstruction) as well as their usage in the High-Level Trigger (HLT). The major event of the past three months was the first “Physics/Trigger week” in Apri...

  3. Towards the Physical Map of the Trypanosoma cruzi Nuclear Genome: Construction of YAC and BAC Libraries of the Reference Clone T. cruzi CL-Brener

    Directory of Open Access Journals (Sweden)

    I Ferrari

    1997-11-01

    Full Text Available Strategies to construct the physical map of the Trypanosoma cruzi nuclear genome have to capitalize on three main advantages of the parasite genome, namely (a its small size, (b the fact that all chromosomes can be defined, and many of them can be isolated by pulse field gel electrophoresis, and (c the fact that simple Southern blots of electrophoretic karyotypes can be used to map sequence tagged sites and expressed sequence tags to chromosomal bands. A major drawback to cope with is the complexity of T. cruzi genetics, that hinders the construction of a comprehensive genetic map. As a first step towards physical mapping, we report the construction and partial characterization of a T. cruzi CL-Brener genomic library in yeast artificial chromosomes (YACs that consists of 2,770 individual YACs with a mean insert size of 365 kb encompassing around 10 genomic equivalents. Two libraries in bacterial artificial chromosomes (BACs have been constructed, BACI and BACII. Both libraries represent about three genome equivalents. A third BAC library (BAC III is being constructed. YACs and BACs are invaluable tools for physical mapping. More generally, they have to be considered as a common resource for research in Chagas disease

  4. Adapted Intervention Mapping: A Strategic Planning Process for Increasing Physical Activity and Healthy Eating Opportunities in Schools via Environment and Policy Change

    Science.gov (United States)

    Belansky, Elaine S.; Cutforth, Nick; Chavez, Robert; Crane, Lori A.; Waters, Emily; Marshall, Julie A.

    2013-01-01

    Background: School environment and policy changes have increased healthy eating and physical activity; however, there has been modest success in translating research ?ndings to practice. The School Environment Project tested whether an adapted version of Intervention Mapping (AIM) resulted in school change. Methods: Using a pair randomized design,…

  5. PHYSICS

    CERN Multimedia

    D. Acosta

    2010-01-01

    A remarkable amount of progress has been made in Physics since the last CMS Week in June given the exponential growth in the delivered LHC luminosity. The first major milestone was the delivery of a variety of results to the ICHEP international conference held in Paris this July. For this conference, CMS prepared 15 Physics Analysis Summaries on physics objects and 22 Summaries on new and interesting physics measurements that exploited the luminosity recorded by the CMS detector. The challenge was incorporating the largest batch of luminosity that was delivered only days before the conference (300 nb-1 total). The physics covered from this initial running period spanned hadron production measurements, jet production and properties, electroweak vector boson production, and even glimpses of the top quark. Since then, the accumulated integrated luminosity has increased by a factor of more than 100, and all groups have been working tremendously hard on analysing this dataset. The September Physics Week was held ...

  6. PHYSICS

    CERN Multimedia

    J. Incandela

    There have been numerous developments in the physics area since the September CMS week. The biggest single event was the Physics/Trigger week in the end of Octo¬ber, whereas in terms of ongoing activities the “2007 analyses” went into high gear. This was in parallel with participation in CSA07 by the physics groups. On the or¬ganizational side, the new conveners of the physics groups have been selected, and a new database for man¬aging physics analyses has been deployed. Physics/Trigger week The second Physics-Trigger week of 2007 took place during the week of October 22-26. The first half of the week was dedicated to working group meetings. The ple¬nary Joint Physics-Trigger meeting took place on Wednesday afternoon and focused on the activities of the new Trigger Studies Group (TSG) and trigger monitoring. Both the Physics and Trigger organizations are now focused on readiness for early data-taking. Thus, early trigger tables and preparations for calibr...

  7. PHYSICS

    CERN Multimedia

    P. Sphicas

    The CPT project came to an end in December 2006 and its original scope is now shared among three new areas, namely Computing, Offline and Physics. In the physics area the basic change with respect to the previous system (where the PRS groups were charged with detector and physics object reconstruction and physics analysis) was the split of the detector PRS groups (the old ECAL-egamma, HCAL-jetMET, Tracker-btau and Muons) into two groups each: a Detector Performance Group (DPG) and a Physics Object Group. The DPGs are now led by the Commissioning and Run Coordinator deputy (Darin Acosta) and will appear in the correspond¬ing column in CMS bulletins. On the physics side, the physics object groups are charged with the reconstruction of physics objects, the tuning of the simulation (in collaboration with the DPGs) to reproduce the data, the provision of code for the High-Level Trigger, the optimization of the algorithms involved for the different physics analyses (in collaboration with the analysis gr...

  8. Prebiotic Low Sugar Chocolate Dairy Desserts: Physical and Optical Characteristics and Performance of PARAFAC and PCA Preference Map.

    Science.gov (United States)

    Morais, E C; Esmerino, E A; Monteiro, R A; Pinheiro, C M; Nunes, C A; Cruz, A G; Bolini, Helena M A

    2016-01-01

    The addition of prebiotic and sweeteners in chocolate dairy desserts opens up new opportunities to develop dairy desserts that besides having a lower calorie intake still has functional properties. In this study, prebiotic low sugar dairy desserts were evaluated by 120 consumers using a 9-point hedonic scale, in relation to the attributes of appearance, aroma, flavor, texture, and overall liking. Internal preference map using parallel factor analysis (PARAFAC) and principal component analysis (PCA) was performed using the consumer data. In addition, physical (texture profile) and optical (instrumental color) analyses were also performed. Prebiotic dairy desserts containing sucrose and sucralose were equally liked by the consumers. These samples were characterized by firmness and gumminess, which can be considered drivers of liking by the consumers. Optimization of the prebiotic low sugar dessert formulation should take in account the choice of ingredients that contribute in a positive manner for these parameters. PARAFAC allowed the extraction of more relevant information in relation to PCA, demonstrating that consumer acceptance analysis can be evaluated by simultaneously considering several attributes. Multiple factor analysis reported Rv value of 0.964, suggesting excellent concordance for both methods.

  9. Physical mapping of 5S and 18S ribosomal DNA in three species of Agave (Asparagales, Asparagaceae

    Directory of Open Access Journals (Sweden)

    Victor Manuel Gomez-Rodriguez

    2013-08-01

    Full Text Available Agave Linnaeus, 1753 is endemic of America and is considered one of the most important crops in Mexico due to its key role in the country’s economy. Cytogenetic analysis was carried out in A. tequilana Weber, 1902 ‘Azul’, A. cupreata Trelease et Berger, 1915 and A. angustifolia Haworth, 1812. The analysis showed that in all species the diploid chromosome number was 2n = 60, with bimodal karyotypes composed of five pairs of large chromosomes and 25 pairs of small chromosomes. Furthermore, different karyotypical formulae as well as a secondary constriction in a large chromosome pair were found in all species. Fluorescent in situ hybridization (FISH was used for physical mapping of 5S and 18S ribosomal DNA (rDNA. All species analyzed showed that 5S rDNA was located in both arms of a small chromosome pair, while 18S rDNA was associated with the secondary constriction of a large chromosome pair. Data of FISH analysis provides new information about the position and number of rDNA loci and helps for detection of hybrids in breeding programs as well as evolutionary studies.

  10. A five-fold pig bacterial artificial chromosome library:a resource for positional cloning and physical mapping

    Institute of Scientific and Technical Information of China (English)

    LIU Wei; LI Ning; ZHANG Ying; LIU Zhaoliang; GUO Li; WANG Xiaobo; FEI Jing; FENG Jidong; ZHAO Rui; HU Xiaoxiang

    2006-01-01

    A pig BAC library was constructed with genomic DNA from a male Erhualian pig. After partial digestion with Hind Ⅲ or BamH I the fragments obtained were cloned into the pBeloBAC11 vector. The library consists of 184320 clones which stored in 480pieces 384-well plates (20 plates per superpool). A two-step 4-dimension PCR screening system was established to screen the positive clones. An average insert size of 128 kb was estimated from 105 randomly isolated clones, which indicates that the library is more than five times of genomic coverage. For the demonstration of the probability to pick out any unique genes or DNA markers from the library, 10single-copy genes were screened out and the positive clones were yielded between 1 and 8 with an average of 3.6. Positive superpools were obtained for 32 microsatellite markers selected from different regions of pig genome. The number of positive superpools for each marker varies from 1 to 9 with an average of 4.78. This BAC library provides an additional resource for pig physical mapping and gene identification.

  11. THE BLIND STUDENT AND HIS BODY FEELINGS: WAYS OF BEING AND PERCEIVING THE SCHOOL THROUGH TACTILE MAPS DURING PHYSICAL EDUCATION CLASSES

    Directory of Open Access Journals (Sweden)

    Ruy Antônio Wanderley Rodrigues de Miranda

    2016-03-01

    Full Text Available Historically, physical education in Brazil has been coming through a long process for achieving its position in regular schools. Conquering this place is owed to a large set of debates about the most varied pedagogical concepts.  This study aims at analyzing the body feelings of a blind student and phenomenologically describing this student’s perceptions of school spaces when influenced by the use of tactile maps. The study adopted a qualitative approach from a theoretical-methodological perspective of the case study with phenomenological-existential inspiration.  Based on the dialogues in this study, the authors understood that tactile maps, mediated by the student’s body feelings, represented significant importance to boost memorization of school spaces. This allowed more reliable guidance and safer mobility to that blind student and his own challenges of overcoming physical and attitudinal barriers when he needed to move around daily at school and during physical education classes.

  12. Mapping physical properties of Swiss forest soils by robust external-drift kriging from legacy soil data

    Science.gov (United States)

    Papritz, Andreas; Ramirez Lopez, Leo; Baltensweiler, Andri; Walthert, Lorenz

    2015-04-01

    Climate change scenario predict for Switzerland increasing summer temperature and decreasing precipitation. In coming decades forests will therefore likely experience more often drought. However, it is not clear to what extent these changes will occur and where in Switzerland they will be most pronounced. Soil-Vegetation-Atmosphere-Transfer (SVAT) models allow to explore likely changes in the water regime of forest under changing climate. Such process models require information of soil physical properties that largely control water storage in forest soils. Spatial information on physical properties of forest soils is currently lacking in Switzerland. Therefore one objective of the project "Soils and water regime of Swiss forests and forest sites under present and future climate BOWA-CH" (http://www.wsl.ch/fe/boden/projekte/bowa_ch/index_EN) was to predict basic physical properties of forest soils at high spatial resolution for the whole Swiss territory. Based on legacy data of about 2000 forest soil profiles, we mapped particle size composition, volumetric content of rock fragments, soil organic carbon (SOC) content and soil density for fixed-depth soil layers (0-10, 10-30, 30-60, ..., 120-150 cm) by robust external drift kriging (Nussbaum et al., 2014). Comprehensive, digitally available information on climate, topography, vegetation and geology were used as covariates for statistical modelling. Preliminary sets of covariates were chosen by LASSO, and the selection was refined by cross-validating the model for the external drift. External validation with 20 % of the data revealed that clay and sand content, soil density and SOC could be predicted with acceptable precision. Predictions of rock fragment content and silt content were less precise, and the developed model failed to spatially predict soil depth. This is unfortunate because soil depth and rock fragment content largely control water storage in soils. Nussbaum, M., Papritz, A., Baltensweiler, A

  13. PHYSICS

    CERN Multimedia

    Submitted by

    Physics Week: plenary meeting on physics groups plans for startup (14–15 May 2008) The Physics Objects (POG) and Physics Analysis (PAG) Groups presented their latest developments at the plenary meeting during the Physics Week. In the presentations particular attention was given to startup plans and readiness for data-taking. Many results based on the recent cosmic run were shown. A special Workshop on SUSY, described in a separate section, took place the day before the plenary. At the meeting, we had also two special DPG presentations on “Tracker and Muon alignment with CRAFT” (Ernesto Migliore) and “Calorimeter studies with CRAFT” (Chiara Rovelli). We had also a report from Offline (Andrea Rizzi) and Computing (Markus Klute) on the San Diego Workshop, described elsewhere in this bulletin. Tracking group (Boris Mangano). The level of sophistication of the tracking software increased significantly over the last few months: V0 (K0 and Λ) reconstr...

  14. A physical map of 15 loci on human chromosome 5q23-q33 by two-color fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Saltman, D.L.; Dolganov, G.M. (Genelabs Inc. Redwood City, CA (United States)); Warrington, J.A.; Wasmuth, J.J. (Univ. of California, Irvine (United States)); Lovett, M. (Univ. of Texas Southwestern Medical Center, Dallas (United States))

    1993-06-01

    The q23-q33 region of human chromosome 5 encodes a large number of growth factors, growth factor receptors, and hormone/neurotransmitter receptors. This is also the general region into which several disease genes have been mapped, including diastrophic dysplasia, Treacher Collins syndrome, hereditary startle disease, the myeloid disorders that are associated with the 5q-syndrome, autosomal-dominant forms of hereditary deafness, and limb girdle muscular dystrophy. The authors have developed a framework physical map of this region using cosmid clones isolated from the Los Alamos arrayed chromosome 5-specific library. Entry points into this library included 14 probes to genes within this interval and one anonymous polymorphic marker locus. A physical map has been constructed using fluorescence in situ hybridization of these cosmids on metaphase and interphase chromosomes, and this is in good agreement with the radiation hybrid map of the region. The derived order of loci across the region is cen-IL4-IL5-IRF1-IL3-IL9-EGR1-CD14-FGFA-GRL-D5S207-ADRB2-SPARC-RPS14-CSF1R-ADRA1, and the total distance spanned by these loci is approximately 15 Mb. The framework map, genomic clones, and contig expansion within 5q23-q33 should provide valuable resources for the eventual isolation of the clinically relevant loci that reside in this region. 31 refs., 3 figs., 2 tabs.

  15. A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing.

    Science.gov (United States)

    Khorasani, Maryam Zadeh; Hennig, Steffen; Imre, Gabriele; Asakawa, Shuichi; Palczewski, Stefanie; Berger, Anja; Hori, Hiroshi; Naruse, Kiyoshi; Mitani, Hiroshi; Shima, Akihiro; Lehrach, Hans; Wittbrodt, Jochen; Kondoh, Hisato; Shimizu, Nobuyoshi; Himmelbauer, Heinz

    2004-07-01

    In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21,121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization.

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

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, M.P.; Nemeth, A.H.; Campbell, L.; Raut, C.P.; Davies, K.E. (Institute of Molecular Medicine, Oxford (United Kingdom)); Weissenbach, J. (Unite de Genetique Moleculaire Humaine, Paris (France))

    1994-05-15

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

  17. A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

    Directory of Open Access Journals (Sweden)

    Kuhn David N

    2011-08-01

    Full Text Available Abstract Background The fermented dried seeds of Theobroma cacao (cacao tree are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. Results Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105 span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map

  18. PHYSICS

    CERN Multimedia

    D. Futyan

    A lot has transpired on the “Physics” front since the last CMS Bulletin. The summer was filled with preparations of new Monte Carlo samples based on CMSSW_3, the finalization of all the 10 TeV physics analyses [in total 50 analyses were approved] and the preparations for the Physics Week in Bologna. A couple weeks later, the “October Exercise” commenced and ran through an intense two-week period. The Physics Days in October were packed with a number of topics that are relevant to data taking, in a number of “mini-workshops”: the luminosity measurement, the determination of the beam spot and the measurement of the missing transverse energy (MET) were the three main topics.  Physics Week in Bologna The second physics week in 2009 took place in Bologna, Italy, on the week of Sep 7-11. The aim of the week was to review and establish how ready we are to do physics with the early collisions at the LHC. The agenda of the week was thus pac...

  19. PHYSICS

    CERN Multimedia

    D. Futyan

    A lot has transpired on the “Physics” front since the last CMS Bulletin. The summer was filled with preparations of new Monte Carlo samples based on CMSSW_3, the finalization of all the 10 TeV physics analyses [in total 50 analyses were approved] and the preparations for the Physics Week in Bologna. A couple weeks later, the “October Exercise” commenced and ran through an intense two-week period. The Physics Days in October were packed with a number of topics that are relevant to data taking, in a number of “mini-workshops”: the luminosity measurement, the determination of the beam spot and the measurement of the missing transverse energy (MET) were the three main topics.   Physics Week in Bologna The second physics week in 2009 took place in Bologna, Italy, on the week of Sep 7-11. The aim of the week was to review and establish (we hoped) the readiness of CMS to do physics with the early collisions at the LHC. The agenda of the...

  20. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza

    Science.gov (United States)

    The Oryza Map Alignment Project (OMAP) provides the first comprehensive experimental system for understanding the evolution, physiology and biochemistry of a full genus in plants or animals. We have constructed twelve deep-coverage BAC libraries that are representative of both diploid and tetraploid...

  1. [CHL15--a new gene controlling the replication of chromosomes in saccharomycetes yeast: cloning, physical mapping, sequencing, and sequence analysis].

    Science.gov (United States)

    Kuprina, N Iu; Krol', E S; Koriabin, M Iu; Shestopalov, B V; Bliskovskiĭ, V V; Bannikov, V M; Gizatullin, R Z; Kirillov, A V; Kravtsov, V Iu; Zakhar'ev, V M

    1993-01-01

    We have analyzed the CHL15 gene, earlier identified in a screen for yeast mutants with increased loss of chromosome III and artificial circular and linear chromosomes in mitosis. Mutations in the CHL15 gene lead to a 100-fold increase in the rate of chromosome III loss per cell division and a 200-fold increase in the rate of marker homozygosis on this chromosome by mitotic recombination. Analysis of segregation of artificial circular minichromosome and artificially generated nonessential marker chromosome fragment indicated that sister chromatid loss (1:0 segregation) is a main reason of chromosome destabilization in the chl15-1 mutant. A genomic clone of CHL15 was isolated and used to map its physical position on chromosome XVI. Nucleotide sequence analysis of CHL15 revealed a 2.8-kb open reading frame with a 105-kD predicted protein sequence. At the N-terminal region of the protein sequences potentially able to form DNA-binding domains defined as zinc-fingers were found. The C-terminal region of the predicted protein displayed a similarity to sequence of regulatory proteins known as the helix-loop-helix (HLH) proteins. Data on partial deletion analysis suggest that the HLH domain is essential for the function of the CHL15 gene product. Analysis of the upstream untranslated region of CHL15 revealed the presence of the hexamer element, ACGCGT (an MluI restriction site) controlling both the periodic expression and coordinate regulation of the DNA synthesis genes in budding yeast. Deletion in the RAD52 gene, the product of which is involved in double-strand break/recombination repair and replication, leads to a considerable decrease in the growth rate of the chl15 mutant. We suggest that CHL15 is a new DNA synthesis gene in the yeast Saccharomyces cerevisiae.

  2. PHYSICS

    CERN Document Server

    J. Incandela

    The all-plenary format of the CMS week in Cyprus gave the opportunity to the conveners of the physics groups to present the plans of each physics analysis group for tackling early physics analyses. The presentations were complete, so all are encouraged to browse through them on the Web. There is a wealth of information on what is going on, by whom and on what basis and priority. The CMS week was followed by two CMS “physics events”, the ICHEP08 days and the physics days in July. These were two weeks dedicated to either the approval of all the results that would be presented at ICHEP08, or to the review of all the other Monte-Carlo based analyses that were carried out in the context of our preparations for analysis with the early LHC data (the so-called “2008 analyses”). All this was planned in the context of the beginning of a ramp down of these Monte Carlo efforts, in anticipation of data.  The ICHEP days are described below (agenda and talks at: http://indic...

  3. PHYSICS

    CERN Multimedia

    Joe Incandela

    There have been two plenary physics meetings since the December CMS week. The year started with two workshops, one on the measurements of the Standard Model necessary for “discovery physics” as well as one on the Physics Analysis Toolkit (PAT). Meanwhile the tail of the “2007 analyses” is going through the last steps of approval. It is expected that by the end of January all analyses will have converted to using the data from CSA07 – which include the effects of miscalibration and misalignment. January Physics Days The first Physics Days of 2008 took place on January 22-24. The first two days were devoted to comprehensive re¬ports from the Detector Performance Groups (DPG) and Physics Objects Groups (POG) on their planning and readiness for early data-taking followed by approvals of several recent studies. Highlights of POG presentations are included below while the activities of the DPGs are covered elsewhere in this bulletin. January 24th was devo...

  4. Physical and genetic mapping of the CMT4A locus and exclusion of PMP-2 as the defect in CMT4A

    Energy Technology Data Exchange (ETDEWEB)

    Othmane, K.B.; Loeb, D.; Roses, A.D.; Pericak-Vance, M.A.; Vance, J.M. [Duke Univ. Medical Center, Durham, NC (United States)] [and others

    1995-07-20

    We have previously localized one form of the autosomal recessive Charcot-Marie-Tooth disease type 4 (CMT4A) to a 5-cM region of chromosome 8q13-q21. We now report the formation of a 7-Bp YAC contig spanning the region. This contig was used to map nine additional microsatellites and six STSs to this region, and subsequent haplotype analysis has narrowed the CMT4A flanking interval to less than 1 cM. In addition, using SSCP and our physical map, we have demonstrated that the myelin protein PMP-2, mapped by FISH to this region, is not the defect in CMT4A. 27 refs., 3 figs., 1 tab.

  5. Physics

    CERN Document Server

    Cullen, Katherine

    2005-01-01

    Defined as the scientific study of matter and energy, physics explains how all matter behaves. Separated into modern and classical physics, the study attracts both experimental and theoretical physicists. From the discovery of the process of nuclear fission to an explanation of the nature of light, from the theory of special relativity to advancements made in particle physics, this volume profiles 10 pioneers who overcame tremendous odds to make significant breakthroughs in this heavily studied branch of science. Each chapter contains relevant information on the scientist''s childhood, research, discoveries, and lasting contributions to the field and concludes with a chronology and a list of print and Internet references specific to that individual.

  6. Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping.

    Science.gov (United States)

    Książkiewicz, Michał; Zielezinski, Andrzej; Wyrwa, Katarzyna; Szczepaniak, Anna; Rychel, Sandra; Karlowski, Wojciech; Wolko, Bogdan; Naganowska, Barbara

    The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula, Glycine max, Lotus japonicus, Phaseolus vulgaris, and Cajanus cajan) were identified. The comparative mapping of the two largest lupin GRRs provides novel evidence for ancient duplications in all of the studied species. These regions are conserved among representatives of the main clades of Papilionoideae. Furthermore, despite the complex evolution of legumes, some segments of the nuclear genome were not substantially modified and retained their quasi-ancestral structures. Cytogenetic markers anchored in these regions constitute a platform for heterologous mapping of legume genomes.

  7. PHYSICS

    CERN Multimedia

    D. Acosta

    2011-01-01

    Since the last CMS Week, all physics groups have been extremely active on analyses based on the full 2010 dataset, with most aiming for a preliminary measurement in time for the winter conferences. Nearly 50 analyses were approved in a “marathon” of approval meetings during the first two weeks of March, and the total number of approved analyses reached 90. The diversity of topics is very broad, including precision QCD, Top, and electroweak measurements, the first observation of single Top production at the LHC, the first limits on Higgs production at the LHC including the di-tau final state, and comprehensive searches for new physics in a wide range of topologies (so far all with null results unfortunately). Most of the results are based on the full 2010 pp data sample, which corresponds to 36 pb-1 at √s = 7 TeV. This report can only give a few of the highlights of a very rich physics program, which is listed below by physics group...

  8. PHYSICS

    CERN Multimedia

    Chris Hill

    2012-01-01

    The months that have passed since the last CMS Bulletin have been a very busy and exciting time for CMS physics. We have gone from observing the very first 8TeV collisions produced by the LHC to collecting a dataset of the collisions that already exceeds that recorded in all of 2011. All in just a few months! Meanwhile, the analysis of the 2011 dataset and publication of the subsequent results has continued. These results come from all the PAGs in CMS, including searches for the Higgs boson and other new phenomena, that have set the most stringent limits on an ever increasing number of models of physics beyond the Standard Model including dark matter, Supersymmetry, and TeV-scale gravity scenarios, top-quark physics where CMS has overtaken the Tevatron in the precision of some measurements, and bottom-quark physics where CMS made its first discovery of a new particle, the Ξ*0b baryon (candidate event pictured below). Image 2:  A Ξ*0b candidate event At the same time POGs and PAGs...

  9. PHYSICS

    CERN Multimedia

    Guenther Dissertori

    The time period between the last CMS week and this June was one of intense activity with numerous get-together targeted at addressing specific issues on the road to data-taking. The two series of workshops, namely the “En route to discoveries” series and the “Vertical Integration” meetings continued.   The first meeting of the “En route to discoveries” sequence (end 2007) had covered the measurements of the Standard Model signals as necessary prerequisite to any claim of signals beyond the Standard Model. The second meeting took place during the Feb CMS week and concentrated on the commissioning of the Physics Objects, whereas the third occurred during the April Physics Week – and this time the theme was the strategy for key new physics signatures. Both of these workshops are summarized below. The vertical integration meetings also continued, with two DPG-physics get-togethers on jets and missing ET and on electrons and photons. ...

  10. Applying the Intervention Mapping protocol to develop a kindergarten-based, family-involved intervention to increase European preschool children's physical activity levels: the ToyBox-study.

    Science.gov (United States)

    De Craemer, M; De Decker, E; De Bourdeaudhuij, I; Verloigne, M; Duvinage, K; Koletzko, B; Ibrügger, S; Kreichauf, S; Grammatikaki, E; Moreno, L; Iotova, V; Socha, P; Szott, K; Manios, Y; Cardon, G

    2014-08-01

    Although sufficient physical activity is beneficial for preschoolers' health, activity levels in most preschoolers are low. As preschoolers spend a considerable amount of time at home and at kindergarten, interventions should target both environments to increase their activity levels. The aim of the current paper was to describe the six different steps of the Intervention Mapping protocol towards the systematic development and implementation of the physical activity component of the ToyBox-intervention. This intervention is a kindergarten-based, family-involved intervention implemented across six European countries. Based on the results of literature reviews and focus groups with parents/caregivers and kindergarten teachers, matrices of change objectives were created. Then, theory-based methods and practical strategies were selected to develop intervention materials at three different levels: (i) individual level (preschoolers); (ii) interpersonal level (parents/caregivers) and (iii) organizational level (teachers). This resulted in a standardized intervention with room for local and cultural adaptations in each participating country. Although the Intervention Mapping protocol is a time-consuming process, using this systematic approach may lead to an increase in intervention effectiveness. The presented matrices of change objectives are useful for future programme planners to develop and implement an intervention based on the Intervention Mapping protocol to increase physical activity levels in preschoolers.

  11. PHYSICS

    CERN Multimedia

    Darin Acosta

    2010-01-01

    The collisions last year at 900 GeV and 2.36 TeV provided the long anticipated collider data to the CMS physics groups. Quite a lot has been accomplished in a very short time. Although the delivered luminosity was small, CMS was able to publish its first physics paper (with several more in preparation), and commence the commissioning of physics objects for future analyses. Many new performance results have been approved in advance of this CMS Week. One remarkable outcome has been the amazing agreement between out-of-the-box data with simulation at these low energies so early in the commissioning of the experiment. All of this is testament to the hard work and preparation conducted beforehand by many people in CMS. These analyses could not have happened without the dedicated work of the full collaboration on building and commissioning the detector, computing, and software systems combined with the tireless work of many to collect, calibrate and understand the data and our detector. To facilitate the efficien...

  12. PHYSICS

    CERN Multimedia

    D. Acosta

    2010-01-01

    The Physics Groups are actively engaged on analyses of the first data from the LHC at 7 TeV, targeting many results for the ICHEP conference taking place in Paris this summer. The first large batch of physics approvals is scheduled for this CMS Week, to be followed by four more weeks of approvals and analysis updates leading to the start of the conference in July. Several high priority analysis areas were organized into task forces to ensure sufficient coverage from the relevant detector, object, and analysis groups in the preparation of these analyses. Already some results on charged particle correlations and multiplicities in 7 TeV minimum bias collisions have been approved. Only one small detail remains before ICHEP: further integrated luminosity delivered by the LHC! Beyond the Standard Model measurements that can be done with these data, the focus changes to the search for new physics at the TeV scale and for the Higgs boson in the period after ICHEP. Particle Flow The PFT group is focusing on the ...

  13. PHYSICS

    CERN Multimedia

    C. Hill

    2012-01-01

      2012 has started off as a very busy year for the CMS Physics Groups. Planning for the upcoming higher luminosity/higher energy (8 TeV) operation of the LHC and relatively early Rencontres de Moriond are the high-priority activities for the group at the moment. To be ready for the coming 8-TeV data, CMS has made a concerted effort to perform and publish analyses on the 5 fb−1 dataset recorded in 2011. This has resulted in the submission of 16 papers already, including nine on the search for the Higgs boson. In addition, a number of preliminary results on the 2011 dataset have been released to the public. The Exotica and SUSY groups approved several searches for new physics in January, such as searches for W′ and exotic highly ionising particles. These were highlighted at a CERN seminar given on 24th  January. Many more analyses, from all the PAGs, including the newly formed SMP (Standard Model Physics) and FSQ (Forward and Small-x QCD), were approved in February. The ...

  14. PHYSICS

    CERN Multimedia

    L. Demortier

    Physics-wise, the CMS week in December was dominated by discussions of the analyses that will be carried out in the “next six months”, i.e. while waiting for the first LHC collisions.  As presented in December, analysis approvals based on Monte Carlo simulation were re-opened, with the caveat that for this work to be helpful to the goals of CMS, it should be carried out using the new software (CMSSW_2_X) and associated samples.  By the end of the week, the goal for the physics groups was set to be the porting of our physics commissioning methods and plans, as well as the early analyses (based an integrated luminosity in the range 10-100pb-1) into this new software. Since December, the large data samples from CMSSW_2_1 were completed. A big effort by the production group gave a significant number of events over the end-of-year break – but also gave out the first samples with the fast simulation. Meanwhile, as mentioned in December, the arrival of 2_2 meant that ...

  15. PHYSICS

    CERN Multimedia

    the PAG conveners

    2011-01-01

    The delivered LHC integrated luminosity of more than 1 inverse femtobarn by summer and more than 5 by the end of 2011 has been a gold mine for the physics groups. With 2011 data, we have submitted or published 14 papers, 7 others are in collaboration-wide review, and 75 Physics Analysis Summaries have been approved already. They add to the 73 papers already published based on the 2010 and 2009 datasets. Highlights from each physics analysis group are described below. Heavy ions Many important results have been obtained from the first lead-ion collision run in 2010. The published measurements include the first ever indications of Υ excited state suppression (PRL synopsis), long-range correlation in PbPb, and track multiplicity over a wide η range. Preliminary results include the first ever measurement of isolated photons (showing no modification), J/ψ suppression including the separation of the non-prompt component, further study of jet fragmentation, nuclear modification factor...

  16. PHYSICS

    CERN Multimedia

    C. Hill

    2012-01-01

      The period since the last CMS Bulletin has been historic for CMS Physics. The pinnacle of our physics programme was an observation of a new particle – a strong candidate for a Higgs boson – which has captured worldwide interest and made a profound impact on the very field of particle physics. At the time of the discovery announcement on 4 July, 2012, prominent signals were observed in the high-resolution H→γγ and H→ZZ(4l) modes. Corroborating excess was observed in the H→W+W– mode as well. The fermionic channel analyses (H→bb, H→ττ), however, yielded less than the Standard Model (SM) expectation. Collectively, the five channels established the signal with a significance of five standard deviations. With the exception of the diphoton channel, these analyses have all been updated in the last months and several new channels have been added. With improved analyses and more than twice the i...

  17. PHYSICS

    CERN Multimedia

    C. Hill

    2013-01-01

    The period since the last CMS bulletin has seen the end of proton collisions at a centre-of-mass energy 8 TeV, a successful proton-lead collision run at 5 TeV/nucleon, as well as a “reference” proton run at 2.76 TeV. With these final LHC Run 1 datasets in hand, CMS Physics Analysis Groups have been busy analysing these data in preparation for the winter conferences. Moreover, despite the fact that the pp run only concluded in mid-December (and there was consequently less time to complete data analyses), CMS again made a strong showing at the Rencontres de Moriond in La Thuile (EW and QCD) where nearly 40 new results were presented. The highlight of these preliminary results was the eagerly anticipated updated studies of the properties of the Higgs boson discovered in July of last year. Meanwhile, preparations for Run 2 and physics performance studies for Phase 1 and Phase 2 upgrade scenarios are ongoing. The Higgs analysis group produced updated analyses on the full Run 1 dataset (~25 f...

  18. PHYSICS

    CERN Multimedia

    J. D'Hondt

    The Electroweak and Top Quark Workshop (16-17th of July) A Workshop on Electroweak and Top Quark Physics, dedicated on early measurements, took place on 16th-17th July. We had more than 40 presentations at the Workshop, which was an important milestone for 2007 physics analyses in the EWK and TOP areas. The Standard Model has been tested empirically by many previous experiments. Observables which are nowadays known with high precision will play a major role for data-based CMS calibrations. A typical example is the use of the Z to monitor electron and muon reconstruction in di-lepton inclusive samples. Another example is the use of the W mass as a constraint for di-jets in the kinematic fitting of top-quark events, providing information on the jet energy scale. The predictions of the Standard Model, for what concerns proton collisions at the LHC, are accurate to a level that the production of W/Z and top-quark events can be used as a powerful tool to commission our experiment. On the other hand the measure...

  19. PHYSICS

    CERN Multimedia

    C. Hill

    2013-01-01

    In the period since the last CMS Bulletin, the LHC – and CMS – have entered LS1. During this time, CMS Physics Analysis Groups have performed more than 40 new analyses, many of which are based on the complete 8 TeV dataset delivered by the LHC in 2012 (and in some cases on the full Run 1 dataset). These results were shown at, and well received by, several high-profile conferences in the spring of 2013, including the inaugural meeting of the Large Hadron Collider    Physics Conference (LHCP) in Barcelona, and the 26th International Symposium on Lepton Photon Interactions at High Energies (LP) in San Francisco. In parallel, there have been significant developments in preparations for Run 2 of the LHC and on “future physics” studies for both Phase 1 and Phase 2 upgrades of the CMS detector. The Higgs analysis group produced five new results for LHCP including a new H-to-bb search in VBF production (HIG-13-011), ttH with H to γ&ga...

  20. PHYSICS

    CERN Multimedia

    Christopher Hill

    2013-01-01

    Since the last CMS Bulletin, the CMS Physics Analysis Groups have completed more than 70 new analyses, many of which are based on the complete Run 1 dataset. In parallel the Snowmass whitepaper on projected discovery potential of CMS for HL-LHC has been completed, while the ECFA HL-LHC future physics studies has been summarised in a report and nine published benchmark analyses. Run 1 summary studies on b-tag and jet identification, quark-gluon discrimination and boosted topologies have been documented in BTV-13-001 and JME-13-002/005/006, respectively. The new tracking alignment and performance papers are being prepared for submission as well. The Higgs analysis group produced several new results including the search for ttH with H decaying to ZZ, WW, ττ+bb (HIG-13-019/020) where an excess of ~2.5σ is observed in the like-sign di-muon channel, and new searches for high-mass Higgs bosons (HIG-13-022). Search for invisible Higgs decays have also been performed both using the associ...

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Qunfeng Lou

    Full Text Available 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

  3. Use of Genetic and Physical Mapping to Locate the Spinal Muscular Atrophy Locus between Two New Highly Polymorphic DNA Markers

    OpenAIRE

    Clermont, Olivier; Burlet, Philippe; Burglen, Lydie; Lefebvre, Suzie; Pascal, Fabrice; McPherson, John; Wasmuth, John J.; Cohen, Daniel; Le Paslier, Denis; Weissenbach, Jean; Lathrop, Mark; Munnich, Arnold; Melki, Judith

    1994-01-01

    The gene for autosomal recessive forms of spinal muscular atrophy (SMA) has recently been mapped to chromosome 5ql3, within a 4-cM region between the blocks D5S465/D5S125 and MAP-1B/D5S112. We identified two new highly polymorphic microsatellite DNA markers—namely, AFM265wf5 (D5S629) and AFM281yh9 (D5S637)—which are the closest markers to the SMA locus. Multilocus analysis by the location-score method was used to establish the best estimate of the SMA gene location. Our data suggest that the ...

  4. Near-infrared chemical imaging (NIR-CI) on roll compacted ribbons and tablets--multivariate mapping of physical and chemical properties.

    Science.gov (United States)

    Souihi, Nabil; Nilsson, David; Josefson, Mats; Trygg, Johan

    2015-04-10

    Near-infrared chemical imaging (NIR-CI) is an attractive technique within the pharmaceutical industry, where tools are continuously in demand to assess the quality of the intermediate and final products. The present paper demonstrates how NIR-CI in combination with multivariate methods was utilized to spatially map physical properties and content of roll compacted ribbons and tablets. Additionally, extracted textural parameters from tablet images were correlated to the design parameters of the roll compaction process as well as to the physical properties of the granules. The results established the use of NIR-CI as a complementary nondestructive tool to determine the ribbon density and map the density distribution across the width and along the length of the ribbons. For the tablets, the compaction pressure developed during compression increased with the lateral distance from the center. Therefore, NIR-CI can be an effective tool to provide information about the spatial distribution of the compaction pressures on the surface of the tablet. Moreover, low roll compaction roll force correlated to a heterogeneous type of texture in the API chemical image. Overall, texture analysis of the tablets enabled efficient investigation of the spatial variation and could be used to advance process understanding. Finally, orthogonal projections to latent structures (O2PLS) model facilitated the understanding of the interrelationships between textural features, design parameters and physical properties data by separately joint and unique variations.

  5. Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

    Institute of Scientific and Technical Information of China (English)

    WANG Xu-sheng; ZHU Jun; MANSUETO Locedie; BRUSKIEWICH Richard

    2005-01-01

    Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

  6. PHYSICS

    CERN Multimedia

    V.Ciulli

    2011-01-01

    The main programme of the Physics Week held between 16th and 20th May was a series of topology-oriented workshops on di-leptons, di-photons, inclusive W, and all-hadronic final states. The goal of these workshops was to reach a common understanding for the set of objects (ID, cleaning...), the handling of pile-up, calibration, efficiency and purity determination, as well as to revisit critical common issues such as the trigger. Di-lepton workshop Most analysis groups use a di-lepton trigger or a combination of single and di-lepton triggers in 2011. Some groups need to collect leptons with as low PT as possible with strong isolation and identification requirements as for Higgs into WW at low mass, others with intermediate PT values as in Drell-Yan studies, or high PT as in the Exotica group. Electron and muon reconstruction, identification and isolation, was extensively described in the workshop. For electrons, VBTF selection cuts for low PT and HEEP cuts for high PT were discussed, as well as more complex d...

  7. Two-dimensional gas chromatography/mass spectrometry, physical property modeling and automated production of component maps to assess the weathering of pollutants.

    Science.gov (United States)

    Antle, Patrick M; Zeigler, Christian D; Livitz, Dimitri G; Robbat, Albert

    2014-10-17

    Local conditions influence how pollutants will weather in subsurface environments and sediment, and many of the processes that comprise environmental weathering are dependent upon these substances' physical and chemical properties. For example, the effects of dissolution, evaporation, and organic phase partitioning can be related to the aqueous solubility (SW), vapor pressure (VP), and octanol-water partition coefficient (KOW), respectively. This study outlines a novel approach for estimating these physical properties from comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC/MS) retention index-based polyparameter linear free energy relationships (LFERs). Key to robust correlation between GC measurements and physical properties is the accurate and precise generation of retention indices. Our model, which employs isovolatility curves to calculate retention indices, provides improved retention measurement accuracy for families of homologous compounds and leads to better estimates of their physical properties. Results indicate that the physical property estimates produced from this approach have the same error on a logarithmic-linear scale as previous researchers' log-log estimates, yielding a markedly improved model. The model was embedded into a new software program, allowing for automated determination of these properties from a single GC×GC analysis with minimal model training and parameter input. This process produces component maps that can be used to discern the mechanism and progression of how a particular site weathers due to dissolution, organic phase partitioning, and evaporation into the surrounding environment.

  8. The ionized gas in the central region of NGC 5253: 2D mapping of the physical and chemical properties

    CERN Document Server

    Monreal-Ibero, Ana; Vilchez, Jose M

    2012-01-01

    ABRIDGED: NGC5253 was previously studied by our group with the aim to elucidate in detail the starburst interaction processes. Some open issues regarding the 2D structure of the main properties of the ionized gas remain to be addressed. Using IFS data obtained with FLAMES, we derived 2D maps for different tracers of electron density (n_e), electron temperature (T_e) and ionization degree. The maps for n_e as traced by several line ratios are compatible with a 3D stratified view of the nebula with the highest n_e in the innermost layers and a decrease of n_e outwards. To our knowledge, this is the first time that a T_e map based on [SII] lines for an extragalactic object is presented. The joint interpretation of our two T_e maps is consistent with a T_e structure in 3D with higher temperatures close to the main ionizing source surrounded by a colder and more diffuse component. The highest ionization degree is found at the peak of emission for the gas with relatively high ionization in the main GHIIR and lower ...

  9. Genetic and physical mapping of the Chediak-Higashi syndrome on chromosome 1q42-43

    Energy Technology Data Exchange (ETDEWEB)

    Barrat, F.J.; Auloge, L.; Pastural, E. [INSERM, Paris (France)] [and others

    1996-09-01

    The Chediak-Higashi syndrome (CHS) is a severe autosomal recessive condition, features of which are partial oculocutaneous albinism, increased susceptibility to infections, deficient natural killer cell activity, and the presence of large intracytoplasmic granulations in various cell types. Similar genetic disorders have been described in other species, including the beige mouse. On the basis of the hypothesis that the murine chromosome 13 region containing the beige locus was homologous to human chromosome 1, we have mapped the CHS locus to a 5-cM interval in chromosome segment 1q42.1-q42.2. The highest LOD score was obtained with the marker D1S235 (Z{sub max} = 5.38; {theta} = 0). Haplotype analysis enabled us to establish D1S2680 and D1S163, respectively, as the telomeric and the centromeric flanking markers. Multipoint linkage analysis confirms the localization of the CHS locus in this interval. Three YAC clones were found to cover the entire region in a contig established by YAC end-sequence characterization and sequence-tagged site mapping. The YAC contig contains all genetic markers that are nonrecombinant for the disease in the nine CHS families studied. This mapping confirms the previous hypothesis that the same gene defect causes CHS in human and beige phenotype in mice and provides a genetic framework for the identification of candidate genes. 36 refs., 4 figs., 1 tab.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rosier, M.F.; Martin, A.; Houlgatte, R. [Genetique Moleculaire et Biologie du Development, Villejuif (France)] [and others

    1994-11-01

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

  11. Construction and characterization of large-insert genomic libraries (BAC and fosmid) from the Ascidian Botryllus schlosseri and initial physical mapping of a histocompatibility locus.

    Science.gov (United States)

    de Tomaso, Anthony W; Weissman, Irving L

    2003-01-01

    The colonial protochordate Botryllus schlosseri is genetically manipulable and represents a potential model organism for a variety of biological disciplines, including immunology, stem cell biology and development. This article presents the construction and characterization of both BAC and fosmid genomic libraries of the 725-Mbp B. schlosseri genome. The BAC library currently consists of 2x genome coverage with an average insert size of 80 kb. The fosmid library is at 11x genome coverage with an average insert of 40 kb. B. schlosseri is a small organism containing a large number of compounds that hinder DNA purification. Thus a number of protocols had to be modified in order to make purified, high molecular weight inserts for cloning, including both gel purification and insert concentration techniques. Both libraries were characterized by using them in initial physical mapping of a single histocompatibility locus, and were found to be representative and functional. These libraries are important tools for physical mapping and positional cloning in the B. schlosseri genome, and the techniques adapted to make them are suitable for use on other organisms in which high molecular weight DNA is difficult to purify.

  12. Genetic and physical mapping of 2q35 in the region of NRAMP and IL8R genes: Identification of a polymorphic repeat in exon 2 of NRAMP

    Energy Technology Data Exchange (ETDEWEB)

    White, J.K.; Shaw, M.A.; Barton, C.H. [Addenbrooke`s Hospital, Cambridge (United Kingdom)] [and others

    1994-11-15

    Recent interest has focused on the region of conserved synteny between mouse chromosome 1 and human 2q33-q37, particularly over the region encoding the murine macrophage resistance gene Ity/Lsh/Bcg (candidate Nramp) and members of the Il8r interleukin-8 (IL8) receptor gene cluster. In this paper, identification of a restriction fragment length polymorphism in the Il8RB gene in 35 pedigrees previously typed for markers in the 2q33-37 interval provided evidence (lod scores > 3) for linkage between Il8RB and the 2q34-135 markers FN1, TNP1, VIL1, and DES. Physical mapping, using yeast artificial chromosomes isolated with VIL1, confirmed that IL8RA, IL8RB and the IL8RB pseudogene map within the NRAMP-VIL1 interval, with the physical distance (155 kb) from 5{prime} LSH to 3{prime} VIL1 representing {approx}3-fold that observed in the mouse. Partial sequencing of NRAMP confirmed the presence of the N-terminal proline/serine-rich putative SH3 binding domain in exon 2 of the human gene. Further analysis of Brazilian leprosy and visceral leishmaniasis pedigrees identified a rare second allele varying in a 9-nucleotide repeat motif of the exon 2 sequence but segregating independently of the disease phenotype. 38 refs., 4 figs., 3 tabs.

  13. -Deformed nonlinear maps

    Indian Academy of Sciences (India)

    Ramaswamy Jaganathan; Sudeshna Sinha

    2005-03-01

    Motivated by studies on -deformed physical systems related to quantum group structures, and by the elements of Tsallis statistical mechanics, the concept of -deformed nonlinear maps is introduced. As a specific example, a -deformation procedure is applied to the logistic map. Compared to the canonical logistic map, the resulting family of -logistic maps is shown to have a wider spectrum of interesting behaviours, including the co-existence of attractors – a phenomenon rare in one-dimensional maps.

  14. Physical mapping of BK virus DNA with SacI, MboII, and AluI restriction endonucleases.

    Science.gov (United States)

    Yang, R C; Wu, R

    1978-12-01

    A new restriction endonuclease, SacI from Streptomyces achromogenes cleaves BK virus (strain MM) DNA into 3 fragments, whereas MboII from Moraxella bovis and AluI from Arthrobacter luteus give 22 and 30 fragments, respectively. All these specific DNA fragments were ordered and mapped on the viral genome by two methods first, by the reciprocal digestion method using uniformly 32P-labeled DNA; and second, by the partial digestion technique using the single-end 32P-labeled DNA. This study, together with those reported earlier, defined the location of 90 cleavage sites on the BK virus DNA.

  15. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

    Directory of Open Access Journals (Sweden)

    Bharti Arvind K

    2008-12-01

    Full Text Available Abstract Background Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR and methylation spanning linker libraries (MSLL. These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends. Results A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig, while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%. These two techniques were compared with other gene-enrichment methods, and shown to be complementary. Conclusion MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of

  16. Connecting Three Pivotal Concepts in K-12 Science State Standards and Maps of Conceptual Growth to Research in Physics Education

    CERN Document Server

    Singh, Chandralekha

    2016-01-01

    This paper describes three conceptual areas in physics that are particularly important targets for educational interventions in K-12 science. These conceptual areas are force and motion, conservation of energy, and geometrical optics, which were prominent in the US national and four US state standards that we examined. The four US state standards that were analyzed to explore the extent to which the K-12 science standards differ in different states were selected to include states in different geographic regions and of different sizes. The three conceptual areas that were common to all the four state standards are conceptual building blocks for other science concepts covered in the K-12 curriculum. Since these three areas have been found to be ripe with deep student misconceptions that are resilient to conventional physics instruction, the nature of difficulties in these areas is described in some depth, along with pointers towards approaches that have met with some success in each conceptual area.

  17. Preduction of Vehicle Mobility on Large-Scale Soft-Soil Terrain Maps Using Physics-Based Simulation

    Science.gov (United States)

    2016-08-02

    Approved for public release; distribution is unlimited. (#28138) Physics- Based Soil Models • Finite element models – Advantages • Element size can be...function used to evaluate (interpolate) each particle properties and fluxes using neighboring particles. – Advantages • Can easily account for large...mechanics governing equations. – Advantages • Can easily account for large material deformation, flow, and separation/reattachment. – Disadvantages

  18. Map of infiltration of the Paraíba do Sul basin using physical elements and precipitation

    Directory of Open Access Journals (Sweden)

    George de Paula Bernardes

    2008-04-01

    Full Text Available This paper presents a methodological approach to characterize the infiltrations conditions of a portion of Paraiba do Sul river basin (7,600 km2 using Geographic Information Systems tools. To each landscape feature (rock, structure, relief, soil, and land-use and to the spatial distribution of precipitation, an infiltration potential scale factor that ranges from higher influence (5 to lower influence (1 was applied considering its geographical position. The results showed that higher infiltration capacity areas are located in Serra da Bocaina associated to Serra do Mar relief in the Northeast region and Southeast region as well associated to gentle hills and sandstones along the Paraíba do Sul river. The creation of an Infiltration Map may contribute to the development of long-term territorial plans and water resource management plans in order to support future implementation of non-structural and structural measures at both regional and local scales.

  19. Mapping and modeling the urban landscape in Bangkok, Thailand: Physical-spectral-spatial relations of population-environmental interactions

    Science.gov (United States)

    Shao, Yang

    This research focuses on the application of remote sensing, geographic information systems, statistical modeling, and spatial analysis to examine the dynamics of urban land cover, urban structure, and population-environment interactions in Bangkok, Thailand, with an emphasis on rural-to-urban migration from rural Nang Rong District, Northeast Thailand to the primate city of Bangkok. The dissertation consists of four main sections: (1) development of remote sensing image classification and change-detection methods for characterizing imperviousness for Bangkok, Thailand from 1993-2002; (2) development of 3-D urban mapping methods, using high spatial resolution IKONOS satellite images, to assess high-rises and other urban structures; (3) assessment of urban spatial structure from 2-D and 3-D perspectives; and (4) an analysis of the spatial clustering of migrants from Nang Rong District in Bangkok and the neighborhood environments of migrants' locations. Techniques are developed to improve the accuracy of the neural network classification approach for the analysis of remote sensing data, with an emphasis on the spectral unmixing problem. The 3-D building heights are derived using the shadow information on the high-resolution IKONOS image. The results from the 2-D and 3-D mapping are further examined to assess urban structure and urban feature identification. This research contributes to image processing of remotely-sensed images and urban studies. The rural-urban migration process and migrants' settlement patterns are examined using spatial statistics, GIS, and remote sensing perspectives. The results show that migrants' spatial clustering in urban space is associated with the source village and a number of socio-demographic variables. In addition, the migrants' neighborhood environments in urban setting are modeled using a set of geographic and socio-demographic variables, and the results are scale-dependent.

  20. Characterization and mapping of surface physical properties of Mars from CRISM multi-angular data: application to Gusev Crater and Meridiani Planum

    CERN Document Server

    Fernando, J; Pilorget, C; Pinet, P; Ceamanos, X; Douté, S; Daydou, Y; Costard, F

    2014-01-01

    The analysis of the surface texture from the particle (grain size, shape and internal structure) to its organization (surface roughness) provides information on the geological processes. CRISM multi-angular observations (varied emission angles) allow to characterize the surface scattering behavior which depends on the composition but also the material physical properties (e.g., grain size, shape, internal structure, the surface roughness). After an atmospheric correction by the Multi-angle Approach for Retrieval of the Surface Reflectance from CRISM Observations, the surface reflectances at different geometries are analyzed by inverting the Hapke photometric model depending on the single scattering albedo, the 2-term phase function, the macroscopic roughness and the 2-term opposition effects. Surface photometric maps are created to observe the spatial variations of surface scattering properties as a function of geological units at the CRISM spatial resolution (200m/pixel). An application at the Mars Explorati...

  1. Fructose-1,6-bisphosphatase: Genetic and physical mapping to human chromosome 9q22.3 and evaluation in non-insulin-dependent diabetes mellitus

    Energy Technology Data Exchange (ETDEWEB)

    Rothschild, C.B.; Akots, G.; Roh, B. [Wake Forest Univ., Winston-Salem, NC (United States)] [and others

    1995-09-01

    PCR primers specific to the human liver fructose-1,6-bisphosphatase (FBP) gene were designed and used to isolate a cosmid clone. Physical mapping of the FBP cosmid by FISH, and genetic mapping of an associated GA repeat polymorphism (PIC = 0.35), located the liver FBP gene to chromosome 9q22.3 with no recombination between FBP and the index markers D9S196 (Z{sub max} = 13.2), D9S280 (Z{sub max} = 11.7), D9S287 (Z{sub max} = 15.6), and D9S176 (Z{sub max} = 14.4). Amplification using FBP exon-specific primers with a YAC contig from this region of chromosome 9 further refined the placement of FBP genomic sequences to an approximately 1.7-cM region flanked by D9S280 and D9S287, near the gene for Fanconi anemia group C. Precise localization of the FBP gene enabled evaluation of FBP as a candidate gene for maturity-onset diabetes of the young (MODY) and non-insulin-dependent diabetes (NIDDM) in both Caucasian and African-American families, using the highly informative markers D9S287 and D9S176. Although FBP is a rate-limiting enzyme in gluconeogenesis, using both parametric and nonparametric analysis there was no evidence for linkage of FBP to diabetes in these families. 30 refs., 4 figs., 2 tabs.

  2. Physical Mapping of Amplified Copies of the 5-Enolpyruvylshikimate-3-Phosphate Synthase Gene in Glyphosate-Resistant Amaranthus tuberculatus1[OPEN

    Science.gov (United States)

    Dillon, Andrew; Varanasi, Vijay K.; Koo, Dal-Hoe; Nakka, Sridevi; Peterson, Dallas E.; Friebe, Bernd

    2017-01-01

    Recent and rapid evolution of resistance to glyphosate, the most widely used herbicides, in several weed species, including common waterhemp (Amaranthus tuberculatus), poses a serious threat to sustained crop production. We report that glyphosate resistance in A. tuberculatus was due to amplification of the 5-enolpyruvylshikimate-3-P synthase (EPSPS) gene, which encodes the molecular target of glyphosate. There was a positive correlation between EPSPS gene copies and its transcript expression. We analyzed the distribution of EPSPS copies in the genome of A. tuberculatus using fluorescence in situ hybridization on mitotic metaphase chromosomes and interphase nuclei. Fluorescence in situ hybridization analysis mapped the EPSPS gene to pericentromeric regions of two homologous chromosomes in glyphosate sensitive A. tuberculatus. In glyphosate-resistant plants, a cluster of EPSPS genes on the pericentromeric region on one pair of homologous chromosomes was detected. Intriguingly, two highly glyphosate-resistant plants harbored an additional chromosome with several EPSPS copies besides the native chromosome pair with EPSPS copies. These results suggest that the initial event of EPSPS gene duplication may have occurred because of unequal recombination mediated by repetitive DNA. Subsequently, gene amplification may have resulted via several other mechanisms, such as chromosomal rearrangements, deletion/insertion, transposon-mediated dispersion, or possibly by interspecific hybridization. This report illustrates the physical mapping of amplified EPSPS copies in A. tuberculatus. PMID:27956489

  3. Physical mapping of the restriction fragments obtained from bacteriophage T4 dC-DNA with the restriction endonucleases SmaI, KpnI and BglII.

    Science.gov (United States)

    Kiko, H; Niggemann, E; Rüger, W

    1979-01-01

    The cytosine-containing DNA of a mutant of bacteriophage T4 was digested with restriction endonucleases SmaI, KpnI and BglII producing 5, 7 and 13 fragments respectively. Complete physical maps of the T4 genome were constructed with the enzymes SmaI and KpnI and an almost complete map with the enzyme BglII.

  4. Physical mapping of 18S and 5S genes in pelagic species of the genera Caranx and Carangoides (Carangidae).

    Science.gov (United States)

    Jacobina, U P; Bertollo, L A C; Bello Cioffi, M; Molina, W F

    2014-11-14

    In Carangidae, Caranx is taxonomically controversial because of slight morphological differences among species, as well as because of its relationship with the genus Carangoides. Cytogenetic data has contributed to taxonomic and phylogenetic classification for some groups of fish. In this study, we examined the chromosomes of Caranx latus, Caranx lugubris, and Carangoides bartholomaei using classical methods, including conventional staining, C-banding, silver staining for nuclear organizer regions, base-specific fluorochrome, and 18S and 5S ribosomal sequence mapping using in situ hybridization. These 3 species showed chromosome numbers of 2n = 48, simple nuclear organizer regions (pair 1), and mainly centromeric heterochomatin. However, C. latus (NF = 50) and C. bartholomaei (NF = 50) showed a structurally conserved karyotype compared with C. lugubris (NF = 54), with a larger number of 2-armed chromosomes. The richness of GC-positive heterochromatic segments and sites in 5S rDNA in specific locations compared to the other 2 species reinforce the higher evolutionary dynamism in C. lugubris. Cytogenetic aspects shared between C. latus and C. bartholomaei confirm the remarkable phylogenetic proximity between these genera.

  5. Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum race 3 in cowpea [Vigna unguiculata (L.) Walp].

    Science.gov (United States)

    Pottorff, Marti; Wanamaker, Steve; Ma, Yaqin Q; Ehlers, Jeffrey D; Roberts, Philip A; Close, Timothy J

    2012-01-01

    Fusarium oxysporum f.sp. tracheiphilum (Fot) is a soil-borne fungal pathogen that causes vascular wilt disease in cowpea. Fot race 3 is one of the major pathogens affecting cowpea production in California. Identification of Fot race 3 resistance determinants will expedite delivery of improved cultivars by replacing time-consuming phenotypic screening with selection based on perfect markers, thereby generating successful cultivars in a shorter time period. Resistance to Fot race 3 was studied in the RIL population California Blackeye 27 (resistant) x 24-125B-1 (susceptible). Biparental mapping identified a Fot race 3 resistance locus, Fot3-1, which spanned 3.56 cM on linkage group one of the CB27 x 24-125B-1 genetic map. A marker-trait association narrowed the resistance locus to a 1.2 cM region and identified SNP marker 1_1107 as co-segregating with Fot3-1 resistance. Macro and microsynteny was observed for the Fot3-1 locus region in Glycine max where six disease resistance genes were observed in the two syntenic regions of soybean chromosomes 9 and 15. Fot3-1 was identified on the cowpea physical map on BAC clone CH093L18, spanning approximately 208,868 bp on BAC contig250. The Fot3-1 locus was narrowed to 0.5 cM distance on the cowpea genetic map linkage group 6, flanked by SNP markers 1_0860 and 1_1107. BAC clone CH093L18 was sequenced and four cowpea sequences with similarity to leucine-rich repeat serine/threonine protein kinases were identified and are cowpea candidate genes for the Fot3-1 locus. This study has shown how readily candidate genes can be identified for simply inherited agronomic traits when appropriate genetic stocks and integrated genomic resources are available. High co-linearity between cowpea and soybean genomes illustrated that utilizing synteny can transfer knowledge from a reference legume to legumes with less complete genomic resources. Identification of Fot race 3 resistance genes will enable transfer into high yielding cowpea varieties

  6. Characterization and physical mapping of 18S and 5S ribosomal genes in Indian major carps (Pisces, Cyprinidae).

    Science.gov (United States)

    Ravindra Kumar; Kushwaha, Basdeo; Nagpure, Naresh S

    2013-06-01

    Characterization of the major (18S) and minor (5S) ribosomal RNA genes were carried out in three commercially important Indian major carp (IMC) species, viz. Catla catla, Labeo rohita and Cirrhinus mrigala along with their physical localizations using dual colour fluorescence in situ hybridization. The diploid chromosome number in the above carps was confirmed to be 50 with inter-species karyo-morphological variations. The 18S rDNA signals were observed on 3 pair of chromosomes in C. catla and L. rohita, and two pairs in C. mrigala. The 5S rDNA signal was found on single pair of chromosome in all the species with variation in their position on chromosomes. The sequencing of 18S rDNA generated 1804, 1805 and 1805 bp long fragments, respectively, in C. catla, L. rohita and C. mrigala with more than 98% sequence identity among them. Similarly, sequencing of 5S rDNA generated 191 bp long fragments in the three species with 100% identity in coding region and 23.2% overall variability in non-transcribed spacer region. Thus, these molecular markers could be used as species-specific markers for taxonomic identification and might help in understanding the genetic diversity, genome organization and karyotype evolution of these species.

  7. Karyotype analysis and physical mapping of 45S rDNA in eight species of Sophora,Robinia,and Amorpha

    Institute of Scientific and Technical Information of China (English)

    LIU Bo; CHEN Chengbin; LI Xiulan; QI Liwang; HAN Suying

    2006-01-01

    The karyotype analysis and physical locations of 45S rDNA were carried out by means of fluorescence in situ hybridization in three species,and two forms of Sophora,two species of Robina,and one species of Amorpha.S.japonica L.,S.japonica L.f.oligophylla Franch.,S.japonica L.f.pendula Loud.,and S.xanthantha C.Y.Ma.are all tetraploids with 2n=28.There were four 45S rDNA sites in pericentromeric regions of two Pairs of chromosomes in each of them.S.rubriflora Tsoong.is a triploid with 2n=21,and three sites were located in each satellite of group 5 chromosomes.In R.pseudoacacia L.(2n=2x=22),we examined four intensive signals in telomeric regions of two pairs of satellite chromosomes.In R.hispida L.(2n=2x=30),there were four other signals in centromeric regions besides those like in R.pseudoacacia.Amorpha fruticosa L.has most chromosomes(2n=40)among the eight materials,however,there were only six 45S rDNA loci and they laid in centromeric regions,and satellites of three pairs of chromosomes.45S rDNA is a valuable chromosomal landmark in karyotype analysis.The distribution and genomic organization Of rDNA in the three genera were also discussed.

  8. HST/STIS observations of the RW Aurigae bipolar jet: mapping the physical parameters close to the source

    CERN Document Server

    Melnikov, Stanislav; Bacciotti, Francesca; Woitas, Jens; Ray, Thomas P

    2009-01-01

    We present the results of new spectral diagnostic investigations applied to high-resolution long-slit spectra of the RW Aur bipolar jet obtained with HST/STIS. The spectra include the forbidden doublets [O I] 6300,6363 \\AA, [S II] 6716,6731 \\AA, and [N II] 6548, 6583 \\AA that we utilized to determine electron density, electron temperature, hydrogen ionisation fraction, total hydrogen density, radial velocity and the mass outflow rate. We were able to extract the parameters as far as 3".9 in the red- and 2".1 in the blueshifted beam. The RW Aur jet appears to be the second densest outflow from a T Tauri star studied so far, but its other properties are quite similar to those found in other jets from young stars. The overall trend of the physical parameters along the first few arcseconds of the RW Aur jet is similar to that of HH 30 and DG Tau and this can reflect analogies in the mechanisms operating in that region, suggesting the same engine is accelerating the jets in the T Tauri stars with outflows. Our stu...

  9. Genetic and physical mapping of the Treacher Collins syndrome locus with respect to loci in the chromosome 5q3 region

    Energy Technology Data Exchange (ETDEWEB)

    Jabs, E.W.; Li, Xiang; Coss, C.; Taylor, E. (Johns Hopkins School of Medicine, Baltimore, MD (United States)); Lovett, M. (Univ. of Texas Southwestern Medical Center, San Antonio, TX (United States)); Yamaoka, L.H.; Speer, M.C. (Duke Univ. Medical Center, Durham, NC (United States)); Cadle, R.; Hall, B. (Univ. of Kentucky, Lexington, KY (United States)); Brown, K. (Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY (United States)) (and others)

    1993-10-01

    Treacher Collins syndrome is an autosomal dominant, craniofacial developmental disorder, and its locus (TCOF1) has been mapped to chromosome 5q3. To refine the location of the gene within this region, linkage analysis was performed among the TCOF1 locus and 12 loci (IL9, FGFA, GRL, D5S207, D5S210, D5S376, CSF1R, SPARC, D5S119, D5S209, D5S527, FGFR4) in 13 Treacher Collins syndrome families. The highest maximum lod score was obtained between loci TCOF1 and D5S210 (Z = 10.52; [theta] = 0.02 [+-] 0.07). The best order, IL9-GRL-D5S207/D5S210-CSF1R-SPARC-D5S119, and genetic distances among these loci were determined in the 40 CEPH families by multipoint linkage analysis. YAC clones were used to establish the order of loci, centromere-5[prime]GRL3[prime]-D5S207-D5S210-D5S376-CSF1R-SPARC-D5S119-telomere. By combining known physical mapping data with ours, the order of chromosome 5q3 markers is centomere-IL9-FGFA-5[prime]GRL3[prime]-D5s207-D5S210-D5S376-CSF1R-SPARC-D5S119-D5S209-FGFR4-telomere. Based on this order, haplotype analysis suggests that the TCOF1 locus resides distal CSF1R and proximal to SPARC within a region less than 1 Mb in size. 29 refs., 2 figs., 2 tabs.

  10. Physical mapping of the split hand/split foot (SHSF) locus on chromosome 7 reveals a relationship between SHSF and the syndromic ectrodactylies

    Energy Technology Data Exchange (ETDEWEB)

    Poorkaj, P.; Nunes, M.E.; Geshuri, D. [Univ. of Washington, Seattle, WA (United States)] [and others

    1994-09-01

    Split hand/split foot (also knows as ectrodactyly) is a human developmental malformation characterized by missing digits and claw-like extremities. An autosomal dominant form of this disorder has been mapped to 7q21.3-q22.1 on the basis of SHSF-associated chromosomal rearrangements: this locus has been designated SHFD1. We have constructed a physical map of the SHFD1 region that consists of contiguous yeast artificial chromosome clones and spans approximately 8 Mb. Somatic cell hybrid and fluorescent in situ hybridization analyses were used to define SHSF-associated chromosomal breakpoints in fourteen patients. A critical interval of about 1 Mb was established for SHFD1 by analysis of six patients with deletions. Translocation and inversion breakpoints in seven other patients were found to localize within a 500-700 kb interval within the critical region. Several candidate genes including DLX5 and DLX6 (members of the Drosophilia Distal-less homeobox-containing gene family) localize to this region. At least four of these genes are expressed in the developing mouse limb bud. Of particular interest is the observation that 8 of the 14 patients studied have syndromic ectrodactyly, which is characterized by the association of SHSF with a variety of other anomalies including cleft lip/palate, ectodermal dysplasia, and renal anomalies. Thus, these data implicate a single gene or cluster of genes at the SHFD1 locus in a wide range of developmental processes and serve to establish a molecular genetic relationship between simple SHSF and a broad group of human birth defects.

  11. HST/STIS observations of the RW Aurigae bipolar jet: mapping the physical parameters close to the source

    Science.gov (United States)

    Melnikov, S. Yu; Eislöffel, J.; Bacciotti, F.; Woitas, J.; Ray, T. P.

    2009-11-01

    Context: We present the results of new spectral diagnostic investigations applied to high-resolution long-slit spectra obtained with the Hubble Space Telescope Imaging Spectrograph (HST/STIS) of the jet from the T Tauri star RW Aur. Aims: Our primary goal is to determine basic physical parameters (electron density ne and electron temperature Te, hydrogen ionisation fraction xe, total hydrogen density nH, radial velocity vr and the mass outflow rate dot Mj) along both the red- and blueshifted lobes of the RW Aur jet. Methods: The input dataset consists of seven long-slit spectra, of 0.1 arcsec spatial resolution, taken with the STIS slit parallel to the jet, and stepped across it. We use the Bacciotti & Eislöffel (1999, A&A, 342, 717) method to analyse the forbidden doublets [O I]λλ6300,6363, [S II]λλ 6716,6731, and [N II]λλ 6548,6583 Å to extract n_e, T_e, x_e, and n_H. Results: We were able to extract the parameters as far as 3.9 arcsec in the red- and 2.1 arcsec in the blueshifted beam. The electron density at the base of both lobes is close to the critical density for [S II] emission but then it decreases gradually with distance from the source. The range of electron temperatures derived for this jet (Te = 10^4-2×104 K) is similar to those generally found in other outflows from young stars. The ionisation fraction xe varies between 0.04 and 0.4, increasing within the first few arcseconds and then decreasing in both lobes. The total hydrogen density, derived as nH = ne / x_e, is on average 3.2×104 cm-3 and shows a gradual decrease along the beam. Variations of the above quantities along the jet lobes appear to be correlated with the position of knots. Combining the derived parameters with vr measured from the HST spectra and other characteristics available for this jet, we estimate dot Mj following two different procedures. The mass-outflow rate dot Mj is moderate and similar in the two lobes, despite the fact that the well-known asymmetry in the radial

  12. Leaf morphology in Cowpea [Vigna unguiculata (L. Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species

    Directory of Open Access Journals (Sweden)

    Pottorff Marti

    2012-06-01

    Full Text Available Abstract Background Cowpea [Vigna unguiculata (L. Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. Results Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape x Vita 7 (hastate leaf shape. A QTL for leaf shape, Hls (hastate leaf shape, was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82 in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89 in a field experiment. The corresponding Hls locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the Hls region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic Hls region in Medicago truncatula and Glycine max. One syntenic locus for Hls was identified on Medicago chromosome 7 while syntenic regions for Hls were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1 gene was observed and is the candidate gene for the Hls locus. The Hls locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25. Conclusions This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in

  13. Development of a pooled probe method for locating small gene families in a physical map of soybean using stress related paralogues and a BAC minimum tile path

    Directory of Open Access Journals (Sweden)

    Shultz Jeffry L

    2006-12-01

    Full Text Available Abstract Background Genome analysis of soybean (Glycine max L. has been complicated by its paleo-autopolyploid nature and conserved homeologous regions. Landmarks of expressed sequence tags (ESTs located within a minimum tile path (MTP of contiguous (contig bacterial artificial chromosome (BAC clones or radiation hybrid set can identify stress and defense related gene rich regions in the genome. A physical map of about 2,800 contigs and MTPs of 8,064 BAC clones encompass the soybean genome. That genome is being sequenced by whole genome shotgun methods so that reliable estimates of gene family size and gene locations will provide a useful tool for finishing. The aims here were to develop methods to anchor plant defense- and stress-related gene paralogues on the MTP derived from the soybean physical map, to identify gene rich regions and to correlate those with QTL for disease resistance. Results The probes included 143 ESTs from a root library selected by subtractive hybridization from a multiply disease resistant soybean cultivar 'Forrest' 14 days after inoculation with Fusarium solani f. sp. glycines (F. virguliforme. Another 166 probes were chosen from a root EST library (Gm-r1021 prepared from a non-inoculated soybean cultivar 'Williams 82' based on their homology to the known defense and stress related genes. Twelve and thirteen pooled EST probes were hybridized to high-density colony arrays of MTP BAC clones from the cv. 'Forrest' genome. The EST pools located 613 paralogues for 201 of the 309 probes used (range 1–13 per functional probe. One hundred BAC clones contained more than one kind of paralogue. Many more BACs (246 contained a single paralogue of one of the 201 probes detectable gene families. ESTs were anchored on soybean linkage groups A1, B1, C2, E, D1a+Q, G, I, M, H, and O. Conclusion Estimates of gene family sizes were more similar to those made by Southern hybridization than by bioinformatics inferences from EST collections

  14. High-resolution meiotic and physical mapping of the Best`s vitelliform macular dystrophy (VMD2) locus to pericentromeric chromosome 11

    Energy Technology Data Exchange (ETDEWEB)

    Weber, B.H.F.; Vogt, G. [Institut fuer Humangenetik, Wuerzburg (Germany); Walker, D. [UBC, Vancouver (Canada)] [and others

    1994-09-01

    Vitelliform macular dystrophy, also known as Best`s disease, is a juvenile-onset macular degeneration with autosomal dominant inheritance. It is characterized by well-demarcated accumulation of lipofuscin-like material within and beneath the retinal pigment epithelium (RPE) and classically results in an egg yolk-like appearance of the macula. Typically, carriers of the disease gene show a specific electrophysiological sign which can be detected by electrooculography (EOG). The EOG measures a standing potential between the cornea and the retina which is primarily generated by the RPE. The histopathological findings as well as the EOG abnormalities suggest that Best`s disease is a generalized disorder of the RPE. The basic biochemical defect is still unknown. As a first step in the positional cloning of the defective gene, the Best`s disease locus was mapped to chromosome 11 between markers at D11S871 and INT2. Subsequently, his region was refined to a 3.7 cM interval flanked by loci D11S903 and PYGM. To further narrow the D11S903-PYGM interval and to obtain an estimate of the physical size of the minimal candidate region, we used a combination of high-resolution PCR hybrid mapping and analysis of recombinant Best`s disease chromosomes. We identified six markers from within the D11S903-PYGM interval that show no recombination with the defective gene in three multigeneration Best`s disease pedigrees. Our hybrid panel localizes these markers on either side of the centromere on chromosome 11. The closest markers flanking the disease gene are at D11S986 in band p12-11.22 and at D11S480 in band q13.2-13.3. Our study demonstrates that the physical size of the Best`s disease region is exceedingly larger than was previously estimated from the genetic data due to the proximity of the defective gene to the centromere of chromosome 11.

  15. The Galactic Census of High- and Medium-mass Protostars. III. 12CO Maps and Physical Properties of Dense Clump Envelopes and Their Embedding GMCs

    Science.gov (United States)

    Barnes, Peter J.; Hernandez, Audra K.; O'Dougherty, Stefan N.; Schap, William J., III; Muller, Erik

    2016-11-01

    We report the second complete molecular line data release from the Census of High- and Medium-mass Protostars (CHaMP), a large-scale, unbiased, uniform mapping survey at sub-parsec resolution, of millimeter-wave line emission from 303 massive, dense molecular clumps in the Milky Way. This release is for all 12CO J = 1 \\to 0 emission associated with the dense gas, the first from Phase II of the survey, which includes 12CO, 13CO, and C18O. The observed clump emission traced by both 12CO and HCO+ (from Phase I) shows very similar morphology, indicating that, for dense molecular clouds and complexes of all sizes, parsec-scale clumps contain Ξ ˜ 75% of the mass, while only 25% of the mass lies in extended (≳10 pc) or “low density” components in these same areas. The mass fraction of all gas above a density of 109 m-3 is {ξ }9 ≳ 50%. This suggests that parsec-scale clumps may be the basic building blocks of the molecular interstellar medium, rather than the standard GMC concept. Using 12CO emission, we derive physical properties of these clumps in their entirety, and compare them to properties from HCO+, tracing their denser interiors. We compare the standard X-factor converting {I}{12{CO}} to {N}{{{H}}2} with alternative conversions, and show that only the latter give whole-clump properties that are physically consistent with those of their interiors. We infer that the clump population is systematically closer to virial equilibrium than when considering only their interiors, with perhaps half being long-lived (10s of Myr), pressure-confined entities that only terminally engage in vigorous massive star formation, supporting other evidence along these lines that was previously published.

  16. An Ammonia Spectral Map of the L1495-B218 Filaments in the Taurus Molecular Cloud : I. Physical Properties of Filaments and Dense cores

    CERN Document Server

    Seo, Young Min; Goldsmith, Paul; Ward-Thompson, Derek; Kirk, Jason M; Schmalzl, Markus; Lee, Jeong-Eun; Friesen, Rachel; Langston, Glen; Masters, Joe; Garwood, Robert W

    2015-01-01

    We present deep NH$_3$ observations of the L1495-B218 filaments in the Taurus molecular cloud covering over a 3 degree angular range using the K-band focal plane array on the 100m Green Bank Telescope. The L1495-B218 filaments form an interconnected, nearby, large complex extending over 8 pc. We observed NH$_3$ (1,1) and (2,2) with a spectral resolution of 0.038 km/s and a spatial resolution of 31$"$. Most of the ammonia peaks coincide with intensity peaks in dust continuum maps at 350 $\\mu$m and 500 $\\mu$m. We deduced physical properties by fitting a model to the observed spectra. We find gas kinetic temperatures of 8 $-$ 15 K, velocity dispersions of 0.05 $-$ 0.25 km/s, and NH$_3$ column densities of 5$\\times$10$^{12}$ $-$ 1$\\times$10$^{14}$ cm$^{-2}$. The CSAR algorithm, which is a hybrid of seeded-watershed and binary dendrogram algorithms, identifies a total of 55 NH$_3$ structures including 39 leaves and 16 branches. The masses of the NH$_3$ sources range from 0.05 M$_\\odot$ to 9.5 M$_\\odot$. The masses...

  17. A regression approach to the mapping of bio-physical characteristics of surface sediment using in situ and airborne hyperspectral acquisitions

    Science.gov (United States)

    Ibrahim, Elsy; Kim, Wonkook; Crawford, Melba; Monbaliu, Jaak

    2017-01-01

    Remote sensing has been successfully utilized to distinguish and quantify sediment properties in the intertidal environment. Classification approaches of imagery are popular and powerful yet can lead to site- and case-specific results. Such specificity creates challenges for temporal studies. Thus, this paper investigates the use of regression models to quantify sediment properties instead of classifying them. Two regression approaches, namely multiple regression (MR) and support vector regression (SVR), are used in this study for the retrieval of bio-physical variables of intertidal surface sediment of the IJzermonding, a Belgian nature reserve. In the regression analysis, mud content, chlorophyll a concentration, organic matter content, and soil moisture are estimated using radiometric variables of two airborne sensors, namely airborne hyperspectral sensor (AHS) and airborne prism experiment (APEX) and and using field hyperspectral acquisitions by analytical spectral device (ASD). The performance of the two regression approaches is best for the estimation of moisture content. SVR attains the highest accuracy without feature reduction while MR achieves good results when feature reduction is carried out. Sediment property maps are successfully obtained using the models and hyperspectral imagery where SVR used with all bands achieves the best performance. The study also involves the extraction of weights identifying the contribution of each band of the images in the quantification of each sediment property when MR and principal component analysis are used.

  18. A regression approach to the mapping of bio-physical characteristics of surface sediment using in situ and airborne hyperspectral acquisitions

    Science.gov (United States)

    Ibrahim, Elsy; Kim, Wonkook; Crawford, Melba; Monbaliu, Jaak

    2017-02-01

    Remote sensing has been successfully utilized to distinguish and quantify sediment properties in the intertidal environment. Classification approaches of imagery are popular and powerful yet can lead to site- and case-specific results. Such specificity creates challenges for temporal studies. Thus, this paper investigates the use of regression models to quantify sediment properties instead of classifying them. Two regression approaches, namely multiple regression (MR) and support vector regression (SVR), are used in this study for the retrieval of bio-physical variables of intertidal surface sediment of the IJzermonding, a Belgian nature reserve. In the regression analysis, mud content, chlorophyll a concentration, organic matter content, and soil moisture are estimated using radiometric variables of two airborne sensors, namely airborne hyperspectral sensor (AHS) and airborne prism experiment (APEX) and and using field hyperspectral acquisitions by analytical spectral device (ASD). The performance of the two regression approaches is best for the estimation of moisture content. SVR attains the highest accuracy without feature reduction while MR achieves good results when feature reduction is carried out. Sediment property maps are successfully obtained using the models and hyperspectral imagery where SVR used with all bands achieves the best performance. The study also involves the extraction of weights identifying the contribution of each band of the images in the quantification of each sediment property when MR and principal component analysis are used.

  19. 新课程理念下一种可能的评价方法--物理概念图%A Possible Evaluation Method under the Concept of the New Curriculum:Physical Concept Map

    Institute of Scientific and Technical Information of China (English)

    韩娟

    2013-01-01

    The paper introduces the basic structure and its theo-retical source of the physical concept map. The paper then re-searches the application of the physical concept maps form the aspects of physical evaluation methods and structure, and points out some issues which need to be discussed in the application.%本文介绍了物理概念图的基本结构及其理论来源,着重从评价方法及结构方面探讨了物理概念图的应用,并指出了其在应用中有待探讨的问题。

  20. Invariants for Parallel Mapping

    Institute of Scientific and Technical Information of China (English)

    YIN Yajun; WU Jiye; FAN Qinshan; HUANG Kezhi

    2009-01-01

    This paper analyzes the geometric quantities that remain unchanged during parallel mapping (i.e., mapping from a reference curved surface to a parallel surface with identical normal direction). The second gradient operator, the second class of integral theorems, the Gauss-curvature-based integral theorems, and the core property of parallel mapping are used to derive a series of parallel mapping invadants or geometri-cally conserved quantities. These include not only local mapping invadants but also global mapping invari-ants found to exist both in a curved surface and along curves on the curved surface. The parallel mapping invadants are used to identify important transformations between the reference surface and parallel surfaces. These mapping invadants and transformations have potential applications in geometry, physics, biome-chanics, and mechanics in which various dynamic processes occur along or between parallel surfaces.

  1. 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

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, S.C.; Bocskai, D.; Cao, Y. [and others

    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.

  2. Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

    Directory of Open Access Journals (Sweden)

    Shultz Jeffry

    2008-07-01

    Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

  3. On palaeogeographic map

    Directory of Open Access Journals (Sweden)

    Zeng-Zhao Feng

    2016-01-01

    Full Text Available The palaeogeographic map is a graphic representation of physical geographical characteristics in geological history periods and human history periods. It is the most important result of palaeogeographic study. The author, as the Editor-in-Chief of Journal of Palaeogeography, Chinese Edition and English Edition, aimed at the problems of the articles submitted to and published in the Journal of Palaeogeography in recent years and the relevant papers and books of others, and integrated with his practice of palaeogeographic study and mapping, wrote this paper. The content mainly includes the data of palaeogeographic mapping, the problems of palaeogeographic mapping method, the “Single factor analysis and multifactor comprehensive mapping method —— Methodology of quantitative lithofacies palaeogeography”, i.e., the “4 steps mapping method”, the nomenclature of each palaeogeographic unit in palaeogeographic map, the explanation of each palaeogeographic unit in palaeogeographic map, the explanation of significance of palaeogeographic map and palaeogeographic article, the evaluative standards of palaeogeographic map and palaeogeographic article, and the self-evaluation. Criticisms and corrections are welcome.

  4. Physical mapping of the herpes simplex virus type 2 nuc- lesion affecting alkaline exonuclease activity by using herpes simplex virus type 1 deletion clones.

    Science.gov (United States)

    Wathen, M W; Hay, J

    1984-07-01

    The nuc- lesion affecting alkaline exonuclease activity in the herpes simplex virus type 2 (HSV-2) mutant ts1348 had previously been mapped to the EcoRI-D restriction enzyme fragment of HSV-1. Eight clones with deletions representing most of HSV-1 EcoRI fragment D were selected with lambda gtWES hybrids. These clones were tested for their ability to rescue the alkaline exonuclease activity of HSV-2 nuc- ts1348 virus. The sequences colinear with the HSV-2 nuc- lesion were found to map between 0.169 and 0.174 map units on the HSV-1 Patton genome, representing an 0.8-kilobase-pair region that is 12.9 to 13.7 kilobase pairs from the left end of HSV-1 EcoRI fragment D.

  5. 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.)

    Science.gov (United States)

    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...

  6. Physical and linkage mapping of the human and murine genes for the [alpha]1 chain of type IX collagen (COL9A1)

    Energy Technology Data Exchange (ETDEWEB)

    Warman, M.L. (Harvard Medical School, Boston, MA (United States) Children' s Hospital/Harvard Medical School, Boston, MA (United States)); Tiller, G.E.; Polumbo, P.A. (Vanderbilt Univ. Medical Center, Nashville, TN (United States)); Seldin, M.F.; Rochelle, J.M. (Duke Univ. Medical Center, Durham, NC (United States)); Knoll, J.H.M.; Cheng, Sou De (Children' s Hospital/Harvard Medical School, Boston, MA (United States)); Olsen, B.R. (Harvard Medical School, Boston, MA (United States))

    1993-09-01

    The IX collagen, a member of the FACIT family of extracellular matrix proteins, is a heterotrimer composed of three genetically distinct [alpha] chains. The cDNAs for the human and mouse [alpha]1(IX) chains have been cloned. In this paper the authors confirm the mapping of the human COL9A1 gene to chromosome 6q12-q13 by fluorescence in situ hybridization utilizing two genomic clones which also contain short tandem repeat polymorphisms. They also report the characterization of these repeats and their incorporation into the chromosome 6 linkage map. The COL9A1 locus shows no recombination with the marker D6Z1 (Z = 27.61 at [theta] = 0) and identifies the most likely locus order of KRAS1P-[D6Z1-COL9A1]-D6S30. In addition, using an interspecific backcross panel, they have mapped murine Col9a1 to mouse chromosome 1. Together with other comparative mapping results, these data suggest that the pericentric region of human chromosome 6 is homologous to the most proximal segment of mouse chromosome 1. These data may facilitate linkage studies with COL9A1 (or col9a1) as a candidate gene for hereditary chondrodysplasias and osteoarthritis. 35 refs., 2 figs., 2 tabs.

  7. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer(Triticum dicoccoides)

    Science.gov (United States)

    Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7A...

  8. Genetic Mapping

    Science.gov (United States)

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers create ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human Genome ...

  9. A comparative study of map use

    DEFF Research Database (Denmark)

    Bouvin, Niels Olof; Brodersen, Ann Christina; Bødker, Susanne;

    2006-01-01

    We present a study comparing the handling of three kinds of maps, each on a physical device: a paper map, a tablet-PC based map, and a cellular phone based one. Six groups of users were asked to locate eight landmarks, looking out a window, and using a particular map. We have begun analyzing video...

  10. Concept Maps

    OpenAIRE

    Schwendimann, Beat Adrian

    2014-01-01

    A concept map is a node-link diagram showing the semantic relationships among concepts. The technique for constructing concept maps is called "concept mapping". A concept map consists of nodes, arrows as linking lines, and linking phrases that describe the relationship between nodes. Two nodes connected with a labeled arrow are called a proposition. Concept maps are versatile graphic organizers that can represent many different forms of relationships between concepts. The relationship between...

  11. Composite Genus One Belyi Maps

    CERN Document Server

    Vidunas, Raimundas

    2016-01-01

    Motivated by a demand for explicit genus 1 Belyi maps from physics, we give an efficient method of explicitly computing genus one Belyi maps by (1) composing covering maps from elliptic curves to the Riemann surface with the simpler, univariate, genus zero Belyi maps as well as by (2) composing further with isogenies of the elliptic curve. This gives many new explicit dessins on the doubly periodic plane, including several which have been realized in the physics literature as so-called brane-tilings in the context of quiver gauge theories.

  12. Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation.

    Science.gov (United States)

    Badenhorst, Daleen; Hillier, LaDeana W; Literman, Robert; Montiel, Eugenia Elisabet; Radhakrishnan, Srihari; Shen, Yingjia; Minx, Patrick; Janes, Daniel E; Warren, Wesley C; Edwards, Scott V; Valenzuela, Nicole

    2015-06-24

    Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.

  13. Localization and physical mapping of a plasmid-borne 23-kb nif gene cluster from Enterobacter agglomerans showing homology to the entire nif gene cluster of Klebsiella pneumoniae M5a1.

    Science.gov (United States)

    Singh, M; Kreutzer, R; Acker, G; Klingmüller, W

    1988-01-01

    A physical and genetical map of the plasmid pEA3 indigenous to Enterobacter agglomerans is presented. pEA3 is a 111-kb large plasmid containing a 23-kb large cluster of nif genes which shows extensive homology (Southern hybridization and heteroduplex analysis) to the entire nif gene cluster of Klebsiella pneumoniae (Kp) M5a1. All the nif genes on pEA3 are organized in the same manner as in K. pneumoniae, except nifJ, which is located on the left end of pEA3 nif gene cluster (near nifQB). A BamHI restriction map of pEA3 and a detailed restriction map of the 23-kb nif region on pEA3 is also presented. The nif genes of pEA3 showed a low level of acetylene reduction in Escherichia coli, demonstrating that these genes are functional and contain the whole genetic information required to fix nitrogen. The origin of vegetative replication (OriV) of pEA3 was localized about 5.5 kb from the right end of the nif gene cluster. In addition to pEA3, large plasmids from four other strains of E. agglomerans showed homology to all the Kp nif genes tested, indicating that in diazotrophic strains of E. agglomerans nif genes are usually located on plasmids. In contrast, in most of the free-living, nitrogen-fixing bacteria the nif genes are on chromosome.

  14. Link maps and map meetings: Scaffolding student learning

    Directory of Open Access Journals (Sweden)

    Christine Lindstrøm

    2009-01-01

    Full Text Available With student numbers decreasing and traditional teaching methods having been found inefficient, it is widely accepted that alternative teaching methods need to be explored in tertiary physics education. In 2006 a different teaching environment was offered to 244 first year students with little or no prior formal instruction in physics. Students were invited to attend additional enrichment classes 1 h a week called map meetings. The focus of these classes was a different type of visual presentation of physics material called link maps. Link maps explicitly show the key concepts covered in lectures and how these interrelate to help novices establish their physics schemata. In each map meeting the link map for the different topic was interactively discussed by the researcher before the students worked on problems in groups using the link map. The class ended with the researcher going through one problem, talking aloud about how to logically attack it. The results were promising. Each week about 20% of the class voluntarily attended map meetings whereas 22% reported that they did not attend due to timetable clashes. Two questionnaires revealed that students thought the classes were helpful for gaining an overview of physics and for developing their problem solving abilities. In the final examination the 32 students who had attended at least eight out of ten map meetings achieved, on average, 9 points out of 90 better in the examination (p=0.004 than a comparison group (N=40 with similar academic background which had not attended map meetings. The results of this study suggest that map meetings are a valuable learning environment for physics novices. Further investigations are currently being undertaken.

  15. Map Projection

    CERN Document Server

    Ghaderpour, Ebrahim

    2014-01-01

    In this paper, we introduce some known map projections from a model of the Earth to a flat sheet of paper or map and derive the plotting equations for these projections. The first fundamental form and the Gaussian fundamental quantities are defined and applied to obtain the plotting equations and distortions in length, shape and size for some of these map projections.

  16. Mapping urban and peri-urban breeding habitats of Aedes mosquitoes using a fuzzy analytical hierarchical process based on climatic and physical parameters.

    Science.gov (United States)

    Sarfraz, Muhammad Shahzad; Tripathi, Nagesh K; Faruque, Fazlay S; Bajwa, Usama Ijaz; Kitamoto, Asanobu; Souris, Marc

    2014-12-01

    The spread of dengue fever depends mainly on the availability of favourable breeding sites for its mosquito vectors around human dwellings. To investigate if the various factors influencing breeding habitats can be mapped from space, dengue indices, such as the container index, the house index and the Breteau index, were calculated from Ministry of Public health data collected three times annually in Phitsanulok, Thailand between 2009 and 2011. The most influential factors were found to be temperature, humidity, rainfall, population density, elevation and land cover. Models were worked out using parameters mostly derived from freely available satellite images and fuzzy logic software with parameter synchronisation and a predication algorithm based on data mining and the Decision Tree method. The models developed were found to be sufficiently flexible to accommodate additional parameters and sampling data that might improve prediction of favourable breeding hotspots. The algorithm applied can not only be used for the prediction of near real-time scenarios with respect to dengue, but can also be applied for monitoring other diseases influenced by environmental and climatic factors. The multi-criteria model presented is a cost-effective way of identifying outbreak hotspots and early warning systems lend themselves for development based on this strategy. The proposed approach demonstrates the successful utilisation of remotely sensed images to map mosquito breeding habitats.

  17. Genetic and physical fine-mapping of the Sc locus conferring indica-japonica hybrid sterility in rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    YANG Cunyi; CHEN Zhongzheng; ZHUANG Chuxiong; MEI Mantong; LIU Yaoguang

    2004-01-01

    Hybrid sterility is a major hindrance to utilizing the heterosis in indica-japonica hybrids. To isolate a gene Sc conferring the hybrid sterility, the locus was mapped using molecular markers and an F2 population derived from a cross between near isogenic lines. A primary linkage analysis showed that Sc was linked closely with 4 markers on chromosome 3, on which the genetic distance between a marker RG227 and Sc was 0.07 cM. Chromosome walking with a rice TAC genomic library was carried out using RG227 as a starting probe, and a contig of ca. 320 kb covering the Sc locus was constructed. Two TAC clones, M45E14 and M90J01 that might cover the Sc locus, were partially sequenced. By searching the rice sequence databases with sequences of the TACs and RG227 a japonica rice BAC sequence, OSJNBb0078P24 was identified. By comparing the TAC and BAC sequences, six new PCR-based markers were developed. With these markers the Sc locus was further mapped to a region of 46 kb. The results suggest that the BAC OSJNBb0078P24 and TAC M45E14 contain the Sc gene. Six ORFs were predicted in the focused 46-kb region.

  18. Stimulation of Ideas through Compound-Based Bibliometrics: Counting and Mapping Chemical Compounds for Analyzing Research Topics in Chemistry, Physics, and Materials Science.

    Science.gov (United States)

    Barth, Andreas; Marx, Werner

    2012-12-01

    Counting compounds (rather than papers or citations) offers a new perspective for quantitative analyses of research activities. First of all, we can precisely define (compound-related) research topics and access the corresponding publications (scientific papers as well as patents) as a measure of research activity. We can also establish the time evolution of the publications dealing with specific compounds or compound classes. Moreover, the mapping of compounds by establishing compound-based landscapes has some potential to visualize the compound basis of research topics for further research activities. We have analyzed the rare earth compounds to give an example of a broad compound class. We present the number of the currently existing compounds and of the corresponding publications as well as the time evolution of the papers and patents. Furthermore, we have analyzed the rare earth cuprates (copper oxides) as an example of a narrower compound class to demonstrate the potential of mapping compounds by compound-based landscapes. We have quantified the various element combinations of the existing compounds and revealed all element combinations not yet realized in the synthesis within this compound class. Finally, we have analyzed the quasicrystal compound category as an example of a compound class that is not defined by a specific element combination or a molecular structure.

  19. Mapping urban and peri-urban breeding habitats of Aedes mosquitoes using a fuzzy analytical hierarchical process based on climatic and physical parameters

    Directory of Open Access Journals (Sweden)

    Muhammad Shahzad Sarfraz

    2014-12-01

    Full Text Available The spread of dengue fever depends mainly on the availability of favourable breeding sites for its mosquito vectors around human dwellings. To investigate if the various factors influencing breeding habitats can be mapped from space, dengue indices, such as the container index, the house index and the Breteau index, were calculated from Ministry of Public health data collected three times annually in Phitsanulok, Thailand between 2009 and 2011. The most influential factors were found to be temperature, humidity, rainfall, population density, elevation and land cover. Models were worked out using parameters mostly derived from freely available satellite images and fuzzy logic software with parameter synchronisation and a predication algorithm based on data mining and the Decision Tree method. The models developed were found to be sufficiently flexible to accommodate additional parameters and sampling data that might improve prediction of favourable breeding hotspots. The algorithm applied can not only be used for the prediction of near real-time scenarios with respect to dengue, but can also be applied for monitoring other diseases influenced by environmental and climatic factors. The multi-criteria model presented is a cost-effective way of identifying outbreak hotspots and early warning systems lend themselves for development based on this strategy. The proposed approach demonstrates the successful utilisation of remotely sensed images to map mosquito breeding habitats.

  20. Physical map of polyoma viral DNA fragments produced by cleavage with a restriction enzyme from Haemophilus aegyptius, endonuclease R-HaeIII.

    Science.gov (United States)

    Summers, J

    1975-04-01

    Digestion of polyoma viral DNA with a restriction enzyme from Haemophilus aegyptius generates at least 22 unique fragments. The fragments have been characterized with respect to size and physical order on the polyoma genome, and the 5' to 3' orientation of the (+) and (-) strands has been determined. A method for specific radiolabeling of adjacent fragments was employed to establish the fragment order. This technique may be useful for ordering the fragments produced by digestion of complex DNAs.

  1. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

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

    Directory of Open Access Journals (Sweden)

    Kahn Tomas

    2003-03-01

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

  3. Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping

    Directory of Open Access Journals (Sweden)

    Souza Manoel T

    2008-01-01

    Full Text Available Abstract Background Many commercial banana varieties lack sources of resistance to pests and diseases, as a consequence of sterility and narrow genetic background. Fertile wild relatives, by contrast, possess greater variability and represent potential sources of disease resistance genes (R-genes. The largest known family of plant R-genes encode proteins with nucleotide-binding site (NBS and C-terminal leucine-rich repeat (LRR domains. Conserved motifs in such genes in diverse plant species offer a means for isolation of candidate genes in banana which may be involved in plant defence. Results A computational strategy was developed for unbiased conserved motif discovery in NBS and LRR domains in R-genes and homologues in monocotyledonous plant species. Degenerate PCR primers targeting conserved motifs were tested on the wild cultivar Musa acuminata subsp. burmannicoides, var. Calcutta 4, which is resistant to a number of fungal pathogens and nematodes. One hundred and seventy four resistance gene analogs (RGAs were amplified and assembled into 52 contiguous sequences. Motifs present were typical of the non-TIR NBS-LRR RGA subfamily. A phylogenetic analysis of deduced amino-acid sequences for 33 RGAs with contiguous open reading frames (ORFs, together with RGAs from Arabidopsis thaliana and Oryza sativa, grouped most Musa RGAs within monocotyledon-specific clades. RFLP-RGA markers were developed, with 12 displaying distinct polymorphisms in parentals and F1 progeny of a diploid M. acuminata mapping population. Eighty eight BAC clones were identified in M. acuminata Calcutta 4, M. acuminata Grande Naine, and M. balbisiana Pisang Klutuk Wulung BAC libraries when hybridized to two RGA probes. Multiple copy RGAs were common within BAC clones, potentially representing variation reservoirs for evolution of new R-gene specificities. Conclusion This is the first large scale analysis of NBS-LRR RGAs in M. acuminata Calcutta 4. Contig sequences were

  4. The Galactic Census of High- and Medium-mass Protostars. III $^{12}$CO Maps and Physical Properties of Dense Clump Envelopes and their Embedding GMCs

    CERN Document Server

    Barnes, Peter J; O'Dougherty, Stefan N; Schap, William J; Muller, Erik

    2016-01-01

    We report the second complete molecular line data release from the {\\em Census of High- and Medium-mass Protostars} (CHaMP), a large-scale, unbiased, uniform mapping survey at sub-parsec resolution, of mm-wave line emission from 303 massive, dense molecular clumps in the Milky Way. This release is for all $^{12}$CO $J$=1$\\rightarrow$0 emission associated with the dense gas, the first from Phase II of the survey, which includes $^{12}$CO, $^{13}$CO, and C$^{18}$O. The observed clump emission traced by both $^{12}$CO and HCO$^+$ (from Phase I) shows very similar morphology, indicating that, for dense molecular clouds and complexes of all sizes, parsec-scale clumps contain $\\Xi$ ~ 75% of the mass, while only 25% of the mass lies in extended (>~ 10 pc) or "low density" components in these same areas. The mass fraction of all gas above a density 10$^9$ m$^{-3}$ is $\\xi_9$ >~ 50%. This suggests that parsec-scale clumps may be the basic building blocks of the molecular ISM, rather than the standard GMC concept. Usin...

  5. Mapping Deeply

    OpenAIRE

    Denis Wood

    2015-01-01

    This is a description of an avant la lettre deep mapping project carried out by a geographer and a number of landscape architecture students in the early 1980s. Although humanists seem to take the “mapping” in deep mapping more metaphorically than cartographically, in this neighborhood mapping project, the mapmaking was taken literally, with the goal of producing an atlas of the neighborhood. In this, the neighborhood was construed as a transformer, turning the stuff of the world (gas, wate...

  6. Collection Mapping.

    Science.gov (United States)

    Harbour, Denise

    2002-01-01

    Explains collection mapping for library media collections. Discusses purposes for creating collection maps, including helping with selection and weeding decisions, showing how the collection supports the curriculum, and making budget decisions; and methods of data collection, including evaluating a collaboratively taught unit with the classroom…

  7. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    of environmental knowledge production. It uses InfoAmazonia, the databased platform on Amazon rainforests, as an example of affective geo-visualization within information mapping that enhances embodiment in the experience of the information. Amazonia is defined as a digitally created affective (map)space within...

  8. Causal mapping

    DEFF Research Database (Denmark)

    Rasmussen, Lauge Baungaard

    2006-01-01

    The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method......The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method...

  9. CALS Mapping

    DEFF Research Database (Denmark)

    Collin, Ib; Nielsen, Povl Holm; Larsen, Michael Holm

    1998-01-01

    To enhance the industrial applications of CALS, CALS Center Danmark has developed a cost efficient and transparent assessment, CALS Mapping, to uncover the potential of CALS - primarily dedicated to small and medium sized enterprises. The idea behind CALS Mapping is that the CALS State...... enterprise is, when applied in a given organisation modified with respect to the industry regarded, hence irrelevant measure parameters are eliminated to avoid redundancy. This assessment of CALS Mapping, quantify the CALS potential of an organisation with the purpose of providing decision support to the top...

  10. Mapping VADEMECUM

    OpenAIRE

    1992-01-01

    The work plan for the implementation of the Convention on Long-Range Transboundary Air Pollution under the UN Economic Commission for Europe (UN ECE) includes the production of maps of critical loads, critical levels, and exceedances as a basis for developing potential abatement strategies for sulphur and nitrogen. This Vademecum is designed to provide guidance to those responsible for calculating and mapping critical loads, critical levels, and exceedances on a national or regional scale. Th...

  11. Linking Mind-maps and Digital Maps with Hypertext

    OpenAIRE

    Klust, Jakub

    2013-01-01

    Information management is an important personal skill, therefore a concept allowing a better information management extended by a digital map was developed in this thesis. It focuses on two independent spaces. The first space is called abstract and handles information in form of spatial diagrams particularly mind-maps consisting of keywords and relations forming for instance a complex structures of ideas. The second space called physical aims to organize information on basis of assigned geogr...

  12. Efficient construction of a physical map by Fiber-FISH of the CLN5 region: Refined assignment and long-range contig covering the critical region on 13q22

    Energy Technology Data Exchange (ETDEWEB)

    Klockars, T.; Savukoski, M.; Isosomppi, J. [National Public Health Institute, Helsinki (Finland)] [and others

    1996-07-01

    The variant form of late infantile neuronal ceroid lipofuscinosis (vLINCL, locus definition CLN5) represents a progressive brain disease with autosomal recessive inheritance. We have previously assigned the CLN5 locus to chromosome 13q21.1-132 between markers D13S160 and D13S162 by linkage analysis in Finnish families. The information on ancient recombination events obtained from linkage disequilibrium provided an efficient tool for further refining the assignment of the CLN5 locus. Isolation of two novel (CA){sub n} markers, COLAC1 and AC224, resulted in a dramatic restriction of the critical DNA region. We utilized the Fiber-FISH technique to orient and order the large DNA clones isolated by STSs and were able to eliminate almost totally the restriction digestion and PFGE step in the construction of the long-range DNA contig. Both linkage disequilibrium data and Fiber-FISH analyses assigned the CLN5 locus to a well-defined 200-kb region. Here we report a complete physical map of about 350 kb covering the critical chromosomal region of CLN5, which will facilitate the final isolation of the CLN5 gene. 31 refs., 4 figs., 2 tabs.

  13. Mapping Deeply

    Directory of Open Access Journals (Sweden)

    Denis Wood

    2015-08-01

    Full Text Available This is a description of an avant la lettre deep mapping project carried out by a geographer and a number of landscape architecture students in the early 1980s. Although humanists seem to take the “mapping” in deep mapping more metaphorically than cartographically, in this neighborhood mapping project, the mapmaking was taken literally, with the goal of producing an atlas of the neighborhood. In this, the neighborhood was construed as a transformer, turning the stuff of the world (gas, water, electricity into the stuff of individual lives (sidewalk graffiti, wind chimes, barking dogs, and vice versa. Maps in the central transformer section of the atlas were to have charted this process in action, as in one showing the route of an individual newspaper into the neighborhood, then through the neighborhood to a home, and finally, as trash, out of the neighborhood in a garbage truck; though few of these had been completed when the project concluded in 1986. Resurrected in 1998 in an episode on Ira Glass’ This American Life, the atlas was finally published, as Everything Sings: Maps for a Narrative Atlas, in 2010 (and an expanded edition in 2013.

  14. Conformal Mapping for Multiple Terminals

    CERN Document Server

    Wang, Weimin; Wang, Qiang; Ren, Hao

    2015-01-01

    Conformal mapping is an important mathematical tool in many physical and engineering fields, especially in electrostatics, fluid mechanics, classical mechanics, and transformation optics. However in the existing textbooks and literatures, it is only adopted to solve the problems which have only two terminals. Two terminals with electric potential differences, pressure difference, optical path difference, etc., can be mapped conformally onto a solvable structure, e.g., a rectangle, where the two terminals are mapped onto two opposite edges of the rectangle. Here we show a conformal mapping method for multiple terminals, which is more common in practical applications. Through accurate analysis of the boundary conditions, additional terminals or boundaries are folded in the inner of the mapped rectangle. Then the solution will not be influenced. The method is described in several typical situations and two application examples are detailed. The first example is an electrostatic actuator with three electrodes. A ...

  15. Cognitive maps

    DEFF Research Database (Denmark)

    Minder, Bettina; Laursen, Linda Nhu; Lassen, Astrid Heidemann

    2014-01-01

    . Conceptual clustering is used to analyse and order information according to concepts or variables from within the data. The cognitive maps identified are validated through the comments of some of the same experts. The study presents three cognitive maps and respective world-views explaining how the design...... and innovation field are related and under which dimensions they differ. The paper draws preliminary conclusions on the implications of the different world- views on the innovation process. With the growing importance of the design approach in innovation e.g. design thinking, a clear conception...

  16. Mole Mapping.

    Science.gov (United States)

    Crippen, Kent J.; Curtright, Robert D.; Brooks, David W.

    2000-01-01

    The abstract nature of the mole and its applications to problem solving make learning the concept difficult for students, and teaching the concept challenging for teachers. Presents activities that use concept maps and graphing calculators as tools for solving mole problems. (ASK)

  17. Projective mapping

    DEFF Research Database (Denmark)

    Dehlholm, Christian; Brockhoff, Per B.; Bredie, Wender Laurentius Petrus

    2012-01-01

    Projective Mapping (Risvik et.al., 1994) and its Napping (Pagès, 2003) variations have become increasingly popular in the sensory field for rapid collection of spontaneous product perceptions. It has been applied in variations which sometimes are caused by the purpose of the analysis and sometime...

  18. Participatory maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    looks at computer-assisted cartography as part of environmental knowledge production. It uses InfoAmazonia, the databased platform on Amazon rainforests, as an example of affective geo-visualization within information mapping that enhances embodiment in the experience of the information. Amazonia...

  19. Covariance mapping techniques

    Science.gov (United States)

    Frasinski, Leszek J.

    2016-08-01

    Recent technological advances in the generation of intense femtosecond pulses have made covariance mapping an attractive analytical technique. The laser pulses available are so intense that often thousands of ionisation and Coulomb explosion events will occur within each pulse. To understand the physics of these processes the photoelectrons and photoions need to be correlated, and covariance mapping is well suited for operating at the high counting rates of these laser sources. Partial covariance is particularly useful in experiments with x-ray free electron lasers, because it is capable of suppressing pulse fluctuation effects. A variety of covariance mapping methods is described: simple, partial (single- and multi-parameter), sliced, contingent and multi-dimensional. The relationship to coincidence techniques is discussed. Covariance mapping has been used in many areas of science and technology: inner-shell excitation and Auger decay, multiphoton and multielectron ionisation, time-of-flight and angle-resolved spectrometry, infrared spectroscopy, nuclear magnetic resonance imaging, stimulated Raman scattering, directional gamma ray sensing, welding diagnostics and brain connectivity studies (connectomics). This review gives practical advice for implementing the technique and interpreting the results, including its limitations and instrumental constraints. It also summarises recent theoretical studies, highlights unsolved problems and outlines a personal view on the most promising research directions.

  20. Physical mapping of three fruit ripening genes:Endopolygalacturonase,ACC oxidase and ACC synthase from apple(Malus x domestica) in an apple rootstock A106(Malus sieboldii

    Institute of Scientific and Technical Information of China (English)

    ZHUJIMEI; SEGARDINER; 等

    1995-01-01

    The apple rootstock,A106(Malus sieboldii),had 17 bivalents in pollen mother cells at meiotic metaphase 1,and 17 chromosomes in a haploid pollen cell.Karyotypes were prepared from root-tip cells with 2n=34 chromosomes,Seven out of 82 karyotypes(8.5%) showed one pari of satellites at the end of the short arm of chromosome 3.C-bands were shown on 6 pairs of chromosomes 2,4,6,8,14,and 16 near the telomeric regions of short arms.Probes for three ripening-related genes from Malus x domestica:endopolygalacturonase(EPG,0.6kb),ACC oxidase(1.2kb),and ACC synthase(2kb)were hybridized in situ to metaphase chromosomes of A106.Hybridization sites for the EPG gene were observed on the long arm of chromosome 14 in 15 out of 16 replicate spreads and proximal to the centromere of chromosomes 6 and 11.For the ACC oxidase gene,hylridization sites were observed in the telomeric region of the short arm of chromosomes 5 and 11 in 87% and 81% of 16 spreads respectively,proxiaml to the centromere of chromosome 1 in 81% of the spreads,and on the long arm of chromosome 13 in 50% of the spreads. Physical mapping of three fruit ripening genes in an apple rootstock A106.Twenty five spreads were studied for the ACC synthase gene and hybridization sites were observed in the telomeric region of the short arm of chromosome 12 in 96% of the spreads.chromosomes 9 and 10 in 76% of the spreads,and chromosome 17 in 56% of the spreads.

  1. MAPPING INNOVATION

    DEFF Research Database (Denmark)

    Thuesen, Christian Langhoff; Koch, Christian

    2011-01-01

    By adopting a theoretical framework from strategic niche management research (SNM) this paper presents an analysis of the innovation system of the Danish Construction industry. The analysis shows a multifaceted landscape of innovation around an existing regime, built around existing ways of working...... and developed over generations. The regime is challenged from various niches and the socio-technical landscape through trends as globalization. Three niches (Lean Construction, BIM and System Deliveries) are subject to a detailed analysis showing partly incompatible rationales and various degrees of innovation...... potential. The paper further discusses how existing policymaking operates in a number of tensions one being between government and governance. Based on the concepts from SNM the paper introduces an innovation map in order to support the development of meta-governance policymaking. By mapping some...

  2. Mapping filmmaking

    DEFF Research Database (Denmark)

    Gilje, Øystein; Frølunde, Lisbeth; Lindstrand, Fredrik

    2010-01-01

    This chapter concerns mapping patterns in regards to how young filmmakers (age 15 – 20) in the Scandinavian countries learn about filmmaking. To uncover the patterns, we present portraits of four young filmmakers who participated in the Scandinavian research project Making a filmmaker. The focus ...... is on their learning practices and how they create ‘learning paths’ in relation to resources in diverse learning contexts, whether formal, non-formal and informal contexts.......This chapter concerns mapping patterns in regards to how young filmmakers (age 15 – 20) in the Scandinavian countries learn about filmmaking. To uncover the patterns, we present portraits of four young filmmakers who participated in the Scandinavian research project Making a filmmaker. The focus...

  3. Hierarchical Reverberation Mapping

    OpenAIRE

    Brendon J. Brewer; Elliott, Tom M.

    2013-01-01

    Reverberation mapping (RM) is an important technique in studies of active galactic nuclei (AGN). The key idea of RM is to measure the time lag $\\tau$ between variations in the continuum emission from the accretion disc and subsequent response of the broad line region (BLR). The measurement of $\\tau$ is typically used to estimate the physical size of the BLR and is combined with other measurements to estimate the black hole mass $M_{\\rm BH}$. A major difficulty with RM campaigns is the large a...

  4. Electrophoretic High Molecular Weight DNA Purification Enables Optical Mapping

    OpenAIRE

    Maydan, Jason; THOMAS, Matthew; Tabanfar, Leyla; Mai, Laura; Poon, Hau-Ling; Pe, Joel; HAHN, KRISTEN; Goji, Noriko; Amoako, Kingsley; Marziali, Andre; Hanson, Dan

    2013-01-01

    Optical mapping generates an ordered restriction map from single, long DNA molecules. By overlapping restriction maps from multiple molecules, a physical map of entire chromosomes and genomes is constructed, greatly facilitating genome assembly in next generation sequencing projects, comparative genomics and strain typing. However, optical mapping relies on a method of preparing high quality DNA >250 kb in length, which can be challenging from some organisms and sample types. Here we demonstr...

  5. Characterization and solvability of quasipolynomial symplectic mappings

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Bermejo, Benito [ESCET (Edificio Departamental II), Universidad Rey Juan Carlos, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain); Brenig, Leon [Service de Physique Theorique et Mathematique, Universite Libre de Bruxelles, Campus Plaine, CP 231, Boulevard du Triomphe, B-1050 Brussels (Belgium)

    2004-02-13

    Quasipolynomial (or QP) mappings constitute a wide generalization of the well-known Lotka-Volterra mappings, of importance in different fields such as population dynamics, physics, chemistry or economy. In addition, QP mappings are a natural discrete-time analogue of the continuous QP systems, which have been extensively used in different pure and applied domains. After presenting the basic definitions and properties of QP mappings in a previous paper, the purpose of this work is to focus on their characterization by considering the existence of symplectic QP mappings. In what follows such QP symplectic maps are completely characterized. Moreover, use of the QP formalism can be made in order to demonstrate that all QP symplectic mappings have an analytical solution that is explicitly and generally constructed. Examples are given.

  6. [Cytogenetic maps and their applications in plants].

    Science.gov (United States)

    Xiong, Huai-Yang; Zhao, Li-Juan; Li, Li-Jia

    2005-07-01

    Integrated cytogenetic maps encompass the information from both genetic maps and cytological maps. It is possible for cytogenetic maps to simultaneously report the cytological and genetic position of a maker. To constructure cytogenetic maps it is necessary to relate the markers mapped across linkage groups to cytological position on chromosomes. Cytogenetic maps have been constructured primarily in two ways. The first general strategy is to utilize the chromosome breakpoints to determine the location of genetically mapped markers on the chromosomes. A second way is by the direct hybridization of genetically mapped sequences onto chromosomes by FISH. In addition, a novel approach is to use RN-cM maps to predict the physical position of genetic markers on the chromosomes. Cytogenetic maps suggest that both the density of genes and the frequency of recombination increase towards the distal regions of chromosome arms, and they play significant roles in revealing gene colinearity between two species, exploring the evolution relationship between both of them and in map-based gene isolation.

  7. Mapping of

    Directory of Open Access Journals (Sweden)

    Sayed M. Arafat

    2014-06-01

    Full Text Available Land cover map of North Sinai was produced based on the FAO-Land Cover Classification System (LCCS of 2004. The standard FAO classification scheme provides a standardized system of classification that can be used to analyze spatial and temporal land cover variability in the study area. This approach also has the advantage of facilitating the integration of Sinai land cover mapping products to be included with the regional and global land cover datasets. The total study area is covering a total area of 20,310.4 km2 (203,104 hectare. The landscape classification was based on SPOT4 data acquired in 2011 using combined multispectral bands of 20 m spatial resolution. Geographic Information System (GIS was used to manipulate the attributed layers of classification in order to reach the maximum possible accuracy. GIS was also used to include all necessary information. The identified vegetative land cover classes of the study area are irrigated herbaceous crops, irrigated tree crops and rain fed tree crops. The non-vegetated land covers in the study area include bare rock, bare soils (stony, very stony and salt crusts, loose and shifting sands and sand dunes. The water bodies were classified as artificial perennial water bodies (fish ponds and irrigated canals and natural perennial water bodies as lakes (standing. The artificial surfaces include linear and non-linear features.

  8. The History Of Genome Mapping In Fragaria Spp.

    Directory of Open Access Journals (Sweden)

    Mohamed Abdel-Rahman Moustafa Abdel-Wahab

    2014-12-01

    Full Text Available This overview summarizes the research programs devoted to mapping the genomes within Fragaria genus. A few genetic linkage maps of diploid and octoploid Fragaria species as well as impressive physical map of F. vesca were developed in the last decade and resulted in the collection of data useful for further fundamental and applied studies. The information concerning the rules for proper preparation of mapping population, the choice of markers useful for generating linkage map, the saturation of existing maps with new markers linked to economically important traits, as well as problems faced during mapping process are presented in this paper.

  9. Mapping Resilience

    DEFF Research Database (Denmark)

    Carruth, Susan

    2015-01-01

    Resilience theory is a growing discipline with great relevance for the discipline of planning, particularly in fields like energy planning that face great uncertainty and rapidly transforming contexts. Building on the work of the Stockholm Resilience Centre, this paper begins by outlining...... the relationship between resilience and energy planning, suggesting that planning in, and with, time is a core necessity in this domain. It then reviews four examples of graphically mapping with time, highlighting some of the key challenges, before tentatively proposing a graphical language to be employed...... by planners when aiming to construct resilient energy plans. It concludes that a graphical language has the potential to be a significant tool, flexibly facilitating cross-disciplinary communication and decision-making, while emphasising that its role is to support imaginative, resilient planning rather than...

  10. A PiggyBac-based recessive screening method to identify pluripotency regulators.

    Directory of Open Access Journals (Sweden)

    Ge Guo

    Full Text Available Phenotype driven genetic screens allow unbiased exploration of the genome to discover new biological regulators. Bloom syndrome gene (Blm deficient embryonic stem (ES cells provide an opportunity for recessive screening due to frequent loss of heterozygosity. We describe a strategy for isolating regulators of mammalian pluripotency based on conversion to homozygosity of PiggyBac gene trap insertions combined with stringent selection for differentiation resistance. From a screen of 2000 mutants we obtained a disruptive integration in the Tcf3 gene. Homozygous Tcf3 mutants showed impaired differentiation and enhanced self-renewal. This phenotype was reverted in a dosage sensitive manner by excision of one or both copies of the gene trap. These results provide new evidence confirming that Tcf3 is a potent negative regulator of pluripotency and validate a forward screening methodology to identify modulators of pluripotent stem cell biology.

  11. Human Mind Maps

    Science.gov (United States)

    Glass, Tom

    2016-01-01

    When students generate mind maps, or concept maps, the maps are usually on paper, computer screens, or a blackboard. Human Mind Maps require few resources and little preparation. The main requirements are space where students can move around and a little creativity and imagination. Mind maps can be used for a variety of purposes, and Human Mind…

  12. An STS-based map of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Hudson, T.J.; Stein, L.D.; Gerety, S.S. [and others

    1995-12-22

    A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid map of the human genome containing 5264 loci. This information was combined with the results of STS-content screening of 10,850 loci against a yeast artificial chromosome library to produce an integrated map, anchored by the radiation hybrid and genetic maps. The map provides radiation hybrid coverage of 99 percent and physical coverage of 94 percent of the human genome. The map also represents an early step in an international project to generate a transcript map of the human genome, with more than 3235 expressed sequences localized. The STSs in the map provide a scaffold for initiating large-scale sequencing of the human genome.

  13. Completely positive maps with memory

    CERN Document Server

    Daffer, S; Cresser, J D; McIver, J K; Daffer, Sonja; Wodkiewicz, Krzysztof; Cresser, James D.; Iver, John K. Mc

    2003-01-01

    The prevailing description for dissipative quantum dynamics is given by the Lindblad form of a Markovian master equation, used under the assumption that memory effects are negligible. However, in certain physical situations, the master equation is essentially of a non-Markovian nature. This paper examines master equations that possess a memory kernel, leading to a replacement of white noise by colored noise. The conditions under which this leads to a completely positive, trace-preserving map are discussed for an exponential memory kernel. A physical model that possesses such an exponential memory kernel is presented. This model contains a classical, fluctuating environment based on random telegraph signal stochastic variables.

  14. Lunar Map Catalog

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Map Catalog includes various maps of the moon's surface, including Apollo landing sites; earthside, farside, and polar charts; photography index maps; zone...

  15. ShakeMap

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — ShakeMap is a product of the USGS Earthquake Hazards Program in conjunction with the regional seismic networks. ShakeMaps provide near-real-time maps of ground...

  16. Mapping: A Course.

    Science.gov (United States)

    Whitmore, Paul M.

    1988-01-01

    Reviews the history of cartography. Describes the contributions of Strabo and Ptolemy in early maps. Identifies the work of Gerhard Mercator as the most important advancement in mapping. Discusses present mapping standards from history. (CW)

  17. Mapping cultural ecosystem services:

    DEFF Research Database (Denmark)

    Paracchini, Maria Luisa; Zulian, Grazia; Kopperoinen, Leena

    2014-01-01

    is required to address the issue, since by definition cultural services (encompassing physical, intellectual, spiritual interactions with biota) need to be analysed from multiple perspectives (i.e. ecological, social, behavioural). A second reason is the lack of data for large-scale assessments, as detailed......Research on ecosystem services mapping and valuing has increased significantly in recent years. However, compared to provisioning and regulating services, cultural ecosystem services have not yet been fully integrated into operational frameworks. One reason for this is that transdisciplinarity...... surveys are a main source of information. Among cultural ecosystem services, assessment of outdoor recreation can be based on a large pool of literature developed mostly in social and medical science, and landscape and ecology studies. This paper presents a methodology to include recreation...

  18. Mapping with the Masses: Google Map Maker

    Science.gov (United States)

    Pfund, J.

    2008-12-01

    After some 15,000 years of map making, which saw the innovations of cardinal directions, map projections for a spherical earth, and GIS analysis, many parts of the world still appear as the "Dark Continent" on modern maps. Google Map Maker intends to shine a light on these areas by tapping into the power of the GeoWeb. Google Map Maker is a website which allows you to collaborate with others on one unified map to add, edit, locate, describe, and moderate map features, such as roads, cities, businesses, parks, schools and more, for certain regions of the world using Google Maps imagery. In this session, we will show some examples of how people are mapping with this powerful tool as well as what they are doing with the data. With Google Map Maker, you can become a citizen cartographer and join the global network of users helping to improve the quality of maps and local information in your region of interest. You are invited to map the world with us!

  19. Eclipse mapping of accretion discs

    OpenAIRE

    Baptista, Raymundo

    2000-01-01

    The eclipse mapping method is an inversion technique that makes use of the information contained in eclipse light curves to probe the structure, the spectrum and the time evolution of accretion discs. In this review I present the basics of the method and discuss its different implementations. I summarize the most important results obtained to date and discuss how they have helped to improve our understanding of accretion physics, from testing the theoretical radial brightness temperature dist...

  20. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  1. Identification of physical models

    DEFF Research Database (Denmark)

    Melgaard, Henrik

    1994-01-01

    The problem of identification of physical models is considered within the frame of stochastic differential equations. Methods for estimation of parameters of these continuous time models based on descrete time measurements are discussed. The important algorithms of a computer program for ML or MAP...... design of experiments, which is for instance the design of an input signal that are optimal according to a criterion based on the information provided by the experiment. Also model validation is discussed. An important verification of a physical model is to compare the physical characteristics...... of the model with the available prior knowledge. The methods for identification of physical models have been applied in two different case studies. One case is the identification of thermal dynamics of building components. The work is related to a CEC research project called PASSYS (Passive Solar Components...

  2. Conformal mapping for multiple terminals

    Science.gov (United States)

    Wang, Weimin; Ma, Wenying; Wang, Qiang; Ren, Hao

    2016-11-01

    Conformal mapping is an important mathematical tool that can be used to solve various physical and engineering problems in many fields, including electrostatics, fluid mechanics, classical mechanics, and transformation optics. It is an accurate and convenient way to solve problems involving two terminals. However, when faced with problems involving three or more terminals, which are more common in practical applications, existing conformal mapping methods apply assumptions or approximations. A general exact method does not exist for a structure with an arbitrary number of terminals. This study presents a conformal mapping method for multiple terminals. Through an accurate analysis of boundary conditions, additional terminals or boundaries are folded into the inner part of a mapped region. The method is applied to several typical situations, and the calculation process is described for two examples of an electrostatic actuator with three electrodes and of a light beam splitter with three ports. Compared with previously reported results, the solutions for the two examples based on our method are more precise and general. The proposed method is helpful in promoting the application of conformal mapping in analysis of practical problems.

  3. Optical Polarimetric Mapping of Ceres

    Science.gov (United States)

    Yang, Bin; Li, Jian-Yang; Kelley, Michael S.

    2016-10-01

    The dwarf planet Ceres, with one quarter of its mass possibly as water, is of particular importance to understanding the origin and the evolution history of water in the inner solar system. It is also a real-life laboratory to study astrobiology. NASA's Dawn is returning detailed geological maps of Ceres until the end of this year. As a complement to the Dawn mission, using SPHERE/ZIMPOL at one of Very Large Telescopes in Chile, we obtained the optical polarimetric maps in the I and V band of the whole surface of Ceres in July and August, 2015. Polarimetric maps of Ceres are sensitive to the physical conditions (such as packing density and particle size distribution) and composition of its surface regolith. The comparative studies between our polarimetric maps and Dawn maps help us to understand the geological evolution and the space weathering processes on Ceres' surface. At the time of the ZIMPOL observations, with the best spatial resolution of about 0.02 arcsecond (equivalent to 30 km), we effectively obtained about 700 independent measurements of the surface in one polarimetric set. I will present the SPHERE observations and discuss our major findings.

  4. Mapping social values of ecosystem services: What is behind the map?

    Directory of Open Access Journals (Sweden)

    Laura Nahuelhual

    2016-09-01

    Full Text Available A growing interest in mapping the social value of ecosystem services (ES is not yet methodologically aligned with what is actually being mapped. We critically examine aspects of the social value mapping process that might influence map outcomes and limit their practical use in decision making. We rely on an empirical case of participatory mapping, for a single ES (recreation opportunities, which involves diverse stakeholders such as planners, researchers, and community representatives. Value elicitation relied on an individual open-ended interview and a mapping exercise. Interpretation of the narratives and GIS calculations of proximity, centrality, and dispersion helped in exploring the factors driving participants' answers. Narratives reveal diverse value types. Whereas planners highlighted utilitarian and aesthetic values, the answers from researchers revealed naturalistic values as well. In turn community representatives acknowledged symbolic values. When remitted to the map, these values were constrained to statements toward a much narrower set of features of the physical (e.g., volcanoes and built landscape (e.g., roads. The results suggest that mapping, as an instrumental approach toward social valuation, may capture only a subset of relevant assigned values. This outcome is the interplay between participants' characteristics, including their acquaintance with the territory and their ability with maps, and the mapping procedure itself, including the proxies used to represent the ES and the value typology chosen, the elicitation question, the cartographic features displayed on the base map, and the spatial scale.

  5. Mapping the Heart

    Science.gov (United States)

    Hulse, Grace

    2012-01-01

    In this article, the author describes how her fourth graders made ceramic heart maps. The impetus for this project came from reading "My Map Book" by Sara Fanelli. This book is a collection of quirky, hand-drawn and collaged maps that diagram a child's world. There are maps of her stomach, her day, her family, and her heart, among others. The…

  6. USGS Map Indices Overlay Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Map Indices service from The National Map (TNM) consists of 1x1 Degree, 30x60 Minute (100K), 15 Minute (63K), 7.5 Minute (24K), and 3.75 Minute grid...

  7. Limitations of Passively Mapping Logical Network Topologies

    Directory of Open Access Journals (Sweden)

    Ayodeji J. Akande

    2017-02-01

    Full Text Available Understanding logical network connectivity is essential in network topology mapping especially in a fast growing network where knowing what is happening on the network is critical for security purposes and where knowing how network resources are being used is highly important. Mapping logical communication topology is important for network auditing, network maintenance and governance, network optimization, and network security. However, the process of capturing network traffic to generate the logical network topology may have a great influence on the operation of the network. In hierarchically structured networks such as control systems, typical active network mapping techniques are not employable as they can affect time-sensitive cyber-physical processes, hence, passive network mapping is required. Though passive network mapping does not modify or disrupt existing traffic, current passive mapping techniques ignore many practical issues when used to generate logical communication topologies. In this paper, we present a methodology which compares topologies from an idealized mapping process with what is actually achievable using passive network mapping and identify some of the factors that can cause inaccuracies in logical maps derived from passively monitored network traffic. We illustrate these factors using a case study involving a hierarchical control network.

  8. A gene map of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Schuler, G.D.; Boguski, M.S. [National Library of Medicine, Bethesda, MD (United States); Stewart, E.A. [Stanford Univ. School of Medicine, CA (United States)] [and others

    1996-10-25

    The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. 45 refs., 4 figs., 3 tabs.

  9. Google Maps: You Are Here

    Science.gov (United States)

    Jacobsen, Mikael

    2008-01-01

    Librarians use online mapping services such as Google Maps, MapQuest, Yahoo Maps, and others to check traffic conditions, find local businesses, and provide directions. However, few libraries are using one of Google Maps most outstanding applications, My Maps, for the creation of enhanced and interactive multimedia maps. My Maps is a simple and…

  10. VEGETATION MAPPING IN WETLANDS

    Directory of Open Access Journals (Sweden)

    F. PEDROTTI

    2004-01-01

    Full Text Available The current work examines the main aspects of wetland vegetation mapping, which can be summarized as analysis of the ecological-vegetational (ecotone gradients; vegetation complexes; relationships between vegetation distribution and geomorphology; vegetation of the hydrographic basin lo which the wetland in question belongs; vegetation monitoring with help of four vegetation maps: phytosociological map of the real and potential vegetation, map of vegetation dynamical tendencies, map of vegetation series.

  11. Web Mapping Using Logo on Map

    Directory of Open Access Journals (Sweden)

    Ximing Hou

    2012-12-01

    Full Text Available The newly proposed Logo on Map (LoM system consists of three modules: picture extraction module (PEM, logo matching module (LMM and web mapping module (WMM. Since the first two modules were covered in our previous paper, the third module WMM is described here to present a complete LoM system. Current research is focused on geo-location distribution of brands on Google Maps. Pictures taken by ordinary people are extracted using Picture Extraction Module (PEM. The pictures containing relevant logos are obtained via Logo Matching Module (LMM. Brand distributions are overlaid on Google Maps. In this paper, GPS and brands are briefly described, and the implementation of Web Mapping Module (WMM based on Google Maps API is detailed. Then several experiments are carried out on the selected top brands. Finally the LMM-pictures are mapped on the Google Maps and the geographical distributions of the brands are visualised. Brand uniqueness is discussed and conclusion is drawn that with unique brand names web mapping can visually reflect the real economic activities of a company in the world.

  12. Particle physics

    CERN Document Server

    Martin, Brian R

    2017-01-01

    An accessible and carefully structured introduction to Particle Physics, including important coverage of the Higgs Boson and recent progress in neutrino physics. Fourth edition of this successful title in the Manchester Physics series. Includes information on recent key discoveries including : An account of the discovery of exotic hadrons, beyond the simple quark model; Expanded treatments of neutrino physics and CP violation in B-decays; An updated account of ‘physics beyond the standard model’, including the interaction of particle physics with cosmology; Additional problems in all chapters, with solutions to selected problems available on the book’s website; Advanced material appears in optional starred sections.

  13. Statistical Physics

    CERN Document Server

    Mandl, Franz

    1988-01-01

    The Manchester Physics Series General Editors: D. J. Sandiford; F. Mandl; A. C. Phillips Department of Physics and Astronomy, University of Manchester Properties of Matter B. H. Flowers and E. Mendoza Optics Second Edition F. G. Smith and J. H. Thomson Statistical Physics Second Edition E. Mandl Electromagnetism Second Edition I. S. Grant and W. R. Phillips Statistics R. J. Barlow Solid State Physics Second Edition J. R. Hook and H. E. Hall Quantum Mechanics F. Mandl Particle Physics Second Edition B. R. Martin and G. Shaw The Physics of Stars Second Edition A. C. Phillips Computing for Scient

  14. Quantum Simulations of Physics Problems

    CERN Document Server

    Somma, R D; Knill, E; Gubernatis, J; Somma, Rolando; Ortiz, Gerardo; Knill, Emanuel; Gubernatis, James

    2003-01-01

    If a large Quantum Computer (QC) existed today, what type of physical problems could we efficiently simulate on it that we could not simulate on a classical Turing machine? In this paper we argue that a QC could solve some relevant physical "questions" more efficiently. The existence of one-to-one mappings between different algebras of observables or between different Hilbert spaces allow us to represent and imitate any physical system by any other one (e.g., a bosonic system by a spin-1/2 system). We explain how these mappings can be performed showing quantum networks useful for the efficient evaluation of some physical properties, such as correlation functions and energy spectra.

  15. Algebra and topology for applications to physics

    Science.gov (United States)

    Rozhkov, S. S.

    1987-01-01

    The principal concepts of algebra and topology are examined with emphasis on applications to physics. In particular, attention is given to sets and mapping; topological spaces and continuous mapping; manifolds; and topological groups and Lie groups. The discussion also covers the tangential spaces of the differential manifolds, including Lie algebras, vector fields, and differential forms, properties of differential forms, mapping of tangential spaces, and integration of differential forms.

  16. Mapping in the cloud

    CERN Document Server

    Peterson, Michael P

    2014-01-01

    This engaging text provides a solid introduction to mapmaking in the era of cloud computing. It takes students through both the concepts and technology of modern cartography, geographic information systems (GIS), and Web-based mapping. Conceptual chapters delve into the meaning of maps and how they are developed, covering such topics as map layers, GIS tools, mobile mapping, and map animation. Methods chapters take a learn-by-doing approach to help students master application programming interfaces and build other technical skills for creating maps and making them available on the Internet. Th

  17. Mapping with Drupal

    CERN Document Server

    Palazzolo, Alan

    2011-01-01

    Build beautiful interactive maps on your Drupal website, and tell engaging visual stories with your data. This concise guide shows you how to create custom geographical maps from top to bottom, using Drupal 7 tools and out-of-the-box modules. You'll learn how mapping works in Drupal, with examples on how to use intuitive interfaces to map local events, businesses, groups, and other custom data. Although building maps with Drupal can be tricky, this book helps you navigate the system's complexities for creating sophisticated maps that match your site design. Get the knowledge and tools you ne

  18. Coded MapReduce

    OpenAIRE

    Li, Songze; Maddah-Ali, Mohammad Ali; Avestimehr, A. Salman

    2015-01-01

    MapReduce is a commonly used framework for executing data-intensive jobs on distributed server clusters. We introduce a variant implementation of MapReduce, namely "Coded MapReduce", to substantially reduce the inter-server communication load for the shuffling phase of MapReduce, and thus accelerating its execution. The proposed Coded MapReduce exploits the repetitive mapping of data blocks at different servers to create coding opportunities in the shuffling phase to exchange (key,value) pair...

  19. Some Semi - Equivelar Maps

    CERN Document Server

    Upadhyay, Ashish K; Maity, Dipendu

    2011-01-01

    Semi-Equivelar maps are generalizations of Archimedean Solids (as are equivelar maps of the Platonic solids) to the surfaces other than $2-$Sphere. We classify some semi equivelar maps on surface of Euler characteristic -1 and show that none of these are vertex transitive. We establish existence of 12-covered triangulations for this surface. We further construct double cover of these maps to show existence of semi-equivelar maps on the surface of double torus. We also construct several semi-equivelar maps on the surfaces of Euler characteristics -8 and -10 and on non-orientable surface of Euler characteristics -2.

  20. Parabolic-like maps

    CERN Document Server

    Lomonaco, Luciana Luna Anna

    2011-01-01

    In this paper we introduce the notion of parabolic-like mapping, which is an object similar to a polynomial-like mapping, but with a parabolic external class, i.e. an external map with a parabolic fixed point. We prove a straightening theorem for parabolic-like maps, which states that any parabolic-like map of degree 2 is hybrid conjugate to a member of the family Per_1(1), and this member is unique (up to holomorphic conjugacy) if the filled Julia set of the parabolic-like map is connected.

  1. Physical activity

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/001941.htm Physical activity To use the sharing features on this page, please enable JavaScript. Physical activity -- which includes an active lifestyle and routine exercise -- ...

  2. The philosophy of physics

    CERN Document Server

    Rickles, Dean

    2016-01-01

    Does the future exist already? What is space? Are time machines physically possible? What is quantum mechanical reality like? Are there many universes? Is there a 'true' geometry of the universe? Why does there appear to be an arrow of time? Do humans play a special role in the world? In this unique introductory book, Dean Rickles guides the reader through these and other core questions that keep philosophers of physics up at night. He discusses the three pillars of modern physics (quantum mechanics, statistical mechanics, and the theories of relativity), in addition to more cutting-edge themes such as econophysics, quantum gravity, quantum computers, and gauge theories. The book's approach is based on the idea that philosophy of physics is a kind of 'interpretation game' in which we try to map physical theories onto our world. But the rules of this game often lead to a multiplicity of possible victors: rarely do we encounter a simple answer. The Philosophy of Physics offers a highly accessible introduction...

  3. Discretization and implicit mapping dynamics

    CERN Document Server

    Luo, Albert C J

    2015-01-01

    This unique book presents the discretization of continuous systems and implicit mapping dynamics of periodic motions to chaos in continuous nonlinear systems. The stability and bifurcation theory of fixed points in discrete nonlinear dynamical systems is reviewed, and the explicit and implicit maps of continuous dynamical systems are developed through the single-step and multi-step discretizations. The implicit dynamics of period-m solutions in discrete nonlinear systems are discussed. The book also offers a generalized approach to finding analytical and numerical solutions of stable and unstable periodic flows to chaos in nonlinear systems with/without time-delay. The bifurcation trees of periodic motions to chaos in the Duffing oscillator are shown as a sample problem, while the discrete Fourier series of periodic motions and chaos are also presented. The book offers a valuable resource for university students, professors, researchers and engineers in the fields of applied mathematics, physics, mechanics,...

  4. Physical ergonomics

    NARCIS (Netherlands)

    Looze, M. de; Koningsveld, E.

    2013-01-01

    Physical ergonomics deals with the physical load on the human body when performing activities like work, sports, jobs at home or dealing with products. With regard to the exposure to physical loads and its potential effects on the human body, the presented framework is helpful. In this article we ex

  5. 2006~2010年我国体育教育训练学研究知识图谱分析%Analysis on Physical Education and Training Research Based on Mapping Knowledge From 2006 to 2010

    Institute of Scientific and Technical Information of China (English)

    姚宪国

    2013-01-01

    The paper analyzes the bibliometric index and focus by the study on physical education and training research paper from 2006 to 2010 based on bibliometric methods and visualization. The paper gets the important institutions and influent authors and journals, identifies research fonts and knowledge basis, and decides the research focus that includes physical teaching, basketball, football, table tennis, physical talents, kinematics, etc.%采用文献计量学方法及可视化技术,对2006~2010年间我国体育教育训练学研究论文进行分析,发现相关研究的计量学指标分布以及研究热点,得出我国体育教育训练学研究的重要机构以及有影响力的作者、期刊,识别该领域的研究基础和前沿,并确定该领域的研究热点.

  6. MapBook

    Data.gov (United States)

    National Aeronautics and Space Administration — Beginning with the systematic mapping of the lunar surface more than three decades ago, this database contains over 1600 maps of the planets and satellites of the...

  7. NGS Survey Control Map

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Survey Control Map provides a map of the US which allows you to find and display geodetic survey control points stored in the database of the National...

  8. Letter of Map Revision

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The National Flood Hazard Layer (NFHL) data incorporates all Digital Flood Insurance Rate Map(DFIRM) databases published by FEMA, and any Letters Of Map Revision...

  9. NAIP Status Maps Gallery

    Data.gov (United States)

    Farm Service Agency, Department of Agriculture — NAIP Status Maps Gallery. These maps illustrate what aerial imagery collection is planned, whats been collected, when it is available and how it is available. These...

  10. Mapping Medicare Disparities Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CMS Office of Minority Health has designed an interactive map, the Mapping Medicare Disparities Tool, to identify areas of disparities between subgroups of...

  11. Improving wetland mapping techniques

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Mapping wetland extent, structure and invasives using radar imagery. Acquiring optical, thermal, LIDAR, and RADAR images and analysis for improved wetland mapping,...

  12. Recovery Action Mapping Tool

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Recovery Action Mapping Tool is a web map that allows users to visually interact with and query actions that were developed to recover species listed under the...

  13. Mapping Mutations on Phylogenies

    DEFF Research Database (Denmark)

    Nielsen, Rasmus

    2005-01-01

    This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety...... of different applications, for example, in the detection of correlated evolution and to identify selection acting on DNA sequences. However, many uses of parsimony mappings have been criticized because they focus on only one of many possible mappings and/or because they do not incorporate statistical...... uncertainty in the mapping. Recently developed probabilistic methods can incorporate statistical uncertainty in the character mappings. In these methods, focus is on a probability distribution of mutational mappings instead of a single estimate of the mutational mapping....

  14. Particle Physics

    CERN Document Server

    Martin, B R

    2008-01-01

    An essential introduction to particle physics, with coverage ranging from the basics through to the very latest developments, in an accessible and carefully structured text. Particle Physics: Third Edition is a revision of a highly regarded introduction to particle physics. In its two previous editions this book has proved to be an accessible and balanced introduction to modern particle physics, suitable for those students needed a more comprehensive introduction to the subject than provided by the 'compendium' style physics books. In the Third Edition the standard mod

  15. Physical Systems

    CERN Document Server

    Belkind, Ori

    2012-01-01

    Based on the concept of a physical system, this book offers a new philosophical interpretation of classical mechanics and the Special Theory of Relativity. According to Belkind's view the role of physical theory is to describe the motions of the parts of a physical system in relation to the motions of the whole. This approach provides a new perspective into the foundations of physical theory, where motions of parts and wholes of physical systems are taken to be fundamental, prior to spacetime, material properties and laws of motion. He defends this claim with a constructive project, deriving b

  16. Understanding physics

    CERN Document Server

    Mansfield, Michael

    2011-01-01

    Understanding Physics - Second edition is a comprehensive, yet compact, introductory physics textbook aimed at physics undergraduates and also at engineers and other scientists taking a general physics course. Written with today's students in mind, this text covers the core material required by an introductory course in a clear and refreshing way. A second colour is used throughout to enhance learning and understanding. Each topic is introduced from first principles so that the text is suitable for students without a prior background in physics. At the same time the book is designed to enable

  17. Cosmoparticle physics

    CERN Document Server

    Khlopov, M Yu

    1999-01-01

    Since the 1980s the cross-disciplinary, multidimensional field of links between cosmology and particle physics has been widely recognised by theorists, studying cosmology, particle and nuclear physics, gravity, as well as by astrophysicists, astronomers, space physicists, experimental particle and nuclear physicists, mathematicians and engineers.The relationship between cosmology and particle physics is now one of the important topics of discussion at any scientific meeting both on astrophysics and high energy physics.Cosmoparticle physics is the result of the mutual relationship between cosmo

  18. Game physics

    CERN Document Server

    Eberly, David H

    2010-01-01

    ""Game Physics, 2nd Edition"" provides clear descriptions of the mathematics and algorithms needed to create a powerful physics engine - while providing a solid reference for all of the math you will encounter anywhere in game development: quaternions, linear algebra, and calculus. Implementing physical simulations for real-time games is a complex task that requires a solid understanding of a wide range of concepts from the fields of mathematics and physics. Previously, the relevant information could only be gleaned through obscure research papers. Thanks to ""Game Physics"", all this informa

  19. Lying with Maps

    OpenAIRE

    Monmonier, Mark

    2005-01-01

    Darrell Huff’s How to Lie with Statistics was the inspiration for How to Lie with Maps, in which the author showed that geometric distortion and graphic generalization of data are unavoidable elements of cartographic representation. New examples of how ill-conceived or deliberately contrived statistical maps can greatly distort geographic reality demonstrate that lying with maps is a special case of lying with statistics. Issues addressed include the effects of map scale on geometry and featu...

  20. Curriculum Mapping. Focus On

    Science.gov (United States)

    Molineaux, Rebecca

    2008-01-01

    This "Focus On" discusses curriculum mapping, a process that allows educators to align the curriculum both within and across grades and to ensure that the curriculum is in line with school, local, and state standards. It outlines the steps of the curriculum mapping process from planning the mapping initiative to creating and editing curriculum…

  1. Reading Angles in Maps

    Science.gov (United States)

    Izard, Véronique; O'Donnell, Evan; Spelke, Elizabeth S.

    2014-01-01

    Preschool children can navigate by simple geometric maps of the environment, but the nature of the geometric relations they use in map reading remains unclear. Here, children were tested specifically on their sensitivity to angle. Forty-eight children (age 47:15-53:30 months) were presented with fragments of geometric maps, in which angle sections…

  2. Diffusion Based Photon Mapping

    DEFF Research Database (Denmark)

    Schjøth, Lars; Olsen, Ole Fogh; Sporring, Jon

    2006-01-01

    . To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....

  3. Diffusion Based Photon Mapping

    DEFF Research Database (Denmark)

    Schjøth, Lars; Fogh Olsen, Ole; Sporring, Jon

    2007-01-01

    . To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....

  4. Mapping a Changing World.

    Science.gov (United States)

    Stoltman, Joseph P.

    1992-01-01

    Addresses the importance of maps for instruction in both history and geography. Suggests that maps have gotten recent attention because of the rapid political changes occurring in Europe and the quincentenary of Columbus' voyage. Discusses different map projections and the importance of media and satellite display of real pictures of the world.…

  5. Hierarchical Reverberation Mapping

    CERN Document Server

    Brewer, Brendon J

    2013-01-01

    Reverberation mapping (RM) is an important technique in studies of active galactic nuclei (AGN). The key idea of RM is to measure the time lag $\\tau$ between variations in the continuum emission from the accretion disc and subsequent response of the broad line region (BLR). The measurement of $\\tau$ is typically used to estimate the physical size of the BLR and is combined with other measurements to estimate the black hole mass $M_{\\rm BH}$. A major difficulty with RM campaigns is the large amount of data needed to measure $\\tau$. Recently, Fine et al (2012) introduced a new approach to RM where the BLR light curve is sparsely sampled, but this is counteracted by observing a large sample of AGN, rather than a single system. The results are combined to infer properties of the sample of AGN. In this letter we implement this method using a hierarchical Bayesian model and contrast this with the results from the previous stacked cross-correlation technique. We find that our inferences are more precise and allow fo...

  6. Mapping the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.

    1989-06-01

    The following pages aim to lay a foundation for understanding the excitement surrounding the ''human genome project,'' as well as to convey a flavor of the ongoing efforts and plans at the Human Genome Center at the Lawrence Berkeley Laboratory. Our own work, of course, is only part of a broad international effort that will dramatically enhance our understanding of human molecular genetics before the end of this century. In this country, the bulk of the effort will be carried out under the auspices of the Department of Energy and the National Institutes of Health, but significant contributions have already been made both by nonprofit private foundations and by private corporation. The respective roles of the DOE and the NIH are being coordinated by an inter-agency committee, the aims of which are to emphasize the strengths of each agency, to facilitate cooperation, and to avoid unnecessary duplication of effort. The NIH, for example, will continue its crucial work in medical genetics and in mapping the genomes of nonhuman species. The DOE, on the other hand, has unique experience in managing large projects, and its national laboratories are repositories of expertise in physics, engineering, and computer science, as well as the life sciences. The tools and techniques the project will ultimately rely on are thus likely to be developed in multidisciplinary efforts at laboratories like LBL. Accordingly, we at LBL take great pride in this enterprise -- an enterprise that will eventually transform our understanding of ourselves.

  7. An Introduction to the Space Mapping Technique

    DEFF Research Database (Denmark)

    Bakr, Mohamed H.; Bandler, John W.; Madsen, Kaj;

    2001-01-01

    The space mapping technique is intended for optimization of engineering models which involve very expensive function evaluations. It is assumed that two different models of the same physical system are available: Besides the expensive model of primary interest (denoted the fine model), access...

  8. Improved mapping of the travelling salesman problem for quantum annealing

    Science.gov (United States)

    Troyer, Matthias; Heim, Bettina; Brown, Ethan; Wecker, David

    2015-03-01

    We consider the quantum adiabatic algorithm as applied to the travelling salesman problem (TSP). We introduce a novel mapping of TSP to an Ising spin glass Hamiltonian and compare it to previous known mappings. Through direct perturbative analysis, unitary evolution, and simulated quantum annealing, we show this new mapping to be significantly superior. We discuss how this advantage can translate to actual physical implementations of TSP on quantum annealers.

  9. Radiation hybrid map of barley chromosome 3H

    Science.gov (United States)

    Assembly of the barley genome is complicated by its large size (5.1 Gb) and proportion of repetitive elements (84%). This process is facilitated by high resolution maps for aligning BAC contigs along chromosomes. Available genetic maps; however, do not provide accurate information on the physical po...

  10. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  11. Cosmopolitan linkage disequilibrium maps

    Directory of Open Access Journals (Sweden)

    Gibson Jane

    2005-03-01

    Full Text Available Abstract Linkage maps have been invaluable for the positional cloning of many genes involved in severe human diseases. Standard genetic linkage maps have been constructed for this purpose from the Centre d'Etude du Polymorphisme Humain and other panels, and have been widely used. Now that attention has shifted towards identifying genes predisposing to common disorders using linkage disequilibrium (LD and maps of single nucleotide polymorphisms (SNPs, it is of interest to consider a standard LD map which is somewhat analogous to the corresponding map for linkage. We have constructed and evaluated a cosmopolitan LD map by combining samples from a small number of populations using published data from a 10-megabase region on chromosome 20. In support of a pilot study, which examined a number of small genomic regions with a lower density of markers, we have found that a cosmopolitan map, which serves all populations when appropriately scaled, recovers 91 to 95 per cent of the information within population-specific maps. Recombination hot spots appear to have a dominant role in shaping patterns of LD. The success of the cosmopolitan map might be attributed to the co-localisation of hot spots in all populations. Although there must be finer scale differences between populations due to other processes (mutation, drift, selection, the results suggest that a whole-genome standard LD map would indeed be a useful resource for disease gene mapping.

  12. University physics

    CERN Document Server

    Arfken, George

    1984-01-01

    University Physics provides an authoritative treatment of physics. This book discusses the linear motion with constant acceleration; addition and subtraction of vectors; uniform circular motion and simple harmonic motion; and electrostatic energy of a charged capacitor. The behavior of materials in a non-uniform magnetic field; application of Kirchhoff's junction rule; Lorentz transformations; and Bernoulli's equation are also deliberated. This text likewise covers the speed of electromagnetic waves; origins of quantum physics; neutron activation analysis; and interference of light. This publi

  13. Ultrasonic physics

    CERN Document Server

    Richardson, E G

    1962-01-01

    Ultrasonic Physics, Second Edition, provides an introduction to the fundamental principles of ultrasonic physics. The book opens with a discussion of the sources of ultrasound. This is followed by separate chapters on the properties and detection of ultrasonic radiation; measurement of propagation constants, i.e., the velocity and absorption, of ultrasound; ultrasound propagation in gases, liquids, and solids; and ultrasound propagation in aerosols, suspensions, and emulsions. The final chapter covers miscellaneous physical and physico-chemical actions, including dispersion and coagulation of

  14. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  15. Neutrino physics

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Deborah A.; /Fermilab

    2008-09-01

    The field of neutrino physics has expanded greatly in recent years with the discovery that neutrinos change flavor and therefore have mass. Although there are many neutrino physics results since the last DIS workshop, these proceedings concentrate on recent neutrino physics results that either add to or depend on the understanding of Deep Inelastic Scattering. They also describe the short and longer term future of neutrino DIS experiments.

  16. Action physics

    Science.gov (United States)

    McGinness, Lachlan P.; Savage, C. M.

    2016-09-01

    More than a decade ago, Edwin Taylor issued a "call to action" that presented the case for basing introductory university mechanics teaching around the principle of stationary action [E. F. Taylor, Am. J. Phys. 71, 423-425 (2003)]. We report on our response to that call in the form of an investigation of the teaching and learning of the stationary action formulation of physics in a first-year university course. Our action physics instruction proceeded from the many-paths approach to quantum physics to ray optics, classical mechanics, and relativity. Despite the challenges presented by action physics, students reported it to be accessible, interesting, motivational, and valuable.

  17. Physical Activity

    DEFF Research Database (Denmark)

    Andersen, Lars Bo; Anderssen, Sigmund Alfred; Wisløff, Ulrik

    2014-01-01

    Andersen LB, Anderssen SA, Wisløff U, Hellénius M-L, Fogelholm M, Ekelund U. (Expert Group) Nordic Nutrition Recommendations 2012. Integrating nutrition and physical activity. Chapter: Physical Activity p. 195-217.Nordic Counsil of Ministers.......Andersen LB, Anderssen SA, Wisløff U, Hellénius M-L, Fogelholm M, Ekelund U. (Expert Group) Nordic Nutrition Recommendations 2012. Integrating nutrition and physical activity. Chapter: Physical Activity p. 195-217.Nordic Counsil of Ministers....

  18. Computational physics

    CERN Document Server

    Newman, Mark

    2013-01-01

    A complete introduction to the field of computational physics, with examples and exercises in the Python programming language. Computers play a central role in virtually every major physics discovery today, from astrophysics and particle physics to biophysics and condensed matter. This book explains the fundamentals of computational physics and describes in simple terms the techniques that every physicist should know, such as finite difference methods, numerical quadrature, and the fast Fourier transform. The book offers a complete introduction to the topic at the undergraduate level, and is also suitable for the advanced student or researcher who wants to learn the foundational elements of this important field.

  19. Few-body physics

    OpenAIRE

    Briceño, Raúl A.

    2014-01-01

    Few-body hadronic observables play an essential role in a wide number of processes relevant for both particle and nuclear physics. In order for Lattice QCD to offer insight into the interpretation of few-body states, a theoretical infrastructure must be developed to map Euclidean-time correlation functions to the desired Minkowski-time few-body observables. In this talk, I review the formal challenges associated with the studies of such systems via Lattice QCD, as first introduced by Maiani a...

  20. Mapping alpha-Particle X-Ray Fluorescence Spectrometer (Map-X)

    Science.gov (United States)

    Blake, D. F.; Sarrazin, P.; Bristow, T.

    2014-01-01

    Many planetary surface processes (like physical and chemical weathering, water activity, diagenesis, low-temperature or impact metamorphism, and biogenic activity) leave traces of their actions as features in the size range 10s to 100s of micron. The Mapping alpha-particle X-ray Spectrometer ("Map-X") is intended to provide chemical imaging at 2 orders of magnitude higher spatial resolution than previously flown instruments, yielding elemental chemistry at or below the scale length where many relict physical, chemical, and biological features can be imaged and interpreted in ancient rocks.

  1. Video Game Genre Affordances for Physics Education

    Science.gov (United States)

    Anagnostou, Kostas; Pappa, Anastasia

    2011-01-01

    In this work, the authors analyze the video game genres' features and investigate potential mappings to specific didactic approaches in the context of Physics education. To guide the analysis, the authors briefly review the main didactic approaches for Physics and identify qualities that can be projected into game features. Based on the…

  2. Imagined Physics

    DEFF Research Database (Denmark)

    Merritt, Timothy; Nørgaard, Mie; Laursen, Christian;

    2015-01-01

    to this book focuses on the human responses to objects that change shape in response to input from users, environment, or other circumstances. In this chapter we discuss the term "imagined physics", meaning how actuated devices are in one sense tied to their physical form, yet through the use of actuators...

  3. Sports Physicals

    Science.gov (United States)

    ... more specific about athletic issues. During a regular physical, however, your doctor will address your overall well-being, which may include things that are unrelated to sports. You can ask your doctor to give you both types of ... if your sports physical exam doesn't reveal any problems, it's always ...

  4. Understanding physics

    CERN Document Server

    Cassidy, David; Rutherford, James

    2002-01-01

    Understanding Physics provides a thorough grounding in contemporary physics while placing physics into its social and historical context Based in large part on the highly respected Project Physics Course developed by two of the authors, it also integrates the results of recent pedagogical research The text thus - teaches about the basic phenomena in the physical world and the concepts developed to explain them - shows that science is a rational human endeavor with a long and continuing tradition, involving many different cultures and people - develops facility in critical thinking, reasoned argumentation, evaluation of evidence, mathematical modeling, and ethical values The treatment emphasizes not only what we know but also how we know it, why we believe it, and what effects that knowledge has - Why do we believe the Earth and planets revolve around the Sun? - Why do we believe that matter is made of atoms? - How do relativity theory and quantum mechanics alter our conception of Nature and in what ways do th...

  5. Map Projection Transitions

    Directory of Open Access Journals (Sweden)

    Nedjeljko Frančula

    2013-06-01

    Full Text Available Map Projection Transitions is a very successful web application about map projections. The web page (http://www.jasondavies.com/maps/transition pre­sents a world map with graticule and country borders in the oblique Aitoff projection, with the South Pole. The map is not static, but animated. The South Pole moves toward the bottom and Earth rotates around its poles. The animation lasts five seconds, after which the projection changes and movement continues for five seconds, after which the projection changes again. Names of projections appear in a separate window. There are a total of 56 projections. The South Pole eventually becomes invisible and the North Pole appears at the top. Various parts of Earth appear in the center of the map by rotating around the poles.

  6. Grid Mapping Method of Multi-physics Coupled Modeling for Near Space Vehicle%临近空间飞行器多物理场耦合建模的网格映射方法

    Institute of Scientific and Technical Information of China (English)

    刘璟; 王玲; 胡东飞; 铁鸣; 吴旭生

    2012-01-01

    临近空间飞行器的研制面临许多复杂的问题和挑战,涉及总体、气动、结构、控制、防热、动力等多个学科和专业领域的相互作用、高度耦合的子系统.全系统、全流程的仿真验证与性能评估能够为设计工作提供重要依据,缩短研制周期.而气动、结构、防热等专业的仿真建模和模型解算基于有限体积法或有限元方法,依赖于不同的工具软件,且网格的划分方法不同.本文研究了临近空间高超声速飞行器多物理场耦合建模方法,研究并实现了异构网格耦合界面之间与耦合域之间的信息传递方法,从而实现了临近空间高超声速飞行器的多物理场耦合建模与仿真.%The development of near space vehicle is confronting many complex problems and challenges, involving many different subsystems which are highly interactive and coupled, such as overall design, aerodynamics , structure, thermal protection, control, dynamics and so on. The simulation validation and performance evaluation based on whole system and whole flow can provide important gist for the design, also accelerating the developing cycle. However, the simulation modeling and computation of subjects such as aerodynamics, structure and thermal protection are based on the finite volume method or the finite element method, depending on different software tools, and the partition methods of mesh are different as well. The coupled modeling method of multi-physics in the field of near space hypersonic vehicle is researched by implementing the method of message-passing which involves coupling interfaces of heterogeneous mesh and coupled region. The method of coupling modeling and simulation is implemented, which involves multi-physics in the fields of near space hypersonic vehicle.

  7. Multi-moment maps

    DEFF Research Database (Denmark)

    Swann, Andrew Francis; Madsen, Thomas Bruun

    2012-01-01

    We introduce a notion of moment map adapted to actions of Lie groups that preserve a closed three-form. We show existence of our multi-moment maps in many circumstances, including mild topological assumptions on the underlying manifold. Such maps are also shown to exist for all groups whose secon......-torus symmetry in terms of tri-symplectic geometry of four-manifolds. (C) 2012 Elsevier Inc. All rights reserved....

  8. Classification of Lipschitz mappings

    CERN Document Server

    Piasecki, Lukasz

    2013-01-01

    The Lipschitz Condition Nonlinear spectral radius Uniformly lipschitzian mappings Basic Facts on Banach Spaces Convexity The operator norm Dual spaces, reexivity, the weak, and weak* topologiesMean Lipschitz Condition Nonexpansive and mean nonexpansive mappings in Banach spaces General case On the Lipschitz Constants for Iterates of Mean Lipschitzian Mappings A bound for Lipschitz constants of iterates A bound for the constant k∞(T)Moving averages in Bana

  9. Obesity Prevalence Maps

    Science.gov (United States)

    ... Breastfeeding Micronutrient Malnutrition State and Local Programs Adult Obesity Prevalence Maps Recommend on Facebook Tweet Share Compartir Obesity Prevalence in 2015 Varies Across States and Territories ...

  10. Similarity transformations of MAPs

    Directory of Open Access Journals (Sweden)

    Andersen Allan T.

    1999-01-01

    Full Text Available We introduce the notion of similar Markovian Arrival Processes (MAPs and show that the event stationary point processes related to two similar MAPs are stochastically equivalent. This holds true for the time stationary point processes too. We show that several well known stochastical equivalences as e.g. that between the H 2 renewal process and the Interrupted Poisson Process (IPP can be expressed by the similarity transformations of MAPs. In the appendix the valid region of similarity transformations for two-state MAPs is characterized.

  11. Statistical physics

    CERN Document Server

    Wannier, Gregory H

    2010-01-01

    Until recently, the field of statistical physics was traditionally taught as three separate subjects: thermodynamics, statistical mechanics, and kinetic theory. This text, a forerunner in its field and now a classic, was the first to recognize the outdated reasons for their separation and to combine the essentials of the three subjects into one unified presentation of thermal physics. It has been widely adopted in graduate and advanced undergraduate courses, and is recommended throughout the field as an indispensable aid to the independent study and research of statistical physics.Designed for

  12. Interpreting Physics

    CERN Document Server

    MacKinnon, Edward

    2012-01-01

    This book is the first to offer a systematic account of the role of language in the development and interpretation of physics. An historical-conceptual analysis of the co-evolution of mathematical and physical concepts leads to the classical/quatum interface. Bohrian orthodoxy stresses the indispensability of classical concepts and the functional role of mathematics. This book analyses ways of extending, and then going beyond this orthodoxy orthodoxy. Finally, the book analyzes how a revised interpretation of physics impacts on basic philosophical issues: conceptual revolutions, realism, and r

  13. Neutrino physics

    CERN Document Server

    Hernandez, P

    2016-01-01

    This is the writeup of the lectures on neutrino physics delivered at various schools: TASI and Trieste in 2013 and the CERN-Latin American School in 2015. The topics discussed in this lecture include: general properties of neutrinos in the SM, the theory of neutrino masses and mixings (Dirac and Majorana), neutrino oscillations both in vacuum and in matter, as well as an overview of the experimental evidence for neutrino masses and of the prospects in neutrino oscillation physics. We also briefly review the relevance of neutri- nos in leptogenesis and in beyond-the-Standard-Model physics.

  14. Plasma physics

    CERN Document Server

    Drummond, James E

    2013-01-01

    A historic snapshot of the field of plasma physics, this fifty-year-old volume offers an edited collection of papers by pioneering experts in the field. In addition to assisting students in their understanding of the foundations of classical plasma physics, it provides a source of historic context for modern physicists. Highly successful upon its initial publication, this book was the standard text on plasma physics throughout the 1960s and 70s.Hailed by Science magazine as a ""well executed venture,"" the three-part treatment ranges from basic plasma theory to magnetohydrodynamics and microwa

  15. Higgs Physics

    CERN Document Server

    Grojean, C

    2016-01-01

    The cause of the screening of the weak interactions at long distances puzzled the high-energy community for more nearly half a century. With the discovery of the Higgs boson a new era started with direct experimental information on the physics behind the breaking of the electroweak symmetry. This breaking plays a fundamental role in our understanding of particle physics and sits at the high-energy frontier beyond which we expect new physics that supersedes the Standard Model. The Higgs boson (inclusive and differential) production and decay rates offer a new way to probe this frontier.

  16. Complex systems: physics beyond physics

    CERN Document Server

    Holovatch, Yurij; Thurner, Stefan

    2016-01-01

    Complex systems are characterized by specific time-dependent interactions among their many constituents. As a consequence they often manifest rich, non-trivial and unexpected behavior. Examples arise both in the physical and non-physical world. The study of complex systems forms a new interdisciplinary research area that cuts across physics, biology, ecology, economics, sociology, and the humanities. In this paper we review the essence of complex systems from a physicist's point of view, and try to clarify what makes them conceptually different from systems that are traditionally studied in physics. Our goal is to demonstrate how the dynamics of such systems may be conceptualized in quantitative and predictive terms by extending notions from statistical physics and how they can often be captured in a framework of co-evolving multiplex network structures. We mention three areas of complex-systems science that are currently studied extensively, the science of cities, dynamics of societies, and the representatio...

  17. Mapping geogenic radon potential by regression kriging.

    Science.gov (United States)

    Pásztor, László; Szabó, Katalin Zsuzsanna; Szatmári, Gábor; Laborczi, Annamária; Horváth, Ákos

    2016-02-15

    Radon ((222)Rn) gas is produced in the radioactive decay chain of uranium ((238)U) which is an element that is naturally present in soils. Radon is transported mainly by diffusion and convection mechanisms through the soil depending mainly on the physical and meteorological parameters of the soil and can enter and accumulate in buildings. Health risks originating from indoor radon concentration can be attributed to natural factors and is characterized by geogenic radon potential (GRP). Identification of areas with high health risks require spatial modeling, that is, mapping of radon risk. In addition to geology and meteorology, physical soil properties play a significant role in the determination of GRP. In order to compile a reliable GRP map for a model area in Central-Hungary, spatial auxiliary information representing GRP forming environmental factors were taken into account to support the spatial inference of the locally measured GRP values. Since the number of measured sites was limited, efficient spatial prediction methodologies were searched for to construct a reliable map for a larger area. Regression kriging (RK) was applied for the interpolation using spatially exhaustive auxiliary data on soil, geology, topography, land use and climate. RK divides the spatial inference into two parts. Firstly, the deterministic component of the target variable is determined by a regression model. The residuals of the multiple linear regression analysis represent the spatially varying but dependent stochastic component, which are interpolated by kriging. The final map is the sum of the two component predictions. Overall accuracy of the map was tested by Leave-One-Out Cross-Validation. Furthermore the spatial reliability of the resultant map is also estimated by the calculation of the 90% prediction interval of the local prediction values. The applicability of the applied method as well as that of the map is discussed briefly.

  18. Molecular mapping of chromosomes 17 and X

    Energy Technology Data Exchange (ETDEWEB)

    Barker, D.F.

    1991-01-15

    Progress toward the construction of high density genetic maps of chromosomes 17 and X has been made by isolating and characterizing a relatively large set of polymorphic probes for each chromosome and using these probes to construct genetic maps. We have mapped the same polymorphic probes against a series of chromosome breakpoints on X and 17. The probes could be assigned to over 30 physical intervals on the X chromosome and 7 intervals on 17. In many cases, this process resulted in improved characterization of the relative locations of the breakpoints with respect to each other and the definition of new physical intervals. The strategy for isolation of the polymorphic clones utilized chromosome specific libraries of 1--15 kb segments from each of the two chromosomes. From these libraries, clones were screened for those detecting restriction fragment length polymorphisms. The markers were further characterized, the chromosomal assignments confirmed and in most cases segments of the original probes were subcloned into plasmids to produce probes with improved signal to noise ratios for use in the genetic marker studies. The linkage studies utilize the CEPH reference families and other well-characterized families in our collection which have been used for genetic disease linkage work. Preliminary maps and maps of portions of specific regions of 17 and X are provided. We have nearly completed a map of the 1 megabase Mycoplasma arthritidis genome by applying these techniques to a lambda phage library of its genome. We have found bit mapping to be an efficient means to organize a contiguous set of overlapping clones from a larger genome.

  19. Complete mapping of crystallization pathways during cholesterol precipitation from model bile: influence of physical-chemical variables of pathophysiologic relevance and identification of a stable liquid crystalline state in cold, dilute and hydrophilic bile salt-containing systems.

    Science.gov (United States)

    Wang, D Q; Carey, M C

    1996-03-01

    Using complementary physical-chemical techniques we defined five different crystallization pathways as functions of time (30 days) and increasing lecithin (egg yolk) content in pathophysiologically relevant model biles super-saturated (cholesterol saturation indices, 1.2 - 2.7) by dilution of approximately equal to 29 g/dl bile salt-lecithin-cholesterol micellar solutions. As evidenced by quasi-elastic light-scattering spectroscopy, supersaturation was heralded by the appearance of unilamellar vesicles. With the lowest lecithin contents, arc-like crystals with habit and density (d 1.030 g/mL) consistent with anhydrous cholesterol appeared first and evolved via helical and tubular crystals to form plate-like cholesterol monohydrate crystals (d 1.045 g/mL). With higher lecithin fractions, cholesterol monohydrate crystals appeared earlier than arc and other transitional crystals. With typical physiological lecithin contents, early liquid crystals (d 1.020 g/mL) were followed by cholesterol monohydrate crystals and subsequent appearances of arc and other intermediate crystals. With higher lecithin contents, liquid crystals were followed by cholesterol monohydrate crystals only, and at the highest lecithin mole fractions, liquid crystals appeared that did not generate solid crystals. Added calcium increased solid crystal number in proportion to its concentration (5 - 20 mM) but did not influence appearance times, crystallization pathways, or micellar cholesterol solubilities. Decreases in temperature (37 degrees --> 4 degrees C), total lipid concentration (7.3 --> 2.4 g/dL), and bile salt hydrophobicity (3 alpha, 12 alpha --> 3 alpha, 7 alpha, 12 alpha --> 3 alpha, 7 beta hydroxylated taurine conjugates) progressively shifted all crystallization pathways to lower lecithin contents, retarded crystallization, and decreased micellar cholesterol solubilities. The lecithin content of mother biles decreased markedly during crystallization especially where liquid crystals were

  20. Physics olympiad

    Science.gov (United States)

    Five high school physics students will represent the U.S. at the 20th International Physics Olympiad, July 14-25 in Warsaw, Poland. The Olympiad has been held annually since 1967; this is the fourth year the U.S. will compete. The American Association of Physics Teachers administers the U.S. program; AGU is a principal sponsoring organization of the Olympiad, as is the American Institute of Physics.The students are Derrick Bass, North Miami Beach High School, Miami Beach, Fla.; Steven Gubser, Cherry Creek High School, Englewood, Colo.; Jason Jacobs, Baldwin Senior High School, Baldwin, N.Y.; Jessica Millar, West High School, Madison, Wise; and James Sarvis, Thomas Jefferson High School, Alexandria, Va.

  1. Physical Abuse

    Science.gov (United States)

    ... be acquaintances, sons, daughters, grandchildren, or others. Physical abuse that is perpetrated by spouses or intimate partners in order to gain power and control over the victim is described in ...

  2. Magic Physics?

    Science.gov (United States)

    Featonby, David

    2010-01-01

    This article examines several readily available "magic tricks" which base their "trickery" on physics principles, and questions the use of the word "magic" in the 21st century, both in popular children's science and in everyday language. (Contains 18 figures.)

  3. Engineering physics

    CERN Document Server

    Mukherji, Uma

    2015-01-01

    ENGINEERING PHYSICS is designed as a textbook for first year engineering students of a two semester course in Applied Physics according to new revised syllabus. However the scope of this book is not only limited to undergraduate engineering students and science students, it can also serve as a reference book for practicing scientists.Advanced technological topics like LCD, Squid, Maglev system, Electron microscopes, MRI, Photonics - Photonic fibre, Nano-particles, CNT, Quantum computing etc., are explained with basic underlying principles of Physics.This text explained following topics with numerous solved, unsolved problems and questions from different angles. Part-I contains crystal structure, Liquid crystal, Thermo-electric effect, Thermionic emission, Ultrasonic, Acoustics, semiconductor and magnetic materials. Whereas Part-2 contains Optics, X-rays, Electron optics, Dielectric materials, Quantum Physics and Schrodinger wave equation, Laser, Fibre-optics and Holography, Radio-activity, Super-conductivity,...

  4. Physical mathematics

    CERN Document Server

    Cahill, Kevin

    2013-01-01

    Unique in its clarity, examples and range, Physical Mathematics explains as simply as possible the mathematics that graduate students and professional physicists need in their courses and research. The author illustrates the mathematics with numerous physical examples drawn from contemporary research. In addition to basic subjects such as linear algebra, Fourier analysis, complex variables, differential equations and Bessel functions, this textbook covers topics such as the singular-value decomposition, Lie algebras, the tensors and forms of general relativity, the central limit theorem and Kolmogorov test of statistics, the Monte Carlo methods of experimental and theoretical physics, the renormalization group of condensed-matter physics and the functional derivatives and Feynman path integrals of quantum field theory.

  5. Statistical physics

    CERN Document Server

    Sadovskii, Michael V

    2012-01-01

    This volume provides a compact presentation of modern statistical physics at an advanced level. Beginning with questions on the foundations of statistical mechanics all important aspects of statistical physics are included, such as applications to ideal gases, the theory of quantum liquids and superconductivity and the modern theory of critical phenomena. Beyond that attention is given to new approaches, such as quantum field theory methods and non-equilibrium problems.

  6. Neutrino Physics

    CERN Document Server

    Xing, Zhi-Zhong

    2014-01-01

    I give a theoretical overview of some basic properties of massive neutrinos in these lectures. Particular attention is paid to the origin of neutrino masses, the pattern of lepton flavor mixing, the feature of leptonic CP violation and the electromagnetic properties of massive neutrinos. I highlight the TeV seesaw mechanisms as a possible bridge between neutrino physics and collider physics in the era characterized by the Large Hadron Collider.

  7. Nuclear Physics

    Science.gov (United States)

    Contents: V Dinucleons, published in The Physical Review , v93 n4 p908-909, 15 Feb 1954; Concentration of a Cyclotron Beam by Strong Focusing Lenses...published in The Review of Scientific Instruments, v25 n4 p365-367, Apr 1954; and Photon Splitting in a Nuclear Electrostatic Field, published in The Physical Review , v94 n2 p367-368, 15 Apr 1954.

  8. Ultrasound physics.

    Science.gov (United States)

    Shriki, Jesse

    2014-01-01

    Bedside ultrasound has become an important modality for obtaining critical information in the acute care of patients. It is important to understand the physics of ultrasound in order to perform and interpret images at the bedside. The physics of both continuous wave and pulsed wave sound underlies diagnostic ultrasound. The instrumentation, including transducers and image processing, is important in the acquisition of appropriate sonographic images. Understanding how these concepts interplay with each other enables practitioners to obtain the best possible images.

  9. Near real-time skin deformation mapping

    Science.gov (United States)

    Kacenjar, Steve; Chen, Suzie; Jafri, Madiha; Wall, Brian; Pedersen, Richard; Bezozo, Richard

    2013-02-01

    A novel in vivo approach is described that provides large area mapping of the mechanical properties of the skin in human patients. Such information is important in the understanding of skin health, cosmetic surgery[1], aging, and impacts of sun exposure. Currently, several methods have been developed to estimate the local biomechanical properties of the skin, including the use of a physical biopsy of local areas of the skin (in vitro methods) [2, 3, and 4], and also the use of non-invasive methods (in vivo) [5, 6, and 7]. All such methods examine localized areas of the skin. Our approach examines the local elastic properties via the generation of field displacement maps of the skin created using time-sequence imaging [9] with 2D digital imaging correlation (DIC) [10]. In this approach, large areas of the skin are reviewed rapidly, and skin displacement maps are generated showing the contour maps of skin deformation. These maps are then used to precisely register skin images for purposes of diagnostic comparison. This paper reports on our mapping and registration approach, and demonstrates its ability to accurately measure the skin deformation through a described nulling interpolation process. The result of local translational DIC alignment is compared using this interpolation process. The effectiveness of the approach is reported in terms of residual RMS, image entropy measures, and differential segmented regional errors.

  10. Quasipolynomial generalization of Lotka-Volterra mappings

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Bermejo, Benito; Brenig, Leon [Service de Physique Theorique et Mathematique, Universite Libre de Bruxelles, Campus Plaine - CP 231, Brussels (Belgium)]. E-mails: bhernand@ulb.ac.be; lbrenig@ulb.ac.be

    2002-07-05

    In recent years, it has been shown that Lotka-Volterra mappings constitute a valuable tool from both the theoretical and the applied points of view, with developments in very diverse fields such as physics, population dynamics, chemistry and economy. The purpose of this work is to demonstrate that many of the most important ideas and algebraic methods that constitute the basis of the quasipolynomial formalism (originally conceived for the analysis of ordinary differential equations) can be extended into the mapping domain. The extension of the formalism into the discrete-time context is remarkable as far as the quasipolynomial methodology had never been shown to be applicable beyond the differential case. It will be demonstrated that Lotka-Volterra mappings play a central role in the quasipolynomial formalism for the discrete-time case. Moreover, the extension of the formalism into the discrete-time domain allows a significant generalization of Lotka-Volterra mappings as well as a whole transfer of algebraic methods into the discrete-time context. The result is a novel and more general conceptual framework for the understanding of Lotka-Volterra mappings as well as a new range of possibilities that become open not only for the theoretical analysis of Lotka-Volterra mappings and their generalizations, but also for the development of new applications. (author)

  11. Evolution of a Laser Hybrid Welding Map

    Science.gov (United States)

    Kaplan, Alexander F. H.; Frostevarg, Jan; Ilar, Torbjörn; Bang, Hee-Seon; Bang, Han-Sur

    Laser arc hybrid welding combines the advantages but also the complex physical mechanisms of gas metal arc welding and laser keyhole welding. From manifold mainly experimental but also theoretical research results a map with versatile functions was initiated for the first time. The purpose is to survey the overall context and to facilitate navigation to the various phenomena that are shown through case studies accompanied by theoretical explanations and guidelines for optimization. Though not complete, the map enables systematic and graphical navigation to relevant publications. Based on a fundamental structure of the map, which was decided early, it is inherently extendable in the future by adding existing and new knowledge, also from other research groups, enabling evolution. The fundament of the map structure comprises gouge thickness, joint type and metal grade, in coherence with product and weld designers' starting points. The next hierarchy level of the map offers options in the joint type as well as in hybrid welding techniques. The latter contains techniques like double-sided welding, pulse shaping management of the arc or laser, CMT arcs, tandem arcs, or remelting of undercuts. In addition to laser-arc hybrid welding, other hybrid laser techniques like multilayer hot-wire laser welding of narrow gaps or hybrid laser friction stir welding can be taken into account. At the other end of the hierarchy, the map offers via a database-like archive electronic navigation to research results like weld macrographs, high speed imaging or numerical simulation results of the welding process.

  12. A first glimpse of wild lupin karyotype variation as revealed by comparative cytogenetic mapping

    Directory of Open Access Journals (Sweden)

    Karolina Susek

    2016-07-01

    Full Text Available Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n=32-52, basic chromosome numbers (x=5-7, 9, 13 and in nuclear genome size (2C DNA=0.97-2.68 pg. Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution.In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all ‘single-locus’ in L. angustifolius, in the wild lupins these clones proved to be ‘single-locus’, ‘single-locus’ with additional signals, ‘repetitive’ or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g. L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the

  13. Occupancy Grid Map Merging Using Feature Maps

    Science.gov (United States)

    2010-11-01

    Gonzalez, “Toward a unified bayesian approach to hybrid metric-topological SLAM,” IEEE Transactions on Robotics , 24(2), April 2008, 259-270. [14] G...Risetti, C. Stachniss, and W. Burgard, “Improved Techniques for grid mapping with Rao-Blackwellized Particle Filter,” IEEE Transactions on Robotics , 23

  14. On circle map coupled map lattice

    CERN Document Server

    Ahmed, E

    2002-01-01

    Circle map in one and two dimensions is studied. Both its stability, synchronization using bounded control and persistence is discussed. This work is expected to be applicable in ecology where spatial effects are known to be important. Also it will be relevant to systems where delay effects are not negligible.

  15. Acoustic mapping velocimetry

    Science.gov (United States)

    Muste, M.; Baranya, S.; Tsubaki, R.; Kim, D.; Ho, H.; Tsai, H.; Law, D.

    2016-05-01

    Knowledge of sediment dynamics in rivers is of great importance for various practical purposes. Despite its high relevance in riverine environment processes, the monitoring of sediment rates remains a major and challenging task for both suspended and bed load estimation. While the measurement of suspended load is currently an active area of testing with nonintrusive technologies (optical and acoustic), bed load measurement does not mark a similar progress. This paper describes an innovative combination of measurement techniques and analysis protocols that establishes the proof-of-concept for a promising technique, labeled herein Acoustic Mapping Velocimetry (AMV). The technique estimates bed load rates in rivers developing bed forms using a nonintrusive measurements approach. The raw information for AMV is collected with acoustic multibeam technology that in turn provides maps of the bathymetry over longitudinal swaths. As long as the acoustic maps can be acquired relatively quickly and the repetition rate for the mapping is commensurate with the movement of the bed forms, successive acoustic maps capture the progression of the bed form movement. Two-dimensional velocity maps associated with the bed form migration are obtained by implementing algorithms typically used in particle image velocimetry to acoustic maps converted in gray-level images. Furthermore, use of the obtained acoustic and velocity maps in conjunction with analytical formulations (e.g., Exner equation) enables estimation of multidirectional bed load rates over the whole imaged area. This paper presents a validation study of the AMV technique using a set of laboratory experiments.

  16. BenMAP Downloads

    Science.gov (United States)

    Download the current and legacy versions of the BenMAP program. Download configuration and aggregation/pooling/valuation files to estimate benefits. BenMAP-CE is free and open source software, and the source code is available upon request.

  17. Statistical air quality mapping

    NARCIS (Netherlands)

    Kassteele, van de J.

    2006-01-01

    This thesis handles statistical mapping of air quality data. Policy makers require more and more detailed air quality information to take measures to improve air quality. Besides, researchers need detailed air quality information to assess health effects. Accurate and spatially highly resolved maps

  18. Quaternionic versus complex maps

    Energy Technology Data Exchange (ETDEWEB)

    Asorey, M [Departamento de Fisica Teorica, Universidad de Zaragoza 50009 Zaragoza (Spain); Scolarici, G [Dipartimento di Fisica dell' Universita del Salento and INFN, Sezione di Lecce, I-73100 Lecce (Italy); Solombrino, L [Dipartimento di Fisica dell' Universita del Salento and INFN, Sezione di Lecce, I-73100 Lecce (Italy)

    2007-11-15

    We discuss the relation between completely positive quaternionic maps and the corresponding complex maps obtained via projection operation. In order to illustrate this formalism, we reobtain the (complex) qubit subdynamics of maximally entangled Bell states, as complex projection of unitary dynamics between quaternionic pure states.

  19. Pore size distribution mapping

    OpenAIRE

    Strange, John H.; J. Beau W. WEBBER; Schmidt, S.D.

    1996-01-01

    Pore size distribution mapping has been demonstrated using NMR cryoporometry\\ud in the presence of a magnetic field gradient, This novel method is extendable to 2D and 3D mapping. It offers a unique nondestructive method of obtaining full pore-size distributions in the range 3 to 100 nm at any point within a bulk sample. \\ud

  20. MUTYH Associated Polyposis (MAP)

    DEFF Research Database (Denmark)

    Poulsen, Marie Louise Mølgaard; Bisgaard, M L

    2008-01-01

    MUTYH Associated Polyposis (MAP), a Polyposis predisposition caused by biallelic mutations in the Base Excision Repair (BER) gene MUTYH, confers a marked risk of colorectal cancer (CRC). The MAP phenotype is difficult to distinguish from other hereditary CRC syndromes. Especially from Familial...

  1. Simplifying Massive Contour Maps

    DEFF Research Database (Denmark)

    Arge, Lars; Deleuran, Lasse Kosetski; Mølhave, Thomas;

    2012-01-01

    We present a simple, efficient and practical algorithm for constructing and subsequently simplifying contour maps from massive high-resolution DEMs, under some practically realistic assumptions on the DEM and contours.......We present a simple, efficient and practical algorithm for constructing and subsequently simplifying contour maps from massive high-resolution DEMs, under some practically realistic assumptions on the DEM and contours....

  2. Map-A-Planet

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Map-A-Planet website allows users to create and download custom image maps of planets and satellites from a variety of missions in an easy to use web interface

  3. Android Mapping Application

    Directory of Open Access Journals (Sweden)

    Abdalwhab Bakheet

    2014-04-01

    Full Text Available Location-aware and mapping applications have gone f rom a desirable feature to an essential part of any smart phone. Whether a user is checking into a social network, looking for a pharmacy in the middle of the night, or located in somewhere and needs help, the key is always the same: location. In this project, an Android mapping application is developed. The application is able to display the map of the whole world while online or, display a pre-downloaded map while offline, track the user’s location, display a compass to determine north, send the user’s location to others in case of emergency using SMS, receive and interpret received location from the message, display it on the map, and notify the user by the reception of the location. The application was developed using agile methodol ogy. It, met its objectives and successfully passed 91% of the final system test, recording that some limitations were discovered, the application needs further testing and can be implem ented for particular company or university using their own maps or editing the maps in OSM (op en street maps.

  4. Diffusion Based Photon Mapping

    DEFF Research Database (Denmark)

    Schjøth, Lars; Sporring, Jon; Fogh Olsen, Ole

    2008-01-01

    . To address this problem, we introduce a photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way, we preserve important illumination features, while...

  5. The Modern Geomorphological Map

    NARCIS (Netherlands)

    Seijmonsbergen, A.C.; Switzer, A.; Kennedy, D.M.

    2013-01-01

    Classical geomorphological maps are representations of the spatial distribution of landforms, materials and of the processes responsible for their formation, in a single paper map. They contain a wealth of information that is generally documented with the aid of symbol and color legends. Uniformity

  6. The CHUVA Lightning Mapping Campaign

    Science.gov (United States)

    Goodman, Steven J.; Blakeslee, Richard J.; Bailey, Jeffrey C.; Carey, Lawrence D.; Hoeller, Hartmut; Albrecht, Rachel I.; Morales, Carlos; Pinto, Osmar; Saba, Marcelo M.; Naccarato, Kleber; Hembury, Nikki; Nag, Amitabh; Heckman, Stan; Holzworth, Robert H.; Rudlosky, Scott D.; Betz, Hans-Dieter; Said, Ryan; Rauenzahn, Kim

    2011-01-01

    The primary science objective for the CHUVA lightning mapping campaign is to combine measurements of total lightning activity, lightning channel mapping, and detailed information on the locations of cloud charge regions of thunderstorms with the planned observations of the CHUVA (Cloud processes of tHe main precipitation systems in Brazil: A contribUtion to cloud resolVing modeling and to the GPM (GlobAl Precipitation Measurement) field campaign. The lightning campaign takes place during the CHUVA intensive observation period October-December 2011 in the vicinity of S o Luiz do Paraitinga with Brazilian, US, and European government, university and industry participants. Total lightning measurements that can be provided by ground-based regional 2-D and 3-D total lightning mapping networks coincident with overpasses of the Tropical Rainfall Measuring Mission Lightning Imaging Sensor (LIS) and the SEVIRI (Spinning Enhanced Visible and Infrared Imager) on the Meteosat Second Generation satellite in geostationary earth orbit will be used to generate proxy data sets for the next generation US and European geostationary satellites. Proxy data, which play an important role in the pre-launch mission development and in user readiness preparation, are used to develop and validate algorithms so that they will be ready for operational use quickly following the planned launch of the GOES-R Geostationary Lightning Mapper (GLM) in 2015 and the Meteosat Third Generation Lightning Imager (LI) in 2017. To date there is no well-characterized total lightning data set coincident with the imagers. Therefore, to take the greatest advantage of this opportunity to collect detailed and comprehensive total lightning data sets, test and validate multi-sensor nowcasting applications for the monitoring, tracking, warning, and prediction of severe and high impact weather, and to advance our knowledge of thunderstorm physics, extensive measurements from lightning mapping networks will be collected

  7. Geologic map of Mars

    Science.gov (United States)

    Tanaka, Kenneth L.; Skinner, James A.; Dohm, James M.; Irwin, Rossman P.; Kolb, Eric J.; Fortezzo, Corey M.; Platz, Thomas; Michael, Gregory G.; Hare, Trent M.

    2014-01-01

    This global geologic map of Mars, which records the distribution of geologic units and landforms on the planet's surface through time, is based on unprecedented variety, quality, and quantity of remotely sensed data acquired since the Viking Orbiters. These data have provided morphologic, topographic, spectral, thermophysical, radar sounding, and other observations for integration, analysis, and interpretation in support of geologic mapping. In particular, the precise topographic mapping now available has enabled consistent morphologic portrayal of the surface for global mapping (whereas previously used visual-range image bases were less effective, because they combined morphologic and albedo information and, locally, atmospheric haze). Also, thermal infrared image bases used for this map tended to be less affected by atmospheric haze and thus are reliable for analysis of surface morphology and texture at even higher resolution than the topographic products.

  8. Bodily maps of emotions.

    Science.gov (United States)

    Nummenmaa, Lauri; Glerean, Enrico; Hari, Riitta; Hietanen, Jari K

    2014-01-14

    Emotions are often felt in the body, and somatosensory feedback has been proposed to trigger conscious emotional experiences. Here we reveal maps of bodily sensations associated with different emotions using a unique topographical self-report method. In five experiments, participants (n = 701) were shown two silhouettes of bodies alongside emotional words, stories, movies, or facial expressions. They were asked to color the bodily regions whose activity they felt increasing or decreasing while viewing each stimulus. Different emotions were consistently associated with statistically separable bodily sensation maps across experiments. These maps were concordant across West European and East Asian samples. Statistical classifiers distinguished emotion-specific activation maps accurately, confirming independence of topographies across emotions. We propose that emotions are represented in the somatosensory system as culturally universal categorical somatotopic maps. Perception of these emotion-triggered bodily changes may play a key role in generating consciously felt emotions.

  9. Iconicity as structure mapping.

    Science.gov (United States)

    Emmorey, Karen

    2014-09-19

    Linguistic and psycholinguistic evidence is presented to support the use of structure-mapping theory as a framework for understanding effects of iconicity on sign language grammar and processing. The existence of structured mappings between phonological form and semantic mental representations has been shown to explain the nature of metaphor and pronominal anaphora in sign languages. With respect to processing, it is argued that psycholinguistic effects of iconicity may only be observed when the task specifically taps into such structured mappings. In addition, language acquisition effects may only be observed when the relevant cognitive abilities are in place (e.g. the ability to make structural comparisons) and when the relevant conceptual knowledge has been acquired (i.e. information key to processing the iconic mapping). Finally, it is suggested that iconicity is better understood as a structured mapping between two mental representations than as a link between linguistic form and human experience.

  10. Chaos control by using Motor Maps.

    Science.gov (United States)

    Arena, Paolo; Fortuna, Luigi; Frasca, Mattia

    2002-09-01

    In this paper a new method for chaos control is proposed, consisting of an unsupervised neural network, namely a Motor Map. In particular a feedback entrainment scheme is adopted: a chaotic system with a given parameter set generates the reference trajectory for another chaotic system with different parameters to be controlled: the Motor Map is required to provide the appropriate time-varying gain value for the feedback signal. The state of the controlled system is considered as input to the Motor Map. Particular efforts have been paid to the feasibility of the implementation. Indeed, the simulations performed have been oriented to design a Motor Map suitable for an hardware realization, thus some restrictive hypotheses, such as for example a low number of neurons, have been assumed. A huge number of simulations has been carried out by considering as system to be controlled a Double Scroll Chua Attractor as well as other chaotic attractors. Several reference trajectories have also been considered: a limit cycle generated by a Chua's circuit with different parameters values, a double scroll Chua attractor, a chaotic attractor of the family of the Chua's circuit attractors. In all the simulations instead of controlling the whole state space, only two state variables have been fed back. Good results in terms of settling time (namely, the period in which the map learns the control task) and steady state errors have been obtained with a few neurons. The Motor Map based adaptive controller offers high performances, specially in the case when the reference trajectory is switched into another one. In this case, a specialization of the neurons constituting the Motor Map is observed: while a group of neurons learns the appropriate control law for a reference trajectory, another group specializes itself to control the system when the other trajectory is used as a reference. A discrete components electronic realization of the Motor Map is presented and experimental results

  11. Mental Mapping: A Classroom Strategy

    Science.gov (United States)

    Solomon, Les

    1978-01-01

    Examines potential uses of mental maps in the classroom by reviewing research efforts, providing an example of the differences between mental maps of two student groups, and suggesting how to use mental maps in the geography curriculum. Mental mapping (or cognitive mapping) refers to individuals' processes of collecting, storing, and retrieving…

  12. The geologic mapping of asteroid Vesta

    Science.gov (United States)

    Williams, D.; Yingst, A.; Garry, B.

    2014-07-01

    As part of NASA's Dawn mission [1,2] we conducted a geologic mapping campaign to provide a systematic, cartography-based initial characterization of the global and regional geology of asteroid Vesta. The goal of geological maps is to place observations of surface features into their stratigraphic context to develop a geologic history of the evolution of planetary surfaces. Geologic mapping reduces the complexity of heterogeneous planetary surfaces into comprehensible portions, defining and characterizing discrete material units based upon physical attributes related to the geologic processes that produced them, and enabling identification of the relative roles of various processes (impact cratering, tectonism, volcanism, erosion and deposition) in shaping planetary surfaces [3,4]. The Dawn Science Team produced cartographic products of Vesta from the Framing Camera images, including global mosaics as well as 15 regional quadrangles [5], which served as bases for the mapping. We oversaw the geologic mapping campaign during the Nominal Mission, including production of a global geologic map at scale 1:500,000 using images from the High Altitude Mapping Orbit [6] and 15 quadrangle geologic maps at scale 1:250,000 using images from the Low Altitude Mapping Orbit [7]. The goal was to support the Dawn Team by providing geologic and stratigraphic context of surface features and supporting the analysis of data from the Visible and Infrared Spectrometer (VIR) and the Gamma Ray and Neutron Detector (GRaND). Mapping was done using ArcGIS™ software, in which quadrangle mapping built on interpretations derived from the global geologic map but were updated and modified to take advantage of the highest spatial resolution data. Despite challenges (e.g., Vesta's highly sloped surface [8] deforms impact craters and produces mass movements that buries contacts), we were successfully able to map the whole surface of Vesta and identify a geologic history as represented in our maps and

  13. nowCOAST's Map Service for Political Map Overlays

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Map Information: This nowCOAST map service provides map overlays depicting the boundaries of U.S. states, territories, counties and townships/county subdivisions,...

  14. nowCOAST's Map Service for Transportation Map Overlays

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Map Information: This nowCOAST map service provides maps depicting the locations of major world airport runways, major U.S. seaports, and latitude/longitude grid...

  15. Plasma physics

    CERN Document Server

    Cairns, R A

    1985-01-01

    This book is intended as an introduction to plasma physics at a level suitable for advanced undergraduates or beginning postgraduate students in physics, applied mathematics or astrophysics. The main prerequisite is a knowledge of electromagnetism and of the associated mathematics of vector calculus. SI units are used throughout. There is still a tendency amongst some plasma physics researchers to· cling to C.g.S. units, but it is the author's view that universal adoption of SI units, which have been the internationally agreed standard since 1960, is to be encouraged. After a short introductory chapter, the basic properties of a plasma con­ cerning particle orbits, fluid theory, Coulomb collisions and waves are set out in Chapters 2-5, with illustrations drawn from problems in nuclear fusion research and space physics. The emphasis is on the essential physics involved and (he theoretical and mathematical approach has been kept as simple and intuitive as possible. An attempt has been made to draw attention t...

  16. Chromosome mapping by FISH to metaphase and interphase nuclei. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Trask, B.

    1997-08-01

    The overall specific aims of this project were: (1) to determine the large-scale structure of interphase and metaphase chromosomes, in order to establish new capabilities for genome mapping by fluorescence in situ hybridization (FISH); (2) to detect chromosome abnormalities associated with genetic disease and map DNA sequences relative to them in order to facilitate the identification of new genes with disease-causing mutations; (3) to establish medium resolution physical maps of selected chromosomal regions using a combined metaphase and interphase mapping strategy and to corroborate physical and genetic maps and integrate these maps with the cytogenetic map; (4) to analyze the polymorphism and sequence evolution of subtelomeric regions of human chromosomes; (5) to establish a state-of-the-art FISH and image processing facility in the Department of Molecular Biotechnology, University of Washington, in order to map DNA sequences rapidly and accurately to benefit the Human Genome Project.

  17. Biometric recognition via fixation density maps

    Science.gov (United States)

    Rigas, Ioannis; Komogortsev, Oleg V.

    2014-05-01

    This work introduces and evaluates a novel eye movement-driven biometric approach that employs eye fixation density maps for person identification. The proposed feature offers a dynamic representation of the biometric identity, storing rich information regarding the behavioral and physical eye movement characteristics of the individuals. The innate ability of fixation density maps to capture the spatial layout of the eye movements in conjunction with their probabilistic nature makes them a particularly suitable option as an eye movement biometrical trait in cases when free-viewing stimuli is presented. In order to demonstrate the effectiveness of the proposed approach, the method is evaluated on three different datasets containing a wide gamut of stimuli types, such as static images, video and text segments. The obtained results indicate a minimum EER (Equal Error Rate) of 18.3 %, revealing the perspectives on the utilization of fixation density maps as an enhancing biometrical cue during identification scenarios in dynamic visual environments.

  18. Medical Physics

    OpenAIRE

    Voto Bernales, Juan; Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Lima, Perú

    2014-01-01

    Medical Physics is to study the physical phenomena that occur in the body and exert action on the agents. It also addresses the manner taught natural agents in the study and exploration of the human body and in the way in the same agents for use in the treatment of disease can be used. La Física Médica tiene por objeto estudiar los fenómenos físicos que se realizan en el organismo y la acción que sobre el ejercen los agentes. Se ocupa, además, de enseñar la manera cómo pueden utilizarse lo...

  19. Nuclear Physics

    CERN Document Server

    Savage, Martin J

    2016-01-01

    Lattice QCD is making good progress toward calculating the structure and properties of light nuclei and the forces between nucleons. These calculations will ultimately refine the nuclear forces, particularly in the three- and four-nucleon sector and the short-distance interactions of nucleons with electroweak currents, and allow for a reduction of uncertainties in nuclear many-body calculations of nuclei and their reactions. After highlighting their importance, particularly to the Nuclear Physics and High-Energy Physics experimental programs, I discuss the progress that has been made toward achieving these goals and the challenges that remain.

  20. Molecular physics

    CERN Document Server

    Demtröder, Wolfgang

    2008-01-01

    The richly illustrated book comprehensively explains the important principles of diatomic and polyatomic molecules and their spectra in two separate, distinct parts. The first part concentrates on the theoretical aspects of molecular physics, such as the vibration, rotation, electronic states, potential curves, and spectra of molecules. The different methods of approximation for the calculation of electronic wave functions and their energy are also covered. The introduction of basics terms used in group theory and their meaning in molecular physics enables an elegant description of polyatomic

  1. Mathematical physics

    CERN Document Server

    Geroch, Robert

    1985-01-01

    Mathematical Physics is an introduction to such basic mathematical structures as groups, vector spaces, topological spaces, measure spaces, and Hilbert space. Geroch uses category theory to emphasize both the interrelationships among different structures and the unity of mathematics. Perhaps the most valuable feature of the book is the illuminating intuitive discussion of the ""whys"" of proofs and of axioms and definitions. This book, based on Geroch's University of Chicago course, will be especially helpful to those working in theoretical physics, including such areas as relativity, particle

  2. Molecular mapping of chromosomes 17 and X

    Energy Technology Data Exchange (ETDEWEB)

    Barker, D.F.

    1989-01-01

    The basic aims of this project are the construction of high density genetic maps of chromosomes 17 and X and the utilization of these maps for the subsequent isolation of a set of physically overlapping DNA segment clones. The strategy depends on the utilization of chromosome specific libraries of small (1--15 kb) segments from each of the two chromosomes. Since the time of submission of our previous progress report, we have refined the genetic map of markers which we had previously isolated for chromosome 17. We have completed our genetic mapping in CEPH reference and NF1 families of 15 markers in the pericentric region of chromosome 17. Physical mapping results with three probes, were shown be in very close genetic proximity to the NF1 gene, with respect to two translocation breakpoints which disrupt the activity of the gene. All three of the probes were found to lie between the centromere and the most proximal translocation breakpoint, providing important genetic markers proximal to the NF1 gene. Our primary focus has shifted to the X chromosome. We have isolated an additional 30 polymorphic markers, bringing the total number we have isolated to over 80. We have invested substantial effort in characterizing the polymorphisms at each of these loci and constructed plasmid subclones which reveal the polymorphisms for nearly all of the loci. These subclones are of practical value in that they produce simpler and stronger patterns on human genomic Southern blots, thus improving the efficiency of the genetic mapping experiments. These subclones may also be of value for deriving DNA sequence information at each locus, necessary for establishing polymerase chain reaction primers specific for each locus. Such information would allow the use of each locus as a sequence tagged site.

  3. Fractional standard map

    Energy Technology Data Exchange (ETDEWEB)

    Edelman, Mark, E-mail: edelman@cims.nyu.ed [Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 (United States)] [Department of Physics, Stern College at Yeshiva University, 245 Lexington Avenue, New York, NY 10016 (United States); Tarasov, Vasily E. [Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 (United States)] [Skobeltsyn Institute of Nuclear Physics, Moscow State University, Moscow 119991 (Russian Federation)

    2009-12-28

    Properties of the phase space of the standard map with memory are investigated. This map was obtained from a kicked fractional differential equation. Depending on the value of the map parameter and the fractional order of the derivative in the original differential equation, this nonlinear dynamical system demonstrates attractors (fixed points, stable periodic trajectories, slow converging and slow diverging trajectories, ballistic trajectories, and fractal-like structures) and/or chaotic trajectories. At least one type of fractal-like sticky attractors in the chaotic sea was observed.

  4. Map: Geospatial paradigm

    Directory of Open Access Journals (Sweden)

    Ikonović Vesna

    2006-01-01

    Full Text Available There are different definitions of map. There is no one which is accepted in whole world or at least from the most cartographers. In the paper it will be given several definitions which are, at the best way, (according to the author’s opinion reflecting essence of map as a model of reality. Map as a universal meaning of researching can’t serve only for representing particular geospace (spatial system or some its element, or to give only clear view about geographical dispersion of objects, phenomena and processes, but have to make possible studying the patterns of that dispersion, as well as their mutual connections and conditions.

  5. The Problem of Map Illiteracy.

    Science.gov (United States)

    Ryan, James D.

    1985-01-01

    Describes an approach to eliminating "map illiteracy" in college students. Map illiteracy is defined as the inability to read and draw meaning from simple maps used in history texts and teaching. (JDH)

  6. Northern Hemisphere Synoptic Weather Maps

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Daily Series of Synoptic Weather Maps. Part I consists of plotted and analyzed daily maps of sea-level and 500-mb maps for 0300, 0400, 1200, 1230, 1300, and 1500...

  7. Review of the Space Mapping Approach to Engineering Optimization and Modeling

    DEFF Research Database (Denmark)

    Bakr, M. H.; Bandler, J. W.; Madsen, Kaj

    2000-01-01

    We review the Space Mapping (SM) concept and its applications in engineering optimization and modeling. The aim of SM is to avoid computationally expensive calculations encountered in simulating an engineering system. The existence of less accurate but fast physically-based models is exploited. S......-based Modeling (SMM). These include Space Derivative Mapping (SDM), Generalized Space Mapping (GSM) and Space Mapping-based Neuromodeling (SMN). Finally, we address open points for research and future development....

  8. Eclipse mapping of accretion discs

    CERN Document Server

    Baptista, R

    2000-01-01

    The eclipse mapping method is an inversion technique that makes use of the information contained in eclipse light curves to probe the structure, the spectrum and the time evolution of accretion discs. In this review I present the basics of the method and discuss its different implementations. I summarize the most important results obtained to date and discuss how they have helped to improve our understanding of accretion physics, from testing the theoretical radial brightness temperature distribution and measuring mass accretion rates to showing the evolution of the structure of a dwarf novae disc through its outburst cycle, from isolating the spectrum of a disc wind to revealing the geometry of disc spiral shocks. I end with an outline of the future prospects.

  9. Complex systems: physics beyond physics

    Science.gov (United States)

    Holovatch, Yurij; Kenna, Ralph; Thurner, Stefan

    2017-03-01

    Complex systems are characterised by specific time-dependent interactions among their many constituents. As a consequence they often manifest rich, non-trivial and unexpected behaviour. Examples arise both in the physical and non-physical worlds. The study of complex systems forms a new interdisciplinary research area that cuts across physics, biology, ecology, economics, sociology, and the humanities. In this paper we review the essence of complex systems from a physicists' point of view, and try to clarify what makes them conceptually different from systems that are traditionally studied in physics. Our goal is to demonstrate how the dynamics of such systems may be conceptualised in quantitative and predictive terms by extending notions from statistical physics and how they can often be captured in a framework of co-evolving multiplex network structures. We mention three areas of complex-systems science that are currently studied extensively, the science of cities, dynamics of societies, and the representation of texts as evolutionary objects. We discuss why these areas form complex systems in the above sense. We argue that there exists plenty of new ground for physicists to explore and that methodical and conceptual progress is needed most.

  10. Flipped Physics

    Science.gov (United States)

    Kettle, Maria

    2013-01-01

    This paper defines flipped learning and then examines its practical implementation in AS and A2 level physics classes, that is, classes for 16-18 year olds. The effect of this teaching style on student learning behaviour and its impact on test results are evaluated. The paper recounts the difficulties of implementing it and evaluates student…

  11. Atomic physics

    CERN Document Server

    Born, Max

    1989-01-01

    The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.

  12. Unifying Physics

    Science.gov (United States)

    Goradia, Shantilal

    2013-04-01

    Century old GR fails to unify quantum physics, nuclear force or distinguish between the mass of living bodies from inert mass. Probabilistic gravity [1] explains strong coupling (nuclear force). The natural log of the age of the universe, 10E60 in Planck times, equaling 137 (1/Alpha) extends physics to deeper science, if we stand on the shoulders of giants like Feynman and Gamow. Implications of [1] are that it is not the earth, but M and S numbers of the particles of the earth are remotely interacting with corresponding numbers of the particles of the moon and the sun respectively, neglecting other heavenly bodies in this short draft. This new physics is likely to enable creative scientific minds to throw light on a theoretical basis for an otherwise arbitrary cosmological constant, uniformity of microwave background, further vindication of Boltzmann, quantum informatics, Einstein’s later publicized views and more, eliminating the need to spend money for implicitly nonexistent quantum gravity and graviton.[4pt] [1] Journal of Physical Science and Applications 2 (7) (2012) 265-268.

  13. Physics Portfolios

    Science.gov (United States)

    Whitworth, Brooke A.; Bell, Randy L.

    2013-01-01

    Traditionally, teachers assess students' physics understanding through lab activities, responses to open-ended word problems, and tests. But there is another way to measure student understanding, one in which students apply their learning to the world around them. This article shows how to implement student portfolios, which allow students to…

  14. Physical Linguistics.

    Science.gov (United States)

    Tice, Bradley S.

    Physical linguistics is defined as the use of treatments from the field of speech pathology to enhance first and second language production in healthy individuals, resulting in increased quality and strength of phonation and articulation. A series of exercises for treating dysarthria (weakness, paralysis, discoordination, primary and secondary…

  15. Physics News

    CERN Multimedia

    Gianotti, F.

    In spite of the fact that real data will only come in the year 2006, this is a very busy and interesting time for Physics-related activities. A very short overview of these activities is given in this issue of the ATLAS News Letter, while the various topics will be described in more detail in the next issues. The Physics and Combined Performance groups are working in four main areas: 1) Assess the ATLAS potential for physics, with emphasis on new channels and ideas. Recent examples are Extra-dimensions, invisible Higgs decays, heavy ion physics, the expected potential of a "Super-LHC" running at a luminosity of 10^35, etc.. 2) Improve the understanding of the detector performance and optimise the reconstruction algorithms. Examples of issues in the pipeline are: can we tag charm-jet ? What can we gain in the jet energy resolution by combining the calorimeter and tracker information to reconstruct the jet energy ? 3) Follow detector changes and detector-related issues and monitor the impact on the perform...

  16. RHIC physics

    CERN Document Server

    Pajares, C

    1999-01-01

    A brief review of the hadronic phase transitions is presented by emphasizing the physical ideas and the main signatures of the transition in relation to the most significant results of the SPS experiments and the description of the RHIC experiments. (77 refs).

  17. Fundamental Physics

    CERN Document Server

    Ydri, Badis

    2016-01-01

    This book includes my lectures, together with their problem sets and solutions, on 1) classical mechanics (one semester), 2) thermodynamics and statistical mechanics (one semester), and 3) quantum mechanics (one semester), which I have been giving to graduate students of theoretical physics at Annaba University since 2010 .

  18. Complete Quasiconvex Mappings in Polydisc

    Institute of Scientific and Technical Information of China (English)

    LIU Tai-shun; ZHANG Wen-jun

    2006-01-01

    In this paper,a class of biholomorphic mappings called complete quasiconvex mappings is introduced and studied in bounded convex Reinhardt domains of Cn.Through a detailed analysis of the analytic characterization for this class of mappings,it is shown that this class of mappings contains the convex mappings and is also a subset of the class of starlike mappings.In the special case of the polydisc,a decomposition theorem is established for the complete quasiconvex mappings,which in turn is used to derive an improved sufficient condition for the convex mappings.

  19. Mapping posthumanism: an exchange

    OpenAIRE

    2004-01-01

    Introduction: posthumanism in question Noel Castree, Catherine Nash Mapping posthumanism Neil Badmington Modalities of posthumanism Bruce Braun Humanising posthumanism Jonathan Murdoch Humanism's excess: some thoughts on the 'post-human/ist' agenda Sarah Whatmore Organisors: Noel Castree, Catherine Nash

  20. Daily Weather Maps

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Several different government offices have published the Daily weather maps over its history. The publication has also gone by different names over time. The U.S....

  1. Minidoka - Invasive Species Mapping

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Locate and map, via the use of GPS, Rush skeletonweed on the refuge. Located areas then entered into GIS to allow refuge staff to pin point locations and treat this...

  2. FLOODPLAIN MAPPING, Bandera, TEXAS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Floodplain Mapping/Redelineation study deliverables depict and quantify the flood risks for the study area. The primary risk classifications used are the...

  3. TOXMAP®: Environmental Health Maps

    Data.gov (United States)

    U.S. Department of Health & Human Services — TOXMAP® is a Geographic Information System (GIS) that uses maps of the United States and Canada to help users visually explore data primarily from the EPA's Toxics...

  4. USGS map quadrangles

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — USGS map quandrangle boundaries with names and unique identifiers for the 1:24,000 (7.5 minute) quadrangles. Additional attributes provide unique identifiers and...

  5. BaseMap

    Data.gov (United States)

    California Department of Resources — The goal of this project is to provide a convenient base map that can be used as a starting point for CA projects. It's simple, but designed to work at a number of...

  6. Public Waters Inventory Maps

    Data.gov (United States)

    Minnesota Department of Natural Resources — This theme is a scanned and rectified version of the Minnesota DNR - Division of Waters "Public Waters Inventory" (PWI) maps. DNR Waters utilizes a small scale...

  7. The CPD Maps System

    Data.gov (United States)

    Department of Housing and Urban Development — CPD Maps includes data on the locations of existing CDBG, HOME, public housing and other HUD-funded community assets, so that users can view past investments...

  8. MAPPING IN MICRONESIA.

    Science.gov (United States)

    Olsen, Randle W.; Swinnerton, J.R.

    1984-01-01

    The U. S. Geological Survey has recently completed a series of new topographic maps of Micronesia in cooperation with the Trust Territory of the Pacific Islands, the Federal agency administering the islands. Monocolor 1:10,000-scale manuscripts were compiled, from which 1:25,000-scale metric quadrangles were derived with symbology consistent with USGS quadrangle mapping. The publication of these new maps coincides with the impending political changes resulting from self-determination referendums held in Micronesia. Local sources have helped considerably with field logistics and resolution of geographic name controversies. Technical aspects of this project included development of tropical feature symbology, location of cadastral subdivisions and associated boundaries and mapping of many outlying coral reefs.

  9. NOS Bathymetric Maps

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This collection of bathymetric contour maps which represent the seafloor topography includes over 400 individual titles and covers US offshore areas including Hawaii...

  10. Marketplace Enrollment Maps

    Data.gov (United States)

    U.S. Department of Health & Human Services — The maps show the distribution of consumers in a state who enrolled in marketplace plans through federally facilitated, partnership, and supported state-based...

  11. Programming with Hierarchical Maps

    DEFF Research Database (Denmark)

    Ørbæk, Peter

    This report desribes the hierarchical maps used as a central data structure in the Corundum framework. We describe its most prominent features, ague for its usefulness and briefly describe some of the software prototypes implemented using the technology....

  12. National Coastal Mapping Program

    Data.gov (United States)

    Army Corps of Engineers, Department of the Army, Department of Defense — The U. S. Army Corps of Engineers (USACE) National Coastal Mapping Program (NCMP) is designed to provide high-resolution elevation and imagery data along U.S....

  13. PDS Planetary Maps API

    Data.gov (United States)

    National Aeronautics and Space Administration — We are developing a set of NASA Extensions to the Google Maps API—and soon to other frameworks such as OpenLayers as well—that will make these platforms more useful...

  14. Haz-Map

    Data.gov (United States)

    U.S. Department of Health & Human Services — Haz-Map is an occupational health database designed for health and safety professionals and for consumers seeking information about the adverse effects of workplace...

  15. MetaMap

    Data.gov (United States)

    U.S. Department of Health & Human Services — MetaMap is a highly configurable application developed by the Lister Hill National Center for Biomedical Communications at the National Library of Medicine (NLM) to...

  16. Genetic mapping of the dentinogenesis imperfecta type II locus

    Energy Technology Data Exchange (ETDEWEB)

    Crosby, A.H.; Dixon, M.J. [Univ. of Manchester (United Kingdom); Scherpbier-Heddema, T. [Fox Chase Cancer Center, Philadelphia, PA (United States)] [and others

    1995-10-01

    Dentinogenesis imperfecta type II (DGI-II) is an autosomal dominant disorder of dentin formation, which has previously been mapped to chromosome 4q12-21. In the current study, six novel short tandem-repeat polymorphisms (STRPs) have been isolated, five of which show significant evidence of linkage to DGI-II. To determine the order of the STRPs and define the genetic distance between them, nine loci (including polymorphisms for two known genes) were mapped through the CEPH reference pedigrees. The resulting genetic map encompasses 16.3 cM on the sex-averaged map. To combine this map with a physical map of the region, all of the STRPs were mapped through a somatic cell hybrid panel. The most likely location for the DGI-II locus within the fixed marker map is in the D4S2691-D4S2692 interval of 6.6 cM. The presence of a marker that shows no recombination with the DGI-II phenotype between the flanking markers provides an important anchor point for the creation of physical continuity across the DGI-II candidate region. 38 refs., 4 figs., 2 tabs.

  17. Irreversible quantum baker map.

    Science.gov (United States)

    Łoziński, Artur; Pakoński, Prot; Zyczkowski, Karol

    2002-12-01

    We propose a generalization of the model of classical baker map on the torus, in which the images of two parts of the phase space do overlap. This transformation is irreversible and cannot be quantized by means of a unitary Floquet operator. A corresponding quantum system is constructed as a completely positive map acting in the space of density matrices. We investigate spectral properties of this superoperator and their link with the increase of the entropy of initially pure states.

  18. Maps and (no) Simulations

    Science.gov (United States)

    Forest, Etienne

    As the title suggests, I examine the role of maps in accelerator theory, conveniently leaving simulation out of the picture for lack of time and space. This is really a primer on the map-based "Courant Snyder" theory as independently proposed by Dragt's group (author included) and Turchetti's group at Bologna. Quite obviously it is viewed here from the author's own perspective and prejudices.

  19. Olympic Maps Available

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Beijing is publishing a set of Olympic maps covering everything from the location of sporting venues to the city’s history As soon as Zhou Liyi hopped off the train from Shanghai to Beijing, he hurried to Wangfujing Xinhua Book Store,one of the largest of its kind in Beijing,to buy an Olympic map. Zhou is a Shanghai resident who came to Beijing on business and plans to return as a

  20. Wind Resource Maps (Postcard)

    Energy Technology Data Exchange (ETDEWEB)

    2011-07-01

    The U.S. Department of Energy's Wind Powering America initiative provides high-resolution wind maps and estimates of the wind resource potential that would be possible from development of the available windy land areas after excluding areas unlikely to be developed. This postcard is a marketing piece that stakeholders can provide to interested parties; it will guide them to Wind Powering America's online wind energy resource maps.

  1. Irreversible Quantum Baker Map

    CERN Document Server

    Lozinski, A; Zyczkowski, K; Lozinski, Artur; Pakonski, Prot; Zyczkowski, Karol

    2002-01-01

    We propose a generalization of the model of classical baker map on the torus, in which the images of two parts of the phase space do overlap. This transformation is irreversible and cannot be quantized by means of a unitary Floquet operator. A corresponding quantum system is constructed as a completely positive map acting in the space of density matrices. We investigate spectral properties of this super-operator and their link with the increase of the entropy of initially pure states.

  2. Interactive Metro Map Editing.

    Science.gov (United States)

    Wang, Yu-Shuen; Peng, Wan-Yu

    2016-02-01

    Manual editing of a metro map is essential because many aesthetic and readability demands in map generation cannot be achieved by using a fully automatic method. In addition, a metro map should be updated when new metro lines are developed in a city. Considering that manually designing a metro map is time-consuming and requires expert skills, we present an interactive editing system that considers human knowledge and adjusts the layout to make it consistent with user expectations. In other words, only a few stations are controlled and the remaining stations are relocated by our system. Our system supports both curvilinear and octilinear layouts when creating metro maps. It solves an optimization problem, in which even spaces, route straightness, and maximum included angles at junctions are considered to obtain a curvilinear result. The system then rotates each edge to extend either vertically, horizontally, or diagonally while approximating the station positions provided by users to generate an octilinear layout. Experimental results, quantitative and qualitative evaluations, and user studies show that our editing system is easy to use and allows even non-professionals to design a metro map.

  3. Mars synthetic topographic mapping

    Science.gov (United States)

    Wu, S.S.C.

    1978-01-01

    Topographic contour maps of Mars are compiled by the synthesis of data acquired from various scientific experiments of the Mariner 9 mission, including S-band radio-occulation, the ultraviolet spectrometer (UVS), the infrared radiometer (IRR), the infrared interferometer spectrometer (IRIS) and television imagery, as well as Earth-based radar information collected at Goldstone, Haystack, and Arecibo Observatories. The entire planet is mapped at scales of 1:25,000,000 and 1:25,000,000 using Mercator, Lambert, and polar stereographic map projections. For the computation of map projections, a biaxial spheroid figure is adopted. The semimajor and semiminor axes are 3393.4 and 3375.7 km, respectively, with a polar flattening of 0.0052. For the computation of elevations, a topographic datum is defined by a gravity field described in terms of spherical harmonics of fourth order and fourth degree combined with a 6.1-mbar occulation pressure surface. This areoid can be approximated by a triaxial ellipsoid with semimajor axes of A = 3394.6 km and B = 3393.3 km and a semiminor axis of C = 3376.3 km. The semimajor axis A intersects the Martian surface at longitude 105??W. The dynamic flattening of Mars is 0.00525. The contour intercal of the maps is 1 km. For some prominent features where overlapping pictures from Mariner 9 are available, local contour maps at relatively larger scales were also compiled by photogrammetric methods on stereo plotters. ?? 1978.

  4. Creating Heliophysics Concept Maps

    Science.gov (United States)

    Ali, N. A.; Peticolas, L. M.; Paglierani, R.; Mendez, B. J.

    2011-12-01

    The Center for Science Education at University of California Berkeley's Space Sciences Laboratory is creating concept maps for Heliophysics and would like to get input from scientists. The purpose of this effort is to identify key concepts related to Heliophysics and map their progression to show how students' understanding of Heliophysics might develop from Kindergarten through higher education. These maps are meant to tie into the AAAS Project 2061 Benchmarks for Scientific Literacy and National Science Education Standards. It is hoped that the results of this effort will be useful for curriculum designers developing Heliophysics-related curriculum materials and classroom teachers using Heliophysics materials. The need for concept maps was identified as a result of product analysis undertaken by the NASA Heliophysics Forum Team. The NASA Science Education and Public Outreach Forums have as two of their goals to improve the characterization of the contents of the Science Mission Directorate and Public Outreach (SMD E/PO) portfolio (Objective 2.1) and assist SMD in addressing gaps in the portfolio of SMD E/PO products and project activities (Objective 2.2). An important part of this effort is receiving feedback from solar scientists regarding the inclusion of key concepts and their progression in the maps. This session will introduce the draft concept maps and elicit feedback from scientists.

  5. EDITORIAL: Physics competitions Physics competitions

    Science.gov (United States)

    Jordens, H.; Mathelitsch, L.

    2009-11-01

    1. Physics competitions: aims and realizations One aim of physics competitions is to increase the interest of young students, primarily at upper secondary level, to physics and natural sciences in general. A competition has motivational aspects known usually from sports events or games—comparing one's own ability with others, of course with the desire to be better and to win. If competitions reach nationwide and even international levels, additional stimulation is created. Competitions provide greatest attraction to possible winners, to the group of gifted people in a particular field. This implies that science contests are excellent tools for the promotion of talented students. Traditional teaching has been shown to have problems in supporting this group of students. Very often teachers are overstretched with the demands of teaching both low- and high-level students. Extracurricular activities are therefore a good chance to relieve the teacher, and to give talented students the opportunity for appropriate training and challenge. The competitions, however, have a broader impact and address more young people than one might guess from the statements above. Training courses and selection at school level give a larger group of students extra and, to some extent, complimentary education in physics. The degree of complexity of the tasks corresponds very often to the standards of the next level of education in the school system. Interestingly, many physics competitions have their origin in countries beyond the former Iron Curtain. They started as regional and national tournaments, were joined by neighbouring countries and have grown, in some cases, to events with participants from more than 80 countries. Although the features mentioned above are common to the different competitions, there are distinct differences between them [1]. The International Physics Olympiad (IPhO) is the oldest international physics competition for students at upper secondary level [2]. It dates

  6. SYSTEM FOR AUTOMATIC GENERALIZATION OF TOPOGRAPHIC MAPS

    Institute of Scientific and Technical Information of China (English)

    YAN Hao-wen; LI Zhi-lin; AI Ting-hua

    2006-01-01

    With the construction of spatial data infrastructure, automated topographic map generalization becomes an indispensable component in the community of cartography and geographic information science. This paper describes a topographic map generalization system recently developed by the authors. The system has the following characteristics: 1) taking advantage of three levels of automation, i.e. fully automated generalization, batch generalization,and interactive generalization, to undertake two types of processes, i.e. intelligent inference process and repetitive operation process in generalization; 2) making use of two kinds of sources for generalizing rule library, i.e. written specifications and cartographers' experiences, to define a six-element structure to describe the rules; 3) employing a hierarchical structure for map databases, logically and physically; 4) employing a grid indexing technique and undo/redo operation to improve database retrieval and object generalization efficiency. Two examples of topographic map generalization are given to demonstrate the system. It reveals that the system works well. In fact, this system has been used for a number of projects and it has been found that a great improvement in efficiency compared with traditional map generalization process can be achieved.

  7. Mapping genes on human chromosome 20

    Energy Technology Data Exchange (ETDEWEB)

    Keith, T.; Phipps, P.; Serino, K. [Collaborative Research, Inc., Waltham, MA (United States)] [and others

    1994-09-01

    While a substantial number of genes have been physically localized to human chromosome 20, few have been genetically mapped. In the process of developing a genetic linkage map of chromosome 20, we have mapped microsatellite polymorphisms associated with six genes. Three of these had highly informative polymorphisms (greater than 0.70) that were originally identified by other investigators. These include avian sarcoma oncogene homolog (SRC), ribophorin II (RPN2), and phosphoenolpyruvate carboxykinase (PCK1). Polymorphisms associated with two genes were determined following a screen of their DNA sequences in GenBank. These include dinucleotide polymorphisms in introl II of cystatin c (CST3) and in the promoter region of neuroendocrine convertase 2 (NEC2) with heterozygosities of 0.52 and 0.54, respectively. A sixth gene, prodynorphin (PDYN) was mapped following the identification of a dinucleotide repeat polymorphism (heterozygosity of 0.35) in a cosmid subclone from a YAC homologous to the original phage clone. CA-positive cosmid subclones from a YAC for an additional gene, guanine nucleotide binding protein, alpha (GNAS10), have been identified and sequencing is in progress. Similar efforts were utilized to identify a microsatellite polymorphism from a half-YAC cloned by W. Brown and localized by FISH to 20pter. This polymorphism is highly informative, with a heterozygosity of 0.83, and serves to delimit the genetic map of the short arm of this chromosome.

  8. Mapping Nursing language terms of Parkinson's disease

    Directory of Open Access Journals (Sweden)

    Michelle Hyczy de Siqueira Tosin

    2015-06-01

    Full Text Available OBJECTIVE Implementing cross-mapping of Nursing language terms with the terminology of NANDA International, contained in records of patients with Parkinson's disease in rehabilitation. METHOD Descriptive study of cross mapping, carried out in three steps. A simple random sample of 67 files of patients who participated in the rehabilitation in the period between March 2009 and April 2013. RESULTS We identified 454 terms of Nursing language that resulted in 54 diagnoses after cross-mapping, present in 11 of the 13 taxonomy domains. The most mapped diagnosis was "Impaired urinary elimination" (59.7%, followed by "Urgent urinary incontinence" (55.2%, "Willingness to self-control improved health" (50.7%, "Constipation" (47.8% and "Compromised physical mobility" (29.9%. Seven described terms were not mapped due to a corresponding defining characteristic being absent. CONCLUSION It was possible to determine the profile of patients, as well as the complexity of nursing care in the rehabilitation of patients with Parkinson's disease.

  9. Development of base maps' role in soil mapping

    Science.gov (United States)

    Miller, Brad; Brevik, Eric

    2014-05-01

    One of the ultimate goals of soil science is the production of accurate soil maps, but historically these thematic maps have relied upon base maps for positional reference and later for parameters that help predict soil properties. This presentation reviews the history of base maps and the dependence of soil mapping on them. The availability of geographic technology for producing these base maps has constrained and directed the geographic study of soil. A lack of accurate methods for determining location limited early geographic description of soils to narratives. The availability of accurate topographic maps in the late 18th century, fueled by governments' interests in documenting national boundaries and popular interest in world atlases, provided the first base maps for soil geographers. These soil maps primarily used the topographic maps as a spatial reference onto which the thematic details were drawn. Due to the late start of a systematic topographic survey in the United States, early Soil Survey maps depended upon plat maps for spatial reference. The adoption of aerial photographs in the process of soil mapping increased the role of base maps as predictive parameters. In the current geospatial revolution, global positioning systems and geographic information systems have nearly replaced the need for base maps to provide spatial reference. Today, base maps are more likely to be used as parameters in landscape models for predicting the spatial distribution of soil properties and classes. As model parameters for digital soil maps, base maps constitute the library of predictive variables and constrain the supported resolution of the soil map. This change in the relationship between base maps and the soil map is a paradigm shift that affects fundamental definitions of geography, such as scale, resolution, and detectable features. These concepts are the essential tools used to study the spatial characteristics of Earth Systems.

  10. Few-body physics

    CERN Document Server

    Briceño, Raúl A

    2014-01-01

    Few-body hadronic observables play an essential role in a wide number of processes relevant for both particle and nuclear physics. In order for Lattice QCD to offer insight into the interpretation of few-body states, a theoretical infrastructure must be developed to map Euclidean-time correlation functions to the desired Minkowski-time few-body observables. In this talk, I review the formal challenges associated with the studies of such systems via Lattice QCD, as first introduced by Maiani and Testa, and I also review the methodology to circumvent said limitations. The first main example of the latter is the formalism by Luscher to analyze elastic scattering and a second is the method by Lellouch and Luscher to analyze weak decays. I discus recent theoretical generalizations of these frameworks that allow for the determination of scattering amplitudes, resonances, nonlocal contribution to matrix elements, and form factors below and above inelastic thresholds. Finally, I outline outstanding problems, includin...

  11. Conformal mappings and CR mappings on the Engel group

    Institute of Scientific and Technical Information of China (English)

    WU QingYan; WANG Wei

    2009-01-01

    We show that conformal mappings between the Engel groups are CR or anti-CR mappings.This reduces the determination of conformal mappings to a problem in the theory of several complex analysis. The result about the group of CR automorphisms is used to determine the identity component of the group of conformal mappings on the Engel group.

  12. Conformal mappings and CR mappings on the Engel group

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We show that conformal mappings between the Engel groups are CR or anti-CR mappings. This reduces the determination of conformal mappings to a problem in the theory of several complex analysis.The result about the group of CR automorphisms is used to determine the identity component of the group of conformal mappings on the Engel group.

  13. Geologic Mapping of Vesta

    Science.gov (United States)

    Yingst, R. A.; Mest, S. C.; Berman, D. C.; Garry, W. B.; Williams, D. A.; Buczkowski, D.; Jaumann, R.; Pieters, C. M.; De Sanctis, M. C.; Frigeri, A.; Le Corre, L.; Preusker, F.; Raymond, C. A.; Reddy, V.; Russell, C. T.; Roatsch, T.; Schenk, P. M.

    2014-01-01

    We report on a preliminary global geologic map of Vesta, based on data from the Dawn spacecraft's High- Altitude Mapping Orbit (HAMO) and informed by Low-Altitude Mapping Orbit (LAMO) data. This map is part of an iterative mapping effort; the geologic map has been refined with each improvement in resolution. Vesta has a heavily-cratered surface, with large craters evident in numerous locations. The south pole is dominated by an impact structure identified before Dawn's arrival. Two large impact structures have been resolved: the younger, larger Rheasilvia structure, and the older, more degraded Veneneia structure. The surface is also characterized by a system of deep, globe-girdling equatorial troughs and ridges, as well as an older system of troughs and ridges to the north. Troughs and ridges are also evident cutting across, and spiraling arcuately from, the Rheasilvia central mound. However, no volcanic features have been unequivocally identified. Vesta can be divided very broadly into three terrains: heavily-cratered terrain; ridge-and-trough terrain (equatorial and northern); and terrain associated with the Rheasilvia crater. Localized features include bright and dark material and ejecta (some defined specifically by color); lobate deposits; and mass-wasting materials. No obvious volcanic features are evident. Stratigraphy of Vesta's geologic units suggests a history in which formation of a primary crust was followed by the formation of impact craters, including Veneneia and the associated Saturnalia Fossae unit. Formation of Rheasilvia followed, along with associated structural deformation that shaped the Divalia Fossae ridge-and-trough unit at the equator. Subsequent impacts and mass wasting events subdued impact craters, rims and portions of ridge-and-trough sets, and formed slumps and landslides, especially within crater floors and along crater rims and scarps. Subsequent to the formation of Rheasilvia, discontinuous low-albedo deposits formed or were

  14. Geologic mapping of Vesta

    Science.gov (United States)

    Yingst, R. A.; Mest, S. C.; Berman, D. C.; Garry, W. B.; Williams, D. A.; Buczkowski, D.; Jaumann, R.; Pieters, C. M.; De Sanctis, M. C.; Frigeri, A.; Le Corre, L.; Preusker, F.; Raymond, C. A.; Reddy, V.; Russell, C. T.; Roatsch, T.; Schenk, P. M.

    2014-11-01

    We report on a preliminary global geologic map of Vesta, based on data from the Dawn spacecraft's High-Altitude Mapping Orbit (HAMO) and informed by Low-Altitude Mapping Orbit (LAMO) data. This map is part of an iterative mapping effort; the geologic map has been refined with each improvement in resolution. Vesta has a heavily-cratered surface, with large craters evident in numerous locations. The south pole is dominated by an impact structure identified before Dawn's arrival. Two large impact structures have been resolved: the younger, larger Rheasilvia structure, and the older, more degraded Veneneia structure. The surface is also characterized by a system of deep, globe-girdling equatorial troughs and ridges, as well as an older system of troughs and ridges to the north. Troughs and ridges are also evident cutting across, and spiraling arcuately from, the Rheasilvia central mound. However, no volcanic features have been unequivocally identified. Vesta can be divided very broadly into three terrains: heavily-cratered terrain; ridge-and-trough terrain (equatorial and northern); and terrain associated with the Rheasilvia crater. Localized features include bright and dark material and ejecta (some defined specifically by color); lobate deposits; and mass-wasting materials. No obvious volcanic features are evident. Stratigraphy of Vesta's geologic units suggests a history in which formation of a primary crust was followed by the formation of impact craters, including Veneneia and the associated Saturnalia Fossae unit. Formation of Rheasilvia followed, along with associated structural deformation that shaped the Divalia Fossae ridge-and-trough unit at the equator. Subsequent impacts and mass wasting events subdued impact craters, rims and portions of ridge-and-trough sets, and formed slumps and landslides, especially within crater floors and along crater rims and scarps. Subsequent to the formation of Rheasilvia, discontinuous low-albedo deposits formed or were

  15. EDITORIAL: Physics competitions Physics competitions

    Science.gov (United States)

    Jordens, H.; Mathelitsch, L.

    2011-07-01

    International tests on competences, such as TIMSS or PISA, and knowledge of young students have revealed low average scores in many countries, often unexpectedly. One effective measure to increase the average standard of a population is to bring the last third of the group to a higher level. Therefore, many nations put some effort into this activity. This brings the danger that not enough attention is paid to students at the other end, those who are talented. Indeed, it is a very difficult task for a teacher to support the less able and at the same time challenge the gifted students, to lead them to the limits of their abilities and provide for a smooth transition to university study. Physics competitions have been proven to fulfil these last demands to a large degree, and therefore are an important additional and, to some extent, complementary tool for the promotion of talented students. This third special section on physics competitions in European Journal of Physics contains three papers, each dealing with a different form of science contest. The first continues the series of presentations of tasks performed at the International Young Physicists' Tournament, which was held in Vienna in 2011. First place went to the team from Singapore, and they have put their investigation on vertical oscillations of coupled magnets into written form (not required by the tournament, where an oral presentation and a defence and discussion are the central aspects). Their paper shows how rich in physics this problem is, and what level of solutions high-school students can already achieve. Sadly, those responsible for the organization of last year's International Physics Olympiad did not provide us with a report on this competition. This is unfortunate, since the Olympiad in Zagreb was very successful and, in particular, the experimental tasks were creative and demanding. Very similar to the aims and the execution of the Physics Olympiad is the International Olympiad on Astronomy

  16. Particle physics

    CERN Document Server

    Kennedy, Eugene

    2012-01-01

    Stimulated by the Large Hadron Collider and the search for the elusive Higgs Boson, interest in particle physics continues at a high level among scientists and the general public. This book includes theoretical aspects, with chapters outlining the generation model and a charged Higgs boson model as alternative scenarios to the Standard Model. An introduction is provided to postulated axion photon interactions and associated photon dispersion in magnetized media. The complexity of particle physics research requiring the synergistic combination of theory, hardware and computation is described in terms of the e-science paradigm. The book concludes with a chapter tackling potential radiation hazards associated with extremely weakly interacting neutrinos if produced in copious amounts with future high-energy muon-collider facilities.

  17. Reactor Physics

    Energy Technology Data Exchange (ETDEWEB)

    Ait Abderrahim, A

    2001-04-01

    The Reactor Physics and MYRRHA Department of SCK-CEN offers expertise in various areas of reactor physics, in particular in neutronics calculations, reactor dosimetry, reactor operation, reactor safety and control and non-destructive analysis of reactor fuel. This expertise is applied in the Department's own research projects in the VENUS critical facility, in the BR1 reactor and in the MYRRHA project (this project aims at designing a prototype Accelerator Driven System). Available expertise is also used in programmes external to the Department such as the reactor pressure steel vessel programme, the BR2 reactor dosimetry, and the preparation and interpretation of irradiation experiments by means of neutron and gamma calculations. The activities of the Fuzzy Logic and Intelligent Technologies in Nuclear Science programme cover several domains outside the department. Progress and achievements in these topical areas in 2000 are summarised.

  18. Astroparticle physics

    Science.gov (United States)

    Ong, Rene A.

    2013-12-01

    Astroparticle physics is a rapidly developing field that has a high degree of overlap with particle physics and astronomy. This paper summarizes recent results and leading experiments in two selected areas: very high energy astrophysics and dark matter. Both areas have made great progress in the last 5 years due to improved instrumentation and a growing community. In very high energy astrophysics, many sources of GeV and TeV radiation have been detected and the challenge now is to fully understand the processes involved at these sites of extreme particle acceleration. In the area of dark matter, there is a close scientific connection between astroparticle experiments and the Large Hadron Collider (LHC). The combination of the LHC, direct-detection and indirect-detection experiments provide critical complementarity and unprecedented sensitivity in the quest to understand this deep mystery.

  19. Mastering physics

    CERN Multimedia

    2006-01-01

    CERN hosts a series of videoconference masterclasses for high-school students. A screen shot of part of the masterclasses videoconference. For two weeks in the middle of March CERN played host to a series of videoconferences as part of the European Particle Physics Masterclasses 2006. The masterclasses were organized for the second consecutive year by ATLAS physicist Michael Kobel from the Technical University of Dresden and colleagues from the European Particle Physics Outreach Group (EPPOG), and more than 3100 high-school students from the United States and 17 countries in Europe participated. On each of the 14 days, between four and six universities hosted groups of students, providing introductory lectures, institute tours and hands-on exercises including the popular 'Hands on CERN' package for analyzing LEP data. To support these events, a CD containing material in 16 languages was distributed to every student. As a grand finale of the day, the groups of students connected to CERN for a videoconference,...

  20. Terahertz physics

    CERN Document Server

    Lewis, R A

    2012-01-01

    Terahertz physics covers one of the least explored but richest regions of the electromagnetic spectrum. Designed for independent learning, this is the first book to open up this exciting new field to students of science and engineering. Written in a clear and consistent style, the textbook focuses on an understanding of fundamental physical principles at terahertz frequencies and their applications. Part I outlines the foundations of terahertz science, starting with the mathematical representation of oscillations before exploring terahertz-frequency light, terahertz phenomena in matter and the terahertz interactions between light and matter. Part II covers components of terahertz technology, from sources of terahertz frequency radiation, through the manipulation of the radiation, to its detection. Part III deals with applications, including time-domain spectroscopy. Highlighting modern developments and concepts, the book is ideal for self-study. It features precise definitions, clear explanations, instructive...