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Sample records for monopyrrolide map complexes

  1. Z-Selective Olefin Metathesis Processes Catalyzed by a Molybdenum Hexaisopropylterphenoxide Monopyrrolide Complex

    PubMed Central

    Flook, Margaret M.; Jiang, Annie J.; Schrock, Richard R.; Müller, Peter; Hoveyda, Amir H.

    2009-01-01

    The molybdenum-based monoaryloxide monopyrrolide (MAP) species, Mo(NAd)(CHCMe2Ph)(C4H4N)(HIPTO) (2a), which contains “small” imido (Ad = 1-adamantyl) and “large” aryloxide (HIPTO = O-2,6(2,4,6-i-Pr3C6H2)C6H3) ligands, catalyzes Z-selective metathesis reactions as a consequence of intermediate metallacyclobutane species not being able to have a (anti) substituent pointing toward the HIPTO group. ROMP of dicarbomethoxynorbornadiene (DCMNBD) with 2% 2a in toluene leads to >99% cis and >99% syndiotactic poly(DCMNBD), while ROMP of cyclooctene and 1,5-cyclooctadiene (300 equiv)with initiator 2a leads to poly(cyclooctene) and poly(cyclooctadiene) that have cis contents of >99%; all are previously unknown microstructures. Z-selectivity is also observed in the metathesis of cis-4-octene and cis-3-hexene by initiator 2a to give cis-3-heptene. PMID:19462947

  2. Physical mapping of complex genomes

    DOEpatents

    Evans, Glen A.

    1993-01-01

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

  3. Physical mapping of complex genomes

    DOEpatents

    Evans, G.A.

    1993-06-15

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

  4. Grammatical complexity for two-dimensional maps

    NASA Astrophysics Data System (ADS)

    Hagiwara, Ryouichi; Shudo, Akira

    2004-11-01

    We calculate the grammatical complexity of the symbol sequences generated from the Hénon map and the Lozi map using the recently developed methods to construct the pruning front. When the map is hyperbolic, the language of symbol sequences is regular in the sense of the Chomsky hierarchy and the corresponding grammatical complexity takes finite values. It is found that the complexity exhibits a self-similar structure as a function of the system parameter, and the similarity of the pruning fronts is discussed as an origin of such self-similarity. For non-hyperbolic cases, it is observed that the complexity monotonically increases as we increase the resolution of the pruning front.

  5. Hamiltonian maps in the complex plane

    SciTech Connect

    Greene, J.M.; Percival, I.C.

    1981-01-01

    Following Arnol'd's proof of the KAM theorem, an analogy with the vertical pendulum, and some general arguments concerning maps in the complex plane, detailed calculations are presented and illustrated graphically for the standard map at the golden mean frequency. The functional dependence of the coordinate q on the canonical angle variable theta is analytically continued into the complex theta-plane, where natural boundaries are found at constant absolute values of Im theta. The boundaries represent the appearance of chaotic motion in the complex plane. Two independent numerical methods based on Fourier analysis in the angle variable were used, one based on a variation-annihilation method and the other on a double expansion. The results were further checked by direct solution of the complex equations of motion. The numerically simpler, but intrinsically complex, semipendulum and semistandard map are also studied. We conjecture that natural boundaries appear in the analogous analytic continuation of the invariant tori or KAM surfaces of general nonintegrable systems.

  6. Is Mapping of Complex Fractionated Electrograms Obsolete?

    PubMed Central

    Sohal, Manav; Choudhury, Rajin; Taghji, Philippe; Louw, Ruan; Wolf, Michael; Fedida, Joel; Vandekerckhove, Yves; Tavernier, Rene; Duytschaever, Mattias; Knecht, Sébastien

    2015-01-01

    Atrial fibrillation is the most common clinically encountered arrhythmia and catheter ablation has emerged as a viable treatment option in drug-refractory cases. Pulmonary vein isolation is widely regarded as the cornerstone for successful outcomes in paroxysmal AF given that the pulmonary veins are a frequent source of AF triggering. Ablation strategies for persistent AF are less well defined. Mapping and ablation of complex fractionated electrograms (CFAEs) is one strategy that has been proposed as a means of modifying the atrial substrate thought to be critical to the perpetuation of AF. Results of clinical studies have proved conflicting and there are now strong data to suggest that pulmonary vein isolation alone is associated with outcomes comparable to those of pulmonary vein isolation plus CFAE ablation. Several studies have demonstrated that the majority of CFAEs are passive phenomena and therefore not critical to the perpetuation of AF. Conventional mapping technologies (using a bipolar or circular mapping catheter) lack the spatiotemporal resolution to identify mechanisms of AF persistence. The development of wide-field mapping techniques allows simultaneous acquisition of activation data over large areas. This strategy has the potential to better identify regions critical to AF perpetuation, and preliminary data suggest that ablation outcomes are improved when guided by these techniques. While mapping and ablation of all CFAEs is almost certainly obsolete, better identification of regions responsible for AF persistence has the potential to improve outcomes in ablation of persistent AF. PMID:26835111

  7. A Protein Complex Map of Trypanosoma brucei

    PubMed Central

    Mehta, Vaibhav; Najafabadi, Hamed S.; Moshiri, Houtan; Jardim, Armando; Salavati, Reza

    2016-01-01

    The functions of the majority of trypanosomatid-specific proteins are unknown, hindering our understanding of the biology and pathogenesis of Trypanosomatida. While protein-protein interactions are highly informative about protein function, a global map of protein interactions and complexes is still lacking for these important human parasites. Here, benefiting from in-depth biochemical fractionation, we systematically interrogated the co-complex interactions of more than 3354 protein groups in procyclic life stage of Trypanosoma brucei, the protozoan parasite responsible for human African trypanosomiasis. Using a rigorous methodology, our analysis led to identification of 128 high-confidence complexes encompassing 716 protein groups, including 635 protein groups that lacked experimental annotation. These complexes correlate well with known pathways as well as for proteins co-expressed across the T. brucei life cycle, and provide potential functions for a large number of previously uncharacterized proteins. We validated the functions of several novel proteins associated with the RNA-editing machinery, identifying a candidate potentially involved in the mitochondrial post-transcriptional regulation of T. brucei. Our data provide an unprecedented view of the protein complex map of T. brucei, and serve as a reliable resource for further characterization of trypanosomatid proteins. The presented results in this study are available at: www.TrypsNetDB.org. PMID:26991453

  8. Mapping complex traits as a dynamic system

    NASA Astrophysics Data System (ADS)

    Sun, Lidan; Wu, Rongling

    2015-06-01

    Despite increasing emphasis on the genetic study of quantitative traits, we are still far from being able to chart a clear picture of their genetic architecture, given an inherent complexity involved in trait formation. A competing theory for studying such complex traits has emerged by viewing their phenotypic formation as a "system" in which a high-dimensional group of interconnected components act and interact across different levels of biological organization from molecules through cells to whole organisms. This system is initiated by a machinery of DNA sequences that regulate a cascade of biochemical pathways to synthesize endophenotypes and further assemble these endophenotypes toward the end-point phenotype in virtue of various developmental changes. This review focuses on a conceptual framework for genetic mapping of complex traits by which to delineate the underlying components, interactions and mechanisms that govern the system according to biological principles and understand how these components function synergistically under the control of quantitative trait loci (QTLs) to comprise a unified whole. This framework is built by a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function, and provides a quantitative and testable platform for assessing the multiscale interplay between QTLs and development. The method will enable geneticists to shed light on the genetic complexity of any biological system and predict, alter or engineer its physiological and pathological states.

  9. Mapping stochastic processes onto complex networks

    NASA Astrophysics Data System (ADS)

    Shirazi, A. H.; Reza Jafari, G.; Davoudi, J.; Peinke, J.; Reza Rahimi Tabar, M.; Sahimi, Muhammad

    2009-07-01

    We introduce a method by which stochastic processes are mapped onto complex networks. As examples, we construct the networks for such time series as those for free-jet and low-temperature helium turbulence, the German stock market index (the DAX), and white noise. The networks are further studied by contrasting their geometrical properties, such as the mean length, diameter, clustering, and average number of connections per node. By comparing the network properties of the original time series investigated with those for the shuffled and surrogate series, we are able to quantify the effect of the long-range correlations and the fatness of the probability distribution functions of the series on the networks constructed. Most importantly, we demonstrate that the time series can be reconstructed with high precision by means of a simple random walk on their corresponding networks.

  10. Complex Mapping of Aerofoils--A Different Perspective

    ERIC Educational Resources Information Center

    Matthews, Miccal T.

    2012-01-01

    In this article an application of conformal mapping to aerofoil theory is studied from a geometric and calculus point of view. The problem is suitable for undergraduate teaching in terms of a project or extended piece of work, and brings together the concepts of geometric mapping, parametric equations, complex numbers and calculus. The Joukowski…

  11. Quantifying the complexity of the delayed logistic map.

    PubMed

    Masoller, Cristina; Rosso, Osvaldo A

    2011-01-28

    Statistical complexity measures are used to quantify the degree of complexity of the delayed logistic map, with linear and nonlinear feedback. We employ two methods for calculating the complexity measures, one with the 'histogram-based' probability distribution function and the other one with ordinal patterns. We show that these methods provide complementary information about the complexity of the delay-induced dynamics: there are parameter regions where the histogram-based complexity is zero while the ordinal pattern complexity is not, and vice versa. We also show that the time series generated from the nonlinear delayed logistic map can present zero missing or forbidden patterns, i.e. all possible ordinal patterns are realized into orbits.

  12. Geologic map of the Stillwater Complex, Montana: a digital database

    USGS Publications Warehouse

    Page, Norman J.; Nokleberg, Warren J.; digital database by Miller, Robert J.

    2002-01-01

    This report provides a digital version of the Geologic map of the Stillwater Complex, Montana by Page and Nokleberg (1974). Paper copies of the four geologic map sheets from the original report were scanned and initially attributed by Optronics Specialty Co., Inc. (Northridge, CA) and remitted to the U.S. Geological Survey for further attribution and publication of the geospatial digital files. The resulting digital geologic dataset can be queried in a geographic information system (GIS) in many ways to produce a variety of geological maps.

  13. The Limits of Some Infinite Families of Complex Contracting Mappings

    SciTech Connect

    Pagon, Dusan

    2008-11-13

    Self-similarity is strongly presented in modern mathematics and physics. We study a broad class of planar fractals--strongly self-similar sets of points in complex plane, obtained from a unit interval as geometric limits of certain infinite families of contracting mappings. Different 1-1 correspondences between the constructed set and the initial unit interval are established.

  14. 3D Gel Map of Arabidopsis Complex I

    PubMed Central

    Peters, Katrin; Belt, Katharina; Braun, Hans-Peter

    2013-01-01

    Complex I has a unique structure in plants and includes extra subunits. Here, we present a novel study to define its protein constituents. Mitochondria were isolated from Arabidopsis thaliana cell cultures, leaves, and roots. Subunits of complex I were resolved by 3D blue-native (BN)/SDS/SDS-PAGE and identified by mass spectrometry. Overall, 55 distinct proteins were found, seven of which occur in pairs of isoforms. We present evidence that Arabidopsis complex I consists of 49 distinct types of subunits, 40 of which represent homologs of bovine complex I. The nine other subunits represent special proteins absent in the animal linage of eukaryotes, most prominently a group of subunits related to bacterial gamma-type carbonic anhydrases. A GelMap http://www.gelmap.de/arabidopsis-3d-complex-i/ is presented for promoting future complex I research in Arabidopsis thaliana. PMID:23761796

  15. Complex disease and phenotype mapping in the domestic dog

    PubMed Central

    Hayward, Jessica J.; Castelhano, Marta G.; Oliveira, Kyle C.; Corey, Elizabeth; Balkman, Cheryl; Baxter, Tara L.; Casal, Margret L.; Center, Sharon A.; Fang, Meiying; Garrison, Susan J.; Kalla, Sara E.; Korniliev, Pavel; Kotlikoff, Michael I.; Moise, N. S.; Shannon, Laura M.; Simpson, Kenneth W.; Sutter, Nathan B.; Todhunter, Rory J.; Boyko, Adam R.

    2016-01-01

    The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies. PMID:26795439

  16. Complex disease and phenotype mapping in the domestic dog.

    PubMed

    Hayward, Jessica J; Castelhano, Marta G; Oliveira, Kyle C; Corey, Elizabeth; Balkman, Cheryl; Baxter, Tara L; Casal, Margret L; Center, Sharon A; Fang, Meiying; Garrison, Susan J; Kalla, Sara E; Korniliev, Pavel; Kotlikoff, Michael I; Moise, N S; Shannon, Laura M; Simpson, Kenneth W; Sutter, Nathan B; Todhunter, Rory J; Boyko, Adam R

    2016-01-22

    The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies.

  17. Measuring MAP kinase activity in immune complex assays.

    PubMed

    Cherkasova, Vera A

    2006-11-01

    I present an overview of published methods for measuring mitogen activated protein (MAP) kinase activity on endogenous associated substrates, exogenously added substrates as well as determination of activation loop phosphorylation as a read-out of kinase activity in vivo. Detailed procedures for these assays are given for two MAP kinases (MAPKs) Fus3 and Kss1 and compared with other published protocols, including the protocols for Hog1 and Mpk1 MAPKs. Measuring kinase activity in immune complex assays can serve as an approach for identification of potential substrates of protein kinases as well as for detecting other kinase-associated proteins. PMID:16890454

  18. RDF SKETCH MAPS - KNOWLEDGE COMPLEXITY REDUCTION FOR PRECISION MEDICINE ANALYTICS.

    PubMed

    Thanintorn, Nattapon; Wang, Juexin; Ersoy, Ilker; Al-Taie, Zainab; Jiang, Yuexu; Wang, Duolin; Verma, Megha; Joshi, Trupti; Hammer, Richard; Xu, Dong; Shin, Dmitriy

    2016-01-01

    Realization of precision medicine ideas requires significant research effort to be able to spot subtle differences in complex diseases at the molecular level to develop personalized therapies. It is especially important in many cases of highly heterogeneous cancers. Precision diagnostics and therapeutics of such diseases demands interrogation of vast amounts of biological knowledge coupled with novel analytic methodologies. For instance, pathway-based approaches can shed light on the way tumorigenesis takes place in individual patient cases and pinpoint to novel drug targets. However, comprehensive analysis of hundreds of pathways and thousands of genes creates a combinatorial explosion, that is challenging for medical practitioners to handle at the point of care. Here we extend our previous work on mapping clinical omics data to curated Resource Description Framework (RDF) knowledge bases to derive influence diagrams of interrelationships of biomarker proteins, diseases and signal transduction pathways for personalized theranostics. We present RDF Sketch Maps - a computational method to reduce knowledge complexity for precision medicine analytics. The method of RDF Sketch Maps is inspired by the way a sketch artist conveys only important visual information and discards other unnecessary details. In our case, we compute and retain only so-called RDF Edges - places with highly important diagnostic and therapeutic information. To do this we utilize 35 maps of human signal transduction pathways by transforming 300 KEGG maps into highly processable RDF knowledge base. We have demonstrated potential clinical utility of RDF Sketch Maps in hematopoietic cancers, including analysis of pathways associated with Hairy Cell Leukemia (HCL) and Chronic Myeloid Leukemia (CML) where we achieved up to 20-fold reduction in the number of biological entities to be analyzed, while retaining most likely important entities. In experiments with pathways associated with HCL a generated RDF

  19. Simulating and mapping spatial complexity using multi-scale techniques

    USGS Publications Warehouse

    De Cola, L.

    1994-01-01

    A central problem in spatial analysis is the mapping of data for complex spatial fields using relatively simple data structures, such as those of a conventional GIS. This complexity can be measured using such indices as multi-scale variance, which reflects spatial autocorrelation, and multi-fractal dimension, which characterizes the values of fields. These indices are computed for three spatial processes: Gaussian noise, a simple mathematical function, and data for a random walk. Fractal analysis is then used to produce a vegetation map of the central region of California based on a satellite image. This analysis suggests that real world data lie on a continuum between the simple and the random, and that a major GIS challenge is the scientific representation and understanding of rapidly changing multi-scale fields. -Author

  20. From globally coupled maps to complex-systems biology.

    PubMed

    Kaneko, Kunihiko

    2015-09-01

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  1. From globally coupled maps to complex-systems biology

    NASA Astrophysics Data System (ADS)

    Kaneko, Kunihiko

    2015-09-01

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  2. From globally coupled maps to complex-systems biology

    SciTech Connect

    Kaneko, Kunihiko

    2015-09-15

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  3. Global topology of images of finite complex analytic maps

    NASA Astrophysics Data System (ADS)

    Houston, Kevin

    1997-11-01

    Let f[ratio]X[rightward arrow][open face C][open face P]p be a finite complex analytic map into complex projective space, with dimX

  4. Hyperbolic mapping of complex networks based on community information

    NASA Astrophysics Data System (ADS)

    Wang, Zuxi; Li, Qingguang; Jin, Fengdong; Xiong, Wei; Wu, Yao

    2016-08-01

    To improve the hyperbolic mapping methods both in terms of accuracy and running time, a novel mapping method called Community and Hyperbolic Mapping (CHM) is proposed based on community information in this paper. Firstly, an index called Community Intimacy (CI) is presented to measure the adjacency relationship between the communities, based on which a community ordering algorithm is introduced. According to the proposed Community-Sector hypothesis, which supposes that most nodes of one community gather in a same sector in hyperbolic space, CHM maps the ordered communities into hyperbolic space, and then the angular coordinates of nodes are randomly initialized within the sector that they belong to. Therefore, all the network nodes are so far mapped to hyperbolic space, and then the initialized angular coordinates can be optimized by employing the information of all nodes, which can greatly improve the algorithm precision. By applying the proposed dual-layer angle sampling method in the optimization procedure, CHM reduces the time complexity to O(n2) . The experiments show that our algorithm outperforms the state-of-the-art methods.

  5. Mapping the Orion Molecular Cloud Complex in Radio Frequencies

    NASA Astrophysics Data System (ADS)

    Castelaz, Michael W.; Lemly, C.

    2013-01-01

    The purpose of this research project was to create a large-scale intensity map of the Orion Molecular Cloud Complex at a radio frequency of 1420 MHz. A mapping frequency of 1420 MHz was chosen because neutral hydrogen, which is the primary component of the Orion Molecular Complex, naturally emits radio waves at this frequency. The radio spectral data for this project were gathered using a 4.6-m radio telescope whose spectrometer was tuned to 1420 MHz and whose beam width was 2.7 degrees. The map created for this project consisted of an eight-by-eight grid centered on M42 spanning 21.6 degrees per side. The grid consisted of 64 individual squares spanning 2.7 degrees per side (corresponding to the beam width of the telescope). Radio spectra were recorded for each of these individual squares at an IF gain of 18. Each spectrum consisted of intensity on an arbitrary scale from 0 to 10 plotted as a function frequencies ranging from -400 kHz to +100 kHz around the origin of 1420 MHz. The data from all 64 radio spectra were imported into Wolfram Alpha, which was used to fit Gaussian functions to the data. The peak intensity and the frequency at which this peak intensity occurs could then be extracted from the Gaussian functions. Other helpful quantities that could be calculated from the Gaussian functions include flux (integral of Gaussian function over frequency range), average value of intensity (flux integral divided by frequency range), and half maximum of intensity. Because all of the radio spectra were redshifted, the velocities of the hydrogen gas clouds of the Orion Molecular Cloud Complex could be calculated using the Doppler equation. The data extracted from the Gaussian functions were then imported into Mathcad to create 2D grayscale maps with right ascension (RA) on the x-axis, declination on the y-axis, and intensity (or flux, etc.) represented on a scale from black to white (with white representing the highest intensities). These 2D maps were then imported

  6. Local cortical surface complexity maps from spherical harmonic reconstructions.

    PubMed

    Yotter, Rachel A; Nenadic, Igor; Ziegler, Gabriel; Thompson, Paul M; Gaser, Christian

    2011-06-01

    Altered cortical surface complexity and gyrification differences may be a potentially sensitive marker for several neurodevelopmental disorders. We propose to use spherical harmonic (SPH) constructions to measure cortical surface folding complexity. First, we demonstrate that the complexity measure is accurate, by applying our SPH approach and the more traditional box-counting method to von Koch fractal surfaces with known fractal dimension (FD) values. The SPH approach is then applied to study complexity differences between 87 patients with DSM-IV schizophrenia (with stable psychopathology and treated with antipsychotic medication; 48 male/39 female; mean age=35.5 years, SD=11.0) and 108 matched healthy controls (68 male/40 female; mean age=32.1 years, SD=10.0). The global FD for the right hemisphere in the schizophrenia group was significantly reduced. Regionally, reduced complexity was also found in temporal, frontal, and cingulate regions in the right hemisphere, and temporal and prefrontal regions in the left hemisphere. These results are discussed in terms of previously published findings. Finally, the anatomical implications of a reduced FD are highlighted through comparison of two subjects with vastly different complexity maps.

  7. Using endophenotypes for pathway clusters to map complex disease genes.

    PubMed

    Pan, Wen-Harn; Lynn, Ke-Shiuan; Chen, Chun-Houh; Wu, Yi-Lin; Lin, Chung-Yen; Chang, Hsing-Yi

    2006-02-01

    Nature determines the complexity of disease etiology and the likelihood of revealing disease genes. While culprit genes for many monogenic diseases have been successfully unraveled, efforts to map major complex disease genes have not been as productive as hoped. The conceptual framework currently adopted to deal with the heterogeneous nature of complex diseases focuses on using homogeneous internal features of the disease phenotype for mapping. However, phenotypic homogeneity does not equal genotypic homogeneity. In this report, we advocate working with well-measured phenotypes portrayed by amounts of transcripts and activities of gene products or their metabolites, which are pertinent to relatively small pathway clusters. Reliable and controlled measures for oligogenic traits resulting from proper dissection efforts may enhance statistical power. The large amounts of information obtained on gene and protein expression from technological advances can add to the power of gene finding, particularly for diseases with unclear etiology. Data-mining tools for dimension reduction can assist biologists to reveal novel molecular endophenotypes. However, there are still hurdles to overcome, including high cost, relatively poor reproducibility and comparability among platforms, the cross-sectional nature of the information, and the accessibility of human tissues. Concerted efforts are required to carry out large-scale prospective studies that are integrated at the levels of phenotype characterization, high throughput experimental techniques, data analyses, and beyond.

  8. Using mapping entropy to identify node centrality in complex networks

    NASA Astrophysics Data System (ADS)

    Nie, Tingyuan; Guo, Zheng; Zhao, Kun; Lu, Zhe-Ming

    2016-07-01

    The problem of finding the best strategy to attack a network or immunize a population with a minimal number of nodes has attracted much current research interest. The assessment of node importance has been a fundamental issue in the research of complex networks. In this paper, we propose a new concept called mapping entropy (ME) to identify the importance of a node in the complex network. The concept is established according to the local information which considers the correlation among all neighbors of a node. We evaluate the efficiency of the centrality by static and dynamic attacks on standard network models and real-world networks. The simulation result shows that the new centrality is more efficient than traditional attack strategies, whether it is static or dynamic.

  9. 2D Potential theory using complex functions and conformal mapping

    NASA Astrophysics Data System (ADS)

    Le Maire, Pauline; Munschy, Marc

    2016-04-01

    For infinitely horizontally extended bodies, functions that describe potential and field equations (gravity and magnetics) outside bodies are 2D and harmonic. The consequence of this property is that potential and field equations can be written as complex analytic functions. We define these complex functions whose real part is the commonly used real function and imaginary part is its Hilbert transform. Using data or synthetic cases the transformation is easily performed in the Fourier domain by setting to zero all values for negative frequencies. Written as complex functions of the complex variable, equations of potential and field in gravity and magnetics for different kinds of geometries are simple and correspond to powers of the inverse of the distance. For example, it is easily shown that for a tilted dyke, the dip and the apparent inclination have the same effect on the function and consequently that it is not possible, with data, to compute one of both values without knowing the other. Conformal mapping is an original way to display potential field functions. Considering that the complex variable corresponds to the real axis, complex potential field functions resume to a limaçon, a curve formed by the path of the point fixed to a circle when that circle rolls around the outside of another circle. For example, the point corresponding to the maximum distance to the origin of the complex magnetic field due to a cylinder, corresponds to the maximum of the analytic signal as defined by Nabighan in 1972 and its phase corresponds to the apparent inclination. Several applications are shown in different geological contexts using aeromagnetic data.

  10. Interval Mapping of Quantitative Trait Loci Employing Correlated Trait Complexes

    PubMed Central

    Korol, A. B.; Ronin, Y. I.; Kirzhner, V. M.

    1995-01-01

    An approach to increase the resolution power of interval mapping of quantitative trait (QT) loci is proposed, based on analysis of correlated trait complexes. For a given set of QTs, the broad sense heritability attributed to a QT locus (QTL) (say, A/ a) is an increasing function of the number of traits. Thus, for some traits x and y, H(xy)(2) (A/ a) >/= H(x)(2) (A/ a). The last inequality holds even if y does not depend on A/ a at all, but x and y are correlated within the groups AA, Aa and aa due to nongenetic factors and segregation of genes from other chromosomes. A simple relationship connects H(2) (both in single trait and two-trait analysis) with the expected LOD value, ELOD = -1/2N log(1 - H(2)). Thus, situations could exist that from the inequality H(xy)(2) (A/ a) >/= H(x)(2) (A/ a) a higher resolution is provided by the two-trait analysis as compared to the single-trait analysis, in spite of the increased number of parameters. Employing LOD-score procedure to simulated backcross data, we showed that the resolution power of the QTL mapping model can be elevated if correlation between QTs is taken into account. The method allows us to test numerous biologically important hypotheses concerning manifold effects of genomic segments on the defined trait complex (means, variances and correlations). PMID:7672584

  11. Mapping of complex traits by single-nucleotide polymorphisms.

    PubMed Central

    Zhao, L P; Aragaki, C; Hsu, L; Quiaoit, F

    1998-01-01

    Molecular geneticists are developing the third-generation human genome map with single-nucleotide polymorphisms (SNPs), which can be assayed via chip-based microarrays. One use of these SNP markers is the ability to locate loci that may be responsible for complex traits, via linkage/linkage-disequilibrium analysis. In this communication, we describe a semiparametric method for combined linkage/linkage-disequilibrium analysis using SNP markers. Asymptotic results are obtained for the estimated parameters, and the finite-sample properties are evaluated via a simulation study. We also applied this technique to a simulated genome-scan experiment for mapping a complex trait with two major genes. This experiment shows that separate linkage and linkage-disequilibrium analyses correctly detected the signals of both major genes; but the rates of false-positive signals seem high. When linkage and linkage-disequilibrium signals were combined, the analysis yielded much stronger and clearer signals for the presence of two major genes than did two separate analyses. PMID:9634510

  12. On loops in the hyperbolic locus of the complex Hénon map and their monodromies

    NASA Astrophysics Data System (ADS)

    Arai, Zin

    2016-11-01

    We prove John Hubbard's conjecture on the topological complexity of the hyperbolic horseshoe locus of the complex Hénon map. In fact, we show that there exist several non-trivial loops in the locus which generate infinitely many mutually different monodromies. Furthermore, we prove that the dynamics of the real Hénon map is completely determined by the monodromy of the complex Hénon map, providing the parameter of the map is contained in the hyperbolic horseshoe locus.

  13. Comparison of association mapping methods in a complex pedigreed population.

    PubMed

    Sahana, Goutam; Guldbrandtsen, Bernt; Janss, Luc; Lund, Mogens S

    2010-07-01

    Association mapping methods were compared using a simulation with a complex pedigree structure. The pedigree was simulated while keeping the present Danish Holstein population pedigree in view. A total of 15 quantitative trait loci (QTL) with varying effect sizes (10%, 5% and 2% of total genetic variance) were simulated. We compared the single-marker test, haplotype-based analysis, mixed model approach, and Bayesian analysis. The methods were compared for power, precision of location estimates, and type I error rates. Results found the best performance in a Bayesian method that included genetic background effects and simultaneously fitted all single-nucleotide polymorphisms (SNPs) with a variable selection method. A mixed model analysis that fitted genetic background effects and tested one SNP at a time performed nearly as well as the Bayesian method. For the Bayesian method, it proved necessary to collect SNP signals in intervals, to avoid the scattering of a QTL signal over multiple neighboring SNPs. Methods not accounting for genetic background (full pedigree information) performed worse, and methods using haplotypes were considerably worse with a high false-positive rate, probably due to the presence of low-frequency haplotypes. It was necessary to account for full relationships among individuals to avoid excess false discovery. Although the methods were tested on a cattle pedigree, the results are applicable to any population with a complex pedigree structure.

  14. High-resolution genetic mapping of complex traits.

    PubMed Central

    Kruglyak, L; Lander, E S

    1995-01-01

    Positional cloning requires high-resolution genetic mapping. To plan a positional cloning project, one needs to know how many informative meioses will be required to narrow the search for a disease gene to an acceptably small region. For a simple Mendelian trait studied with linkage analysis, the answer is straightforward. In this paper, we address the situation of a complex trait studied with affected-relative-pair methods. We derive mathematical formulas for the size of an appropriate confidence region, as a function of the relative risk attributable to the gene. Using these results, we provide graphs showing the number of relative pairs required to narrow the gene hunt to an interval of a given size. For example, we show that localizing a gene to 1 cM requires a median of 200 sib pairs for a locus causing a fivefold increased risk to an offspring and 700 sib pairs for a locus causing a twofold increased risk. We discuss the implications of these results for the positional cloning of genes underlying complex traits. PMID:7726179

  15. High-resolution genetic mapping of complex traits

    SciTech Connect

    Zruglyak, L.; Lander, E.S. |

    1995-05-01

    Positional cloning requires high-resolution genetic mapping. To plan a positional cloning project, one needs to know how many informative meioses will be required to narrow the search for a disease gene to an acceptably small region. For a simple Mendelian trait studied with linkage analysis, the answer is straightforward. In this paper, we address the situation of a complex trait studied with affected-relative-pair methods. We derive mathematical formulas for the size of an appropriate confidence region, as a function of the relative risk attributable to the gene. Using these results, we provide graphs showing the number of relative pairs required to narrow the gene hunt to an interval of a given size. For example, we show that localizing a gene to a 1 cM requires a median of 200 sib pairs for a locus causing a fivefold increased risk to an offspring and 700 sib pairs for a locus causing a twofold increased risk. We discuss the implications of these results for the positional cloning of genes underlying complex traits. 11 refs., 7 figs., 2 tabs.

  16. Tales of the City: Understanding Urban Complexity through the Medium of Concept Mapping.

    ERIC Educational Resources Information Center

    Gold, John R.; Coaffee, Jon

    1998-01-01

    Describes the use of concept mapping in teaching complex notions in urban geography. Discusses the nature and characteristics of concept mapping, course context, three experimental exercises, and student responses in evaluations. Finds that concept-mapping techniques increased students' understanding. Emphasizes the continuing potential of this…

  17. Nonlinear mapping methods with adjustable computational complexity for hyperspectral image analysis

    NASA Astrophysics Data System (ADS)

    Myasnikov, E. V.

    2015-12-01

    Nonlinear mapping (Sammon mapping) is a well-known dimensionality reduction technique. Recently several nonlinear mapping methods with reduced computational complexity have been proposed but they do not provide a flexible control over a computational complexity. In this paper a nonlinear mapping method with adjustable computational complexity is proposed. The proposed method is based on the hierarchical decomposition of the multidimensional space, priority queues, and simple optimization procedure to provide fast and flexible dimensionality reduction process. The proposed method is compared to an alternative one based on stochastic optimization. The experiments are carried out on well-known hyperspectral images. Studied methods are evaluated in terms of the data mapping error and runtime. Experimental results for both two- and three-dimensional output spaces are presented.

  18. Concept Maps for Improved Science Reasoning and Writing: Complexity Isn’t Everything

    PubMed Central

    Dowd, Jason E.; Duncan, Tanya; Reynolds, Julie A.

    2015-01-01

    A pervasive notion in the literature is that complex concept maps reflect greater knowledge and/or more expert-like thinking than less complex concept maps. We show that concept maps used to structure scientific writing and clarify scientific reasoning do not adhere to this notion. In an undergraduate course for thesis writers, students use concept maps instead of traditional outlines to define the boundaries and scope of their research and to construct an argument for the significance of their research. Students generate maps at the beginning of the semester, revise after peer review, and revise once more at the end of the semester. Although some students revised their maps to make them more complex, a significant proportion of students simplified their maps. We found no correlation between increased complexity and improved scientific reasoning and writing skills, suggesting that sometimes students simplify their understanding as they develop more expert-like thinking. These results suggest that concept maps, when used as an intervention, can meet the varying needs of a diverse population of student writers. PMID:26538388

  19. Concept Maps for Improved Science Reasoning and Writing: Complexity Isn't Everything.

    PubMed

    Dowd, Jason E; Duncan, Tanya; Reynolds, Julie A

    2015-01-01

    A pervasive notion in the literature is that complex concept maps reflect greater knowledge and/or more expert-like thinking than less complex concept maps. We show that concept maps used to structure scientific writing and clarify scientific reasoning do not adhere to this notion. In an undergraduate course for thesis writers, students use concept maps instead of traditional outlines to define the boundaries and scope of their research and to construct an argument for the significance of their research. Students generate maps at the beginning of the semester, revise after peer review, and revise once more at the end of the semester. Although some students revised their maps to make them more complex, a significant proportion of students simplified their maps. We found no correlation between increased complexity and improved scientific reasoning and writing skills, suggesting that sometimes students simplify their understanding as they develop more expert-like thinking. These results suggest that concept maps, when used as an intervention, can meet the varying needs of a diverse population of student writers.

  20. Concept Maps for Improved Science Reasoning and Writing: Complexity Isn't Everything.

    PubMed

    Dowd, Jason E; Duncan, Tanya; Reynolds, Julie A

    2015-01-01

    A pervasive notion in the literature is that complex concept maps reflect greater knowledge and/or more expert-like thinking than less complex concept maps. We show that concept maps used to structure scientific writing and clarify scientific reasoning do not adhere to this notion. In an undergraduate course for thesis writers, students use concept maps instead of traditional outlines to define the boundaries and scope of their research and to construct an argument for the significance of their research. Students generate maps at the beginning of the semester, revise after peer review, and revise once more at the end of the semester. Although some students revised their maps to make them more complex, a significant proportion of students simplified their maps. We found no correlation between increased complexity and improved scientific reasoning and writing skills, suggesting that sometimes students simplify their understanding as they develop more expert-like thinking. These results suggest that concept maps, when used as an intervention, can meet the varying needs of a diverse population of student writers. PMID:26538388

  1. Overcoming complexities for consistent, continental-scale flood mapping

    NASA Astrophysics Data System (ADS)

    Smith, Helen; Zaidman, Maxine; Davison, Charlotte

    2013-04-01

    The EU Floods Directive requires all member states to produce flood hazard maps by 2013. Although flood mapping practices are well developed in Europe, there are huge variations in the scale and resolution of the maps between individual countries. Since extreme flood events are rarely confined to a single country, this is problematic, particularly for the re/insurance industry whose exposures often extend beyond country boundaries. Here, we discuss the challenges of large-scale hydrological and hydraulic modelling, using our experience of developing a 12-country model and set of maps, to illustrate how consistent, high-resolution river flood maps across Europe can be produced. The main challenges addressed include: data acquisition; manipulating the vast quantities of high-resolution data; and computational resources. Our starting point was to develop robust flood-frequency models that are suitable for estimating peak flows for a range of design flood return periods. We used the index flood approach, based on a statistical analysis of historic river flow data pooled on the basis of catchment characteristics. Historical flow data were therefore sourced for each country and collated into a large pan-European database. After a lengthy validation these data were collated into 21 separate analysis zones or regions, grouping smaller river basins according to their physical and climatic characteristics. The very large continental scale basins were each modelled separately on account of their size (e.g. Danube, Elbe, Drava and Rhine). Our methodology allows the design flood hydrograph to be predicted at any point on the river network for a range of return periods. Using JFlow+, JBA's proprietary 2D hydraulic hydrodynamic model, the calculated out-of-bank flows for all watercourses with an upstream drainage area exceeding 50km2 were routed across two different Digital Terrain Models in order to map the extent and depth of floodplain inundation. This generated modelling for

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

    PubMed

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

    2016-07-01

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

  3. Normalized mass mapping of Orbitrap data to define complex, polyglycerol-based raw material compositions.

    PubMed

    Strife, Robert J; Mangels, Michele L

    2010-06-15

    Kendrick Mass Mapping of complex sample compositions, via data derived by Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) at 1,000,000 resolution, is becoming more common. The Orbitrap mass spectrometer (Fourier Transform Axially Harmonic Orbital Trapping) also uses FT methods and indirect detection, though operating at a maximum resolution of 100,000. We define the more general case of Normalized Mass Mapping to any repeating oligomer unit (e.g., C(3)H(6)O(2)) and apply it to Orbitrap-based mapping of a complex polyglycerol ester, 'green' raw material. Mass measurement errors showed sub-ppm precision and accuracy in many cases, parameters that are critical to obtaining well-defined maps. Map-derived, raw-material-characterization parameters such as iodine value are compared with wet-chemical results and show reasonable agreement for our purposes. The methodology appears applicable to raw material control and eliminates wet chemical methods.

  4. Distinct cortical circuit mechanisms for complex forelimb movement and motor map topography.

    PubMed

    Harrison, Thomas C; Ayling, Oliver G S; Murphy, Timothy H

    2012-04-26

    Cortical motor maps are the basis of voluntary movement, but they have proven difficult to understand in the context of their underlying neuronal circuits. We applied light-based motor mapping of Channelrhodopsin-2 mice to reveal a functional subdivision of the forelimb motor cortex based on the direction of movement evoked by brief (10 ms) pulses. Prolonged trains of electrical or optogenetic stimulation (100-500 ms) targeted to anterior or posterior subregions of motor cortex evoked reproducible complex movements of the forelimb to distinct positions in space. Blocking excitatory cortical synaptic transmission did not abolish basic motor map topography, but the site-specific expression of complex movements was lost. Our data suggest that the topography of movement maps arises from their segregated output projections, whereas complex movements evoked by prolonged stimulation require intracortical synaptic transmission.

  5. Mapping the Escherichia coli transcription elongation complex with exonuclease III

    PubMed Central

    Liu, Zhaokun; Artsimovitch, Irina

    2014-01-01

    Summary RNA polymerase interactions with the nucleic acids control every step of the transcription cycle. These contacts mediate RNA polymerase recruitment to promoters; induce pausing during RNA chain synthesis, and control transcription termination. These interactions are dissected using footprinting assays, in which a bound protein protects nucleic acids from the digestion by nucleases or modification by chemical probes. Exonuclease III is frequently employed to study protein-DNA interactions owing to relatively simple procedures and low background. Exonuclease III has been used to determine RNA polymerase position in transcription initiation and elongation complexes and to infer the translocation register of the enzyme. In this chapter, we describe probing the location and the conformation of transcription elongation complexes formed by walking of the RNA polymerase along an immobilized template. PMID:25665555

  6. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    PubMed Central

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-01-01

    Genetic mapping on fully sequenced individuals is transforming our understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating novel genes in models of anxiety, heart disease and multiple sclerosis. The relation between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show the extent and spatial pattern of variation in inbred rats differ significantly from those of inbred mice, and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species. PMID:23708188

  7. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

    PubMed

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H; Koller, Daniel L; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A; Worley, Kim C; Muzny, Donna M; Gibbs, Richard A; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J; Keane, Thomas; Atanur, Santosh S; Aitman, Tim J; Flicek, Paul; Malinauskas, Tomas; Jones, E Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-07-01

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci, a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show that the extent and spatial pattern of variation in inbred rats differ substantially from those of inbred mice and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.

  8. Directing wayfinders with maps: the effects of gender, age, route complexity, and familiarity with the environment.

    PubMed

    Harrell, W A; Bowlby, J W; Hall-Hoffarth, D

    2000-04-01

    The participants were 360 Canadian undergraduates. After receiving written scenarios involving a campus visitor seeking direction to a nearby destination (simple route) or a distant destination (complex route), they drew maps to that destination. The authors varied the visitor's gender, age, and familiarity with campus. They analyzed the content of the students' maps in terms of cardial indicators (compass grid, correct north-south orientation), landmarks, labeled buildings, directional arrows, and supplemental written directions. The men tended to provide more cartographically complete maps than the women, though there were no gender differences in use of landmarks or labeled buildings. The men were significantly more inclined than the women to take visitor characteristics into account, providing more complete maps to visitors navigating complex routes, to newcomers, and to older visitors who were unfamiliar with the campus. The men had more confidence that their maps would successfully lead visitors to their destinations. Route complexity led to greater use of landmarks, labeled buildings, and cardinal indicators. The participants' self-reported familiarity with campus had little effect on their direction giving, except for a greater use of labeled buildings in maps.

  9. Ablation of premature ventricular complexes exclusively guided by three-dimensional noninvasive mapping.

    PubMed

    Erkapic, Damir; Neumann, Thomas

    2015-03-01

    Preprocedural detailed characterization of premature ventricular complexes before ablation, currently limited to the 12-lead electrocardiogram, may aid in planning and improve procedural outcomes. This article summarizes current published data on feasibility, accuracy, and impact on clinical outcomes of a novel, three-dimensional, noninvasive, single-beat mapping system (ECVUE, CardioInsight). ECVUE technology offers premature ventricular complex characterization and localization with clinically relevant accuracy and performance superior to the surface electrocardiogram. With its noninvasive and single beat advantages, ECVUE has the potential to simplify mapping, and reduce ablation and procedural time.

  10. Mapping

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1978-01-01

    Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

  11. Sequence-based physical mapping of complex genomes by whole genome profiling.

    PubMed

    van Oeveren, Jan; de Ruiter, Marjo; Jesse, Taco; van der Poel, Hein; Tang, Jifeng; Yalcin, Feyruz; Janssen, Antoine; Volpin, Hanne; Stormo, Keith E; Bogden, Robert; van Eijk, Michiel J T; Prins, Marcel

    2011-04-01

    We present whole genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. WGP leverages short read sequences derived from restriction fragments of two-dimensionally pooled BAC clones to generate sequence tags. These sequence tags are assigned to individual BAC clones, followed by assembly of BAC contigs based on shared regions containing identical sequence tags. Following in silico analysis of WGP sequence tags and simulation of a map of Arabidopsis chromosome 4 and maize, a WGP map of Arabidopsis thaliana ecotype Columbia was constructed de novo using a six-genome equivalent BAC library. Validation of the WGP map using the Columbia reference sequence confirmed that 350 BAC contigs (98%) were assembled correctly, spanning 97% of the 102-Mb calculated genome coverage. We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data.

  12. QTL mapping of complex binary traits in an advanced intercross line.

    PubMed

    Moradi Marjaneh, M; Martin, I C A; Kirk, E P; Harvey, R P; Moran, C; Thomson, P C

    2012-07-01

    An advanced intercross line (AIL) is an easier and more cost-effective approach compared to recombinant inbred lines for fine mapping of quantitative trait loci (QTL) identified by F(2) designs. In an AIL, a complex binary trait can be mapped through analysis of either continuously distributed proxy traits for the liability of the binary trait or the liability itself, the latter presenting the greater statistical challenge. In another work, we successfully applied both approaches in an AIL to fine map previously identified QTL underlying anatomical parameters of the cardiac inter-atrial septum including patent foramen ovale. Here, we describe the statistical methods that we used to analyse complex binary traits in our AIL design. This is achieved using a likelihood-based method, with the expectation-maximisation algorithm allowing use of standard logistic regression methods for model fitting.

  13. Doppler mapping of an alternating-sign flow with complex geometry using optical coherence tomography

    SciTech Connect

    Proskurin, S G; Potlov, A Yu; Frolov, S V

    2014-01-31

    The method of sign-sensitive mapping of the given range of velocities in a flow with complex geometry based on the principles of optical coherence tomography is described. To produce an alternating-sign flow, the 1% aqueous intralipid solution and the tilted capillary entry with the contraction coefficient 4:1 are used. The mapping is controlled using two parameters, the value of one specific velocity (OSV) for mapping and the accuracy of its determination. The structure image and two OSV images (for positive and negative direction of motion) are obtained as a result of selecting and processing the relevant parts of the signal spectrum. The final image is a result of summing these three images and can be used as a Doppler equivelocity contour map. (radiation scattering)

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

    SciTech Connect

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

    1995-05-01

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

  15. Towards a complex system understanding of bipolar disorder: A map based model of a complex winnerless competition.

    PubMed

    Hadaeghi, Fatemeh; Hashemi Golpayegani, Mohammad Reza; Murray, Greg

    2015-07-01

    Bipolar disorder is characterized by repeated erratic episodes of mania and depression, which can be understood as pathological complex system behavior involving cognitive, affective and psychomotor disturbance. In order to illuminate dynamical aspects of the longitudinal course of the illness, we propose here a novel complex model based on the notion of competition between recurrent maps, which mathematically represent the dynamics of activation in excitatory (Glutamatergic) and inhibitory (GABAergic) pathways. We assume that manic and depressive states can be considered stable sub attractors of a dynamical system through which the mood trajectory moves. The model provides a theoretical framework which can account for a number of complex phenomena of bipolar disorder, including intermittent transition between the two poles of the disorder, rapid and ultra-rapid cycling of episodes and manicogenic effects of antidepressants.

  16. Efficient use of systems mapping without expert knowledge. Comment on "Mapping complex traits as a dynamic system" by L. Sun and R. Wu

    NASA Astrophysics Data System (ADS)

    Li, Zitong; Sillanpää, Mikko J.

    2015-06-01

    Functional mapping [11], pioneered by Rongling Wu and his colleagues, is a statistical framework for studying the association between quantitative trait locus (QTL) and dynamic quantitative traits. Functional mapping integrate phenotype information over multiple time points as a smooth function/curve to study the genetic mechanism behind phenotype development and growth. The comprehensive review of Sun and Wu further generalize the concept of functional mapping to systems mapping and network mapping [8], in which the target output variable is not merely a single trait, but rather a complex biological system comprising various interactive components of a single trait or a set of correlated genes or proteins activating the same pathways/networks. With systems mapping, genetic influence on interactions, causal relationships and/or steady-state of the dynamic biological system behind the complex traits can be investigated.

  17. A comprehensive archaeological map of the world's largest preindustrial settlement complex at Angkor, Cambodia

    PubMed Central

    Evans, Damian; Pottier, Christophe; Fletcher, Roland; Hensley, Scott; Tapley, Ian; Milne, Anthony; Barbetti, Michael

    2007-01-01

    The great medieval settlement of Angkor in Cambodia [9th–16th centuries Common Era (CE)] has for many years been understood as a “hydraulic city,” an urban complex defined, sustained, and ultimately overwhelmed by a complex water management network. Since the 1980s that view has been disputed, but the debate has remained unresolved because of insufficient data on the landscape beyond the great temples: the broader context of the monumental remains was only partially understood and had not been adequately mapped. Since the 1990s, French, Australian, and Cambodian teams have sought to address this empirical deficit through archaeological mapping projects by using traditional methods such as ground survey in conjunction with advanced radar remote-sensing applications in partnership with the National Aeronautics and Space Administration (NASA)/Jet Propulsion Laboratory (JPL). Here we present a major outcome of that research: a comprehensive archaeological map of greater Angkor, covering nearly 3,000 km2, prepared by the Greater Angkor Project (GAP). The map reveals a vast, low-density settlement landscape integrated by an elaborate water management network covering >1,000 km2, the most extensive urban complex of the preindustrial world. It is now clear that anthropogenic changes to the landscape were both extensive and substantial enough to have created grave challenges to the long-term viability of the settlement. PMID:17717084

  18. Mapping the q-voter model: From a single chain to complex networks

    NASA Astrophysics Data System (ADS)

    Jȩdrzejewski, Arkadiusz; Sznajd-Weron, Katarzyna; Szwabiński, Janusz

    2016-03-01

    We propose and compare six different ways of mapping the modified q-voter model to complex networks. Considering square lattices, Barabási-Albert, Watts-Strogatz and real Twitter networks, we ask the question if always a particular choice of the group of influence of a fixed size q leads to different behavior at the macroscopic level. Using Monte Carlo simulations we show that the answer depends on the relative average path length of the network and for real-life topologies the differences between the considered mappings may be negligible.

  19. Complete physical map of the human immunoglobulin heavy chain constant region gene complex

    SciTech Connect

    Hofker, M.H.; Walter, M.A.; Cox, D.W. )

    1989-07-01

    The authors have found by pulsed-field gel electrophoresis that the human immunoglobulin heavy chain constant region gene complex maps entirely to a 350-kilobase (kb) Mlu I fragment. The enzyme Eag I was used with pulsed-field gel electrophoresis alone and in double digests with Spe I to map the region. C{sub {gamma}}3 maps 60 kb to the 3{prime} side of C{sub {delta}}; C{gamma}2 maps 80 kb to the 3{prime} side of C{sub {alpha}}1. C{sub {psi}{gamma}} maps 35 kb to the 3{prime} side of C{sub {alpha}}1 and is in the same transcriptional orientation as the other genes. Although in the cloned DNA many CpG-containing restriction sites were identified, most of these were methylated in peripheral blood leukocytes. The sites that were not methylated were predominantly found in three clusters, or Hpa I tiny fragment islands. A region showing strong linkage disequilibrium between all C{sub {gamma}} genes spans at least 160 kb. The 70-kb C{sub {mu}}-C{sub {gamma}}3 region, however, shows no linkage disequilibrium, possibly indicating a recombination hot spot. The immunoglobulin heavy chain constant region has been almost entirely cloned and mapped, and thus most rearrangements occurring in this region should be detectable.

  20. Ecosystem services provided by a complex coastal region: challenges of classification and mapping

    NASA Astrophysics Data System (ADS)

    Sousa, Lisa P.; Sousa, Ana I.; Alves, Fátima L.; Lillebø, Ana I.

    2016-03-01

    A variety of ecosystem services classification systems and mapping approaches are available in the scientific and technical literature, which needs to be selected and adapted when applied to complex territories (e.g. in the interface between water and land, estuary and sea). This paper provides a framework for addressing ecosystem services in complex coastal regions. The roadmap comprises the definition of the exact geographic boundaries of the study area; the use of CICES (Common International Classification of Ecosystem Services) for ecosystem services identification and classification; and the definition of qualitative indicators that will serve as basis to map the ecosystem services. Due to its complexity, the Ria de Aveiro coastal region was selected as case study, presenting an opportunity to explore the application of such approaches at a regional scale. The main challenges of implementing the proposed roadmap, together with its advantages are discussed in this research. The results highlight the importance of considering both the connectivity of natural systems and the complexity of the governance framework; the flexibility and robustness, but also the challenges when applying CICES at regional scale; and the challenges regarding ecosystem services mapping.

  1. Ecosystem services provided by a complex coastal region: challenges of classification and mapping.

    PubMed

    Sousa, Lisa P; Sousa, Ana I; Alves, Fátima L; Lillebø, Ana I

    2016-03-11

    A variety of ecosystem services classification systems and mapping approaches are available in the scientific and technical literature, which needs to be selected and adapted when applied to complex territories (e.g. in the interface between water and land, estuary and sea). This paper provides a framework for addressing ecosystem services in complex coastal regions. The roadmap comprises the definition of the exact geographic boundaries of the study area; the use of CICES (Common International Classification of Ecosystem Services) for ecosystem services identification and classification; and the definition of qualitative indicators that will serve as basis to map the ecosystem services. Due to its complexity, the Ria de Aveiro coastal region was selected as case study, presenting an opportunity to explore the application of such approaches at a regional scale. The main challenges of implementing the proposed roadmap, together with its advantages are discussed in this research. The results highlight the importance of considering both the connectivity of natural systems and the complexity of the governance framework; the flexibility and robustness, but also the challenges when applying CICES at regional scale; and the challenges regarding ecosystem services mapping.

  2. Ecosystem services provided by a complex coastal region: challenges of classification and mapping

    PubMed Central

    Sousa, Lisa P.; Sousa, Ana I.; Alves, Fátima L.; Lillebø, Ana I.

    2016-01-01

    A variety of ecosystem services classification systems and mapping approaches are available in the scientific and technical literature, which needs to be selected and adapted when applied to complex territories (e.g. in the interface between water and land, estuary and sea). This paper provides a framework for addressing ecosystem services in complex coastal regions. The roadmap comprises the definition of the exact geographic boundaries of the study area; the use of CICES (Common International Classification of Ecosystem Services) for ecosystem services identification and classification; and the definition of qualitative indicators that will serve as basis to map the ecosystem services. Due to its complexity, the Ria de Aveiro coastal region was selected as case study, presenting an opportunity to explore the application of such approaches at a regional scale. The main challenges of implementing the proposed roadmap, together with its advantages are discussed in this research. The results highlight the importance of considering both the connectivity of natural systems and the complexity of the governance framework; the flexibility and robustness, but also the challenges when applying CICES at regional scale; and the challenges regarding ecosystem services mapping. PMID:26964892

  3. Ecosystem services provided by a complex coastal region: challenges of classification and mapping.

    PubMed

    Sousa, Lisa P; Sousa, Ana I; Alves, Fátima L; Lillebø, Ana I

    2016-01-01

    A variety of ecosystem services classification systems and mapping approaches are available in the scientific and technical literature, which needs to be selected and adapted when applied to complex territories (e.g. in the interface between water and land, estuary and sea). This paper provides a framework for addressing ecosystem services in complex coastal regions. The roadmap comprises the definition of the exact geographic boundaries of the study area; the use of CICES (Common International Classification of Ecosystem Services) for ecosystem services identification and classification; and the definition of qualitative indicators that will serve as basis to map the ecosystem services. Due to its complexity, the Ria de Aveiro coastal region was selected as case study, presenting an opportunity to explore the application of such approaches at a regional scale. The main challenges of implementing the proposed roadmap, together with its advantages are discussed in this research. The results highlight the importance of considering both the connectivity of natural systems and the complexity of the governance framework; the flexibility and robustness, but also the challenges when applying CICES at regional scale; and the challenges regarding ecosystem services mapping. PMID:26964892

  4. Full vectorial mapping of the complex electric near-fields of THz resonators

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Arkabrata; Gómez Rivas, Jaime

    2016-11-01

    Using micro-structured photo-conducting probes, we demonstrate full vectorial mapping of the complex electric fields in the near-field region of a resonant structure at THz frequencies. The investigated structure represents the simplest case of a resonator: a metallic rod. We show field amplitude as well as phase maps for the three field components at the half wavelength (λ/2) resonance of the rod. The field as well as the phase distributions are in excellent agreement with our physical understanding of local electric-field distributions in the vicinity of λ/2 resonant structures and are validated by numerical simulations. These measurements can be a platform for performance optimization of the emerging field of THz photonic and plasmonic devices with complex sub-wavelength structures.

  5. Concept Mapping to Assess Learning and Understanding of Complexity in Courses on Global Climate Change

    NASA Astrophysics Data System (ADS)

    Rebich-Hespanha, S.; Gautier, C.

    2010-12-01

    The complex nature of climate change science poses special challenges for educators wishing to broaden and deepen student understanding of the climate system and its sensitivity to and impacts upon human activity. Learners have prior knowledge that may limit their perception and processing of the multiple relationships between processes (e.g., feedbacks) that arise in global change science, and these existing mental models serve as the scaffold for all future learning. Because adoption of complex scientific concepts is not likely if instruction includes presentation of information or concepts that are not compatible with the learners’ prior knowledge, providing effective instruction on this complex topic requires learning opportunities that are anchored upon an evaluation of the limitations and inaccuracies of the learners’ existing understandings of the climate system. The formative evaluation that serves as the basis for planning such instruction can also be useful as a baseline against which to evaluate subsequent learning. We will present concept-mapping activities that we have used to assess students’ knowledge and understanding about global climate change in courses that utilized multiple assessment methods including presentations, writings, discussions, and concept maps. The courses in which these activities were completed use a variety of instructional approaches (including standard lectures and lab assignments and a mock summit) to help students understand the inherently interdisciplinary topic of global climate change, its interwoven human and natural causes, and the connections it has with society through a complex range of political, social, technological and economic factors. Two instances of concept map assessment will be presented: one focused on evaluating student understanding of the major components of the climate system and their interconnections, and the other focused on student understanding of the connections between climate change and

  6. Computational large-scale mapping of protein-protein interactions using structural complexes.

    PubMed

    Shoemaker, Benjamin; Wuchty, Stefan; Panchenko, Anna R

    2013-01-01

    Although the identification of protein interactions by high-throughput methods progresses at a fast pace, "interactome" datasets still suffer from high rates of false positives and low coverage. To map the interactome of any organism, this unit presents a computational framework to predict protein-protein or gene-gene interactions utilizing experimentally determined evidence of structural complexes, atomic details of binding interfaces and evolutionary conservation.

  7. Chain mapping approach of Hamiltonian for FMO complex using associated, generalized and exceptional Jacobi polynomials

    NASA Astrophysics Data System (ADS)

    Mahdian, M.; Arjmandi, M. B.; Marahem, F.

    2016-06-01

    The excitation energy transfer (EET) in photosynthesis complex has been widely investigated in recent years. However, one of the main problems is simulation of this complex under realistic condition. In this paper by using the associated, generalized and exceptional Jacobi polynomials, firstly, we introduce the spectral density of Fenna-Matthews-Olson (FMO) complex. Afterward, we obtain a map that transforms the Hamiltonian of FMO complex as an open quantum system to a one-dimensional chain of oscillatory modes with only nearest neighbor interaction in which the system is coupled only to first mode of chain. The frequency and coupling strength of each mode can be analytically obtained from recurrence coefficient of mentioned orthogonal polynomials.

  8. Geologic map of the Khanneshin carbonatite complex, Helmand Province, Afghanistan, modified from the 1976 original map compilation of V.G. Cheremytsin

    USGS Publications Warehouse

    Tucker, Robert D.; Peters, Stephen G.; Schulz, Klaus J.; Renaud, Karine M.; Stettner, Will R.; Masonic, Linda M.; Packard, Patricia H.

    2011-01-01

    This map is a modified version of the Geological map of the Khanneshin carbonatite complex, scale 1:10,000, which was compiled by V.G. Cheremytsin in 1976. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original map and also visited the field area in September 2009, August 2010, and February 2011. This modified map, which includes cross sections, illustrates the geologic structure of the Khanneshin carbonatite complex. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of that map and a related report, and based on observations made during our field visits. (Refer to the References section in the Map PDF for complete citations of the original map and related report.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

  9. AFRICAN GENETIC DIVERSITY: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping

    PubMed Central

    Campbell, Michael C.; Tishkoff, Sarah A.

    2010-01-01

    Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. PMID:18593304

  10. Learning from Nature - Mapping of Complex Hydrological and Geomorphological Process Systems for More Realistic Modelling of Hazard-related Maps

    NASA Astrophysics Data System (ADS)

    Chifflard, Peter; Tilch, Nils

    2010-05-01

    Introduction Hydrological or geomorphological processes in nature are often very diverse and complex. This is partly due to the regional characteristics which vary over time and space, as well as changeable process-initiating and -controlling factors. Despite being aware of this complexity, such aspects are usually neglected in the modelling of hazard-related maps due to several reasons. But particularly when it comes to creating more realistic maps, this would be an essential component to consider. The first important step towards solving this problem would be to collect data relating to regional conditions which vary over time and geographical location, along with indicators of complex processes. Data should be acquired promptly during and after events, and subsequently digitally combined and analysed. Study area In June 2009, considerable damage occurred in the residential area of Klingfurth (Lower Austria) as a result of great pre-event wetness and repeatedly heavy rainfall, leading to flooding, debris flow deposit and gravitational mass movement. One of the causes is the fact that the meso-scale watershed (16 km²) of the Klingfurth stream is characterised by adverse geological and hydrological conditions. Additionally, the river system network with its discharge concentration within the residential zone contributes considerably to flooding, particularly during excessive rainfall across the entire region, as the flood peaks from different parts of the catchment area are superposed. First results of mapping Hydro(geo)logical surveys across the entire catchment area have shown that - over 600 gravitational mass movements of various type and stage have occurred. 516 of those have acted as a bed load source, while 325 mass movements had not reached the final stage yet and could thus supply bed load in the future. It should be noted that large mass movements in the initial or intermediate stage were predominately found in clayey-silty areas and weathered material

  11. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  12. Mapping of West Siberian taiga wetland complexes using Landsat imagery: implications for methane emissions

    NASA Astrophysics Data System (ADS)

    Evgenievna Terentieva, Irina; Vladimirovich Glagolev, Mikhail; Dmitrievna Lapshina, Elena; Faritovich Sabrekov, Alexandr; Maksyutov, Shamil

    2016-08-01

    High-latitude wetlands are important for understanding climate change risks because these environments sink carbon dioxide and emit methane. However, fine-scale heterogeneity of wetland landscapes poses a serious challenge when generating regional-scale estimates of greenhouse gas fluxes from point observations. In order to reduce uncertainties at the regional scale, we mapped wetlands and water bodies in the taiga zone of The West Siberia Lowland (WSL) on a scene-by-scene basis using a supervised classification of Landsat imagery. Training data consist of high-resolution images and extensive field data collected at 28 test areas. The classification scheme aims at supporting methane inventory applications and includes seven wetland ecosystem types comprising nine wetland complexes distinguishable at the Landsat resolution. To merge typologies, mean relative areas of wetland ecosystems within each wetland complex type were estimated using high-resolution images. Accuracy assessment based on 1082 validation polygons of 10 × 10 pixel size indicated an overall map accuracy of 79 %. The total area of the WSL wetlands and water bodies was estimated to be 52.4 Mha or 4-12 % of the global wetland area. Ridge-hollow complexes prevail in WSL's taiga zone accounting for 33 % of the total wetland area, followed by pine bogs or "ryams" (23 %), ridge-hollow-lake complexes (16 %), open fens (8 %), palsa complexes (7 %), open bogs (5 %), patterned fens (4 %), and swamps (4 %). Various oligotrophic environments are dominant among wetland ecosystems, while poor fens cover only 14 % of the area. Because of the significant change in the wetland ecosystem coverage in comparison to previous studies, a considerable reevaluation of the total CH4 emissions from the entire region is expected. A new Landsat-based map of WSL's taiga wetlands provides a benchmark for validation of coarse-resolution global land cover products and wetland data sets in high latitudes.

  13. Geophysical Survey and Detailed Geologic Mapping of an Eroded Stratovolcano's Central Intrusive Complex, Summer Coon, Co.

    NASA Astrophysics Data System (ADS)

    Harp, A.

    2015-12-01

    Eroded volcanoes expose plumbing systems that provide important information on intrusive geometries, magma propagation directions, and the effects of host rock types and heterogeneities. Summer Coon Volcano, CO, is an Oligocene stratovolcano where erosion has removed much of the original edifice, revealing the intrusive stocks of the central intrusive complex (CIC). Surrounding the CIC are hundreds of radial dikes ranging from basaltic to rhyolitic in composition. Published geologic maps indicate most radial dikes do not connect to the intrusive stocks, supporting published theories that most did not emanate from the central intrusions. However, much of the area surrounding the CIC is covered by alluvium, suggesting that the lack of connection might be an artifact of exposure. We completed a ground magnetic survey and detailed geological mapping to determine if the dikes continue beneath the alluvium and into the intrusive stocks. Linear magnetic anomalies indicate four NW-SE trending rhyodacite dikes continue beneath the alluvium for up to 250 m, and mapping indicates that at least two of the rhyodacite dikes do extend into the CIC. Shorter linear anomalies are attributed to seven NW-SE trending basaltic dikes ~100-500-m-long which are sparsely exposed in the alluvium. Mapping shows that three rhyodacite dikes extend into the CIC and to within 200 m of their possible source, an 800-m-wide granodiorite stock. Additionally, three rhyolitic dikes extend to within several meters of a 200×500-m-wide tuff breccia zone of similar composition, likely their source. In summary, magnetic data and detailed mapping indicate that radial dikes do extend into the central intrusive complex in contrast to some model predictions.

  14. Acoustic emission source location in complex structures using full automatic delta T mapping technique

    NASA Astrophysics Data System (ADS)

    Al-Jumaili, Safaa Kh.; Pearson, Matthew R.; Holford, Karen M.; Eaton, Mark J.; Pullin, Rhys

    2016-05-01

    An easy to use, fast to apply, cost-effective, and very accurate non-destructive testing (NDT) technique for damage localisation in complex structures is key for the uptake of structural health monitoring systems (SHM). Acoustic emission (AE) is a viable technique that can be used for SHM and one of the most attractive features is the ability to locate AE sources. The time of arrival (TOA) technique is traditionally used to locate AE sources, and relies on the assumption of constant wave speed within the material and uninterrupted propagation path between the source and the sensor. In complex structural geometries and complex materials such as composites, this assumption is no longer valid. Delta T mapping was developed in Cardiff in order to overcome these limitations; this technique uses artificial sources on an area of interest to create training maps. These are used to locate subsequent AE sources. However operator expertise is required to select the best data from the training maps and to choose the correct parameter to locate the sources, which can be a time consuming process. This paper presents a new and improved fully automatic delta T mapping technique where a clustering algorithm is used to automatically identify and select the highly correlated events at each grid point whilst the "Minimum Difference" approach is used to determine the source location. This removes the requirement for operator expertise, saving time and preventing human errors. A thorough assessment is conducted to evaluate the performance and the robustness of the new technique. In the initial test, the results showed excellent reduction in running time as well as improved accuracy of locating AE sources, as a result of the automatic selection of the training data. Furthermore, because the process is performed automatically, this is now a very simple and reliable technique due to the prevention of the potential source of error related to manual manipulation.

  15. Aeromagnetic and aeromagnetic-based geologic maps of the Coastal Belt, Franciscan Complex, northern California

    USGS Publications Warehouse

    Langenheim, V.E.; Jachens, R.C.; McLaughlin, R.J.

    2011-01-01

    The Coastal belt of the Franciscan Complex represents a Late Cretaceous to Miocene accretionary prism and overlying slope deposits. Its equivalents may extend from the offshore outer borderland of southern California to north of the Mendocino Triple Junction under the Eel River Basin and in the offshore of Cascadia. The Coastal belt is exposed on land in northern California, yet its structure and stratigraphy are incompletely known because of discontinuous exposure, structural disruption, and lithologically non-distinctive clastic rocks. The intent of this report is to make available, in map form, aeromagnetic data covering the Coastal belt that provide a new dataset to aid in mapping, understanding, and interpreting the incompletely understood geology and structure in northern California. The newly merged aeromagnetic data over the Coastal belt of the Franciscan Complex reveal long, linear anomalies that indicate remarkably coherent structure within a terrane where mapping at the surface indicates complex deformation and that has been described as "broken formation" and, even locally as "melange". The anomalies in the Coastal belt are primarily sourced by volcanic-rich graywackes and exotic blocks of basalt. Some anomalies along the contact of the Coastal belt with the Central belt are likely caused by local interleaving of components of the Coast Ranges ophiolite. These data can be used to map additional exotic blocks within the Coastal belt and to distinguish lithologically indistinct graywackes within the Coastal terrane. Using anomaly asymmetry allows projection of these "layers" into the subsurface. This analysis indicates predominant northeast dips consistent with tectonic interleaving of blocks within a subduction zone.

  16. A reciprocal cross design to map the genetic architecture of complex traits in apomictic plants.

    PubMed

    Yin, Danni; Zhu, Xuli; Jiang, Libo; Zhang, Jian; Zeng, Yanru; Wu, Rongling

    2015-02-01

    Many higher plants of economic and biological importance undergo apomixis in which the maternal tissue of the ovule forms a seed, without experiencing meiosis and fertilization. This feature of apomixis has made it difficult to perform linkage mapping which relies on meiotic recombination. Here, we describe a computational model for mapping quantitative trait loci (QTLs) that control complex traits in apomictic plants. The model is founded on the mixture model-based likelihood in which maternal genotypes are dissolved into two possible components generated by meiotic and apomictic processes, respectively. The EM algorithm was implemented to discern meiotic and apomictic genotypes and, therefore, allow the marker-QTL linkage relationship to be estimated. By capitalizing on reciprocal crosses, the model is renovated to estimate and test imprinting effects of QTLs, providing a better gateway to characterize the genetic architecture of complex traits. The model was validated through computer simulation and further demonstrated for its usefulness by analyzing a real data for an apomictic woody plant. The model has for the first time provided a unique tool for genetic mapping in apomictic plants.

  17. An entropy-driven matrix completion (E-MC) approach to complex network mapping

    NASA Astrophysics Data System (ADS)

    Koochakzadeh, Ali; Pal, Piya

    2016-05-01

    Mapping the topology of a complex network in a resource-efficient manner is a challenging problem with applications in internet mapping, social network inference, and so forth. We propose a new entropy driven algorithm leveraging ideas from matrix completion, to map the network using monitors (or sensors) which, when placed on judiciously selected nodes, are capable of discovering their immediate neighbors. The main challenge is to maximize the portion of discovered network using only a limited number of available monitors. To this end, (i) a new measure of entropy or uncertainty is associated with each node, in terms of the currently discovered edges incident on that node, and (ii) a greedy algorithm is developed to select a candidate node for monitor placement based on its entropy. Utilizing the fact that many complex networks of interest (such as social networks), have a low-rank adjacency matrix, a matrix completion algorithm, namely 1-bit matrix completion, is combined with the greedy algorithm to further boost its performance. The low rank property of the network adjacency matrix can be used to extrapolate a portion of missing edges, and consequently update the node entropies, so as to efficiently guide the network discovery algorithm towards placing monitors on the nodes that can turn out to be more informative. Simulations performed on a variety of real world networks such as social networks and peer networks demonstrate the superior performance of the matrix-completion guided approach in discovering the network topology.

  18. A reciprocal cross design to map the genetic architecture of complex traits in apomictic plants.

    PubMed

    Yin, Danni; Zhu, Xuli; Jiang, Libo; Zhang, Jian; Zeng, Yanru; Wu, Rongling

    2015-02-01

    Many higher plants of economic and biological importance undergo apomixis in which the maternal tissue of the ovule forms a seed, without experiencing meiosis and fertilization. This feature of apomixis has made it difficult to perform linkage mapping which relies on meiotic recombination. Here, we describe a computational model for mapping quantitative trait loci (QTLs) that control complex traits in apomictic plants. The model is founded on the mixture model-based likelihood in which maternal genotypes are dissolved into two possible components generated by meiotic and apomictic processes, respectively. The EM algorithm was implemented to discern meiotic and apomictic genotypes and, therefore, allow the marker-QTL linkage relationship to be estimated. By capitalizing on reciprocal crosses, the model is renovated to estimate and test imprinting effects of QTLs, providing a better gateway to characterize the genetic architecture of complex traits. The model was validated through computer simulation and further demonstrated for its usefulness by analyzing a real data for an apomictic woody plant. The model has for the first time provided a unique tool for genetic mapping in apomictic plants. PMID:25354995

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

    PubMed Central

    2011-01-01

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

  20. Link prediction based on hyperbolic mapping with community structure for complex networks

    NASA Astrophysics Data System (ADS)

    Wang, Zuxi; Wu, Yao; Li, Qingguang; Jin, Fengdong; Xiong, Wei

    2016-05-01

    Link prediction is becoming a concerned topic in the complex network field in recent years. However, the existing link prediction methods are unsatisfactory for processing topological information and have high time complexity. This paper presents a novel method of Link Prediction with Community Structure (LPCS) based on hyperbolic mapping. Different from the existing link prediction methods, to utilize global structure information of the network, LPCS deals with the network from an overall perspective. LPCS takes full advantage of the community structure and its hierarchical organization to map networks into hyperbolic space, and obtains the hyperbolic coordinates which depict the global structure information of the network, then uses hyperbolic distance to describe the similarity between the nodes, finally predicts missing links according to the degree of the similarity between unconnected node pairs. The combination of the hyperbolic geometry framework and the community structure makes LPCS perform well in predicting missing links, and the time complexity of LPCS is linear, which makes LPCS can be applied to handle large scale networks in acceptable time. LPCS outperforms many state-of-the-art link prediction methods in the networks obeying power-law degree distribution.

  1. Linkage map of the human major histocompatibility complex including the tumor necrosis factor genes

    SciTech Connect

    Carroll, M.C.; Katzman, P.; Alicot, E.M.; Koller, B.H.; Geraghty, D.E.; Orr, H.T.; Strominger, J.L.; Spies, T.

    1987-12-01

    The tumor necrosis factor (TNF) ..cap alpha.. and ..beta.. gene pair has been linked in the human major histocompatibility complex to HLA-B, HLA-C, and, tentatively, HLA-E and HLA-A on one side and to the class III complement/steroid 21-hydroxylase gene cluster on the other by pulsed-field gel electrophoresis. The TNF genes are located 200 kilobases (kb) centromeric of HLA-B and about 350 kb telomeric of the class III cluster. Together with previous data on the linkage and structures of the class II and class III regions, a restriction map of the entire human major histocompatibility complex of about 3500 kb has been prepared.

  2. In Vivo Flow Mapping in Complex Vessel Networks by Single Image Correlation

    PubMed Central

    Sironi, Laura; Bouzin, Margaux; Inverso, Donato; D'Alfonso, Laura; Pozzi, Paolo; Cotelli, Franco; Guidotti, Luca G.; Iannacone, Matteo; Collini, Maddalena; Chirico, Giuseppe

    2014-01-01

    We describe a novel method (FLICS, FLow Image Correlation Spectroscopy) to extract flow speeds in complex vessel networks from a single raster-scanned optical xy-image, acquired in vivo by confocal or two-photon excitation microscopy. Fluorescent flowing objects produce diagonal lines in the raster-scanned image superimposed to static morphological details. The flow velocity is obtained by computing the Cross Correlation Function (CCF) of the intensity fluctuations detected in pairs of columns of the image. The analytical expression of the CCF has been derived by applying scanning fluorescence correlation concepts to drifting optically resolved objects and the theoretical framework has been validated in systems of increasing complexity. The power of the technique is revealed by its application to the intricate murine hepatic microcirculatory system where blood flow speed has been mapped simultaneously in several capillaries from a single xy-image and followed in time at high spatial and temporal resolution. PMID:25475129

  3. The L1457 molecular/atomic cloud complex: H I and CO maps.

    PubMed

    Moriarty-Schieven, G H; Andersson, B G; Wannier, P G

    1997-02-01

    L1457 is the closest known molecular cloud (65 pc), and it lies near the edge of the local hot bubble and well out of the Galactic plane (b approximately -34 degrees). We have mapped an 8 degrees x 8 degrees region at 35' resolution and a 3 degrees x 5 degrees region at approximately 2' resolution in H I 21 cm emission. We have also mapped a 2 degrees x 4 degrees region at 2' resolution in 12CO J = 1-0. We find that there is an extended component of atomic gas, clearly associated with the molecular complex and comparable to it in total mass. The H I structure at small scales in the vicinity of the molecular clouds is remarkable, consisting largely of long, narrow filaments less than 20' (0.2 pc) in width and 1 degree-4 degrees in length. A thin (<10') limb-brightened atomic halo is seen to surround the CO at some velocities, but it is ill-defined at other velocities. The halo may be disturbed by external pressure, perhaps from the hot gas in the local bubble. The molecular clouds are part of a large structure approximately 5 degrees x 3 degrees in extent with a small "funnel-shaped" extension to the south. The structure, which we call the L1457 atomic/molecular complex, is dominated by H I in the north and H2 in the south extension. Roughly one-half the mass of the complex is molecular. The structure of this complex at both large- and small-scale suggests that the south end has been recently compressed.

  4. The MAP kinase pathway coordinates crossover designation with disassembly of synaptonemal complex proteins during meiosis.

    PubMed

    Nadarajan, Saravanapriah; Mohideen, Firaz; Tzur, Yonatan B; Ferrandiz, Nuria; Crawley, Oliver; Montoya, Alex; Faull, Peter; Snijders, Ambrosius P; Cutillas, Pedro R; Jambhekar, Ashwini; Blower, Michael D; Martinez-Perez, Enrique; Harper, J Wade; Colaiacovo, Monica P

    2016-02-27

    Asymmetric disassembly of the synaptonemal complex (SC) is crucial for proper meiotic chromosome segregation. However, the signaling mechanisms that directly regulate this process are poorly understood. Here we show that the mammalian Rho GEF homolog, ECT-2, functions through the conserved RAS/ERK MAP kinase signaling pathway in the C. elegans germline to regulate the disassembly of SC proteins. We find that SYP-2, a SC central region component, is a potential target for MPK-1-mediated phosphorylation and that constitutively phosphorylated SYP-2 impairs the disassembly of SC proteins from chromosomal domains referred to as the long arms of the bivalents. Inactivation of MAP kinase at late pachytene is critical for timely disassembly of the SC proteins from the long arms, and is dependent on the crossover (CO) promoting factors ZHP-3/RNF212/Zip3 and COSA-1/CNTD1. We propose that the conserved MAP kinase pathway coordinates CO designation with the disassembly of SC proteins to ensure accurate chromosome segregation.

  5. The MAP kinase pathway coordinates crossover designation with disassembly of synaptonemal complex proteins during meiosis

    PubMed Central

    Nadarajan, Saravanapriah; Mohideen, Firaz; Tzur, Yonatan B; Ferrandiz, Nuria; Crawley, Oliver; Montoya, Alex; Faull, Peter; Snijders, Ambrosius P; Cutillas, Pedro R; Jambhekar, Ashwini; Blower, Michael D; Martinez-Perez, Enrique; Harper, J Wade; Colaiacovo, Monica P

    2016-01-01

    Asymmetric disassembly of the synaptonemal complex (SC) is crucial for proper meiotic chromosome segregation. However, the signaling mechanisms that directly regulate this process are poorly understood. Here we show that the mammalian Rho GEF homolog, ECT-2, functions through the conserved RAS/ERK MAP kinase signaling pathway in the C. elegans germline to regulate the disassembly of SC proteins. We find that SYP-2, a SC central region component, is a potential target for MPK-1-mediated phosphorylation and that constitutively phosphorylated SYP-2 impairs the disassembly of SC proteins from chromosomal domains referred to as the long arms of the bivalents. Inactivation of MAP kinase at late pachytene is critical for timely disassembly of the SC proteins from the long arms, and is dependent on the crossover (CO) promoting factors ZHP-3/RNF212/Zip3 and COSA-1/CNTD1. We propose that the conserved MAP kinase pathway coordinates CO designation with the disassembly of SC proteins to ensure accurate chromosome segregation. DOI: http://dx.doi.org/10.7554/eLife.12039.001 PMID:26920220

  6. Drone based structural mapping at Holuhraun indicates fault reactivation and complexity

    NASA Astrophysics Data System (ADS)

    Mueller, Daniel; Walter, Thomas R.; Steinke, Bastian; Witt, Tanja; Schoepa, Anne; Duerig, Tobi; Gudmundsson, Magnus T.

    2016-04-01

    Accompanied by an intense seismic swarm in August 2014, a dike laterally formed, starting under Icelands Vatnajökull glacier, propagating over a distance of more than 45 km within only two weeks, leading to the largest eruption by volume since the 1783-84 Laki eruption. Along its propagation path, the dike caused intense surface displacements up to meters. Based on seismicity, GPS and InSAR, the propagation has already been analysed and described as segmented lateral dike growth. We now focus on few smaller regions of the dike. We consider the Terrasar-X tandem digital elevation map and aerial photos and find localized zones where structural fissures formed and curved. At these localized, regions we performed a field campaign in summer 2015, applying the close range remote sensing techniques Structure from Motion (SfM) and Terrestrial Laser Scanning (TLS). Over 4 TLS scan were collected, along with over 5,000 aerial images. Point clouds from SfM and TLS are merged and compared, and local structural lineaments analysed. As a result, we obtained an unprecedentedly high-resolution digital elevation map. With this map, we analyse the structural expression of the fissure eruption at the surface and improve understanding on the conditions that influenced the magma propagation path. We elaborate scenarios that lead to complexities of the surface structures and the link to the underlying dike intrusion.

  7. Web mapping system for complex processing and visualization of environmental geospatial datasets

    NASA Astrophysics Data System (ADS)

    Titov, Alexander; Gordov, Evgeny; Okladnikov, Igor

    2016-04-01

    Environmental geospatial datasets (meteorological observations, modeling and reanalysis results, etc.) are used in numerous research applications. Due to a number of objective reasons such as inherent heterogeneity of environmental datasets, big dataset volume, complexity of data models used, syntactic and semantic differences that complicate creation and use of unified terminology, the development of environmental geodata access, processing and visualization services as well as client applications turns out to be quite a sophisticated task. According to general INSPIRE requirements to data visualization geoportal web applications have to provide such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. It should be noted that modern web mapping systems as integrated geoportal applications are developed based on the SOA and might be considered as complexes of interconnected software tools for working with geospatial data. In the report a complex web mapping system including GIS web client and corresponding OGC services for working with geospatial (NetCDF, PostGIS) dataset archive is presented. There are three basic tiers of the GIS web client in it: 1. Tier of geospatial metadata retrieved from central MySQL repository and represented in JSON format 2. Tier of JavaScript objects implementing methods handling: --- NetCDF metadata --- Task XML object for configuring user calculations, input and output formats --- OGC WMS/WFS cartographical services 3. Graphical user interface (GUI) tier representing JavaScript objects realizing web application business logic Metadata tier consists of a number of JSON objects containing technical information describing geospatial datasets (such as spatio-temporal resolution, meteorological parameters, valid processing methods, etc). The middleware tier of JavaScript objects implementing methods for handling geospatial

  8. Structural analysis and mapping of individual protein complexes by infrared nanospectroscopy

    PubMed Central

    Amenabar, Iban; Poly, Simon; Nuansing, Wiwat; Hubrich, Elmar H.; Govyadinov, Alexander A.; Huth, Florian; Krutokhvostov, Roman; Zhang, Lianbing; Knez, Mato; Heberle, Joachim; Bittner, Alexander M.; Hillenbrand, Rainer

    2013-01-01

    Mid-infrared spectroscopy is a widely used tool for material identification and secondary structure analysis in chemistry, biology and biochemistry. However, the diffraction limit prevents nanoscale protein studies. Here we introduce mapping of protein structure with 30 nm lateral resolution and sensitivity to individual protein complexes by Fourier transform infrared nanospectroscopy (nano-FTIR). We present local broadband spectra of one virus, ferritin complexes, purple membranes and insulin aggregates, which can be interpreted in terms of their α-helical and/or β-sheet structure. Applying nano-FTIR for studying insulin fibrils—a model system widely used in neurodegenerative disease research—we find clear evidence that 3-nm-thin amyloid-like fibrils contain a large amount of α-helical structure. This reveals the surprisingly high level of protein organization in the fibril’s periphery, which might explain why fibrils associate. We envision a wide application potential of nano-FTIR, including cellular receptor in vitro mapping and analysis of proteins within quaternary structures. PMID:24301518

  9. Bioclimatic and vegetation mapping of a topographically complex oceanic island applying different interpolation techniques.

    PubMed

    Garzón-Machado, Víctor; Otto, Rüdiger; del Arco Aguilar, Marcelino José

    2014-07-01

    Different spatial interpolation techniques have been applied to construct objective bioclimatic maps of La Palma, Canary Islands. Interpolation of climatic data on this topographically complex island with strong elevation and climatic gradients represents a challenge. Furthermore, meteorological stations are not evenly distributed over the island, with few stations at high elevations. We carried out spatial interpolations of the compensated thermicity index (Itc) and the annual ombrothermic Index (Io), in order to obtain appropriate bioclimatic maps by using automatic interpolation procedures, and to establish their relation to potential vegetation units for constructing a climatophilous potential natural vegetation map (CPNV). For this purpose, we used five interpolation techniques implemented in a GIS: inverse distance weighting (IDW), ordinary kriging (OK), ordinary cokriging (OCK), multiple linear regression (MLR) and MLR followed by ordinary kriging of the regression residuals. Two topographic variables (elevation and aspect), derived from a high-resolution digital elevation model (DEM), were included in OCK and MLR. The accuracy of the interpolation techniques was examined by the results of the error statistics of test data derived from comparison of the predicted and measured values. Best results for both bioclimatic indices were obtained with the MLR method with interpolation of the residuals showing the highest R2 of the regression between observed and predicted values and lowest values of root mean square errors. MLR with correction of interpolated residuals is an attractive interpolation method for bioclimatic mapping on this oceanic island since it permits one to fully account for easily available geographic information but also takes into account local variation of climatic data.

  10. Dissection of a Complex Disease Susceptibility Region Using a Bayesian Stochastic Search Approach to Fine Mapping.

    PubMed

    Wallace, Chris; Cutler, Antony J; Pontikos, Nikolas; Pekalski, Marcin L; Burren, Oliver S; Cooper, Jason D; García, Arcadio Rubio; Ferreira, Ricardo C; Guo, Hui; Walker, Neil M; Smyth, Deborah J; Rich, Stephen S; Onengut-Gumuscu, Suna; Sawcer, Stephen J; Ban, Maria; Richardson, Sylvia; Todd, John A; Wicker, Linda S

    2015-06-01

    Identification of candidate causal variants in regions associated with risk of common diseases is complicated by linkage disequilibrium (LD) and multiple association signals. Nonetheless, accurate maps of these variants are needed, both to fully exploit detailed cell specific chromatin annotation data to highlight disease causal mechanisms and cells, and for design of the functional studies that will ultimately be required to confirm causal mechanisms. We adapted a Bayesian evolutionary stochastic search algorithm to the fine mapping problem, and demonstrated its improved performance over conventional stepwise and regularised regression through simulation studies. We then applied it to fine map the established multiple sclerosis (MS) and type 1 diabetes (T1D) associations in the IL-2RA (CD25) gene region. For T1D, both stepwise and stochastic search approaches identified four T1D association signals, with the major effect tagged by the single nucleotide polymorphism, rs12722496. In contrast, for MS, the stochastic search found two distinct competing models: a single candidate causal variant, tagged by rs2104286 and reported previously using stepwise analysis; and a more complex model with two association signals, one of which was tagged by the major T1D associated rs12722496 and the other by rs56382813. There is low to moderate LD between rs2104286 and both rs12722496 and rs56382813 (r2 ≃ 0:3) and our two SNP model could not be recovered through a forward stepwise search after conditioning on rs2104286. Both signals in the two variant model for MS affect CD25 expression on distinct subpopulations of CD4+ T cells, which are key cells in the autoimmune process. The results support a shared causal variant for T1D and MS. Our study illustrates the benefit of using a purposely designed model search strategy for fine mapping and the advantage of combining disease and protein expression data.

  11. A new broccoli × broccoli immortal mapping population and framework genetic map: tools for breeders and complex trait analysis.

    PubMed

    Walley, Peter Glen; Carder, John; Skipper, Emma; Mathas, Evy; Lynn, James; Pink, David; Buchanan-Wollaston, Vicky

    2012-02-01

    A unique broccoli × broccoli doubled haploid (DH) population has been created from the F(1) of a cross between two DH broccoli lines derived from cultivars Green Duke and Marathon. We genotyped 154 individuals from this population with simple sequence repeat and amplified fragment length polymorphism markers to create a B. oleracea L. var. italica 'intra-crop' specific framework linkage map. The map is composed of nine linkage groups with a total length of 946.7 cM. Previous published B. oleracea maps have been constructed using diverse crosses between morphotypes of B. oleracea; this map therefore represents a useful breeding resource for the dissection of broccoli specific traits. Phenotype data have been collected from the population over five growing seasons; the framework linkage map has been used to locate quantitative trait loci for agronomically important broccoli traits including head weight (saleable yield), head diameter, stalk diameter, weight loss and relative weight loss during storage, as well as traits for broccoli leaf architecture. This population and associated linkage map will aid breeders to directly map agronomically important traits for the improvement of elite broccoli cultivars. PMID:22038485

  12. Geomorphologic map and derived geomorphological evolution model of the Ampato volcanic complex (Southern Peru).

    NASA Astrophysics Data System (ADS)

    Alcalá, J.; Zamorano, J. J.; Palacios, D.

    2012-04-01

    In this work we present the evolution of the Ampato volcanic complex (15°24´-15° 51´S, 73°W; 6.288 m asl) from a geomorphological perspective based on the analysis of landforms, both volcanic and derived from cold processes such as moraines and rock glaciers. In order to do so, a detailed 1:20.000 scale geomorphological map was elaborated by integrating the following techniques: the interpretation of the 1:35.000 scale aerial photographs (Instituto Geográfico Nacional de Perú, 1956) and the analysis of satellite images (Mrsid; NASA, 2000). The cartography was corrected through field work campaigns. A geomorphological cross-section traversing the map from North to South was elaborated in order facilitate the interpretation of the landforms. From the thorough analysis of the landforms represented in the geomorphological map and their relative position we have identified six main volcanic phases, mainly constructive but also, to a lesser extent, destructive (related with a Sant. Helens eruption), interspersed by five large glacial phases. From the three andesitic stratovolcanoes that form the complex (HualcaHualca, Sabancaya and Ampato) we suggest that the oldest of them is HualcaHualca representing the first step of the process over which the other units were placed. The most recent phase corresponds to the main cone of Sabancaya and its sets of domes and large lavas flows. Also we have detected a number of well-preserved vents on the Southern slope of volcano HualcaHualca close to the 1955 glacier tongues. Their presence is an evidence of recent volcanic activity in a volcano considered extinct. The glacial activity has been very active during the Quaternary on the Ampato Complex. The most ancient glacial phase is linked to the Last Glacial Maximum of the Pleistocene. During this event, the paleoglaciers descended down to 3650 m asl and builted moraines of 25- 30 m height. The most recent advance is related to the global event known as Little Ice Age (LIA

  13. Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes.

    PubMed

    Warnecke, T E; Lynch, M D; Karimpour-Fard, A; Lipscomb, M L; Handke, P; Mills, T; Ramey, C J; Hoang, T; Gill, R T

    2010-05-01

    The understanding and engineering of complex phenotypes is a critical issue in biotechnology. Conventional approaches for engineering such phenotypes are often resource intensive, marginally effective, and unable to generate the level of biological understanding desired. Here, we report a new approach for rapidly dissecting a complex phenotype that is based upon the combination of genome-scale growth phenotype data, precisely targeted growth selections, and informatic strategies for abstracting and summarizing data onto coherent biological processes. We measured at high resolution (125 NT) and for the entire genome the effect of increased gene copy number on overall biological fitness corresponding to the expression of a complex phenotype (tolerance to 3-hydroxypropionic acid (3-HP) in Escherichia coli). Genetic level fitness data were then mapped according to various definitions of gene-gene interaction in order to generate network-level fitness data. When metabolic pathways were used to define interactions, we observed that genes within the chorismate and threonine super-pathways were disproportionately enriched throughout selections for 3-HP tolerance. Biochemical and genetic studies demonstrated that alleviation of inhibition of either of these super-pathways was sufficient to mitigate 3-HP toxicity. These data enabled the design of combinatorial modifications that almost completely offset 3-HP toxicity in minimal medium resulting in a 20 g/L and 25-fold increase in tolerance and specific growth, respectively.

  14. Physical mapping of the human t-cell receptor beta gene complex, using yeast artificial chromosomes

    SciTech Connect

    Hashim, Y.; So, A.K.; Kearney, L.

    1995-04-01

    Yeast artificial chromosomes (YACs) were used to construct a physical map of the germline human T-cell {beta} chain gene complex (TCRB). Variable region genes (BV) for the 25 known subfamilies were used as probes to screen the ICRF AM4x YAC library. Of the five positive YACs identified, one YAC designated B3, 820 kilobase pairs (kbp) in size, scored positive for all 25 TCRBV subfamilies plus the constant region genes (BC) when analyzed by pulse field gel electrophoresis. Restriction enzyme mapping of B3 located TCRBV and TCRBC gene regions to 4 Sfi I fragments of 280, 110, 90, and 125 kbp and was in accordance with published data. In addition, comparison of hybridization results of Sfi I-restricted B3 and genomic DNA from the parental cell line GM1416B revealed identical banding patterns. The data thus showed YAC B3 encoded a complete and unrearranged TCRB gene locus of some 600-620 kbp. The map was further resolved by locating restriction sites for Sal I and Bss HII on B3, giving more precise localization of the individual TCRBV gene families. Fluorescent in situ hybridization of B3 to spreads of human metaphase chromosomes localized B3 to 7q35. However, two additional signals were obtained; one attributable to the TCRBV orphon cluster on 9p21, the second to the long arm of chromosome 2. Polymerase chain reaction amplification of a chromosome 2 somatic cell hybrid, using primers for all 25 TCRBV gene families, revealed that the signal was not attributable to a second orphon cluster. It is suggested that B3 is a chimeric YAC with an intact TCRB locus flanked by chromosome 2 sequences. 32 refs., 5 figs., 1 tab.

  15. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

    PubMed Central

    Zhao, Keyan; Tung, Chih-Wei; Eizenga, Georgia C.; Wright, Mark H.; Ali, M. Liakat; Price, Adam H.; Norton, Gareth J.; Islam, M. Rafiqul; Reynolds, Andy; Mezey, Jason; McClung, Anna M.; Bustamante, Carlos D.; McCouch, Susan R.

    2011-01-01

    Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement. PMID:21915109

  16. Electronic sensor and actuator webs for large-area complex geometry cardiac mapping and therapy

    PubMed Central

    Kim, Dae-Hyeong; Ghaffari, Roozbeh; Lu, Nanshu; Wang, Shuodao; Lee, Stephen P.; Keum, Hohyun; D’Angelo, Robert; Klinker, Lauren; Su, Yewang; Lu, Chaofeng; Kim, Yun-Soung; Ameen, Abid; Li, Yuhang; Zhang, Yihui; de Graff, Bassel; Hsu, Yung-Yu; Liu, ZhuangJian; Ruskin, Jeremy; Xu, Lizhi; Lu, Chi; Omenetto, Fiorenzo G.; Huang, Yonggang; Mansour, Moussa; Slepian, Marvin J.; Rogers, John A.

    2012-01-01

    Curved surfaces, complex geometries, and time-dynamic deformations of the heart create challenges in establishing intimate, nonconstraining interfaces between cardiac structures and medical devices or surgical tools, particularly over large areas. We constructed large area designs for diagnostic and therapeutic stretchable sensor and actuator webs that conformally wrap the epicardium, establishing robust contact without sutures, mechanical fixtures, tapes, or surgical adhesives. These multifunctional web devices exploit open, mesh layouts and mount on thin, bio-resorbable sheets of silk to facilitate handling in a way that yields, after dissolution, exceptionally low mechanical moduli and thicknesses. In vivo studies in rabbit and pig animal models demonstrate the effectiveness of these device webs for measuring and spatially mapping temperature, electrophysiological signals, strain, and physical contact in sheet and balloon-based systems that also have the potential to deliver energy to perform localized tissue ablation. PMID:23150574

  17. Electronic sensor and actuator webs for large-area complex geometry cardiac mapping and therapy.

    PubMed

    Kim, Dae-Hyeong; Ghaffari, Roozbeh; Lu, Nanshu; Wang, Shuodao; Lee, Stephen P; Keum, Hohyun; D'Angelo, Robert; Klinker, Lauren; Su, Yewang; Lu, Chaofeng; Kim, Yun-Soung; Ameen, Abid; Li, Yuhang; Zhang, Yihui; de Graff, Bassel; Hsu, Yung-Yu; Liu, Zhuangjian; Ruskin, Jeremy; Xu, Lizhi; Lu, Chi; Omenetto, Fiorenzo G; Huang, Yonggang; Mansour, Moussa; Slepian, Marvin J; Rogers, John A

    2012-12-01

    Curved surfaces, complex geometries, and time-dynamic deformations of the heart create challenges in establishing intimate, nonconstraining interfaces between cardiac structures and medical devices or surgical tools, particularly over large areas. We constructed large area designs for diagnostic and therapeutic stretchable sensor and actuator webs that conformally wrap the epicardium, establishing robust contact without sutures, mechanical fixtures, tapes, or surgical adhesives. These multifunctional web devices exploit open, mesh layouts and mount on thin, bio-resorbable sheets of silk to facilitate handling in a way that yields, after dissolution, exceptionally low mechanical moduli and thicknesses. In vivo studies in rabbit and pig animal models demonstrate the effectiveness of these device webs for measuring and spatially mapping temperature, electrophysiological signals, strain, and physical contact in sheet and balloon-based systems that also have the potential to deliver energy to perform localized tissue ablation. PMID:23150574

  18. Mass mapping of large globin complexes by scanning transmission electron microscopy.

    PubMed

    Wall, Joseph S; Simon, Martha N; Lin, Beth Y; Vinogradov, Serge N

    2008-01-01

    Scanning transmission electron microscopy (STEM) of unstained, freeze-dried biological macromolecules in the dark-field mode provides an image based on the number of electrons elastically scattered by the constituent atoms of the macromolecule. The image of each isolated particle provides information about the projected structure of the latter, and its integrated intensity is directly related to the mass of the selected particle. Particle images can be sorted by shape, providing independent histograms of mass to study assembly/disassembly intermediates. STEM is optimized for low-dose imaging and is suitable for accurate measurement of particle masses over the range from about 30 kDa to 1,000 MDa. This article describes the details of the method developed at the Brookhaven National Laboratory STEM facility and illustrates its application to the mass mapping of large globin complexes.

  19. Airborne mapping of shallow water bathymetry in the optically complex waters of the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Vahtmäe, Ele; Kutser, Tiit

    2016-04-01

    Accurate determination of the water depth is important for marine spatial planning, producing maritime charts for navigation, seabed morphology studies, and carrying out different activities in the coastal waters. Bathymetric data are lacking foremost in the shallow water regions as those areas are often inaccessible to the hydrographic ships carrying out echo sounding measurements. Remote sensing technology can be used as an alternative for shallow water bathymetry mapping. Varieties of empirical methods have been proposed for bathymetry retrieval, where the relationship between remotely sensed radiance of the water body and the water depth at sampled locations was established empirically. Two most widely used depth derivation methods, the linear band model proposed by Lyzenga (1978, 1985, 2006), and the log-transformed band ratio model proposed by Stumpf et al. (2003), were applied to the different preprocessing level airborne Hyspex hyperspectral images from the optically complex Baltic Sea area and evaluated for accuracy. Results showed that the Lyzenga linear band model outperformed the Stumpf log-transformed band ratio model. The best results were achieved with the atmospherically corrected images. The application of glint correction did not improve, but even reduced the accuracy of bathymetric maps.

  20. Extrinsic Sources of Cholinergic Innervation of the Striatal Complex: A Whole-Brain Mapping Analysis

    PubMed Central

    Dautan, Daniel; Hacioğlu Bay, Husniye; Bolam, J. Paul; Gerdjikov, Todor V.; Mena-Segovia, Juan

    2016-01-01

    Acetylcholine in the striatal complex plays an important role in normal behavior and is affected in a number of neurological disorders. Although early studies suggested that acetylcholine in the striatum (STR) is derived almost exclusively from cholinergic interneurons (CIN), recent axonal mapping studies using conditional anterograde tracing have revealed the existence of a prominent direct cholinergic pathway from the pedunculopontine and laterodorsal tegmental nuclei to the dorsal striatum and nucleus accumbens. The identification of the importance of this pathway is essential for creating a complete model of cholinergic modulation in the striatum, and it opens the question as to whether other populations of cholinergic neurons may also contribute to such modulation. Here, using novel viral tracing technologies based on phenotype-specific fluorescent reporter expression in combination with retrograde tracing, we aimed to define other sources of cholinergic innervation of the striatum. Systematic mapping of the projections of all cholinergic structures in the brain (Ch1 to Ch8) by means of conditional tracing of cholinergic axons, revealed that the only extrinsic source of cholinergic innervation arises in the brainstem pedunculopontine and laterodorsal tegmental nuclei. Our results thus place the pedunculopontine and laterodorsal nuclei in a key and exclusive position to provide extrinsic cholinergic modulation of the activity of the striatal systems. PMID:26834571

  1. Airborne mapping of shallow water bathymetry in the optically complex waters of the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Vahtmäe, Ele; Kutser, Tiit

    2016-04-01

    Accurate determination of the water depth is important for marine spatial planning, producing maritime charts for navigation, seabed morphology studies, and carrying out different activities in the coastal waters. Bathymetric data are lacking foremost in the shallow water regions as those areas are often inaccessible to the hydrographic ships carrying out echo sounding measurements. Remote sensing technology can be used as an alternative for shallow water bathymetry mapping. Varieties of empirical methods have been proposed for bathymetry retrieval, where the relationship between remotely sensed radiance of the water body and the water depth at sampled locations was established empirically. Two most widely used depth derivation methods, the linear band model proposed by Lyzenga (1978, 1985, 2006), and the log-transformed band ratio model proposed by Stumpf et al. (2003), were applied to the different preprocessing level airborne Hyspex hyperspectral images from the optically complex Baltic Sea area and evaluated for accuracy. Results showed that the Lyzenga linear band model outperformed the Stumpf log-transformed band ratio model. The best results were achieved with the atmospherically corrected images. The application of glint correction did not improve, but even reduced the accuracy of bathymetric maps.

  2. LARGE-SCALE CO MAPS OF THE LUPUS MOLECULAR CLOUD COMPLEX

    SciTech Connect

    Tothill, N. F. H.; Loehr, A.; Stark, A. A.; Lane, A. P.; Harnett, J. I.; Bourke, T. L.; Myers, P. C.; Parshley, S. C.; Wright, G. A.; Walker, C. K.

    2009-11-01

    Fully sampled degree-scale maps of the {sup 13}CO 2-1 and CO 4-3 transitions toward three members of the Lupus Molecular Cloud Complex-Lupus I, III, and IV-trace the column density and temperature of the molecular gas. Comparison with IR extinction maps from the c2d project requires most of the gas to have a temperature of 8-10 K. Estimates of the cloud mass from {sup 13}CO emission are roughly consistent with most previous estimates, while the line widths are higher, around 2 km s{sup -1}. CO 4-3 emission is found throughout Lupus I, indicating widespread dense gas, and toward Lupus III and IV. Enhanced line widths at the NW end and along the edge of the B 228 ridge in Lupus I, and a coherent velocity gradient across the ridge, are consistent with interaction between the molecular cloud and an expanding H I shell from the Upper-Scorpius subgroup of the Sco-Cen OB Association. Lupus III is dominated by the effects of two HAe/Be stars, and shows no sign of external influence. Slightly warmer gas around the core of Lupus IV and a low line width suggest heating by the Upper-Centaurus-Lupus subgroup of Sco-Cen, without the effects of an H I shell.

  3. Dissecting the genetics of complex inheritance: linkage disequilibrium mapping provides insight into Crohn disease.

    PubMed

    Elding, Heather; Lau, Winston; Swallow, Dallas M; Maniatis, Nikolas

    2011-12-01

    Family studies for Crohn disease (CD) report extensive linkage on chromosome 16q and pinpoint NOD2 as a possible causative locus. However, linkage is also observed in families that do not bear the most frequent NOD2 causative mutations, but no other signals on 16q have been found so far in published genome-wide association studies. Our aim is to identify this missing genetic contribution. We apply a powerful genetic mapping approach to the Wellcome Trust Case-Control Consortium and the National Institute of Diabetes and Digestive and Kidney Diseases genome-wide association data on CD. This method takes into account the underlying structure of linkage disequilibrium (LD) by using genetic distances from LD maps and provides a location for the causal agent. We find genetic heterogeneity within the NOD2 locus and also show an independent and unsuspected involvement of the neighboring gene, CYLD. We find associations with the IRF8 region and the region containing CDH1 and CDH3, as well as substantial phenotypic and genetic heterogeneity for CD itself. The genes are known to be involved in inflammation and immune dysregulation. These findings provide insight into the genetics of CD and suggest promising directions for understanding disease heterogeneity. The application of this method thus paves the way for understanding complex inheritance in general, leading to the dissection of different pathways and ultimately, personalized treatment.

  4. Mapping of Muslim Bagh ophiolite complex (Pakistan) using new remote sensing, and field data

    NASA Astrophysics Data System (ADS)

    Khan, Shuhab D.; Mahmood, Khalid; Casey, John F.

    2007-04-01

    TETHYS is a relational GIS database that combines geophysical, remote sensing, geochemical, and geochronological data, developed as a flexible resource for studying magmatic and geodynamic responses to continental collisions. In this paper, we demonstrate utility of our database by integrating field, remote sensing, and structural data, for detailed mapping and tectonic emplacement of Muslim Bagh ophiolite of western Pakistan. This ophiolite forms the uppermost part of a nappe pile which accreted onto the Indian continental margin during the closure of the Neo-Tethys during a pre-terminal collision that predated the final closure of Tethys during the major collision between India and Eurasia. Utilizing the TETHYS, Landsat, ASTER imagery, and a digital elevation model developed from the ASTER data are used to characterize the lithology and structure of the area. Use of image processing techniques improved the geologic map of the area, for a better understanding of the tectonic emplacement of the Muslim Bagh ophiolite. For the first time we report that the dikes in the Muslim Bagh ophiolite are cutting the metamorphic sole. Our preliminary geochemical data for sheeted dike complex suggest chemical affinities with arc-related rocks. This observation suggests that dikes were intruded in an island arc environment soon after the ophiolite was formed.

  5. Functional Mapping of Protein-Protein Interactions in an Enzyme Complex by Directed Evolution

    PubMed Central

    Roderer, Kathrin; Neuenschwander, Martin; Codoni, Giosiana; Sasso, Severin; Gamper, Marianne; Kast, Peter

    2014-01-01

    The shikimate pathway enzyme chorismate mutase converts chorismate into prephenate, a precursor of Tyr and Phe. The intracellular chorismate mutase (MtCM) of Mycobacterium tuberculosis is poorly active on its own, but becomes >100-fold more efficient upon formation of a complex with the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (MtDS). The crystal structure of the enzyme complex revealed involvement of C-terminal MtCM residues with the MtDS interface. Here we employed evolutionary strategies to probe the tolerance to substitution of the C-terminal MtCM residues from positions 84–90. Variants with randomized positions were subjected to stringent selection in vivo requiring productive interactions with MtDS for survival. Sequence patterns identified in active library members coincide with residue conservation in natural chorismate mutases of the AroQδ subclass to which MtCM belongs. An Arg-Gly dyad at positions 85 and 86, invariant in AroQδ sequences, was intolerant to mutation, whereas Leu88 and Gly89 exhibited a preference for small and hydrophobic residues in functional MtCM-MtDS complexes. In the absence of MtDS, selection under relaxed conditions identifies positions 84–86 as MtCM integrity determinants, suggesting that the more C-terminal residues function in the activation by MtDS. Several MtCM variants, purified using a novel plasmid-based T7 RNA polymerase gene expression system, showed that a diminished ability to physically interact with MtDS correlates with reduced activatability and feedback regulatory control by Tyr and Phe. Mapping critical protein-protein interaction sites by evolutionary strategies may pinpoint promising targets for drugs that interfere with the activity of protein complexes. PMID:25551646

  6. Mapping environmental partitioning properties of nonpolar complex mixtures by use of GC × GC.

    PubMed

    Nabi, Deedar; Gros, Jonas; Dimitriou-Christidis, Petros; Arey, J Samuel

    2014-06-17

    Comprehensive two-dimensional gas chromatography (GC × GC) is effective for separating and quantifying nonpolar organic chemicals in complex mixtures. Here we present a model to estimate 11 environmental partitioning properties for nonpolar analytes based on GC × GC chromatogram retention time information. The considered partitioning properties span several phases including pure liquid, air, water, octanol, hexadecane, particle natural organic matter, dissolved organic matter, and organism lipids. The model training set and test sets are based on a literature compilation of 648 individual experimental partitioning property data. For a test set of 50 nonpolar environmental contaminants, predicted partition coefficients exhibit root-mean-squared errors ranging from 0.19 to 0.48 log unit, outperforming Abraham-type solvation models for the same chemical set. The approach is applicable to nonpolar organic chemicals containing C, H, F, Cl, Br, and I, having boiling points ≤402 °C. The presented model is calibrated, easy to apply, and requires the user only to identify a small set of known analytes that adapt the model to the GC × GC instrument program. The analyst can thus map partitioning property estimates onto GC × GC chromatograms of complex mixtures. For example, analyzed nonpolar chemicals can be screened for long-range transport potential, aquatic bioaccumulation potential, arctic contamination potential, and other characteristic partitioning behaviors. PMID:24901063

  7. Improving wait times to care for individuals with multimorbidities and complex conditions using value stream mapping

    PubMed Central

    Sampalli, Tara; Desy, Michel; Dhir, Minakshi; Edwards, Lynn; Dickson, Robert; Blackmore, Gail

    2015-01-01

    Background: Recognizing the significant impact of wait times for care for individuals with complex chronic conditions, we applied a LEAN methodology, namely – an adaptation of Value Stream Mapping (VSM) to meet the needs of people with multiple chronic conditions and to improve wait times without additional resources or funding. Methods: Over an 18-month time period, staff applied a patient-centric approach that included LEAN methodology of VSM to improve wait times to care. Our framework of evaluation was grounded in the needs and perspectives of patients and individuals waiting to receive care. Patient centric views were obtained through surveys such as Patient Assessment of Chronic Illness Care (PACIC) and process engineering based questions. In addition, LEAN methodology, VSM was added to identify non-value added processes contributing to wait times. Results: The care team successfully reduced wait times to 2 months in 2014 with no wait times for care anticipated in 2015. Increased patient engagement and satisfaction are also outcomes of this innovative initiative. In addition, successful transformations and implementation have resulted in resource efficiencies without increase in costs. Patients have shown significant improvements in functional health following Integrated Chronic Care Service (ICCS) intervention. The methodology will be applied to other chronic disease management areas in Capital Health and the province. Conclusion: Wait times to care in the management of multimoribidities and other complex conditions can add a significant burden not only on the affected individuals but also on the healthcare system. In this study, a novel and modified LEAN methodology has been applied to embed the voice of the patient in care delivery processes and to reduce wait times to care in the management of complex chronic conditions. PMID:26188810

  8. Volcanic and glacial evolution of Chachani-Nocarane complex (Southern Peru) deduced from the geomorphologic map.

    NASA Astrophysics Data System (ADS)

    Alcalá, J.; Zamorano, J. J.; Palacios, D.

    2012-04-01

    The Chachani-Nocarane (16°11'S; 71°31'W; 6.057 m asl) is a large volcanic complex located in the western Central-Andean Cordillera, South of Peru. The date of the last eruption is not known and there are no registers of recent volcanic activity. The complex is shaped by glacial forms belonging to different phases, and periglacial forms (several generations of rock glaciers) which alternate with volcanic forms. The aim of this research is to establish the glacio-volcanic evolution of the volcanic complex Chachani-Nocarane. In order to do so, a detailed 1:20.000 scale geomorphological map was elaborated by integrating the following techniques: interpretation of the 1:35.000 scale aerial photographs (Instituto Geográfico Nacional de Perú, 1956) and the analysis of satellite images (Mrsid; NASA, 2000). Finally, the cartography was corrected though field work campaigns. Through the geomorphologic analysis of the landforms and their relative position, we have identified twelve phases, seven volcanic and five glacial phases. The most ancient volcanic phase is locate to the north area of the study area and correspond with Nocarane and Chingana volcanoes, alignment NW-SE. Above those ensemble the rest of the large delimited geomorphological units overlap. The most recent is located to the SW and consists of a complex series of domes, lava cones and voluminous lavas. Within the glacial phases, the most ancient one is related to the Last Glacial Maximum during the Pleistocene. Over this period, glaciers formed moraines from 3150 to 3600 m asl. The most recent glacier pulsation corresponds to the Little Ice Age (LIA). The moraines related to that event are the closest to the summits, located between 5.100 and 5.300 m asl, and they represent the last trace of glacial activity on the volcanic complex. Currently, this tropical mountain does not have glaciers. The only solid-state water reserves are found in the form of permafrost, as shown by various generations of rock

  9. Two-trait-locus linkage analysis: A powerful strategy for mapping complex genetic traits

    SciTech Connect

    Schork, N.J.; Boehnke, M. ); Terwilliger, J.D.; Ott, J. )

    1993-11-01

    Nearly all diseases mapped to date follow clear Mendelian, single-locus segregation patterns. In contrast, many common familial diseases such as diabetes, psoriasis, several forms of cancer, and schizophrenia are familial and appear to have a genetic component but do not exhibit simple Mendelian transmission. More complex models are required to explain the genetics of these important diseases. In this paper, the authors explore two-trait-locus, two-marker-locus linkage analysis in which two trait loci are mapped simultaneously to separate genetic markers. The authors compare the utility of this approach to standard one-trait-locus, one-marker-locus linkage analysis with and without allowance for heterogeneity. The authors also compare the utility of the two-trait-locus, two-marker-locus analysis to two-trait-locus, one-marker-locus linkage analysis. For common diseases, pedigrees are often bilineal, with disease genes entering via two or more unrelated pedigree members. Since such pedigrees often are avoided in linkage studies, the authors also investigate the relative information content of unilineal and bilineal pedigrees. For the dominant-or-recessive and threshold models that the authors consider, the authors find that two-trait-locus, two-marker-locus linkage analysis can provide substantially more linkage information, as measured by expected maximum lod score, than standard one-trait-locus, one-marker-locus methods, even allowing for heterogeneity, while, for a dominant-or-dominant generating model, one-locus models that allow for heterogeneity extract essentially as much information as the two-trait-locus methods. For these three models, the authors also find that bilineal pedigrees provide sufficient linkage information to warrant their inclusion in such studies. The authors discuss strategies for assessing the significance of the two linkages assumed in two-trait-locus, two-marker-locus models. 37 refs., 1 fig., 4 tabs.

  10. Super-Interpolation With Edge-Orientation-Based Mapping Kernels for Low Complex 2× Upscaling.

    PubMed

    Jae-Seok Choi; Munchurl Kim

    2016-01-01

    With the advent of ultrahigh-definition (UHD) video services, super-resolution (SR) techniques are often required to generate high-resolution (HR) images from low-resolution (LR) images, such as HD images. To generate such HR images and a video of UHD resolutions in limited computing devices with hardware and software, low complex but excellent SR methods are particularly required. In this paper, we present a novel and fast SR method, called super-interpolation (SI), by unifying an interpolation step and a quality-enhancement step. The proposed SI method utilizes edge-orientation (EO)-based pre-learned kernels, which inherits the simplicity of interpolation and the quality enhancement of SR. It performs SR directly from the initial resolution of an input image to the target resolution of an up-scaled output image without requiring any intermediate interpolated image. The proposed SI method involves offline training and online up-scaling phases. In the offline training phase, training LR image patches are clustered based on their edge orientations into different EO classes for which class-dependent linear mapping functions are learned between training LR and HR image patches. In up-scaling phase, an HR output image patch for each LR input image patch is generated by applying an appropriate linear mapping function selected based on the EO of LR input image patch. Our proposed SI method is intensively compared with the ten state-of-the-art SR methods for common image sets and many HD/UHD images. The experimental results show that the SI method yields the smallest running time and requires relatively small hardware resources. It outperforms the six state-of-the-art methods in average (peak signal-to-noise ratio) PSNR/(structural similarity) SSIM, and exhibits competitive or somewhat lower PSNR/SSIM performance compared with the others. PMID:26672039

  11. Fine Mapping Major Histocompatibility Complex Associations in Psoriasis and Its Clinical Subtypes

    PubMed Central

    Okada, Yukinori; Han, Buhm; Tsoi, Lam C.; Stuart, Philip E.; Ellinghaus, Eva; Tejasvi, Trilokraj; Chandran, Vinod; Pellett, Fawnda; Pollock, Remy; Bowcock, Anne M.; Krueger, Gerald G.; Weichenthal, Michael; Voorhees, John J.; Rahman, Proton; Gregersen, Peter K.; Franke, Andre; Nair, Rajan P.; Abecasis, Gonçalo R.; Gladman, Dafna D.; Elder, James T.; de Bakker, Paul I.W.; Raychaudhuri, Soumya

    2014-01-01

    Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10−364). Stepwise analysis revealed multiple HLA-C∗06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C∗12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10−8), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (pomnibus = 2.2 × 10−11), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC. PMID:25087609

  12. Perched Lava Pond Complex on South Rift of Axial Volcano Revealed in AUV Mapping

    NASA Astrophysics Data System (ADS)

    Paduan, J. B.; Clague, D. A.; Caress, D. W.; Thomas, H. J.

    2013-12-01

    An extraordinary lava pond complex is located on Axial Volcano's distal south rift. It was discovered in EM300 multibeam bathymetry collected in 1998, and explored and sampled with ROVs Tiburon in 2005 and Doc Ricketts in 2013. It was surveyed with the MBARI Mapping AUV D. Allan B. in 2011, in a complicated mission first flying above the levees at constant depth, then skimming ~5 m over the levees at a different constant depth to survey the floors, then twice switching to constant altitude mode to map outside the ponds. The AUV navigation was adjusted using the MB-System tool mbnavadjust so that bathymetric features match in overlapping and crossing swaths. The ~1-m resolution AUV bathymetry reveals extremely rough terrain, where low-resolution EM300 data had averaged acoustic returns and obscured details of walls, floors, a breach and surrounding flows, and gives context to the ROV observations and samples. The 6 x 1.5 km pond complex has 4 large and several smaller drained ponds with rims 67 to 106 m above the floors. The combined volume before draining was 0.56 km3. The ponds overflowed to build lobate-flow levees with elongate pillows draping outer flanks, then drained, leaving lava veneer on vertical inner walls. Levee rim depths vary by only 10 m and are deeper around the southern ponds. Deep collapse-pits in the levees suggest porosity of pond walls. The eastern levee of the northeastern pond breached, draining the interconnected ponds, and fed thick, rapidly-emplaced, sheet-flows along the complex's east side. These flows travelled at least 5.5 km down-rift and have 19-33 m deep drained ponds. They extended up-rift as well, forming a 10 x 2.5 km ponded flow with level 'bathtub rings' as high as 35 m above the floor marking that flow's high-stand. Despite the breach, at least 0.066 km3 of the molten interior of the large ponds also drained back down the eruptive fissures, as the pond floors are deeper than the sill and sea floor outside the complex. Tumulus

  13. QTL mapping - Current status and challenges: Comment on "Mapping complex traits as a dynamic system" by L. Sun and R. Wu

    NASA Astrophysics Data System (ADS)

    Liu, Nianjun

    2015-06-01

    One of the important objectives of genetic study is to understand the underlying mechanism of complex traits. However, complex traits are complex in terms of their mechanisms. First, multiple genetic variants are involved in different ways. In addition to the main effects (such as additive and dominant effects), these genetic variants may interact with each other [1-4], they may have pleiotropic effects [5,6], there may be genomic imprinting (a phenomenon where some genes are expressed or repressed depending on their parental origin) [7-9] and epigenetic effects [10-14]. In addition, environment often fits in via gene by environment interaction [15,16]. A more complicated genetic interaction between QTLs is from different genomes, i.e. the genome-genome interaction which may involve genomes from the same organisms or even different organisms [17-19]. Biology is multifactorial and dynamic. Complex traits are closely related to developmental changes in an organism's ontogeny, giving time an important role in the formation of complex traits. From the point of view of ecology, the formation of complex traits is extremely complex involving not only the genes of an individual but also the genotypes of its neighbors that co-occur with it [17,18,20-23]. Such complexity makes QTL mapping very challenging.

  14. The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence from Association Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for ...

  15. Does Visualization Enhance Complex Problem Solving? The Effect of Causal Mapping on Performance in the Computer-Based Microworld Tailorshop

    ERIC Educational Resources Information Center

    Öllinger, Michael; Hammon, Stephanie; von Grundherr, Michael; Funke, Joachim

    2015-01-01

    Causal mapping is often recognized as a technique to support strategic decisions and actions in complex problem situations. Such drawing of causal structures is supposed to particularly foster the understanding of the interaction of the various system elements and to further encourage holistic thinking. It builds on the idea that humans make use…

  16. Global mapping of herpesvirus-host protein complexes reveals a novel transcription strategy for late genes

    PubMed Central

    Davis, Zoe H.; Verschueren, Erik; Jang, Gwendolyn M.; Kleffman, Kevin; Johnson, Jeffrey R.; Park, Jimin; Von Dollen, John; Maher, M. Cyrus; Johnson, Tasha; Newton, William; Jäger, Stefanie; Shales, Michael; Horner, Julie; Hernandez, Ryan D.; Krogan, Nevan J.; Glaunsinger, Britt A.

    2014-01-01

    SUMMARY Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipulate host machinery and how numerous cellular processes are regulated. DNA viruses such as herpesviruses have relatively large coding capacity and thus can target an extensive network of cellular proteins. To identify the host proteins hijacked by this pathogen, we systematically affinity tagged and purified all 89 proteins of Kaposi’s sarcoma-associated herpesvirus (KSHV) from human cells. Mass spectrometry of this material identified over 500 virus-host interactions. KSHV causes AIDS-associated cancers and its interaction network is enriched for proteins linked to cancer and overlaps with proteins that are also targeted by HIV-1. We found that the conserved KSHV protein ORF24 binds to RNA polymerase II and brings it to viral late promoters by mimicking and replacing cellular TATA-box-binding protein (TBP). This is required for herpesviral late gene expression, a complex and poorly understood phase of the viral lifecycle. PMID:25544563

  17. Optimal strategies for mapping complex diseases in the presence of multiple loci.

    PubMed Central

    Goldgar, D E; Easton, D F

    1997-01-01

    Recent advances in genome technology have led to mapping and subsequent isolation, by positional cloning, of a number of genes for common and/or complex human diseases. It therefore will be possible to utilize information about a known locus in the search for additional, perhaps less penetrant, genes for a particular disease. It is also unclear, under these situations, what the optimal sampling strategy should be. To address these questions, we have calculated the expected LOD score for localizing one locus in a variety of two-locus models of disease, for four different pedigree structures, and under three different scenarios regarding knowledge/testing of one of the two loci. These design considerations are evaluated by use of a cost function that incorporates the costs of ascertaining different family structures, the relative costs of genotyping and mutation testing family members, and the amount of information provided by each family structure and testing scenario. The results indicate that, in most cases, affected sib pairs are a particularly poor strategy, especially when linkage or mutation data are available at the known locus. We also demonstrate that prescreening the sample of families for mutations at known susceptibility loci is, in general, a cost-effective strategy. PMID:9150170

  18. Automated two-dimensional liquid chromatographic system for mapping proteins in highly complex mixtures.

    PubMed

    Isobe, T; Uchida, K; Taoka, M; Shinkai, F; Manabe, T; Okuyama, T

    1991-12-27

    An automated two-dimensional liquid chromatographic system was developed for systematic protein separations which could serve for analytical mapping and preparative separations of proteins. The system applies the principles of the column-switching technique, and consists of two different columns connected in tandem through an electrical column switching valve, two pumping systems to operate each column independently and a system controller to perform sequential chromatography on the two columns. A protein mixture is applied to the first-dimensional anion-exchange column and is separated by stepwise elution with an increasing sodium chloride concentration. The eluent is introduced directly to the second-dimensional reversed-phase column, and is further separated by gradient elution with an increasing acetonitrile concentration. The two elution stages are synchronized by a computer program. By this system, very complex protein mixtures such as crude cerebellar extracts were resolved reproducibly into ca. 200 peaks within 12 h. The method can be used for the total analysis of proteins in various tissues and cells without complicated premanupulation of samples, and allows the simultaneous analysis of a protein isolated by chromatography. The isolated protein is most suitable for use in the strategy of protein and gene sequence analysis.

  19. Spectral transformation of ASTER and Landsat TM bands for lithological mapping of Soghan ophiolite complex, south Iran

    NASA Astrophysics Data System (ADS)

    Pournamdari, Mohsen; Hashim, Mazlan; Pour, Amin Beiranvand

    2014-08-01

    Spectral transformation methods, including correlation coefficient (CC) and Optimum Index Factor (OIF), band ratio (BR) and principal component analysis (PCA) were applied to ASTER and Landsat TM bands for lithological mapping of Soghan ophiolitic complex in south of Iran. The results indicated that the methods used evidently showed superior outputs for detecting lithological units in ophiolitic complexes. CC and OIF methods were used to establish enhanced Red-Green-Blue (RGB) color combination bands for discriminating lithological units. A specialized band ratio (4/1, 4/5, 4/7 in RGB) was developed using ASTER bands to differentiate lithological units in ophiolitic complexes. The band ratio effectively detected serpentinite dunite as host rock of chromite ore deposits from surrounding lithological units in the study area. Principal component images derived from first three bands of ASTER and Landsat TM produced well results for lithological mapping applications. ASTER bands contain improved spectral characteristics and higher spatial resolution for detecting serpentinite dunite in ophiolitic complexes. The developed approach used in this study offers great potential for lithological mapping using ASTER and Landsat TM bands, which contributes in economic geology for prospecting chromite ore deposits associated with ophiolitic complexes.

  20. A computational model for sex-specific genetic architecture of complex traits in humans: Implications for mapping pain sensitivity

    PubMed Central

    Wang, Chenguang; Cheng, Yun; Liu, Tian; Li, Qin; Fillingim, Roger B; Wallace, Margaret R; Staud, Roland; Kaplan, Lee; Wu, Rongling

    2008-01-01

    Understanding differences in the genetic architecture of complex traits between the two sexes has significant implications for evolutionary studies and clinical diagnosis. However, our knowledge about sex-specific genetic architecture is limited largely because of a lack of analytical models that can detect and quantify the effects of sex on the complexity of quantitative genetic variation. Here, we derived a statistical model for mapping DNA sequence variants that contribute to sex-specific differences in allele frequencies, linkage disequilibria, and additive and dominance genetic effects due to haplotype diversity. This model allows a genome-wide search for functional haplotypes and the estimation and test of haplotype by sex interactions and sex-specific heritability. The model, validated by simulation studies, was used to detect sex-specific functional haplotypes that encode a pain sensitivity trait in humans. The model could have important implications for mapping complex trait genes and studying the detailed genetic architecture of sex-specific differences. PMID:18416828

  1. Remote mineralogic and lithologic mapping of the Ice River alkaline complex, British Columbia, Canada, using AVIRIS data

    USGS Publications Warehouse

    Bowers, T.L.; Rowan, L.C.

    1996-01-01

    The Ice River Alkaline Complex is a late Paleozoic intrusion of mafic alkaline rocks, syenite, and carbonatite exposed in southeastern British Columbia, Canada. The complex intrudes Cambrian and Ordovician shales, slates, and limestones of the Chancellor and Ottertail Formations and the McKay Group. We examined the alkaline complex and adjacent country rocks using Airborne Visible-Infrared Imaging Spectrometer (AVIRIS) data. The data were first calibrated to relative reflectance and then used to spectrally map mineralogies in the study area by using a linear spectral unmixing program. This technique models each pixel spectrum in an AVIRIS image as a linear combination of unique endmember spectra. We selected endmember spectra from well-exposed and spectrally distinct mineralogic units, vegetation, and snow. Four of the endmembers reflect mineralogic variations within the McKay group in the study area, and may represent lateral and vertical variations of sedimentary or metamorphic facies. Otherwise, the resultant spatial distribution of endmembers shows generally close agreement with the published geologic map, although, in several places, our image-map is more accurate than the published map.

  2. The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses.

    PubMed

    Caballero, Armando; Tenesa, Albert; Keightley, Peter D

    2015-12-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03-0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem.

  3. Sex Differences in Infants' Mapping of Complex Occlusion Sequences: Further Evidence

    ERIC Educational Resources Information Center

    Wilcox, Teresa

    2007-01-01

    Recently, infant researchers have reported sex differences in infants' capacity to map their representation of an occlusion sequence onto a subsequent no-occlusion display. The research reported here sought to identify the extent to which these sex differences are observed in event-mapping tasks and to identify the underlying basis for these…

  4. Inverse period-doubling bifurcations determine complex structure of bursting in a one-dimensional non-autonomous map.

    PubMed

    Han, Xiujing; Chen, Zhenyang; Bi, Qinsheng

    2016-02-01

    We propose a simple one-dimensional non-autonomous map, in which some novel bursting patterns (e.g., "fold/double inverse flip" bursting, "fold/multiple inverse flip" bursting, and "fold/a cascade of inverse flip" bursting) can be observed. Typically, these bursting patterns exhibit complex structures containing a chain of inverse period-doubling bifurcations. The active states related to these bursting can be period-2(n) (n = 1, 2, 3,…) attractors or chaotic attractors, which may evolve to quiescence by a chain of inverse period-doubling bifurcations when the slow excitation decreases through period-doubling bifurcation points of the map. This accounts for the complex inverse period-doubling bifurcation structures observed in bursting patterns. Our findings enrich the possible routes to bursting as well as the underlying mechanisms of bursting.

  5. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries.

    PubMed

    Mbugi, Erasto V; Katale, Bugwesa Z; Streicher, Elizabeth M; Keyyu, Julius D; Kendall, Sharon L; Dockrell, Hazel M; Michel, Anita L; Rweyemamu, Mark M; Warren, Robin M; Matee, Mecky I; van Helden, Paul D; Couvin, David; Rastogi, Nalin

    2016-01-01

    The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA

  6. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries

    PubMed Central

    Mbugi, Erasto V.; Katale, Bugwesa Z.; Streicher, Elizabeth M.; Keyyu, Julius D.; Kendall, Sharon L.; Dockrell, Hazel M.; Michel, Anita L.; Rweyemamu, Mark M.; Warren, Robin M.; Matee, Mecky I.; van Helden, Paul D.; Couvin, David; Rastogi, Nalin

    2016-01-01

    The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA

  7. Thermal mapping: the hydrothermal system of a volcano used to map faults and palaeostructures within stratified ground. The Yasur-Yenkahe volcanic complex (Vanuatu)

    NASA Astrophysics Data System (ADS)

    Amin Douillet, Guilhem; Peltier, Aline; Finizola, Anthony; Brothelande, Elodie; Garaebiti, Esline

    2014-05-01

    Subsurface thermal measurements provide a valuable tool to map hydrothermal-fluid release zones in activevolcanic areas. On explosive volcanoes, where ash fall layers deposit parallel to the ground surface, hydrothermal fluids are trapped in the stratification due to the variations in permeability in deposits of the different explosive phases. Thermal fluids thus travel parallel to the surface close to the ground. This horizontal flux can only escape when faults break the seals of stratification. On the Yasur-Yenkahe volcanic complex (Tanna Island, Vanuatu archipelago), fumaroles andhot springs abound, signs of upraising heat fluxes associated to a well-developed hydrothermal activity. Combinationof high resolution mapping of ground thermal anomalies with geomorphological analysis allows thecharacterization of the structural relationships between the active Yasur volcano and the Yenkahe resurgent dome. A complex system of heat release and hydrothermal fluid circulation below the Yasur-Yenkahe complex isevidenced. Circulation, though propagating vertically as a whole, is funneled by stratification. Thus, the main thermal fluid release is almost exclusively concentrated along structural limits that break the seals inducedby the stratified nature of the ground. Three types of medium/high temperature anomalies have beenevidenced: (1) broad hydrothermalized areas linked with planar stratification that favor lateral spreading,(2) linear segments that represent active faults, and (3) arcuate segments related to paleo-crater rims. Thelimit between the Yasur volcano and the Yenkahe resurgent dome is characterized by an active fault systemaccommodating both the rapid uplift of the Yenkahe block and the overloading induced by the volcanoweight. In such a setting, faults converge below the cone of Yasur, which acts as a focus for the faults. Evidenceof such structures, sometimes hidden in the landscape but detected by thermal measurements, iscritical for risk assessment of

  8. Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex

    PubMed Central

    2012-01-01

    Background The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection. PMID:22621324

  9. Ultrafast inter-ionic charge transfer of transition-metal complexes mapped by femtosecond X-ray powder diffraction

    SciTech Connect

    Freyer, Benjamin; Zamponi, Flavio; Juve, Vincent; Stingl, Johannes; Woerner, Michael; Elsaesser, Thomas; Chergui, Majed

    2013-04-14

    The transient electronic and molecular structure arising from photoinduced charge transfer in transition metal complexes is studied by X-ray powder diffraction with a 100 fs temporal and atomic spatial resolution. Crystals containing a dense array of Fe(II)-tris(bipyridine) ([Fe(bpy){sub 3}]{sup 2+}) complexes and their PF{sub 6}{sup -} counterions display pronounced changes of electron density that occur within the first 100 fs after two-photon excitation of a small fraction of the [Fe(bpy){sub 3}]{sup 2+} complexes. Transient electron density maps derived from the diffraction data reveal a transfer of electronic charge from the Fe atoms and-so far unknown-from the PF{sub 6}{sup -} counterions to the bipyridine units. Such charge transfer (CT) is connected with changes of the inter-ionic and the Fe-bipyridine distances. An analysis of the electron density maps demonstrates the many-body character of charge transfer which affects approximately 30 complexes around a directly photoexcited one. The many-body behavior is governed by the long-range Coulomb forces in the ionic crystals and described by the concept of electronic polarons.

  10. Complex approach to long-term multi-agent mapping in low dynamic environments

    NASA Astrophysics Data System (ADS)

    Shvets, Evgeny A.; Nikolaev, Dmitry P.

    2015-12-01

    In the paper we consider the problem of multi-agent continuous mapping of a changing, low dynamic environment. The mapping problem is a well-studied one, however usage of multiple agents and operation in a non-static environment complicate it and present a handful of challenges (e.g. double-counting, robust data association, memory and bandwidth limits). All these problems are interrelated, but are very rarely considered together, despite the fact that each has drawn attention of the researches. In this paper we devise an architecture that solves the considered problems in an internally consistent manner.

  11. cDNA sequence and mapping of the mouse Copb gene encoding the beta subunit of the COPI coatomer complex.

    PubMed

    LI, W; Elliott, R W; Novak, E K; Swank, R T

    1999-05-01

    COPI-coated vesicles are involved in retrograde-directed selective transport of proteins from the Golgi complex to the endoplasmic reticulum (ER) as well as mediate anterograde transport of cargo proteins within the Golgi or in endosomal trafficking. The COPI protein complex contains an ADP-ribosylation factor (ARF1) and seven coatamer subunits (alpha, beta, beta', gamma, delta, epsilon, zeta-COP). The localization and function of human beta subunit of coatamer (COPB) suggests it is likely a candidate gene of ruby-eye-2 (ru2), which is a mouse model of human Hermansky-Pudlak syndrome characterized by the dysfunction of several subcellular organelles. In this study, we determined the entire coding sequence of mouse (Copb) cDNA by combining an overlapping mouse EST contig with EST walking. beta-COP was found highly conserved in mouse, rat, and human, and it is ubiquitously expressed in mouse. The Copb gene was mapped to mouse Chr 7 at a position of 53.3 cM by radiation hybrid mapping. Our RH mapping data, sequencing of RT-PCR products, and Western blotting exclude the Copb gene as a candidate for ru2.

  12. Restoration of geological surface-UNFOLD method-a validation of complex structural mapping interpretation in the Andean Thrust Belt

    SciTech Connect

    Guillier, B. ); Oller, J.; Mendez, E.; Leconte, J.C.; Letouzey, J.; Specht, M.; Gratier, J.P.

    1993-02-01

    One of the most important problems in petroleum structural geology is dependable interpretation of structural maps obtained by seismic and sub-surface data. One method for validating the geometry of geological structures is the balancing cross-section technique which allows verification of cross-section geometry by a return to its initial horizontal state. However, this can not be used for of 3D halokinesis, shale tectonics, structures formed by polyphased noncoaxial tectonic events, or strike-slip and wrench faulting. An alternative approach is to test the restoration of folded and faulted surfaces to verify 3D structures by balancing geological surfaces represented by a structural map. This method tests the geometry of studied horizon and faults and is based upon the fact that, initially, actual folded/faulted structures were continuous at deposition. The balancing surface program, UNFOLD, restores the actual geological surface to its initial state. Misfits along faults implied poor structural map drawings or strong internal deformation of the geological level. By trial and error method, we returned to the initial data interpretation modifications. This method has been applied to 2D and 3D seismic structural interpretation in different structural styles, environments, rift zones, salt basins, wrench faulting, thrust belt,etc. Some applications to oil field structures in the Andean Thrust Belt have been done to check and validate the complex structural mapping interpretation.

  13. Mapping the Gulf of Maine with side-scan sonar: A new bottom-type classification for complex seafloors

    USGS Publications Warehouse

    Barnhardt, W.A.; Kelley, J.T.; Dickson, S.M.; Belknap, D.F.

    1998-01-01

    The bedrock-framed seafloor in the northwestern Gulf of Maine is characterized by extreme changes in bathymetric relief and covered with a wide variety of surficial materials. Traditional methods of mapping cannot accurately represent the great heterogeneity of such a glaciated region. A new mapping scheme for complex seafloors, based primarily on the interpretation of side-scan sonar imagery, utilizes four easily recognized units: rock, gravel, sand and mud. In many places, however, the seafloor exhibits a complicated mixture or extremely 'patchy' distribution of the four basic units, which are too small to map individually. Twelve composite units, each a two-component mixture of the basic units, were established to represent this patchiness at a small scale (1:100,000). Using a geographic information system, these and all other available data (seismic profiles, grab samples, submersible dives and cores) were referenced to a common geographic base, superimposed on bathymetric contours and then integrated into surficial geologic maps of the regional inner continental shelf. This digital representation of the seafloor comprises a multidimensional, interactive model complete with explicit attributes (depth, bottom type) that allow for detailed analysis of marine environments.

  14. A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria.

    PubMed

    Hoppins, Suzanne; Collins, Sean R; Cassidy-Stone, Ann; Hummel, Eric; Devay, Rachel M; Lackner, Laura L; Westermann, Benedikt; Schuldiner, Maya; Weissman, Jonathan S; Nunnari, Jodi

    2011-10-17

    To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria.

  15. Affected sib-pair interval mapping and exclusion for complex genetic traits: Inferring identity by descent status from relatives

    SciTech Connect

    Hauser, E.R.; Boehnke, M.; Guo, S.W.

    1994-09-01

    Affected sib-pair (ASP) methods provide a useful approach for the initial genetic mapping of complex diseases for which mode of inheritance is uncertain. Risch described a method for interval mapping and exclusion based on the ratio lambda comparing disease risk in the first degree relatives of affected individuals to disease risk in the general population. He assumed marker identity by descent (IBD) status for the ASP could be deduced from parental genotypes. For late onset diseases such as type 2 diabetes, parents may be dead or otherwise unavailable, so that marker IBD status generally cannot be inferred with certainty. Guo has developed efficient methods for probabilistic determination of marker IBD sharing for two or more loci. We have combined and extended the methods of Risch and Guo to carry out interval mapping and exclusion when parents are missing but other relatives such as additional siblings are available. Our method is based on calculating the likelihood of marker data of the ASP and their relatives conditional on the disease status of the ASP, as a function of lambda and the position of the disease locus within the genetic map. We currently are using this method to compare the information to detect or exclude linkage provided by various types of ASP nuclear families -- zero, one, or two typed parents and zero, one, two, or more additional siblings -- as a function of sample size, marker density and informativity, and risk ratio lambda.

  16. Association mapping of complex diseases in linked regions: estimation of genetic effects and feasibility of testing rare variants.

    PubMed

    Wang, William Y S; Cordell, Heather J; Todd, John A

    2003-01-01

    Association mapping in linked regions is a current major approach for the identification of genes for complex diseases. Loci contributing to linkage, even with small values of sibling recurrence risk (lambda(s)), may be equivalent to substantial underlying genetic effects for association studies. For disease alleles with a frequency as low as 1%, highly reliable association studies (80% power for significance level alpha=10(-6)) require only 277, 781, and 1289 families or cases and controls for loci detected with lambda(s) of 1.5, 1.1, and 1.05, respectively, under a multiplicative genetic model. Under alternative models, provided epistatic effects are minor, larger achievable sample sizes will provide sufficient power to map almost any disease gene that may have initially contributed to linkage.

  17. Improved mapping of National Atmospheric Deposition Program wet-deposition in complex terrain using PRISM-gridded data sets

    USGS Publications Warehouse

    Latysh, Natalie E.; Wetherbee, Gregory Alan

    2012-01-01

    High-elevation regions in the United States lack detailed atmospheric wet-deposition data. The National Atmospheric Deposition Program/National Trends Network (NADP/NTN) measures and reports precipitation amounts and chemical constituent concentration and deposition data for the United States on annual isopleth maps using inverse distance weighted (IDW) interpolation methods. This interpolation for unsampled areas does not account for topographic influences. Therefore, NADP/NTN isopleth maps lack detail and potentially underestimate wet deposition in high-elevation regions. The NADP/NTN wet-deposition maps may be improved using precipitation grids generated by other networks. The Parameter-elevation Regressions on Independent Slopes Model (PRISM) produces digital grids of precipitation estimates from many precipitation-monitoring networks and incorporates influences of topographical and geographical features. Because NADP/NTN ion concentrations do not vary with elevation as much as precipitation depths, PRISM is used with unadjusted NADP/NTN data in this paper to calculate ion wet deposition in complex terrain to yield more accurate and detailed isopleth deposition maps in complex terrain. PRISM precipitation estimates generally exceed NADP/NTN precipitation estimates for coastal and mountainous regions in the western United States. NADP/NTN precipitation estimates generally exceed PRISM precipitation estimates for leeward mountainous regions in Washington, Oregon, and Nevada, where abrupt changes in precipitation depths induced by topography are not depicted by IDW interpolation. PRISM-based deposition estimates for nitrate can exceed NADP/NTN estimates by more than 100% for mountainous regions in the western United States.

  18. Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an e...

  19. Mapping of an ophiolite complex by high-resolution visible-infrared spectrometry

    NASA Astrophysics Data System (ADS)

    Combe, Jean-Philippe; Launeau, Patrick; Pinet, Patrick; Despan, Daniela; Harris, Esther; Ceuleneer, Georges; Sotin, Christophe

    2006-08-01

    The Sumail massif of the Oman peridotite has been surveyed by the high spectral resolution imager HyMap. The field measurements have been taken simultaneously to the HyMap campaign with a GER 3700 spectrometer. To compare the two data sets, further calibration and atmospheric correction are made through empirical line corrections. A continuum removal by a modified Gaussian model on reflectance is then performed for each pixel to minimize atmospheric scattering and shadowing effects. Classification from spectral distance is established using field observations and comparisons at full spectral resolution to identify peridotite subunits (harzburgites and dunites) and to distinguish plagioclase-wehrlites from gabbros. Detections of hydrothermal transformations of olivine in serpentines and their alteration in carbonates along fracture networks, characterized by narrow spectral signatures, validate the classification. This demonstrates the utility of the high spectral resolution and the development of appropriate processing methods for geological identifications.

  20. Spatial disaggregation of complex soil map units at regional scale based on soil-landscape relationships

    NASA Astrophysics Data System (ADS)

    Vincent, Sébastien; Lemercier, Blandine; Berthier, Lionel; Walter, Christian

    2015-04-01

    Accurate soil information over large extent is essential to manage agronomical and environmental issues. Where it exists, information on soil is often sparse or available at coarser resolution than required. Typically, the spatial distribution of soil at regional scale is represented as a set of polygons defining soil map units (SMU), each one describing several soil types not spatially delineated, and a semantic database describing these objects. Delineation of soil types within SMU, ie spatial disaggregation of SMU allows improved soil information's accuracy using legacy data. The aim of this study was to predict soil types by spatial disaggregation of SMU through a decision tree approach, considering expert knowledge on soil-landscape relationships embedded in soil databases. The DSMART (Disaggregation and Harmonization of Soil Map Units Through resampled Classification Trees) algorithm developed by Odgers et al. (2014) was used. It requires soil information, environmental covariates, and calibration samples, to build then extrapolate decision trees. To assign a soil type to a particular spatial position, a weighed random allocation approach is applied: each soil type in the SMU is weighted according to its assumed proportion of occurrence in the SMU. Thus soil-landscape relationships are not considered in the current version of DSMART. Expert rules on soil distribution considering the relief, parent material and wetlands location were proposed to drive the procedure of allocation of soil type to sampled positions, in order to integrate the soil-landscape relationships. Semantic information about spatial organization of soil types within SMU and exhaustive landscape descriptors were used. In the eastern part of Brittany (NW France), 171 soil types were described; their relative area in the SMU were estimated, geomorphological and geological contexts were recorded. The model predicted 144 soil types. An external validation was performed by comparing predicted

  1. Using geomorphology to map plant community distribution in complex polygonal tundra landscapes

    NASA Astrophysics Data System (ADS)

    Sloan, V. L.; Gangodagamage, C.; Iversen, C. M.; Norby, R. J.; Wullschleger, S. D.

    2014-12-01

    Climate change over the next century is expected to substantially alter Arctic ecosystem structure and function, resulting in important feedbacks to global climate. Representing Arctic landscapes in the carbon cycle and climate models, however, is challenging because vegetation and soils vary over small spatial scales. Robust approaches are needed for identifying distinct plant communities for fine-scale model parameterizations, and for mapping the distribution of these communities to enable scaling from plot to grid-cell. Here, we demonstrate how a novel technique using LiDAR-derived metrics to delineate micro-topographic features can also be applied to mapping plant community distribution in a polygonal tundra landscape on the Barrow Environmental Observatory (BEO), Alaska. We recorded species composition in 48, 1 x 1 m plots located across contrasting ice-wedge polygon types on the BEO in July 2012. One-way cluster analysis and non-metric multidimensional scaling identified four major plant communities, namely i) tall Carex (sedge) dominated communities, ii) mixed tall graminoid-forb-moss communities, iii) dry graminoid-lichen communities and iv) low-stature, lichen dominated-communities. These communities were strongly linked to micro-topography, corresponding with i) low centers ii) troughs, iii) rims and transitional polygon centers, and iv) high centers. We therefore combined plant community type with geomorphological analyses using high-resolution LiDAR-derived metrics (e.g. slope, curvature, flowpath distances) to delineate micro-topographic features to produce a vegetation map. The map was verified using 24 field survey transects in which plant community boundaries were mapped using DGPS. The approach performed well, with only a small (5%) over-estimate of the extent of trough communities and a corresponding under-estimate of rim and transitional center communities. Overall, these analyses provide a framework which can be used for parameterizing fine

  2. Mapping the interactions and bioactivity of quercetin-(2-hydroxypropyl)-β-cyclodextrin complex.

    PubMed

    Kellici, Tahsin F; Chatziathanasiadou, Maria V; Diamantis, Dimitris; Chatzikonstantinou, Alexandra V; Andreadelis, Ioannis; Christodoulou, Eirini; Valsami, Georgia; Mavromoustakos, Thomas; Tzakos, Andreas G

    2016-09-10

    Natural products have served as a rich source for drug discovery and development. In the last decade their fruitful integration in the drug discovery pipeline declined due to their reduced bioavailability, mainly attributed to their poor aqueous solubility. We synthesized a quercetin (QUE)-(2-hydroxypropyl)-β-cyclodextrin (HP-β-CD) complex that enabled amplification of its solubility and in the same time retained its bioactivity in T24 human bladder cancer cell line. The stability of the complex and the molecular basis of the interactions developed in this host-guest complex were assayed by incorporating an array of analytical techniques and Molecular Dynamics (MD) experiments. 2D DOSY NMR experiment revealed that the diffusion coefficient of free HP-β-CD was 3.55×10(-10)m(2)s(-1) while that of QUE-HP-β-CD inclusion complex 3.09×10(-10)m(2)s(-1), indicating the formation of a complex. Solid and liquid high resolution NMR spectroscopy data showed that the most pronounced differences in chemical shifts at carbons and protons correspondingly during complexation occur in the aromatic ring Α (bearing the two phenolic hydroxyl groups meta to each other). The chemical shift differences in the aromatic ring Β (bearing the two phenolic hydroxyl groups ortho to each other) were less pronounced. The MD results confirmed the experimental data. PMID:27395802

  3. Hepatitis B virus HBx protein activates Ras-GTP complex formation and establishes a Ras, Raf, MAP kinase signaling cascade.

    PubMed Central

    Benn, J; Schneider, R J

    1994-01-01

    Hepatitis B virus produces a small (154-amino acid) transcriptional transactivating protein, HBx, which is required for viral infection and has been implicated in virus-mediated liver oncogenesis. However, the molecular mechanism for HBx activity and its possible influence on cell proliferation have remained obscure. A number of studies suggest that HBx may stimulate transcription by indirectly activating transcription factors, possibly by influencing cell signaling pathways. We now present biochemical evidence that HBx activates Ras and rapidly induces a cytoplasmic signaling cascade linking Ras, Raf, and mitogen-activated protein kinase (MAP kinase), leading to transcriptional transactivation. HBx strongly elevates levels of GTP-bound Ras, activated and phosphorylated Raf, and tyrosine-phosphorylated and activated MAP kinase. Transactivation of transcription factor AP-1 by HBx is blocked by inhibition of Ras or Raf activities but not by inhibition of Ca(2+)- and diacylglycerol-dependent protein kinase C. HBx was also found to stimulate DNA synthesis in serum-starved cells. The hepatitis B virus HBx protein therefore stimulates Ras-GTP complex formation and promotes downstream signaling through Raf and MAP kinases, and may influence cell proliferation. Images PMID:7937954

  4. CauseMap: fast inference of causality from complex time series.

    PubMed

    Maher, M Cyrus; Hernandez, Ryan D

    2015-01-01

    Background. Establishing health-related causal relationships is a central pursuit in biomedical research. Yet, the interdependent non-linearity of biological systems renders causal dynamics laborious and at times impractical to disentangle. This pursuit is further impeded by the dearth of time series that are sufficiently long to observe and understand recurrent patterns of flux. However, as data generation costs plummet and technologies like wearable devices democratize data collection, we anticipate a coming surge in the availability of biomedically-relevant time series data. Given the life-saving potential of these burgeoning resources, it is critical to invest in the development of open source software tools that are capable of drawing meaningful insight from vast amounts of time series data. Results. Here we present CauseMap, the first open source implementation of convergent cross mapping (CCM), a method for establishing causality from long time series data (≳25 observations). Compared to existing time series methods, CCM has the advantage of being model-free and robust to unmeasured confounding that could otherwise induce spurious associations. CCM builds on Takens' Theorem, a well-established result from dynamical systems theory that requires only mild assumptions. This theorem allows us to reconstruct high dimensional system dynamics using a time series of only a single variable. These reconstructions can be thought of as shadows of the true causal system. If reconstructed shadows can predict points from opposing time series, we can infer that the corresponding variables are providing views of the same causal system, and so are causally related. Unlike traditional metrics, this test can establish the directionality of causation, even in the presence of feedback loops. Furthermore, since CCM can extract causal relationships from times series of, e.g., a single individual, it may be a valuable tool to personalized medicine. We implement CCM in Julia, a

  5. CauseMap: fast inference of causality from complex time series.

    PubMed

    Maher, M Cyrus; Hernandez, Ryan D

    2015-01-01

    Background. Establishing health-related causal relationships is a central pursuit in biomedical research. Yet, the interdependent non-linearity of biological systems renders causal dynamics laborious and at times impractical to disentangle. This pursuit is further impeded by the dearth of time series that are sufficiently long to observe and understand recurrent patterns of flux. However, as data generation costs plummet and technologies like wearable devices democratize data collection, we anticipate a coming surge in the availability of biomedically-relevant time series data. Given the life-saving potential of these burgeoning resources, it is critical to invest in the development of open source software tools that are capable of drawing meaningful insight from vast amounts of time series data. Results. Here we present CauseMap, the first open source implementation of convergent cross mapping (CCM), a method for establishing causality from long time series data (≳25 observations). Compared to existing time series methods, CCM has the advantage of being model-free and robust to unmeasured confounding that could otherwise induce spurious associations. CCM builds on Takens' Theorem, a well-established result from dynamical systems theory that requires only mild assumptions. This theorem allows us to reconstruct high dimensional system dynamics using a time series of only a single variable. These reconstructions can be thought of as shadows of the true causal system. If reconstructed shadows can predict points from opposing time series, we can infer that the corresponding variables are providing views of the same causal system, and so are causally related. Unlike traditional metrics, this test can establish the directionality of causation, even in the presence of feedback loops. Furthermore, since CCM can extract causal relationships from times series of, e.g., a single individual, it may be a valuable tool to personalized medicine. We implement CCM in Julia, a

  6. Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato.

    PubMed

    Li, Li; Paulo, Maria-João; van Eeuwijk, Fred; Gebhardt, Christiane

    2010-11-01

    Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ≤ 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ≤ 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed.

  7. Consistent global structures of complex RNA states through multidimensional chemical mapping.

    PubMed

    Cheng, Clarence Yu; Chou, Fang-Chieh; Kladwang, Wipapat; Tian, Siqi; Cordero, Pablo; Das, Rhiju

    2015-06-02

    Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

  8. Consistent global structures of complex RNA states through multidimensional chemical mapping

    PubMed Central

    Cheng, Clarence Yu; Chou, Fang-Chieh; Kladwang, Wipapat; Tian, Siqi; Cordero, Pablo; Das, Rhiju

    2015-01-01

    Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states. DOI: http://dx.doi.org/10.7554/eLife.07600.001 PMID:26035425

  9. Lithologic mapping of the Mordor, NT, Australia ultramafic complex by using the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER)

    USGS Publications Warehouse

    Rowan, L.C.; Mars, J.C.; Simpson, C.J.

    2005-01-01

    Spectral measurements made in the Mordor Pound, NT, Australia study area using the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), in the laboratory and in situ show dominantly Al-OH and ferric-iron VNIR-SWIR absorption features in felsic rock spectra and ferrous-iron and Fe,Mg-OH features in the mafic-ultramafic rock spectra. ASTER ratio images, matched-filter, and spectral-angle mapper processing (SAM) were evaluated for mapping the lithologies. Matched-filter processing in which VNIR + SWIR image spectra were used for reference resulted in 4 felsic classes and 4 mafic-ultramafic classes based on Al-OH or Fe,Mg-OH absorption features and, in some, subtle reflectance differences related to differential weathering and vegetation. These results were similar to those obtained by match-filter analysis of HyMap data from a previous study, but the units were more clearly demarcated in the HyMap image. ASTER TIR spectral emittance data and laboratory emissivity measurements document a wide wavelength range of Si-O spectral features, which reflect the lithological diversity of the Mordor ultramafic complex and adjacent rocks. SAM processing of the spectral emittance data distinguished 2 classes representing the mafic-ultramafic rocks and 4 classes comprising the quartzose to intermediate composition rocks. Utilization of the complementary attributes of the spectral reflectance and spectral emittance data resulted in discrimination of 4 mafic-ultramafic categories; 3 categories of alluvial-colluvial deposits; and a significantly more completely mapped quartzite unit than could be accomplished by using either data set alone. ?? 2005 Elsevier Inc. All rights reserved.

  10. Physical mapping of male fertility and meiotic drive quantitative trait loci in the mouse t complex using chromosome deficiencies.

    PubMed Central

    Planchart, A; You, Y; Schimenti, J C

    2000-01-01

    The t complex spans 20 cM of the proximal region of mouse chromosome 17. A variant form, the t haplotype (t), exists at significant frequencies in wild mouse populations and is characterized by the presence of inversions that suppress recombination with wild-type (+) chromosomes. Transmission ratio distortion and sterility are associated with t and affect males only. It is hypothesized that these phenomena are caused by trans-acting distorter/sterility factors that interact with a responder locus (Tcr(t)) and that the distorter and sterility factors are the same because homozygosity of the distorters causes male sterility. One factor, Tcd1, was previously shown to be amorphic using a chromosome deletion. To overcome limitations imposed by recombination suppression, we used a series of deletions within the t complex in trans to t chromosomes to characterize the Tcd1 region. We find that the distorter activity of Tcd1 is distinct from a linked sterility factor, originally called tcs1. YACs mapped with respect to deletion breakpoints localize tcs1 to a 1.1-Mb interval flanked by D17Aus9 and Tctex1. We present evidence for the existence of multiple proximal t complex regions that exhibit distorter activity. These studies demonstrate the utility of chromosome deletions for complex trait analysis. PMID:10835401

  11. Metallophore mapping in complex matrices by metal isotope coded profiling of organic ligands.

    PubMed

    Deicke, Michael; Mohr, Jan Frieder; Bellenger, Jean-Philippe; Wichard, Thomas

    2014-12-01

    Metal isotope coded profiling (MICP) introduces a universal discovery platform for metal chelating natural products that act as metallophores, ion buffers or sequestering agents. The detection of cation and oxoanion complexing ligands is facilitated by the identification of unique isotopic signatures created by the application of isotopically pure metals.

  12. Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

    PubMed Central

    Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Jia, Limeng; Jackson, Aaron; Moldenhauer, Karen; Yeater, Kathleen; McClung, Anna; Wu, Dianxing

    2012-01-01

    Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice. PMID:22291889

  13. Mutations in MAP3K7 that Alter the Activity of the TAK1 Signaling Complex Cause Frontometaphyseal Dysplasia.

    PubMed

    Wade, Emma M; Daniel, Philip B; Jenkins, Zandra A; McInerney-Leo, Aideen; Leo, Paul; Morgan, Tim; Addor, Marie Claude; Adès, Lesley C; Bertola, Debora; Bohring, Axel; Carter, Erin; Cho, Tae-Joon; Duba, Hans-Christoph; Fletcher, Elaine; Kim, Chong A; Krakow, Deborah; Morava, Eva; Neuhann, Teresa; Superti-Furga, Andrea; Veenstra-Knol, Irma; Wieczorek, Dagmar; Wilson, Louise C; Hennekam, Raoul C M; Sutherland-Smith, Andrew J; Strom, Tim M; Wilkie, Andrew O M; Brown, Matthew A; Duncan, Emma L; Markie, David M; Robertson, Stephen P

    2016-08-01

    Frontometaphyseal dysplasia (FMD) is a progressive sclerosing skeletal dysplasia affecting the long bones and skull. The cause of FMD in some individuals is gain-of-function mutations in FLNA, although how these mutations result in a hyperostotic phenotype remains unknown. Approximately one half of individuals with FMD have no identified mutation in FLNA and are phenotypically very similar to individuals with FLNA mutations, except for an increased tendency to form keloid scars. Using whole-exome sequencing and targeted Sanger sequencing in 19 FMD-affected individuals with no identifiable FLNA mutation, we identified mutations in two genes-MAP3K7, encoding transforming growth factor β (TGF-β)-activated kinase (TAK1), and TAB2, encoding TAK1-associated binding protein 2 (TAB2). Four mutations were found in MAP3K7, including one highly recurrent (n = 15) de novo mutation (c.1454C>T [ p.Pro485Leu]) proximal to the coiled-coil domain of TAK1 and three missense mutations affecting the kinase domain (c.208G>C [p.Glu70Gln], c.299T>A [p.Val100Glu], and c.502G>C [p.Gly168Arg]). Notably, the subjects with the latter three mutations had a milder FMD phenotype. An additional de novo mutation was found in TAB2 (c.1705G>A, p.Glu569Lys). The recurrent mutation does not destabilize TAK1, or impair its ability to homodimerize or bind TAB2, but it does increase TAK1 autophosphorylation and alter the activity of more than one signaling pathway regulated by the TAK1 kinase complex. These findings show that dysregulation of the TAK1 complex produces a close phenocopy of FMD caused by FLNA mutations. Furthermore, they suggest that the pathogenesis of some of the filaminopathies caused by FLNA mutations might be mediated by misregulation of signaling coordinated through the TAK1 signaling complex. PMID:27426733

  14. Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models

    PubMed Central

    2012-01-01

    Background Statistical approaches to describing the behaviour, including the complex relationships between input parameters and model outputs, of nonlinear dynamic models (referred to as metamodelling) are gaining more and more acceptance as a means for sensitivity analysis and to reduce computational demand. Understanding such input-output maps is necessary for efficient model construction and validation. Multi-way metamodelling provides the opportunity to retain the block-wise structure of the temporal data typically generated by dynamic models throughout the analysis. Furthermore, a cluster-based approach to regional metamodelling allows description of highly nonlinear input-output relationships, revealing additional patterns of covariation. Results By presenting the N-way Hierarchical Cluster-based Partial Least Squares Regression (N-way HC-PLSR) method, we here combine multi-way analysis with regional cluster-based metamodelling, together making a powerful methodology for extensive exploration of the input-output maps of complex dynamic models. We illustrate the potential of the N-way HC-PLSR by applying it both to predict model outputs as functions of the input parameters, and in the inverse direction (predicting input parameters from the model outputs), to analyse the behaviour of a dynamic model of the mammalian circadian clock. Our results display a more complete cartography of how variation in input parameters is reflected in the temporal behaviour of multiple model outputs than has been previously reported. Conclusions Our results indicated that the N-way HC-PLSR metamodelling provides a gain in insight into which parameters that are related to a specific model output behaviour, as well as variations in the model sensitivity to certain input parameters across the model output space. Moreover, the N-way approach allows a more transparent and detailed exploration of the temporal dimension of complex dynamic models, compared to alternative 2-way methods

  15. X-ray fluorescence microscopy artefacts in elemental maps of topologically complex samples: Analytical observations, simulation and a map correction method

    NASA Astrophysics Data System (ADS)

    Billè, Fulvio; Kourousias, George; Luchinat, Enrico; Kiskinova, Maya; Gianoncelli, Alessandra

    2016-08-01

    XRF spectroscopy is among the most widely used non-destructive techniques for elemental analysis. Despite the known angular dependence of X-ray fluorescence (XRF), topological artefacts remain an unresolved issue when using X-ray micro- or nano-probes. In this work we investigate the origin of the artefacts in XRF imaging of topologically complex samples, which are unresolved problems in studies of organic matter due to the limited travel distances of low energy XRF emission from the light elements. In particular we mapped Human Embryonic Kidney (HEK293T) cells. The exemplary results with biological samples, obtained with a soft X-ray scanning microscope installed at a synchrotron facility were used for testing a mathematical model based on detector response simulations, and for proposing an artefact correction method based on directional derivatives. Despite the peculiar and specific application, the methodology can be easily extended to hard X-rays and to set-ups with multi-array detector systems when the dimensions of surface reliefs are in the order of the probing beam size.

  16. A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells.

    PubMed

    Dalvai, Mathieu; Loehr, Jeremy; Jacquet, Karine; Huard, Caroline C; Roques, Céline; Herst, Pauline; Côté, Jacques; Doyon, Yannick

    2015-10-20

    Conventional affinity purification followed by mass spectrometry (AP-MS) analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs) to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.

  17. Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

    PubMed Central

    Obado, Samson O.; Brillantes, Marc; Uryu, Kunihiro; Zhang, Wenzhu; Ketaren, Natalia E.; Chait, Brian T.; Field, Mark C.; Rout, Michael P.

    2016-01-01

    The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes. PMID:26891179

  18. The Role of Pedigree Information in Combined Linkage Disequilibrium and Linkage Mapping of Quantitative Trait Loci in a General Complex Pedigree

    PubMed Central

    Lee, S. H.; Van der Werf, J. H. J.

    2005-01-01

    Combined linkage disequilibrium and linkage (LDL) mapping can exploit historical as well as recent and observed recombinations in a recorded pedigree. We investigated the role of pedigree information in LDL mapping and the performance of LDL mapping in general complex pedigrees. We compared using complete and incomplete genotypic data, spanning 5 or 10 generations of known pedigree, and we used bi- or multiallelic markers that were positioned at 1- or 5-cM intervals. Analyses carried out with or without pedigree information were compared. Results were compared with linkage mapping in some of the data sets. Linkage mapping or LDL mapping with sparse marker spacing (∼5 cM) gave a poorer mapping resolution without considering pedigree information compared to that with considering pedigree information. The difference was bigger in a pedigree of more generations. However, LDL mapping with closely linked markers (∼1 cM) gave a much higher mapping resolution regardless of using pedigree information. This study shows that when marker spacing is dense and there is considerable linkage disequilibrium generated from historical recombinations between flanking markers and QTL, the loss of power due to ignoring pedigree information is negligible and mapping resolution is very high. PMID:15677753

  19. Modeling and hazard mapping of complex cascading mass movement processes: the case of glacier lake 513, Carhuaz, Peru

    NASA Astrophysics Data System (ADS)

    Schneider, Demian; Huggel, Christian; García, Javier; Ludeña, Sebastian; Cochachin, Alejo

    2013-04-01

    that complex cascades of mass movement processes can realistically be modeled using different models and model parameters. The method to semi-automatically produce hazard maps is promising and should be applied in other case studies. Verification of model based results in the field remains an important requirement. Results from this study are important for the GLOF early warning system that is currently in an implementation phase, and for risk reduction efforts in general.

  20. Mapping Microbial Populations Relative to Sites of Ongoing Serpentinization: Results from the Tablelands Ophiolite Complex, Canada

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Brazelton, W. J.; Woodruff, Q.; Szponar, N.; Morrill, P. L.

    2010-12-01

    The aqueous alteration of ultramafic rocks (serpentinization) has been suggested to be a favorable process for the habitability of astrobodies in our solar system including subsurface environments of Mars and Europa. Serpentinization produces copious quantities of hydrogen and small organic molecules, and leads to highly reducing, highly alkaline conditions (up to pH 12) and a lack of dissolved inorganic carbon, which both stimulates and challenges microbial activities. Several environments on Earth provide insight into the relationships between serpentinization and microbial life including slow-spreading mid-ocean ridges, subduction zones, and ophiolite materials emplaced along continental margins. The Tablelands, an ophiolite in western Newfoundland, Canada provides an opportunity to carefully document and map the relationships between geochemical energy, microbial growth, and physiology. Alkaline fluids at the Tablelands originate from 500-million year old oceanic crust and accumulate in shallow pools or seep from beneath serpentinized talus. Fluids, rocks, and gases were collected from the Tablelands during a series of field excursions in 2009 and 2010, and geochemical, microscopic, molecular, and cultivation-based approaches were used to study the serpentinite microbial ecosystem. These samples provide an opportunity to generate a comprehensive map of microbial communities and their activities in space and time. Data indicate that a low but detectable stock of microorganisms inhabit high pH pools associated with end-member serpentinite fluids. Enrichment cultures yielded brightly pigmented colonies related to Alphaproteobacteria, presumably carrying out anoxygenic photosynthesis, and Firmicutes, presumably catalyzing the fermentation of organic matter. Culture-independent analyses of SSU rRNA using T-RFLP indicated low diversity communities of Firmicutes and Archaea in standing alkaline pools, communities of Beta- and Gammaproteobacteria at high pH seeps, and

  1. Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.

    PubMed

    Winkelman, Jared T; Winkelman, Bradford T; Boyce, Julian; Maloney, Michael F; Chen, Albert Y; Ross, Wilma; Gourse, Richard L

    2015-09-01

    RNA polymerase binds tightly to DNA to recognize promoters with high specificity but then releases these contacts during the initial stage of transcription. We report a site-specific crosslinking approach to map the DNA path in bacterial transcription intermediates at amino acid and nucleotide resolution. After validating the approach by showing that the DNA path in open complexes (RPO) is the same as in high-resolution X-ray structures, we define the path following substrate addition in "scrunched" complexes (RPITC). The DNA bulges that form within the transcription bubble in RPITC are positioned differently on the two strands. Our data suggest that the non-template strand bulge is extruded into solvent in complexes containing a 5-mer RNA, whereas the template strand bulge remains within the template strand tunnel, exerting stress on interactions between the β flap, β' clamp, and σ3.2. We propose that this stress contributes to σ3.2 displacement from the RNA exit channel, facilitating promoter escape. PMID:26257284

  2. Identification and mapping of two divergent, unlinked major histocompatibility complex class II B genes in Xiphophorus fishes.

    PubMed Central

    McConnell, T J; Godwin, U B; Norton, S F; Nairn, R S; Kazianis, S; Morizot, D C

    1998-01-01

    We have isolated two major histocompatibility complex (MHC) class II B genes from the inbred fish strain Xiphophorus maculatus Jp 163 A. We mapped one of these genes, designated here as DXB, to linkage group III, linked to a malic enzyme locus, also syntenic with human and mouse MHC. Comparison of genomic and cDNA clones shows the gene consists of six exons and five introns. The encoded beta1 domain has three amino acids deleted and a cytoplasmic tail nine amino acids longer than in other teleost class II beta chains, more similar to HLA-DRB, clawed frog Xela-F3, and nurse shark Gici-B. Key residues for disulfide bonds, glycosylation, and interaction with alpha chains are conserved. These same features are also present in a swordtail (Xiphophorus helleri) genomic DXB PCR clone. A second type of class II B clone was amplified by PCR from X. maculatus and found to be orthologous to class II genes identified in other fishes. This DAB-like gene is 63% identical to the X. maculatus DXB sequence in the conserved beta2-encoding exon and was mapped to new unassigned linkage group LG U24. The DXB gene, then, represents an unlinked duplicated locus not previously identified in teleosts. PMID:9691047

  3. Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of Chromera velia.

    PubMed

    Janouskovec, Jan; Sobotka, Roman; Lai, De-Hua; Flegontov, Pavel; Koník, Peter; Komenda, Josef; Ali, Shahjahan; Prásil, Ondrej; Pain, Arnab; Oborník, Miroslav; Lukes, Julius; Keeling, Patrick J

    2013-11-01

    The canonical photosynthetic plastid genomes consist of a single circular-mapping chromosome that encodes a highly conserved protein core, involved in photosynthesis and ATP generation. Here, we demonstrate that the plastid genome of the photosynthetic relative of apicomplexans, Chromera velia, departs from this view in several unique ways. Core photosynthesis proteins PsaA and AtpB have been broken into two fragments, which we show are independently transcribed, oligoU-tailed, translated, and assembled into functional photosystem I and ATP synthase complexes. Genome-wide transcription profiles support expression of many other highly modified proteins, including several that contain extensions amounting to hundreds of amino acids in length. Canonical gene clusters and operons have been fragmented and reshuffled into novel putative transcriptional units. Massive genomic coverage by paired-end reads, coupled with pulsed-field gel electrophoresis and polymerase chain reaction, consistently indicate that the C. velia plastid genome is linear-mapping, a unique state among all plastids. Abundant intragenomic duplication probably mediated by recombination can explain protein splits, extensions, and genome linearization and is perhaps the key driving force behind the many features that defy the conventional ways of plastid genome architecture and function.

  4. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

    SciTech Connect

    Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

    1992-12-01

    A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 {sup 32}P- or {sup 33}P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.

  5. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

    SciTech Connect

    Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

    1992-01-01

    A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 [sup 32]P- or [sup 33]P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.

  6. How to dissect complex traits and how to choose suitable mapping resources for system genetics?. Comment on "Mapping complex traits as a dynamic system" by L. Sun and R. Wu

    NASA Astrophysics Data System (ADS)

    van Eeuwijk, Fred

    2015-06-01

    Sun and Wu [1] present an integral approach to the mapping of complex traits. Phenotypic traits are components belonging to a system together with other components, with all these components being interconnected and interacting over time and across levels of biological organisation. Following the terminology of Sun and Wu, the system initiates with variation at the level of DNA sequences and terminates with variation at the level of end point phenotypes. In between, we find variation at the levels of gene-expression, proteins, and metabolites. Before arriving at the end point phenotypes, many biochemical pathways need to be regulated and endophenotypes synthesised. To resolve the genetic architecture of complex traits, they need to be studied in relation to their underlying components, their interactions with other traits, and their development over time. Crucial is the identification of the mechanisms that govern the system and how quantitative trait loci (QTL) influence those mechanisms. Sun and Wu propose for any biological system a methodological framework that predicts physiological and pathological phenotypes as well as the consequences of genetic and environmental changes and interventions. This framework consists in a system of differential equations that drives variation in components and their mutual interactions and leads to developmental and functional changes. The differential equations allow capturing the dynamics of end point phenotypes and endophenotypes in relation to time and/or environmental factors. Simultaneously, QTLs underlie the constants in the differential equations and thereby can change developmental trajectories and environmental dependencies.

  7. Mapping the Structure and Dynamics of Genomics-Related MeSH Terms Complex Networks

    PubMed Central

    Siqueiros-García, Jesús M.; Hernández-Lemus, Enrique; García-Herrera, Rodrigo; Robina-Galatas, Andrea

    2014-01-01

    It has been proposed that the history and evolution of scientific ideas may reflect certain aspects of the underlying socio-cognitive frameworks in which science itself is developing. Systematic analyses of the development of scientific knowledge may help us to construct models of the collective dynamics of science. Aiming at scientific rigor, these models should be built upon solid empirical evidence, analyzed with formal tools leading to ever-improving results that support the related conclusions. Along these lines we studied the dynamics and structure of the development of research in genomics as represented by the entire collection of genomics-related scientific papers contained in the PubMed database. The analyzed corpus consisted in more than 49,000 articles published in the years 1987 (first appeareance of the term Genomics) to 2011, categorized by means of the Medical Subheadings (MeSH) content-descriptors. Complex networks were built where two MeSH terms were connected if they are descriptors of the same article(s). The analysis of such networks revealed a complex structure and dynamics that to certain extent resembled small-world networks. The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project. We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks. In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-stucture, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms. PMID:24699262

  8. Mapping the structure and dynamics of genomics-related MeSH terms complex networks.

    PubMed

    Siqueiros-García, Jesús M; Hernández-Lemus, Enrique; García-Herrera, Rodrigo; Robina-Galatas, Andrea

    2014-01-01

    It has been proposed that the history and evolution of scientific ideas may reflect certain aspects of the underlying socio-cognitive frameworks in which science itself is developing. Systematic analyses of the development of scientific knowledge may help us to construct models of the collective dynamics of science. Aiming at scientific rigor, these models should be built upon solid empirical evidence, analyzed with formal tools leading to ever-improving results that support the related conclusions. Along these lines we studied the dynamics and structure of the development of research in genomics as represented by the entire collection of genomics-related scientific papers contained in the PubMed database. The analyzed corpus consisted in more than 49,000 articles published in the years 1987 (first appearance of the term Genomics) to 2011, categorized by means of the Medical Subheadings (MeSH) content-descriptors. Complex networks were built where two MeSH terms were connected if they are descriptors of the same article(s). The analysis of such networks revealed a complex structure and dynamics that to certain extent resembled small-world networks. The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project. We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks. In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-structure, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms. PMID:24699262

  9. Radiological Mapping of the Alkaline Intrusive Complex of Jombo, South Coastal Kenya by In-Situ Gamma-Ray Spectrometry

    NASA Astrophysics Data System (ADS)

    Kaniu, Ian; Darby, Iain G.; Kalambuka Angeyo, Hudson

    2016-04-01

    Carbonatites and alkaline intrusive complexes are rich in a variety of mineral deposits such as rare earth elements (REEs), including Nb, Zr and Mn. These are often associated with U and Th bearing minerals, including monazite, samarskite and pyrochlore. Mining waste resulting from mineral processing activities can be highly radioactive and therefore poses a risk to human health and environment. The Jombo complex located in Kenya's south coastal region is potentially one of the richest sources of Nb and REEs in the world. It consists of the main intrusion at Jombo hill, three associated satellite intrusions at Mrima, Kiruku and Nguluku hills, and several dykes. The complex is highly heterogeneous with regard to its geological formation as it is characterized by alkaline igneous rocks and carbonatites which also influence its radio-ecological dynamics. In-situ gamma spectrometry offers a low-cost, rapid and spatially representative radioactivity estimate across a range of landscapes compared to conventional radiometric techniques. In this work, a wide ranging radiological survey was conducted in the Jombo complex as follow up on previous studies[1,2], to determine radiation exposure levels and source distributions, and perform radiological risk assessments. The in-situ measurements were carried out using a 2.0 l NaI(Tl) PGIS-2 portable detector from Pico Envirotec Inc integrated with GPS, deployed for ground (back-pack) and vehicular gamma-ray spectrometry. Preliminary results of radiological distribution and mapping will be presented. [1] Patel, J. P. (1991). Discovery and Innovation, 3(3): 31-35. [2] Kebwaro, J. M. et. al. (2011). J. Phys. Sci., 6(13): 3105-3110.

  10. Mapping the Complex Phase Behaviors of Aqueous Mixtures of κ-Carrageenan and Type B Gelatin.

    PubMed

    Cao, Yiping; Wang, Lu; Zhang, Ke; Fang, Yapeng; Nishinari, Katsuyoshi; Phillips, Glyn O

    2015-07-30

    We report a detailed and complete phase diagram for an aqueous mixture of oppositely charged gelling biopolymers, type B gelatin and κ-carrageenan (KC) at pH 7.0. The phase diagram is studied in the ionic strength-temperature coordinate by means of turbidity, rheological and differential scanning calorimetric measurements, and macroscopic phase compositional analysis. Seven phase regions are identified, including (I) compatible region, (II) electrostatically induced associative phase separation (EIAPS) region, (III) hydrogen bonding induced associative phase separation (HBIAPS) region, (IV) coexistence of EIAPS and HBIAPS, (V) segregative phase separation (SPS) region, (VI) coexistence of HBIAPS and SPS, and (VII) SPS trapped by gelation. The HBIAPS reported for the first time here is attributed to the extensive hydrogen bonding formation between gelatin and KC above their conformational transition temperatures, as probed by addition of urea and methylene blue as well as by 2D (1)H-(1)H NOESY NMR. NaCl is found to have dual effects on HBIAPS. The electrostatic complexation at lower ionic strength facilitates the formation of hydrogen bonds between gelatin and KC and hence the HBIAPS. It is believed that the local structural arrangement of gelatin molecules or the change in local solvent environment prior to triple helix formation during cooling enables the formation of hydrogen bonds with KC.

  11. Exon junction complex subunits are required to splice Drosophila MAP kinase, a large heterochromatic gene

    PubMed Central

    Roignant, Jean-Yves; Treisman, Jessica E.

    2010-01-01

    Summary The exon junction complex (EJC) is assembled on spliced mRNAs upstream of exon-exon junctions, and can regulate their subsequent translation, localization, or degradation. We isolated mutations in Drosophila mago nashi (mago), which encodes a core EJC subunit, based on their unexpectedly specific effects on photoreceptor differentiation. Loss of Mago prevents Epidermal growth factor receptor signaling, due to a large reduction in MAPK mRNA levels. MAPK expression also requires the EJC subunits Y14 and eIF4AIII, and EJC-associated splicing factors. Mago depletion does not affect the transcription or stability of MAPK mRNA, but alters its splicing pattern. MAPK expression from an exogenous promoter requires Mago only when the template includes introns. MAPK is the primary functional target of mago in eye development; in cultured cells, Mago knockdown disproportionately affects other large genes located in heterochromatin. These data support a nuclear role for EJC components in splicing a specific subset of introns. PMID:20946982

  12. Mapping forest stand complexity for woodland caribou habitat assessment using multispectral airborne imagery

    NASA Astrophysics Data System (ADS)

    Zhang, W.; Hu, B.; Woods, M.

    2014-11-01

    The decline of the woodland caribou population is a result of their habitat loss. To conserve the habitat of the woodland caribou and protect it from extinction, it is critical to accurately characterize and monitor its habitat. Conventionally, products derived from low to medium spatial resolution remote sensing data, such as land cover classification and vegetation indices are used for wildlife habitat assessment. These products fail to provide information on the structure complexities of forest canopies which reflect important characteristics of caribou's habitats. Recent studies have employed the LiDAR system (Light Detection And Ranging) to directly retrieve the three dimensional forest attributes. Although promising results have been achieved, the acquisition cost of LiDAR data is very high. In this study, utilizing the very high spatial resolution imagery in characterizing the structural development the of forest canopies was exploited. A stand based image texture analysis was performed to predict forest succession stages. The results were demonstrated to be consistent with those derived from LiDAR data.

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

    PubMed

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

    2016-08-01

    Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping. PMID:27144898

  14. Mapping the complex kinematics of LL objects in the Orion nebula

    NASA Astrophysics Data System (ADS)

    Henney, William J.; García-Díaz, Ma. T.; O'Dell, C. R.; Rubin, Robert H.

    2013-01-01

    LL Orionis-type objects (LL objects) are hyperbolic bowshocks visible around young stars in the outer Orion nebula, many of which are also associated with curved, highly collimated jets. The bowshocks are clearly due to the supersonic interaction between an outflow from the young star and an environmental flow from the core of the nebula, but the exact nature of these flows has not yet been established. We present the first high-resolution optical spectra of two of these objects, LL 1 and LL 2, together with their associated Herbig-Haro (HH) jets, HH 888 and HH 505. We combine multiple long-slit echelle spectra in the Hα 6563 Å and [N ii] 6584 Å lines to produce velocity maps of the two objects at a resolution of 4text{arcsec} × 2text{arcsec} × 11 {km s^{-1}}. The gas motions within both stellar bowshocks are of rather low velocity (10-20 km s-1), but there are important differences between the two objects. LL 1 shows a high degree of symmetry, whereas LL 2 has very asymmetric kinematics that seem to follow velocity gradients in the surrounding nebula. We also measure the line-of-sight velocity for multiple knots in the HH 888 and HH 505 jets, and combine our spectroscopy with new and existing proper-motion measurements to reconstruct the three-dimensional kinematics of the jets. The knot motions in both jets are very similar: both flows are inclined at 40° to 60° from the plane of the sky, with exclusively redshifted knots to the north and exclusively blueshifted knots to the south. In both cases, one also sees a deceleration along the length of the jets, from >200 km s-1 close to the respective stars down to <100 km s-1 farther out. The marked contrasts that we find between the kinematics of the jets and the kinematics of the stellar bowshocks are evidence that the two phenomena are not causally related. Regular patterns in the dynamic ages of the HH 505 knots imply periodic ejections on three different time-scales: 50, 12 and 4 yr. We use line ratios and

  15. Disentangling regular and chaotic motion in the standard map using complex network analysis of recurrences in phase space.

    PubMed

    Zou, Yong; Donner, Reik V; Thiel, Marco; Kurths, Jürgen

    2016-02-01

    Recurrence in the phase space of complex systems is a well-studied phenomenon, which has provided deep insights into the nonlinear dynamics of such systems. For dissipative systems, characteristics based on recurrence plots have recently attracted much interest for discriminating qualitatively different types of dynamics in terms of measures of complexity, dynamical invariants, or even structural characteristics of the underlying attractor's geometry in phase space. Here, we demonstrate that the latter approach also provides a corresponding distinction between different co-existing dynamical regimes of the standard map, a paradigmatic example of a low-dimensional conservative system. Specifically, we show that the recently developed approach of recurrence network analysis provides potentially useful geometric characteristics distinguishing between regular and chaotic orbits. We find that chaotic orbits in an intermittent laminar phase (commonly referred to as sticky orbits) have a distinct geometric structure possibly differing in a subtle way from those of regular orbits, which is highlighted by different recurrence network properties obtained from relatively short time series. Thus, this approach can help discriminating regular orbits from laminar phases of chaotic ones, which presents a persistent challenge to many existing chaos detection techniques. PMID:26931601

  16. Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes - a new strategy for OLED materials.

    PubMed

    Ewen, Pascal R; Sanning, Jan; Koch, Tobias; Doltsinis, Nikos L; Strassert, Cristian A; Wegner, Daniel

    2014-01-01

    The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM) and spectroscopy (STS) are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters) with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II) complexes adsorbed on Au(111). The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices.

  17. A scheme for the uniform mapping and monitoring of earth resources and environmental complexes using ERTS-1 imagery

    NASA Technical Reports Server (NTRS)

    Poulton, C. E. (Principal Investigator); Welch, R. I.

    1973-01-01

    There are no author-identified significant results in this report. Progress on plans for the development and testing of a practical procedure and system for the uniform mapping and monitoring of natural ecosystems and environmental complexes from space-acquired imagery is discussed. With primary emphasis on ERTS-1 imagery, but supported by appropriate aircraft photography as necessary, the objectives are to accomplish the following: (1) Develop and test in a few selected sites and areas of the western United States a standard format for an ecological and land use legend for making natural resource inventories on a simulated global basis. (2) Based on these same limited geographic areas, identify the potentialities and limitations of the legend concept for the recognition and annotation of ecological analogs and environmental complexes. An additional objective is to determine the optimum combination of space photography, aerial photography, ground data, human data analysis, and automatic data analysis for estimating crop yield in the rice growing areas of California and Louisiana.

  18. Disentangling regular and chaotic motion in the standard map using complex network analysis of recurrences in phase space.

    PubMed

    Zou, Yong; Donner, Reik V; Thiel, Marco; Kurths, Jürgen

    2016-02-01

    Recurrence in the phase space of complex systems is a well-studied phenomenon, which has provided deep insights into the nonlinear dynamics of such systems. For dissipative systems, characteristics based on recurrence plots have recently attracted much interest for discriminating qualitatively different types of dynamics in terms of measures of complexity, dynamical invariants, or even structural characteristics of the underlying attractor's geometry in phase space. Here, we demonstrate that the latter approach also provides a corresponding distinction between different co-existing dynamical regimes of the standard map, a paradigmatic example of a low-dimensional conservative system. Specifically, we show that the recently developed approach of recurrence network analysis provides potentially useful geometric characteristics distinguishing between regular and chaotic orbits. We find that chaotic orbits in an intermittent laminar phase (commonly referred to as sticky orbits) have a distinct geometric structure possibly differing in a subtle way from those of regular orbits, which is highlighted by different recurrence network properties obtained from relatively short time series. Thus, this approach can help discriminating regular orbits from laminar phases of chaotic ones, which presents a persistent challenge to many existing chaos detection techniques.

  19. Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes – a new strategy for OLED materials

    PubMed Central

    Ewen, Pascal R; Sanning, Jan; Koch, Tobias; Doltsinis, Nikos L

    2014-01-01

    Summary The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM) and spectroscopy (STS) are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters) with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II) complexes adsorbed on Au(111). The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices. PMID:25551053

  20. Evaluation of Changes in Effluent Quality from Industrial Complexes on the Korean Nationwide Scale Using a Self-Organizing Map

    PubMed Central

    Bae, Mi-Jung; Kim, Jun-Su; Park, Young-Seuk

    2012-01-01

    One of the major issues related to the environment in the 21st century is sustainable development. The innovative economic growth policy has supported relatively successful economic development, but poor environmental conservation efforts, have consequently resulted in serious water quality pollution issues. Hence, assessments of water quality and health are fundamental processes towards conserving and restoring aquatic ecosystems. In this study, we characterized spatial and temporal changes in water quality (specifically physico-chemical variables plus priority and non-priority pollutants) of discharges from industrial complexes on a national scale in Korea. The data were provided by the Water Quality Monitoring Program operated by the Ministry of Environment, Korea and were measured from 1989 to 2008 on a monthly basis at 61 effluent monitoring sites located at industrial complexes. Analysis of monthly and annual changes in water quality, using the seasonal Mann-Kendall test, indicated an improvement in water quality, which was inferred from a continuous increase in dissolved oxygen and decrease in other water quality factors. A Self-Organizing Map, which is an unsupervised artificial neural network, also indicated an improvement of effluent water quality, by showing spatial and temporal differences in the effluent water quality as well as in the occurrence of priority pollutants. Finally, our results suggested that continued long-term monitoring is necessary to establish plans and policies for wastewater management and health assessment. PMID:22690190

  1. A genetic linkage map of mouse chromosome 2 extending from thrombospondin to paired box gene 1, including the H3 minor histocompatibility complex

    SciTech Connect

    Zuberi, A.R.; Nguyen, H.Q.; Auman, H.J.

    1996-04-01

    The classical minor histocompatibility 3(H3) locus was originally defined by the phenotype of skin graft rejection, which is complex genetic trait. H3 is now known to be a gene complex comprised of a minimum of two functionally interdependent alloantigen-encoding loci, H3a and H3b. H3a encodes a peptide recognized by cytotoxic T cells, and H3b encodes a peptide that stimulates helper T cells. The H3 complex also contains the {beta}{sub 2}-microglobulin gene (B2m), and polymorphisms in B2m contribute to the tissue rejection phenotype. We describe a high-density genetic linkage map of a 16-cM region of mouse Chromosome 2 from thromospondin (Thbs1) to paired box gene 1 (Pax1). This genetic map includes H3a, H3b, and B2m. Other genes and anonymous loci have also been placed on the map. H3a maps between D2Mit444 and B2m in close vicinity to several known genes. H3b maps 12 cM distal to H3a, and the proprotein convertase subtilisin/kexin type 2 gene (Pcsk2; formerly Nec2) cosegregates with H3b in a high-resolution backcross panel. The H3 complex spans a region that shows conserved synteny to human chromosomes 15q, 2q, and 20p. 59 refs., 4 figs., 1 tab.

  2. The Complexity of the ERK/MAP-Kinase Pathway and the Treatment of Melanoma Skin Cancer

    PubMed Central

    Wellbrock, Claudia; Arozarena, Imanol

    2016-01-01

    The central role played by the ERK/MAPK pathway downstream of RAS in human neoplasias is best exemplified in the context of melanoma skin cancer. Signaling through the MAPK pathway is crucial for the proliferation of melanocytes, the healthy pigment cells that give rise to melanoma. However, hyper-activation of the MAPK-pathway is found in over 90% of melanomas with approximately 50% of all patients displaying mutations in the kinase BRAF, and approximately 28% of all patients harboring mutations in the MAPK-pathway up-stream regulator NRAS. This finding has led to the development of BRAF and MEK inhibitors whose application in the clinic has shown unprecedented survival responses. Unfortunately the responses to MAPK pathway inhibitors are transient with most patients progressing within a year and a median progression free survival of 7–10 months. The disease progression is due to the development of drug-resistance based on various mechanisms, many of them involving a rewiring of the MAPK pathway. In this article we will review the complexity of MAPK signaling in melanocytic cells as well as the mechanisms of action of different MAPK-pathway inhibitors and their correlation with clinical response. We will reflect on mechanisms of innate and acquired resistance that limit patient's response, with a focus on the MAPK signaling network. Because of the resurgence of antibody-based immune-therapies there is a growing feeling of failure in the targeted therapy camp. However, recent studies have revealed new windows of therapeutic opportunity for melanoma sufferers treated with drugs targeting the MAPK pathway, and these opportunities will be discussed. PMID:27200346

  3. Interpreting participatory Fuzzy Cognitive Maps as complex networks in the social-ecological systems of the Amazonian forests

    NASA Astrophysics Data System (ADS)

    Varela, Consuelo; Tarquis, Ana M.; Blanco-Gutiérrez, Irene; Estebe, Paloma; Toledo, Marisol; Martorano, Lucieta

    2015-04-01

    Social-ecological systems are linked complex systems that represent interconnected human and biophysical processes evolving and adapting across temporal and spatial scales. In the real world, social-ecological systems pose substantial challenges for modeling. In this regard, Fuzzy Cognitive Maps (FCMs) have proven to be a useful method for capturing the functioning of this type of systems. FCMs are a semi-quantitative type of cognitive map that represent a system composed of relevant factors and weighted links showing the strength and direction of cause-effects relationships among factors. Therefore, FCMs can be interpreted as complex system structures or complex networks. In this sense, recent research has applied complex network concepts for the analysis of FCMs that represent social-ecological systems. Key to FCM the tool is its potential to allow feedback loops and to include stakeholder knowledge in the construction of the tool. Also, previous research has demonstrated their potential to represent system dynamics and simulate the effects of changes in the system, such as policy interventions. For illustrating this analysis, we have developed a series of participatory FCM for the study of the ecological and human systems related to biodiversity conservation in two case studies of the Amazonian region, the Bolivia lowlands of Guarayos and the Brazil Tapajos National forest. The research is carried out in the context of the EU project ROBIN1 and it is based on the development of a series of stakeholder workshops to analyze the current state of the socio-ecological environment in the Amazonian forest, reflecting conflicts and challenges for biodiversity conservation and human development. Stakeholders included all relevant actors in the local case studies, namely farmers, environmental groups, producer organizations, local and provincial authorities and scientists. In both case studies we illustrate the use of complex networks concepts, such as the adjacency

  4. Spatial digital database of the geologic map of Catalina Core Complex and San Pedro Trough, Pima, Pinal, Gila, Graham, and Cochise counties, Arizona

    USGS Publications Warehouse

    Dickinson, William R.; digital database by Hirschberg, Douglas M.; Pitts, G. Stephen; Bolm, Karen S.

    2002-01-01

    The geologic map of Catalina Core Complex and San Pedro Trough by Dickinson (1992) was digitized for input into a geographic information system (GIS) by the U.S. Geological Survey staff and contractors in 2000-2001. This digital geospatial database is one of many being created by the U.S. Geological Survey as an ongoing effort to provide geologic information in a geographic information system (GIS) for use in spatial analysis. The resulting digital geologic map database data can be queried in many ways to produce a variety of geologic maps and derivative products. Digital base map data (topography, roads, towns, rivers, lakes, and so forth) are not included; they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:125,000 (for example, 1:100,000 or 1:24,000). The digital geologic map plot files that are provided herein are representations of the database. The map area is located in southern Arizona. This report lists the geologic map units, the methods used to convert the geologic map data into a digital format, the ArcInfo GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. The manuscript and digital data review by Lorre Moyer (USGS) is greatly appreciated.

  5. Oceanic core complexes in the Philippine Sea: results from Japan's extended continental shelf mapping

    NASA Astrophysics Data System (ADS)

    Ohara, Y.; Yoshida, T.; Nishizawa, A.

    2013-12-01

    The United Nations Commission on the Limits of the Continental Shelf (CLCS) issued its recommendations on Japan's extended continental shelf in April 2012, confirming Japan's rights over the vast areas within the Philippine Sea and Pacific Plates. Japan submitted information on the limits of its continental shelf beyond the EEZ to the CLCS on November 2008, which was the result of 25 years of nation's continental shelf survey project since 1983, involving all of Japan's agency relevant to geosciences. The huge geological and geophysical data obtained through the project give the scientists unprecedented opportunity to study the geology and tectonics of the Philippine Sea and Pacific Plates. In this contribution, we show such an example from the Philippine Sea Plate, relevant to the global mid-ocean ridge problem. Oceanic core complexes (OCC) are dome-shaped bathymetric highs identified in mid-ocean ridges, interpreted as portions of the lower crust and/or upper mantle denuded via low-angle detachment faulting. OCCs are characterized morphologically by axis-normal striations (corrugations, or mullion structure) on the dome, and exposures of mantle peridotite and/or lower crustal gabbro. A strikingly giant OCC (named 'Godzilla Megamullion') was discovered in the Parece Vela Basin by the continental shelf survey project in 2001. Godzilla Megamullion is morphologically the largest OCC in the world, consisting mainly of fertile mantle peridotite along its entire length of over 125 km. Following its discovery in 2001, several academic cruises investigated the structure in detail, providing numerous important findings relevant to mid-ocean ridge tectono-magmatic processes and Philippine Sea evolution, including the slow- to ultraslow-spreading environment for denudation of the detachment fault (< 2.5 cm/y) and associated decreasing degree of partial melting of the peridotites towards the termination of Godzilla Megamullion. In addition to Godzilla Megamullion, several

  6. Colorado Late Cenozoic Fault and Fold Database and Internet Map Server: User-friendly technology for complex information

    USGS Publications Warehouse

    Morgan, K.S.; Pattyn, G.J.; Morgan, M.L.

    2005-01-01

    Internet mapping applications for geologic data allow simultaneous data delivery and collection, enabling quick data modification while efficiently supplying the end user with information. Utilizing Web-based technologies, the Colorado Geological Survey's Colorado Late Cenozoic Fault and Fold Database was transformed from a monothematic, nonspatial Microsoft Access database into a complex information set incorporating multiple data sources. The resulting user-friendly format supports easy analysis and browsing. The core of the application is the Microsoft Access database, which contains information compiled from available literature about faults and folds that are known or suspected to have moved during the late Cenozoic. The database contains nonspatial fields such as structure type, age, and rate of movement. Geographic locations of the fault and fold traces were compiled from previous studies at 1:250,000 scale to form a spatial database containing information such as length and strike. Integration of the two databases allowed both spatial and nonspatial information to be presented on the Internet as a single dataset (http://geosurvey.state.co.us/pubs/ceno/). The user-friendly interface enables users to view and query the data in an integrated manner, thus providing multiple ways to locate desired information. Retaining the digital data format also allows continuous data updating and quick delivery of newly acquired information. This dataset is a valuable resource to anyone interested in earthquake hazards and the activity of faults and folds in Colorado. Additional geologic hazard layers and imagery may aid in decision support and hazard evaluation. The up-to-date and customizable maps are invaluable tools for researchers or the public.

  7. Isolation, characterization, and mapping of gene encoding dihydrolipoyl succinyltransferase (E2k) of human [alpha]-ketoglutarate dehydrogenase complex

    SciTech Connect

    Ali, G.; Cai, Xingang; Sheu, Kwan-Fu R.; Blass, J.P. ); Wasco, W.; Gaston, S.M.; Tanzi, R.E.; Cooper, A.J.L.; Gusella, J.F. ); Szabo, P. )

    1994-03-01

    The authors have isolated and sequenced cDNAs representing the full-length (2987-bp) gene for dihydrolipoyl succinyltransferase (E2k component) of the human [alpha]-ketoglutarate dehydrogenase complex (KHDHC) from a human fetal brain cDNA library. The E2k cDNA was mapped to human chromosome 14 using a somatic cell hybrid panel, and more precisely to band 14q24.3 by in situ hybridization. This cDNA also cross-hybridized to an apparent E2k pseudogene on chromosome 1p31. Northern analysis revealed the E2k gene to be ubiquitously expressed in peripheral tissues and brain. Interestingly, chromosome 14q24.3 has recently been reported to contain gene defects for an early-onset form of familial Alzheimer's disease and for Machado-Joseph disease. Future studies will be necessary to determine whether the E2K gene plays a role in either of these two disorders.

  8. Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

    PubMed Central

    Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

    2015-01-01

    Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

  9. The physical map of the chromosome of a serogroup A strain of Neisseria meningitidis shows complex rearrangements relative to the chromosomes of the two mapped strains of the closely related species N. gonorrhoeae.

    PubMed Central

    Dempsey, J A; Wallace, A B; Cannon, J G

    1995-01-01

    A physical map of the chromosome of N. meningitidis Z2491 (serogroup A, subgroup IV-1) has been constructed. Z2491 DNA was digested with NheI, SpeI, SgfI, PacI, BglII, or PmeI, resulting in a limited number of fragments that were resolved by contour-clamped homogeneous electric field (CHEF) electrophoresis. The estimated genome size for this strain was 2,226 kb. To construct the map, probes corresponding to single-copy genes or sequences were used on Southern blots of chromosomal DNA digested with the different mapping enzymes and subjected to CHEF electrophoresis. By determining which fragments from different digests hybridized to each specific probe, it was possible to walk back and forth between digests to form a circular macrorestriction map. The intervals between mapped restriction sites range from 10 to 143 kb in size. A total of 117 markers have been placed on the map; 75 represent identified genes, with the remaining markers defined by anonymous cloned fragments of neisserial DNA. Comparison of the arrangement of genetic loci in Z2491 with that in gonococcal strain FA1090, for which a physical map was previously constructed, revealed complex genomic rearrangements between the two strains. Although gene order is generally conserved over much of the chromosome, a region of approximately 500 kb shows translocation and/or inversion of multiple blocks of markers between the two strains. Even within the relatively conserved portions of the maps, several genetic markers are in different positions in Z2491 and FA1090. PMID:7592413

  10. Oxygen isotope mapping of the Archean Sturgeon Lake caldera complex and VMS-related hydrothermal system, Northwestern Ontario, Canada

    NASA Astrophysics Data System (ADS)

    Holk, Gregory J.; Taylor, Bruce E.; Galley, Alan G.

    2008-08-01

    The hydrothermal and magmatic evolution of the Sturgeon Lake caldera complex is graphically documented by a regional-scale (525 km2) analysis of oxygen isotopes. Spatial variations in whole-rock oxygen isotope compositions provide a thermal map of the cumulative effects of multiple stages of hydrothermal metasomatism before, during, and after volcanogenic massive sulfide (VMS) mineralization. There is a progressive, upward increase in δ18O from less than 2‰ to greater than 15‰ through a 5-km-thick section above the Biedelman Bay subvolcanic intrusive complex. This isotopic trend makes it clear that at least the earlier phases of this intrusive complex were coeval with the overlying VMS-hosting cauldron succession and provided thermal energy to drive a convective hydrothermal circulation system. The sharp contrast in δ18O values between late stage phases of the Biedelman Bay intrusion and immediate hanging wall strata indicates that the main phase of VMS-related hydrothermal activity took place before late-stage resurgence in the cauldron-related magmatic activity. Mineralogical and isotopic evidence indicates the presence of both syn- and postmineralization hydrothermal activity defined by the presence of widespread semiconformable and more restricted discordant alteration zones that affect the pre- and syncauldron strata. The semiconformable alteration zones formed during early stages of hydrothermal circulation and are defined by widespread silicification and carbonatization in association with relatively high δ18O values. The discordant alteration assemblages, containing Al-silicate minerals with chloritoid and/or Fe-rich carbonate or chlorite, centered on synvolcanic faults represent restricted zones of both seawater inflow and hydrothermal fluid upflow. A rapid increase in δ18O values (˜7-9‰) over a short distance (<200 m) suggests marked cooling of hydrothermal fluid from ˜350°C to less than 130°C either just before or during discharge onto the

  11. Complex B1 Mapping and Electrical Properties Imaging of the Human Brain using a 16-channel Transceiver Coil at 7T

    PubMed Central

    Zhang, Xiaotong; Van de Moortele, Pierre-Francois; Schmitter, Sebastian; He, Bin

    2012-01-01

    The electric properties (EPs) of biological tissue provide important diagnostic information within radio and microwave frequencies, and also play an important role in specific absorption rate (SAR) calculation which is a major safety concern at ultrahigh field (UHF). The recently proposed electrical properties tomography (EPT) technique aims to reconstruct EPs in biological tissues based on B1 measurement. However, for individual coil element in multi-channel transceiver coil which is increasingly utilized at UHF, current B1-mapping techniques could not provide adequate information (magnitude and absolute phase) of complex transmit and receive B1 which are essential for EPT, electric field, and quantitative SAR assessment. In this study, using a 16-channel transceiver coil at 7T, based on hybrid B1-mapping techniques within the human brain, a complex B1-mapping method has been developed, and in-vivo EPs imaging of the human brain has been demonstrated by applying a logarithm-based inverse algorithm. Computer simulation studies as well as phantom and human experiments have been conducted at 7T. The average bias and standard deviation for reconstructed conductivity in vivo were 28% and 67%, and 10% and 43% for relative permittivity, respectively. The present results suggest the feasibility and reliability of proposed complex B1-mapping technique and EPs reconstruction method. PMID:22692921

  12. Frequent Premature Ventricular Complexes Originating from the Left Ventricular Summit Successfully Ablated from the Proximal Great Cardiac Vein Using an Impedance-based Electroanatomical Mapping System.

    PubMed

    Nagata, Yoshihisa; Ogawa, Masahiro; Goto, Shunichiro; Morii, Joji; Imaizumi, Satoshi; Yasuda, Tomoo; Matsumoto, Naomichi; Saku, Keijiro

    2016-01-01

    We herein report a 58-year-old woman with frequent premature ventricular complexes (PVCs) originating from the left ventricular summit. The earliest ventricular activation of spontaneous PVCs was recorded in the proximal site of the great cardiac vein, which was simultaneously mapped and conducted using an impedance-based electroanatomical mapping system. Irrigated radiofrequency with a starting power output of 20 W and maximal temperature set at 40°C was applied with 10 Ω impedance fall, resulting in total disappearance of the frequent PVCs. The patient has remained free from PVCs for 18 months without requiring antiarrhythmic drug therapy. PMID:27374677

  13. Major Histocompatibility Complex Genes Map to Two Chromosomes in an Evolutionarily Ancient Reptile, the Tuatara Sphenodon punctatus

    PubMed Central

    Miller, Hilary C.; O’Meally, Denis; Ezaz, Tariq; Amemiya, Chris; Marshall-Graves, Jennifer A.; Edwards, Scott

    2015-01-01

    Major histocompatibility complex (MHC) genes are a central component of the vertebrate immune system and usually exist in a single genomic region. However, considerable differences in MHC organization and size exist between different vertebrate lineages. Reptiles occupy a key evolutionary position for understanding how variation in MHC structure evolved in vertebrates, but information on the structure of the MHC region in reptiles is limited. In this study, we investigate the organization and cytogenetic location of MHC genes in the tuatara (Sphenodon punctatus), the sole extant representative of the early-diverging reptilian order Rhynchocephalia. Sequencing and mapping of 12 clones containing class I and II MHC genes from a bacterial artificial chromosome library indicated that the core MHC region is located on chromosome 13q. However, duplication and translocation of MHC genes outside of the core region was evident, because additional class I MHC genes were located on chromosome 4p. We found a total of seven class I sequences and 11 class II β sequences, with evidence for duplication and pseudogenization of genes within the tuatara lineage. The tuatara MHC is characterized by high repeat content and low gene density compared with other species and we found no antigen processing or MHC framework genes on the MHC gene-containing clones. Our findings indicate substantial differences in MHC organization in tuatara compared with mammalian and avian MHCs and highlight the dynamic nature of the MHC. Further sequencing and annotation of tuatara and other reptile MHCs will determine if the tuatara MHC is representative of nonavian reptiles in general. PMID:25953959

  14. Major Histocompatibility Complex Genes Map to Two Chromosomes in an Evolutionarily Ancient Reptile, the Tuatara Sphenodon punctatus.

    PubMed

    Miller, Hilary C; O'Meally, Denis; Ezaz, Tariq; Amemiya, Chris; Marshall-Graves, Jennifer A; Edwards, Scott

    2015-05-07

    Major histocompatibility complex (MHC) genes are a central component of the vertebrate immune system and usually exist in a single genomic region. However, considerable differences in MHC organization and size exist between different vertebrate lineages. Reptiles occupy a key evolutionary position for understanding how variation in MHC structure evolved in vertebrates, but information on the structure of the MHC region in reptiles is limited. In this study, we investigate the organization and cytogenetic location of MHC genes in the tuatara (Sphenodon punctatus), the sole extant representative of the early-diverging reptilian order Rhynchocephalia. Sequencing and mapping of 12 clones containing class I and II MHC genes from a bacterial artificial chromosome library indicated that the core MHC region is located on chromosome 13q. However, duplication and translocation of MHC genes outside of the core region was evident, because additional class I MHC genes were located on chromosome 4p. We found a total of seven class I sequences and 11 class II β sequences, with evidence for duplication and pseudogenization of genes within the tuatara lineage. The tuatara MHC is characterized by high repeat content and low gene density compared with other species and we found no antigen processing or MHC framework genes on the MHC gene-containing clones. Our findings indicate substantial differences in MHC organization in tuatara compared with mammalian and avian MHCs and highlight the dynamic nature of the MHC. Further sequencing and annotation of tuatara and other reptile MHCs will determine if the tuatara MHC is representative of nonavian reptiles in general.

  15. Thermographic mapping of a complex vernacular settlement: the case study of Casalnuovo District within the Sassi of Matera (Italy)

    NASA Astrophysics Data System (ADS)

    Cardinale, Tiziana; Balestra, Alessandro; Cardinale, Nicola

    2015-04-01

    appropriate cognitive apparatus has been set up for the entire technical process, first of all making use of infrared thermography. It is an affordable, fast and hence widespread method to detect temperature distributions on the surfaces of buildings. In the investigation of historical structures, where a restoration or conservation treatment can cause irreversible damage to the structure, it is considered to be of most importance. So we have made a thermographic mapping and we have analyzed the thermal conditions of approximately 15 caves, with the presence of rising moisture and condensation moisture. The ability to investigate a so complex reality offers an important opportunity for the knowledge, valorization and fruition of the cultural landscape of Matera, where you can disassemble the constituents of full and empty spaces with the consideration that the whole is not merely the sum of the parts.

  16. Integrating Map Algebra and Statistical Modeling for Spatio-Temporal Analysis of Monthly Mean Daily Incident Photosynthetically Active Radiation (PAR) over a Complex Terrain

    PubMed Central

    Evrendilek, Fatih

    2007-01-01

    This study aims at quantifying spatio-temporal dynamics of monthly mean daily incident photosynthetically active radiation (PAR) over a vast and complex terrain such as Turkey. The spatial interpolation method of universal kriging, and the combination of multiple linear regression (MLR) models and map algebra techniques were implemented to generate surface maps of PAR with a grid resolution of 500 × 500 m as a function of five geographical and 14 climatic variables. Performance of the geostatistical and MLR models was compared using mean prediction error (MPE), root-mean-square prediction error (RMSPE), average standard prediction error (ASE), mean standardized prediction error (MSPE), root-mean-square standardized prediction error (RMSSPE), and adjusted coefficient of determination (R2adj.). The best-fit MLR- and universal kriging-generated models of monthly mean daily PAR were validated against an independent 37-year observed dataset of 35 climate stations derived from 160 stations across Turkey by the Jackknifing method. The spatial variability patterns of monthly mean daily incident PAR were more accurately reflected in the surface maps created by the MLR-based models than in those created by the universal kriging method, in particular, for spring (May) and autumn (November). The MLR-based spatial interpolation algorithms of PAR described in this study indicated the significance of the multifactor approach to understanding and mapping spatio-temporal dynamics of PAR for a complex terrain over meso-scales.

  17. Plastic mine detecting radar system using complex-valued self-organizing map that deals with multiple-frequency interferometric images.

    PubMed

    Hara, Takahiro; Hirose, Akira

    2004-01-01

    Ground penetrating radars (GPR's) have been often applied to underground object imaging. However, conventional radar systems do not work sufficiently to detect anti-personnel plastic landmines. We propose a novel radar imaging system, which processes adaptively interferometric front-end data obtained at multiple-frequency points. The system deals with interferometric images using complex-valued self-organizing map (C-SOM). We demonstrate a successful visualization of a plastic mine buried near the ground surface. PMID:15555861

  18. Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

    PubMed

    Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

    2015-09-01

    Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells.

  19. A methodology for eliciting, representing, and analysing stakeholder knowledge for decision making on complex socio-ecological systems: from cognitive maps to agent-based models.

    PubMed

    Elsawah, Sondoss; Guillaume, Joseph H A; Filatova, Tatiana; Rook, Josefine; Jakeman, Anthony J

    2015-03-15

    This paper aims to contribute to developing better ways for incorporating essential human elements in decision making processes for modelling of complex socio-ecological systems. It presents a step-wise methodology for integrating perceptions of stakeholders (qualitative) into formal simulation models (quantitative) with the ultimate goal of improving understanding and communication about decision making in complex socio-ecological systems. The methodology integrates cognitive mapping and agent based modelling. It cascades through a sequence of qualitative/soft and numerical methods comprising: (1) Interviews to elicit mental models; (2) Cognitive maps to represent and analyse individual and group mental models; (3) Time-sequence diagrams to chronologically structure the decision making process; (4) All-encompassing conceptual model of decision making, and (5) computational (in this case agent-based) Model. We apply the proposed methodology (labelled ICTAM) in a case study of viticulture irrigation in South Australia. Finally, we use strengths-weakness-opportunities-threats (SWOT) analysis to reflect on the methodology. Results show that the methodology leverages the use of cognitive mapping to capture the richness of decision making and mental models, and provides a combination of divergent and convergent analysis methods leading to the construction of an Agent Based Model.

  20. A methodology for eliciting, representing, and analysing stakeholder knowledge for decision making on complex socio-ecological systems: from cognitive maps to agent-based models.

    PubMed

    Elsawah, Sondoss; Guillaume, Joseph H A; Filatova, Tatiana; Rook, Josefine; Jakeman, Anthony J

    2015-03-15

    This paper aims to contribute to developing better ways for incorporating essential human elements in decision making processes for modelling of complex socio-ecological systems. It presents a step-wise methodology for integrating perceptions of stakeholders (qualitative) into formal simulation models (quantitative) with the ultimate goal of improving understanding and communication about decision making in complex socio-ecological systems. The methodology integrates cognitive mapping and agent based modelling. It cascades through a sequence of qualitative/soft and numerical methods comprising: (1) Interviews to elicit mental models; (2) Cognitive maps to represent and analyse individual and group mental models; (3) Time-sequence diagrams to chronologically structure the decision making process; (4) All-encompassing conceptual model of decision making, and (5) computational (in this case agent-based) Model. We apply the proposed methodology (labelled ICTAM) in a case study of viticulture irrigation in South Australia. Finally, we use strengths-weakness-opportunities-threats (SWOT) analysis to reflect on the methodology. Results show that the methodology leverages the use of cognitive mapping to capture the richness of decision making and mental models, and provides a combination of divergent and convergent analysis methods leading to the construction of an Agent Based Model. PMID:25622296

  1. Exploring the Impact of Visual Complexity Levels in 3d City Models on the Accuracy of Individuals' Orientation and Cognitive Maps

    NASA Astrophysics Data System (ADS)

    Rautenbach, V.; Çöltekin, A.; Coetzee, S.

    2015-08-01

    In this paper we report results from a qualitative user experiment (n=107) designed to contribute to understanding the impact of various levels of complexity (mainly based on levels of detail, i.e., LoD) in 3D city models, specifically on the participants' orientation and cognitive (mental) maps. The experiment consisted of a number of tasks motivated by spatial cognition theory where participants (among other things) were given orientation tasks, and in one case also produced sketches of a path they `travelled' in a virtual environment. The experiments were conducted in groups, where individuals provided responses on an answer sheet. The preliminary results based on descriptive statistics and qualitative sketch analyses suggest that very little information (i.e., a low LoD model of a smaller area) might have a negative impact on the accuracy of cognitive maps constructed based on a virtual experience. Building an accurate cognitive map is an inherently desired effect of the visualizations in planning tasks, thus the findings are important for understanding how to develop better-suited 3D visualizations such as 3D city models. In this study, we specifically discuss the suitability of different levels of visual complexity for development planning (urban planning), one of the domains where 3D city models are most relevant.

  2. Two-Dimensional Spreads of Synaptonemal Complexes from Solanaceous Plants. VI. High-Resolution Recombination Nodule Map for Tomato (Lycopersicon Esculentum)

    PubMed Central

    Sherman, J. D.; Stack, S. M.

    1995-01-01

    We have produced a high-resolution physical recombination map for tomato chromosomes by determining the frequency and distribution of recombination nodules (RNs) on tomato synaptonemal complexes (SCs). We present evidence that there is a 1:1 relationship between RNs and chiasmata. Every SC has at least one RN. There are no RNs at the ends of SCs, in kinetochores, or in the heterochromatic short arm of SC 2 that carries the nucleolus organizer. RNs are more common per unit length of SC in euchromatin compared with SC in heterochromatin. The average number of RNs per SC and the average number of RNs per SC arm are directly correlated with the length of SC in euchromatin. When SCs have only one RN, that RN occurs on the long arm more frequently than predicted based on SC arm length. Patterns of multiple RNs on SCs indicate RN (crossover) interference. RNs probably can occur anywhere on SCs in euchromatin, but RNs are not distributed randomly along SCs in euchromatin or in heterochromatin. The lengths of tomato's physical recombination (RN) map, classical genetic linkage map, and molecular linkage map all differ from each other for a variety of reasons. PMID:8647403

  3. A Linkage Map Reveals a Complex Basis for Segregation Distortion in an Interpopulation Cross in the Moss Ceratodon purpureus

    PubMed Central

    McDaniel, Stuart F.; Willis, John H.; Shaw, A. Jonathan

    2007-01-01

    We report the construction of a linkage map for the moss Ceratodon purpureus (n = 13), based on a cross between geographically distant populations, and provide the first experimental confirmation of maternal chloroplast inheritance in bryophytes. From a mapping population of 288 recombinant haploid gametophytes, genotyped at 121 polymorphic AFLP loci, three gene-based nuclear loci, one chloroplast marker, and sex, we resolved 15 linkage groups resulting in a map length of ∼730 cM. We estimate that the map covers more than three-quarters of the C. purpureus genome. Approximately 35% of the loci were sex linked, not including those in recombining pseudoautosomal regions. Nearly 45% of the loci exhibited significant segregation distortion (α = 0.05). Several pairs of unlinked distorted loci showed significant deviations from multiplicative genotypic frequencies, suggesting that distortion arises from genetic interactions among loci. The distorted autosomal loci all exhibited an excess of the maternal allele, suggesting that these interactions may involve nuclear–cytoplasmic factors. The sex ratio of the progeny was significantly male biased, and the pattern of nonrandom associations among loci indicates that this results from interactions between the sex chromosomes. These results suggest that even in interpopulation crosses, multiple mechanisms act to influence segregation ratios. PMID:17603096

  4. Comparison of copper and zinc in vitro bioaccessibility from cyanobacteria rich in proteins and a synthetic supplement containing gluconate complexes: LC-MS mapping of bioaccessible copper complexes.

    PubMed

    Wojcieszek, Justyna; Witkoś, Katarzyna; Ruzik, Lena; Pawlak, Katarzyna

    2016-01-01

    An analytical procedure was proposed to estimate bioaccessibility of copper and zinc in Spirulina Pacifica tablets with respect to that of copper and zinc in gluconate complexes. Spirulina is the common name for diet supplements produced primarily from two species of cyanobacteria, namely Arthrospira platensis and Arthrospira maxima. Spirulina tablets are an excellent source of proteins, vitamins and minerals. To obtain information about the bioavailability of these elements, an in vitro bioaccessibility test was performed by application of a two-step protocol which simulated the gastric (pepsin) and intestinal (pancreatin) digestion. The species obtained were investigated by size exclusion chromatography on a chromatograph coupled to a mass spectrometer with inductively coupled plasma (SEC-ICP-MS) and an on-capillary liquid chromatograph coupled to an electrospray mass spectrometer (μ-HPLC-ESI-MS). Both copper and zinc were found to be highly bioaccessible in Spirulina tablets (90-111%) and those containing gluconate complexes (103% for Cu and 62% for Zn). In Spirulina tablets, copper was found to form two types of complex: (1) polar ones with glycine and aspartic acid and (2) more hydrophobic ones containing amino acids with cyclic hydrocarbons (phenylalanine, histidine, proline and tyrosine). Zinc and copper were also proved to form complexes during the digestion process with products of pepsin digestion, but the stability of these complexes is lower than that of the complexes formed in Spirulina. The results proving the involvement of proteins in the enhancement of copper and zinc bioaccessibility will be useful for the design of new copper and zinc supplements.

  5. Comparison of copper and zinc in vitro bioaccessibility from cyanobacteria rich in proteins and a synthetic supplement containing gluconate complexes: LC-MS mapping of bioaccessible copper complexes.

    PubMed

    Wojcieszek, Justyna; Witkoś, Katarzyna; Ruzik, Lena; Pawlak, Katarzyna

    2016-01-01

    An analytical procedure was proposed to estimate bioaccessibility of copper and zinc in Spirulina Pacifica tablets with respect to that of copper and zinc in gluconate complexes. Spirulina is the common name for diet supplements produced primarily from two species of cyanobacteria, namely Arthrospira platensis and Arthrospira maxima. Spirulina tablets are an excellent source of proteins, vitamins and minerals. To obtain information about the bioavailability of these elements, an in vitro bioaccessibility test was performed by application of a two-step protocol which simulated the gastric (pepsin) and intestinal (pancreatin) digestion. The species obtained were investigated by size exclusion chromatography on a chromatograph coupled to a mass spectrometer with inductively coupled plasma (SEC-ICP-MS) and an on-capillary liquid chromatograph coupled to an electrospray mass spectrometer (μ-HPLC-ESI-MS). Both copper and zinc were found to be highly bioaccessible in Spirulina tablets (90-111%) and those containing gluconate complexes (103% for Cu and 62% for Zn). In Spirulina tablets, copper was found to form two types of complex: (1) polar ones with glycine and aspartic acid and (2) more hydrophobic ones containing amino acids with cyclic hydrocarbons (phenylalanine, histidine, proline and tyrosine). Zinc and copper were also proved to form complexes during the digestion process with products of pepsin digestion, but the stability of these complexes is lower than that of the complexes formed in Spirulina. The results proving the involvement of proteins in the enhancement of copper and zinc bioaccessibility will be useful for the design of new copper and zinc supplements. PMID:26597916

  6. A neural network model for the development of simple and complex cell receptive fields within cortical maps of orientation and ocular dominance.

    PubMed

    Olson, S J; Grossberg, S

    1998-03-01

    Prenatal development of the primary visual cortex leads to simple cells with spatially distinct and oriented ON and OFF subregions. These simple cells are organized into spatial maps of orientation and ocular dominance that exhibit singularities, fractures, and linear zones. On a finer spatial scale, simple cells occur that are sensitive to similar orientations but opposite contrast polarities, and exhibit both even-symmetric and odd-symmetric receptive fields. Pooling of outputs from oppositely polarized simple cells leads to complex cells that respond to both contrast polarities. A neural network model is described which simulates how simple and complex cells self-organize starting from unsegregated and unoriented geniculocortical inputs during prenatal development. Neighboring simple cells that are sensitive to opposite contrast polarities develop from a combination of spatially short-range inhibition and high-gain recurrent habituative excitation between cells that obey membrane equations. Habituation, or depression, of synapses controls reset of cell activations both through enhanced ON responses and OFF antagonistic rebounds. Orientation and ocular dominance maps form when high-gain medium-range recurrent excitation and long-range inhibition interact with the short-range mechanisms. The resulting structure clarifies how simple and complex cells contribute to perceptual processes such as texture segregation and perceptual grouping.

  7. A molecular map of the chicken major histocompatibility complex: the class II beta genes are closely linked to the class I genes and the nucleolar organizer.

    PubMed Central

    Guillemot, F; Billault, A; Pourquié, O; Béhar, G; Chaussé, A M; Zoorob, R; Kreibich, G; Auffray, C

    1988-01-01

    We have cloned in a cosmid vector four DNA clusters covering 320 kb of the chicken MHC (B complex), including five class II (B-L) beta genes defining two related isotypic families. Additional B complex genes have been revealed using tissue-specific cDNA probes. A cosmid fragment has been used to isolate a cDNA for a class I (B-F) transcript. This transcript, that is by far the most divergent known member of the class I gene family, hybridized to six B-F genes present in the cosmids. One of the clusters was shown to contain two rRNA transcriptional units from the nucleolar organizer region (NOR), marking the telomeric boundary of the B complex. None of the other B complex genes hybridizes to, or has the transcriptional characteristics of mammalian MHC class II alpha or class III genes. The map we have obtained shows that the B complex does not contain well defined class I and class II regions since B-F and B-L beta genes are closely associated with unrelated genes. Moreover, class II beta genes are very closely linked to class I genes in two clusters, and to the NOR in a third one. Images PMID:3141149

  8. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry.

    PubMed

    Guan, Xiaoyan; Noble, Kyle A; Tao, Yeqing; Roux, Kenneth H; Sathe, Shridhar K; Young, Nicolas L; Marshall, Alan G

    2015-06-01

    The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments. PMID:26169135

  9. Catalyst-Controlled Stereoselective Olefin Metathesis as a Principal Strategy in Multi-Step Synthesis Design. A Concise Route to (+)-Neopeltolide**

    PubMed Central

    Yu, Miao; Schrock, Richard R.

    2014-01-01

    Mo-, W- and Ru-based complexes that control the stereochemical outcome of olefin metathesis reactions have been recently introduced. However, the complementary nature of these systems through their combined use in multistep complex molecule synthesis has not been illustrated. Here, we disclose a concise diastereo- and enantioselective route that furnishes the anti-proliferative natural product neopeltolide. Catalytic transformations are employed to address every stereochemical issue. Among the featured processes are an enantioselective ring-opening/cross-metathesis promoted by a Mo monopyrrolide aryloxide (MAP) complex and a macrocyclic ring-closing metathesis affording a trisubstituted alkene catalyzed by a Mo bis-aryloxide species. Furthermore, Z-selective cross-metathesis reactions, facilitated by Mo and Ru complexes, have been employed in stereoselective synthesis of the acyclic dienyl moiety of the target molecule. PMID:25377347

  10. Linkage Maps of the dwarf and Normal Lake Whitefish (Coregonus clupeaformis) Species Complex and Their Hybrids Reveal the Genetic Architecture of Population Divergence

    PubMed Central

    Rogers, S. M.; Isabel, N.; Bernatchez, L.

    2007-01-01

    Elucidating the genetic architecture of population divergence may reveal the evolution of reproductive barriers and the genomic regions implicated in the process. We assembled genetic linkage maps for the dwarf and Normal lake whitefish species complex and their hybrids. A total of 877 AFLP loci and 30 microsatellites were positioned. The homology of mapped loci between families supported the existence of 34 linkage groups (of 40n expected) exhibiting 83% colinearity among linked loci between these two families. Classes of AFLP markers were not randomly distributed among linkage groups. Both AFLP and microsatellites exhibited deviations from Mendelian expectations, with 30.4% exhibiting significant segregation distortion across 28 linkage groups of the four linkage maps in both families (P < 0.00001). Eight loci distributed over seven homologous linkage groups were significantly distorted in both families and the level of distortion, when comparing homologous loci of the same phase between families, was correlated (Spearman R = 0.378, P = 0.0021). These results suggest that substantial divergence incurred during allopatric glacial separation and subsequent sympatric ecological specialization has resulted in several genomic regions that are no longer complementary between dwarf and Normal populations issued from different evolutionary glacial lineages. PMID:17110497

  11. Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics.

    PubMed

    Melani, Rafael D; Skinner, Owen S; Fornelli, Luca; Domont, Gilberto B; Compton, Philip D; Kelleher, Neil L

    2016-07-01

    Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics. PMID:27178327

  12. Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics.

    PubMed

    Melani, Rafael D; Skinner, Owen S; Fornelli, Luca; Domont, Gilberto B; Compton, Philip D; Kelleher, Neil L

    2016-07-01

    Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics.

  13. Tracing the path of DNA substrates in active Tetrahymena telomerase holoenzyme complexes: mapping of DNA contact sites in the RNA subunit.

    PubMed

    Goldin, Svetlana; Kertesz Rosenfeld, Karin; Manor, Haim

    2012-08-01

    Telomerase, the enzyme that extends single-stranded telomeric DNA, consists of an RNA subunit (TER) including a short template sequence, a catalytic protein (TERT) and accessory proteins. We used site-specific UV cross-linking to map the binding sites for DNA primers in TER within active Tetrahymena telomerase holoenzyme complexes. The mapping was performed at single-nucleotide resolution by a novel technique based on RNase H digestion of RNA-DNA hybrids made with overlapping complementary oligodeoxynucleotides. These data allowed tracing of the DNA path through the telomerase complexes from the template to the TERT binding element (TBE) region of TER. TBE is known to bind TERT and to be involved in the template 5'-boundary definition. Based on these findings, we propose that upstream sequences of each growing telomeric DNA chain are involved in regulation of its growth arrest at the 5'-end of the RNA template. The upstream DNA-TBE interaction may also function as an anchor for the subsequent realignment of the 3'-end of the DNA with the 3'-end of the template to enable initiation of synthesis of a new telomeric repeat.

  14. Canceled connections: Lesion-derived network mapping helps explain differences in performance on a complex decision-making task.

    PubMed

    Sutterer, Matthew J; Bruss, Joel; Boes, Aaron D; Voss, Michelle W; Bechara, Antoine; Tranel, Daniel

    2016-05-01

    Studies of patients with brain damage have highlighted a broad neural network of limbic and prefrontal areas as important for adaptive decision-making. However, some patients with damage outside these regions have impaired decision-making behavior, and the behavioral impairments observed in these cases are often attributed to the general variability in behavior following brain damage, rather than a deficit in a specific brain-behavior relationship. A novel approach, lesion-derived network mapping, uses healthy subject resting-state functional connectivity (RSFC) data to infer the areas that would be connected with each patient's lesion area in healthy adults. Here, we used this approach to investigate whether there was a systematic pattern of connectivity associated with decision-making performance in patients with focal damage in areas not classically associated with decision-making. These patients were categorized a priori into "impaired" or "unimpaired" groups based on their performance on the Iowa Gambling Task (IGT). Lesion-derived network maps based on the impaired patients showed overlap in somatosensory, motor and insula cortices, to a greater extent than patients who showed unimpaired IGT performance. Akin to the classic concept of "diaschisis" (von Monakow, 1914), this focus on the remote effects that focal damage can have on large-scale distributed brain networks has the potential to inform not only differences in decision-making behavior, but also other cognitive functions or neurological syndromes where a distinct phenotype has eluded neuroanatomical classification and brain-behavior relationships appear highly heterogeneous. PMID:26994344

  15. A High-Confidence Interaction Map Identifies SIRT1 as a Mediator of Acetylation of USP22 and the SAGA Coactivator Complex

    PubMed Central

    Armour, Sean M.; Bennett, Eric J.; Braun, Craig R.; Zhang, Xiao-Yong; McMahon, Steven B.; Gygi, Steven P.; Harper, J. Wade

    2013-01-01

    Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex. PMID:23382074

  16. Fourier-domain Jones-matrix mapping of a complex degree of mutual anisotropy in differentiation of biological tissues' pathological states.

    PubMed

    Ushenko, Yu A; Trifonyuk, L Yu; Dubolazov, A V; Karachevtsev, A O

    2014-04-01

    This article presents the theoretical background of an azimuthally stable method of Jones-matrix mapping of histological sections of a uterine wall biopsy on the basis of spatial-frequency selection of the mechanisms of linear and circular birefringence. The diagnostic application of a new correlation parameter--a complex degree of mutual anisotropy--is analytically substantiated. The method of measuring coordinate distributions of a complex degree of mutual anisotropy with further spatial filtration of their high- and low-frequency components is developed. The interconnections of such distributions with linear and circular birefringence parameters of the uterine-wall-endometrium histological sections are found. The comparative results of measuring the coordinate distributions of a complex degree of mutual anisotropy formed by fibrillar networks of myosin and collagen fibrils of uterus wall tissue of different pathological states--pre-cancer (dysplasia) and cancer (adenocarcinoma)--are shown. The values and ranges of change of the statistical (moments of the first to fourth orders) parameters of complex degree of mutual-anisotropy coordinate distributions are studied. The objective criteria of diagnosing the pathology and differentiation of its severity degree are determined. PMID:24787205

  17. The Monster and Lover?Girl: Mapping Complex Relations in Preschool Children's Digital Video Productions

    ERIC Educational Resources Information Center

    McClure, Marissa

    2013-01-01

    In this article, I propose that research which focuses on young children's experiences with the interactivity of new media not only furthers findings about young children's digital lives but also enriches the conclusion that children's engagement with artmaking--in general and in traditional ways--is richly complex, affective, and…

  18. Two novel mouse genes--Nubp2, mapped to the t-complex on chromosome 17, and Nubp1, mapped to chromosome 16--establish a new gene family of nucleotide-binding proteins in eukaryotes.

    PubMed

    Nakashima, H; Grahovac, M J; Mazzarella, R; Fujiwara, H; Kitchen, J R; Threat, T A; Ko, M S

    1999-09-01

    Two novel mouse genes and one novel human gene that define distinctive eukaryotic nucleotide-binding proteins (NUBP) and are related to the mrp gene of prokaryotes are characterized. Phylogenetic analyses of the genes, encoding a short form (Nubp2) and a long form (Nubp1) of NUBP, clearly establish them as a new NUBP/MRP gene family that is well conserved throughout phylogeny. In addition to conserved ATP/GTP-binding motifs A (P-loop) and A', members of this family share at least two highly conserved sequence motifs, NUBP/MRP motifs alpha and beta. Only one type of NUBP/MRP gene has been observed thus far in prokaryotes, but there are two types in eukaryotes. One group includes mouse Nubp1, human NBP, yeast NBP35, and Caenorhabditis elegans F10G8.6 and is characterized by a unique N-terminal sequence with four cysteine residues that is lacking in the other group, which includes mouse Nubp2, human NUBP2, and yeast YIA3w. Northern blot analyses of the two mouse genes show distinctive patterns consistent with this classification. Mouse Nubp2 is mapped to the t-complex region of mouse Chromosome 17, whereas Nubp1 is mapped to the proximal region of mouse Chromosome 16. Interestingly, both regions are syntenic with human chromosome 16p13.1-p13.3, suggesting that a chromosomal breakage between Nubp2 and Nubp1 probably occurred during the evolution of mouse chromosomes.

  19. A Complex Recombination Pattern in the Genome of Allotetraploid Brassica napus as Revealed by a High-Density Genetic Map

    PubMed Central

    Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus. PMID:25356735

  20. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

    PubMed

    Cai, Guangqin; Yang, Qingyong; Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

  1. High-Resolution Genetic Mapping of Complex Traits from a Combined Analysis of F2 and Advanced Intercross Mice

    PubMed Central

    Parker, Clarissa C.; Carbonetto, Peter; Sokoloff, Greta; Park, Yeonhee J.; Abney, Mark; Palmer, Abraham A.

    2014-01-01

    Genetic influences on anxiety disorders are well documented; however, the specific genes underlying these disorders remain largely unknown. To identify quantitative trait loci (QTL) for conditioned fear and open field behavior, we used an F2 intercross (n = 490) and a 34th-generation advanced intercross line (AIL) (n = 687) from the LG/J and SM/J inbred mouse strains. The F2 provided strong support for several QTL, but within wide chromosomal regions. The AIL yielded much narrower QTL, but the results were less statistically significant, despite the larger number of mice. Simultaneous analysis of the F2 and AIL provided strong support for QTL and within much narrower regions. We used a linear mixed-model approach, implemented in the program QTLRel, to correct for possible confounding due to familial relatedness. Because we recorded the full pedigree, we were able to empirically compare two ways of accounting for relatedness: using the pedigree to estimate kinship coefficients and using genetic marker estimates of “realized relatedness.” QTL mapping using the marker-based estimates yielded more support for QTL, but only when we excluded the chromosome being scanned from the marker-based relatedness estimates. We used a forward model selection procedure to assess evidence for multiple QTL on the same chromosome. Overall, we identified 12 significant loci for behaviors in the open field and 12 significant loci for conditioned fear behaviors. Our approach implements multiple advances to integrated analysis of F2 and AILs that provide both power and precision, while maintaining the advantages of using only two inbred strains to map QTL. PMID:25236452

  2. Tyrosine kinase/p21ras/MAP-kinase pathway activation by estradiol-receptor complex in MCF-7 cells.

    PubMed Central

    Migliaccio, A; Di Domenico, M; Castoria, G; de Falco, A; Bontempo, P; Nola, E; Auricchio, F

    1996-01-01

    The mechanism by which estradiol acts on cell multiplication is still unclear. Under conditions of estradiol-dependent growth, estradiol treatment of human mammary cancer MCF-7 cells triggers rapid and transient activation of the mitogen-activated (MAP) kinases, erk-1 and erk-2, increases the active form of p21ras, tyrosine phosphorylation of Shc and p190 protein and induces association of p190 to p21ras-GAP. Both Shc and p190 are substrates of activated src and once phosphorylated, they interact with other proteins and upregulate p21ras. Estradiol activates the tyrosine kinase/p21ras/MAP-kinase pathway in MCF-7 cells with kinetics which are similar to those of peptide mitogens. It is only after introduction of the human wild-type 67 kDa estradiol receptor cDNA that Cos cells become estradiol-responsive in terms of erk-2 activity. This finding, together with the inhibition by the pure anti-estrogen ICI 182 780 of the stimulatory effect of estradiol on each step of the pathway in MCF-7 cells proves that the classic estradiol receptor is responsible for the transduction pathway activation. Transfection experiments of Cos cells with the estradiol receptor cDNA and in vitro experiments with c-src show that the estradiol receptor activates c-src and this activation requires occupancy of the receptor by hormone. Our experiments suggest that c-src is an initial and integral part of the signaling events mediated by the estradiol receptor. Images PMID:8635462

  3. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

    PubMed

    Cai, Guangqin; Yang, Qingyong; Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus. PMID:25356735

  4. Improved Discrimination of Volcanic Complexes, Tectonic Features, and Regolith Properties in Mare Serenitatis from Earth-Based Radar Mapping

    NASA Technical Reports Server (NTRS)

    Campbell, Bruce A.; Hawke, B. Ray; Morgan, Gareth A.; Carter, Lynn M.; Campbell, Donald B.; Nolan, Michael

    2014-01-01

    Radar images at 70 cm wavelength show 4-5 dB variations in backscatter strength within regions of relatively uniform spectral reflectance properties in central and northern Mare Serenitatis, delineating features suggesting lava flow margins, channels, and superposition relationships. These backscatter differences are much less pronounced at 12.6 cm wavelength, consistent with a large component of the 70 cm echo arising from the rough or blocky transition zone between the mare regolith and the intact bedrock. Such deep probing is possible because the ilmenite content, which modulates microwave losses, of central Mare Serenitatis is generally low (2-3% by weight). Modeling of the radar returns from a buried interface shows that an average regolith thickness of 10m could lead to the observed shifts in 70 cm echo power with a change in TiO2 content from 2% to 3%. This thickness is consistent with estimates of regolith depth (10-15m) based on the smallest diameter for which fresh craters have obvious blocky ejecta. The 70 cm backscatter differences provide a view of mare flow-unit boundaries, channels, and lobes unseen by other remote sensing methods. A localized pyroclastic deposit associated with Rima Calippus is identified based on its low radar echo strength. Radar mapping also improves delineation of units for crater age dating and highlights a 250 km long, east-west trending feature in northern Mare Serenitatis that we suggest is a large graben flooded by late-stage mare flows.

  5. Human brain mapping under increasing cognitive complexity using regional cerebral blood flow measurements and positron emission tomography.

    PubMed

    Law, Ian

    2007-11-01

    Measurement of the regional cerebral blood flow (rCBF) is an important parameter in the evaluation of cerebral function. With positron emission tomography (PET) rCBF has predominantly been quantified using the short-lived radiotracer oxygen-15 labelled water (H 2 15 O) and an adaptation of the Kety one-tissue compartment autoradiographic model. The values attained in putative grey matter, however, are systematically underestimated because of the limited scanner resolution. For this reason we applied a dynamic kinetic two-tissue compartment model including a fast and a slow flow component each with a perfusable tissue fraction. In the fast component rCBF was 2-2.5 times greater than grey matter values using traditional autoradiography in both human and monkey. Visual stimulation in human gave a corrected rCBF increase of approximately 40%. Visual stimulation was also used to indirectly validate carbon-10 labelled carbondioxide ( 10 CO 2 ), a new very short-lived rCBF PET tracer with a half-life of only 19.3 seconds. This allowed an increase in the number of independent PET scans per subject from 12-14 using H 2 15 O to 64 using 10 CO 2 . The experiment demonstrated a maximal activation response in the visual cortex at a 10-15 Hz stimulation frequency. The use of the rCBF PET mapping technique is illustrated by studies of the organization of language and the oculomotor system. With respect to the former, we found confirmation of neuropsychological evidence of the involvement of the left supramarginal/angular gyrus in reading in Japanese of a phonologically based script system, Kana, and of the left posterior inferior temporal gyrus in reading of a morphogram based script system, Kanji. Concerning the organization of the oculomotor system we found overlapping areas in fronto-parietal cortex involved in maintaining visual fixation, and performing visually guided and imagined eye movements. These data show that overt eye movements are not a prerequisite of the

  6. Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa).

    PubMed

    Sánchez-Sevilla, José F; Horvath, Aniko; Botella, Miguel A; Gaston, Amèlia; Folta, Kevin; Kilian, Andrzej; Denoyes, Beatrice; Amaya, Iraida

    2015-01-01

    Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed '232' × '1392' mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options. PMID:26675207

  7. Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa).

    PubMed

    Sánchez-Sevilla, José F; Horvath, Aniko; Botella, Miguel A; Gaston, Amèlia; Folta, Kevin; Kilian, Andrzej; Denoyes, Beatrice; Amaya, Iraida

    2015-01-01

    Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed '232' × '1392' mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options.

  8. Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)

    PubMed Central

    Sánchez-Sevilla, José F.; Horvath, Aniko; Botella, Miguel A.; Gaston, Amèlia; Folta, Kevin; Kilian, Andrzej; Denoyes, Beatrice; Amaya, Iraida

    2015-01-01

    Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed ‘232’ × ‘1392’ mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options. PMID:26675207

  9. Disentangling different functional roles of evoked K-complex components: Mapping the sleeping brain while quenching sensory processing.

    PubMed

    Laurino, Marco; Menicucci, Danilo; Piarulli, Andrea; Mastorci, Francesca; Bedini, Remo; Allegrini, Paolo; Gemignani, Angelo

    2014-02-01

    During non-REM sleep the largest EEG response evoked by sensory stimulation is the K-complex (eKC), composed of an initial positive bump (P200) followed by a bistable cortical response: a giant negative deflection (N550) and a large positive one (P900), respectively reflecting down states and up states of < 1 Hz oscillations.Sensory-modality-independent topology of N550 and P900, with maximal detection rate on fronto-central areas, has been consistently reported, suggesting that sensory inputs arise to the cortex avoiding specific primary sensory areas. However, these studies neglected latencies of all KC components as a function of electrode sites.Our aim is to identify, component by component, which topological/dynamical properties of eKCs depend on stimulus modality and which are mainly related to local cortical properties. We measured temporal and morphological features of acoustic, tactile and visual eKCs to disentangle specific sensory excitatory activities from aspecific responses due to local proneness to bistability, measured by means of the N550 descending steepness (synchronization in falling into down state).While confirming the sensory-modality independence of N550 and P900 topology with maximal detection rate in fronto-central areas, four main original results emerge from this study: (i) the topology of P200 latency depends on the sensory modality with earliest waves in the stimulation-related primary sensory areas; (ii) P200 rapidly travels as a cortical excitation; (iii) P200-like excitations when KCs are not evoked are detected over the scalp with significantly smaller amplitudes in fronto-central areas, compared to eKC P200s; and (iv) N550 latency mirrors its mean local steepness which is a function of topological proneness to bistability.From these results we can describe the emergence N550/P900 complex as the interplay between a waxing P200 cortical travel and higher fronto-central proneness to bistability.In conclusion, eKCs exhibit a

  10. Developing a high-resolution wind map for a complex terrain with a coupled MM5/CALMET system

    NASA Astrophysics Data System (ADS)

    Yim, Steve H. L.; Fung, Jimmy C. H.; Lau, Alexis K. H.; Kot, S. C.

    2007-03-01

    This study investigates the wind energy potential in Hong Kong, a region with a complex terrain, by coupling the prognostic MM5 mesoscale model with the CALMET diagnostic model to produce high-resolution wind fields. Hourly wind fields were simulated for the entire year of 2004. The MM5 simulations were performed on a nested grid from 40.5 km down to 1.5 km horizontal resolution. The CALMET meteorological model was used in a domain that includes the entire Hong Kong region with a high horizontal resolution of 100 m. The MM5 model wind field (1.5 km horizontal resolution) output was input into the CALMET diagnostic meteorological model every hour along with an objective analysis procedure using all available observations. Verification was achieved through two steps. In the first step, the data from three meteorological surface stations that were not assimilated into the CALMET model were compared horizontally with the simulated wind fields. In the second step, the simulated wind fields were compared vertically with the vertical wind profile collected from two upper air sounding stations. The results of this study identified the locations of the highest wind energy potential in HK down to 100 m resolution.

  11. SNP-based mapping arrays reveal high genomic complexity in monoclonal gammopathies, from MGUS to myeloma status.

    PubMed

    López-Corral, L; Sarasquete, M E; Beà, S; García-Sanz, R; Mateos, M V; Corchete, L A; Sayagués, J M; García, E M; Bladé, J; Oriol, A; Hernández-García, M T; Giraldo, P; Hernández, J; González, M; Hernández-Rivas, J M; San Miguel, J F; Gutiérrez, N C

    2012-12-01

    Genetic events mediating transformation from premalignant monoclonal gammopathies (MG) to multiple myeloma (MM) are unknown. To obtain a comprehensive genomic profile of MG from the early to late stages, we performed high-resolution analysis of purified plasma cells from 20 MGUS, 20 smoldering MM (SMM) and 34 MM by high-density 6.0 SNP array. A progressive increase in the incidence of copy number abnormalities (CNA) from MGUS to SMM and to MM (median 5, 7.5 and 12 per case, respectively) was observed (P=0.006). Gains on 1q, 3p, 6p, 9p, 11q, 19p, 19q and 21q along with 1p, 16q and 22q deletions were significantly less frequent in MGUS than in MM. Although 11q and 21q gains together with 16q and 22q deletions were apparently exclusive of MM status, we observed that these abnormalities were also present in minor subclones in MGUS. Overall, a total of 65 copy number-neutral LOH (CNN-LOH) were detected. Their frequency was higher in active MM than in the asymptomatic entities (P=0.047). A strong association between genetic lesions and fragile sites was also detected. In summary, our study shows an increasing genomic complexity from MGUS to MM and identifies new chromosomal regions involved in CNA and CNN-LOH. PMID:22565645

  12. Mapping gas-phase organic reactivity and concomitant secondary organic aerosol formation: chemometric dimension reduction techniques for the deconvolution of complex atmospheric data sets

    NASA Astrophysics Data System (ADS)

    Wyche, K. P.; Monks, P. S.; Smallbone, K. L.; Hamilton, J. F.; Alfarra, M. R.; Rickard, A. R.; McFiggans, G. B.; Jenkin, M. E.; Bloss, W. J.; Ryan, A. C.; Hewitt, C. N.; MacKenzie, A. R.

    2015-07-01

    .e. toluene) oxidation and "more realistic" plant mesocosm systems, demonstrates that such an ensemble of chemometric mapping has the potential to be used for the classification of more complex spectra of unknown origin. More specifically, the addition of mesocosm data from fig and birch tree experiments shows that isoprene and monoterpene emitting sources, respectively, can be mapped onto the statistical model structure and their positional vectors can provide insight into their biological sources and controlling oxidative chemistry. The potential to extend the methodology to the analysis of ambient air is discussed using results obtained from a zero-dimensional box model incorporating mechanistic data obtained from the Master Chemical Mechanism (MCMv3.2). Such an extension to analysing ambient air would prove a powerful asset in assisting with the identification of SOA sources and the elucidation of the underlying chemical mechanisms involved.

  13. Application of remote sensing to the photogeologic mapping of the region of the Itatiaia alkaline complex. M.S. Thesis; [Minas Gerais, Rio De Janeiro, Sao Paulo, and Itatiaia, Brazil

    NASA Technical Reports Server (NTRS)

    Dejesusparada, N. (Principal Investigator); Rodrigues, J. E.

    1981-01-01

    Remote sensing methods applied to geologically complex areas, through interaction of ground truth and information obtained from multispectral LANDSAT images and radar mosaics were evaluated. The test area covers parts of Minos Gerais, Rio De Janeiro and Sao Paulo states and contains the alkaline complex of Itatiaia and surrounding Precambrian terrains. Geological and structural mapping was satisfactory; however, lithological varieties which form the massif's could not be identified. Photogeological lineaments were mapped, some of which represent the boundaries of stratigraphic units. Automatic processing was used to classify sedimentary areas, which includes the talus deposits of the alkaline massifs.

  14. Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail

    PubMed Central

    2012-01-01

    Background As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome. Results The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene. Conclusions These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix. PMID:23066875

  15. Lesion-symptom mapping of a complex figure copy task: A large-scale PCA study of the BCoS trial

    PubMed Central

    Chen, Haobo; Pan, Xiaoping; Lau, Johnny King Lam; Bickerton, Wai-Ling; Pradeep, Boddana; Taheri, Maliheh; Humphreys, Glyn; Rotshtein, Pia

    2016-01-01

    Complex figure copying is a commonly used neuropsychological test. Here we explored the neural basis of the factors underlying complex figure copying (CFC), using data from the Birmingham Cognitive Screen (BCoS) in a large group of sub-acute, ischemic stroke patients (239). We computed two analyses: in the first we assessed the contribution of co-morbid deficits (i.e. in gesture processing, object use, visual neglect, pictures naming and sustained attention) to the lesions associated with CFC. In a second analysis a Principle Component Analysis (PCA) was used to isolate different underlying task components and to link to clinical neuroimaging scans. A voxel-based morphometry (VBM) analysis showed that poor CFC performance was associated with lesions to bi-lateral thalamus, lingual, right fusiform and right inferior parietal cortices (rIPC). The latter association with the posterior parietal cortex was diminished after controlling for neglect. Follow up analysis showed the neglect partially mediated the correlation of CFC and rIPC. The PCA revealed three main underlying components: (1) a component associated with high-level motor control common to different measures of apraxia and linked to the left postcentral gyrus, the right thalamus and middle frontal gyrus; (2) a visuo-motor transformation component unique to the CFC and associated with lesions to the posterior occipital and sensory cortices; (3) a component associated with multistep object use tasks which was correlated with lesions to the left inferior frontal orbital gyrus, the right fusiform and cerebellum. Using clinical symptoms, cognitive profiles and lesion mapping we showed that beyond visual perception, CFC performance is supported by three functional networks: one for high-level motor control, a visuo-motor transformation component, and multistep object use network. PMID:27182489

  16. Mapping of the associated phenotype of an absent granular layer in ichthyosis vulgaris to the epidermal differentiation complex on chromosome 1.

    PubMed

    Compton, John G; DiGiovanna, John J; Johnston, Kay A; Fleckman, Philip; Bale, Sherri J

    2002-12-01

    Ichthyosis vulgaris (IV) is a mild to severe scaling disorder of uncertain etiology estimated to affect as many as 1 : 250 in the population. Family studies have shown that in many cases IV follows an autosomal dominant inheritance pattern, but gene mapping studies have not been reported. To investigate the genetic basis for inherited IV, we have performed gene linkage studies in two multigenerational families where affected individuals have clinical features of IV but distinct histological features. The epidermis in this disorder characteristically displays non-specific orthohyperkeratosis. Notably, a subset of IV patients with a reduced or absent granular epidermal layer (AGL) have been reported, and decreased filaggrin levels have been described in others. The prominent role of profilaggrin in human keratohyalin suggests that defects in the gene for profilaggrin (FLG), its processing of profillagrin to filaggrin, or a gene involved in profilaggrin regulation may underlie or modify the pathology in IV. Family 1 had seven individuals with IV, severe heat intolerance and epidermis with 1-3 granular layers (consistent with normal epidermal histology). Ichthyosis vulgaris in this family did not segregate with FLG or other genes in the epidermal differentiation complex. In contrast, five of the six IV patients in Family 2, all siblings, had epidermis with no granular layer. Significant evidence was obtained for linkage of IV with the associated AGL phenotype to the epidermal differentiation complex (which includes FLG) assuming either a recessive (max Lod 3.4) or dominant (max Lod 3.6) inheritance model. Sequence analysis of FLG did not reveal a mutation in the amino or carboxyl terminal portions of the coding sequence adjacent to filaggrin repeats. The AGL may represent an endophenotype for IV, and the presence of a modifier of IV pathology at this locus is discussed.

  17. Comparative chromosome mapping of the rRNA genes and telomeric repeats in three Italian pine voles of the Microtus savii s.l. complex (Rodentia, Cricetidae)

    PubMed Central

    Gornung, Ekaterina; Bezerra, Alexandra M. R.; Castiglia, Riccardo

    2011-01-01

    Abstract The Microtus (Terricola) savii s. l. complex is a group of five species/subspecies of the Italian pine voles, which diverged at different times either with or without chromosomal differentiation. The evidence of chromosomal diversification has so far concerned the shape of the sex chromosomes, especially the X chromosome. Three taxa of the group, Microtus savii savii, Microtus savii nebrodensis, and Microtus savii tolfetanus have identical karyotypes with metacentric X chromosomes. The X chromosomes of Microtus brachycercus and Microtus brachycercus niethammericus are, respectively, subtelocentric and acrocentric in shape. The Microtus savii complex has been long an object of conventional karyological studies, but comparative molecular cytogenetic data were completely missing. Therefore, we conducted a comparative chromosomal mapping of rRNA genes (rDNA) and telomeric repeats in three of the five taxa of the group: Microtus savii savii, Microtus savii nebrodensis, and Microtus brachycercus niethammericus, each of which belongs to a distinct mitochondrial clade.The survey revealed that differentiation of the clades was accompanied by remarkable changes with regard to the number and locations of the rDNA sites. Thus, Microtus savii savii and Microtus savii nebrodensis have especially high numbers of rDNA sites, which are located in the centromeric regions of, correspondingly, 18 and 13 chromosome pairs, whereas Microtus brachycercus niethammericus shows variable (8–10) and heteromorphic rDNA sites on both centromeric and telomeric regions. Interstitial telomeric sites (ITS), which are believed to indicate possible breakpoints of recurring chromosomal rearrangements, are present on the largest biarmed chromosomes and on the metacentric X chromosomes in Microtus savii savii and Microtus savii nebrodensis. These preliminary results are discussed in the context of recent advances in phylogeny of the group, as well as the rDNA genomic organization and X

  18. A velocity map imaging study of gold-rare gas complexes: Au-Ar, Au-Kr, and Au-Xe

    NASA Astrophysics Data System (ADS)

    Hopkins, W. Scott; Woodham, Alex P.; Plowright, Richard J.; Wright, Timothy G.; Mackenzie, Stuart R.

    2010-06-01

    The ultraviolet photodissociation dynamics of the gold-rare gas atom van der Waals complexes (Au-RG, RG=Ar, Kr, and Xe) have been studied by velocity map imaging. Photofragmentation of Au-Ar and Au-Kr at several wavelengths permits extrapolation to zero of the total kinetic energy release (TKER) spectra as monitored in the Au(P23/2∘[5d106p]) fragment channel, facilitating the determination of ground state dissociation energies of D0″(Au-Ar)=149±13 cm-1 and D0″(Au-Kr)=240±19 cm-1, respectively. In the same spectral region, transitions to vibrational levels of an Ω'=1/2 state of the Au-Xe complex result in predissociation to the lower Au(P21/2∘[5d106p])+Xe(S10[5p6]) fragment channel for which TKER extrapolation yields a value of D0″(Au-Xe)=636±27 cm-1. Asymmetric line shapes for transitions to the v'=14 level of this state indicate coupling to the Au(P23/2∘[5d106p])+Xe(S10[5p6]) continuum, which allows us to refine this value to D0″(Au-Xe)=607±5 cm-1. The dissociation dynamics of this vibrational level have been studied at the level of individual isotopologues by fitting the observed excitation spectra to Fano profiles. These fits reveal a remarkable variation in the predissociation dynamics for different Au-Xe isotopologues. For Au-Ar and Au-Xe, the determined ground state dissociation energies are in good agreement with recent theoretical calculations; the agreement of the Au-Kr value with theory is less satisfactory.

  19. Lesion-symptom mapping of a complex figure copy task: A large-scale PCA study of the BCoS trial.

    PubMed

    Chen, Haobo; Pan, Xiaoping; Lau, Johnny King Lam; Bickerton, Wai-Ling; Pradeep, Boddana; Taheri, Maliheh; Humphreys, Glyn; Rotshtein, Pia

    2016-01-01

    Complex figure copying is a commonly used neuropsychological test. Here we explored the neural basis of the factors underlying complex figure copying (CFC), using data from the Birmingham Cognitive Screen (BCoS) in a large group of sub-acute, ischemic stroke patients (239). We computed two analyses: in the first we assessed the contribution of co-morbid deficits (i.e. in gesture processing, object use, visual neglect, pictures naming and sustained attention) to the lesions associated with CFC. In a second analysis a Principle Component Analysis (PCA) was used to isolate different underlying task components and to link to clinical neuroimaging scans. A voxel-based morphometry (VBM) analysis showed that poor CFC performance was associated with lesions to bi-lateral thalamus, lingual, right fusiform and right inferior parietal cortices (rIPC). The latter association with the posterior parietal cortex was diminished after controlling for neglect. Follow up analysis showed the neglect partially mediated the correlation of CFC and rIPC. The PCA revealed three main underlying components: (1) a component associated with high-level motor control common to different measures of apraxia and linked to the left postcentral gyrus, the right thalamus and middle frontal gyrus; (2) a visuo-motor transformation component unique to the CFC and associated with lesions to the posterior occipital and sensory cortices; (3) a component associated with multistep object use tasks which was correlated with lesions to the left inferior frontal orbital gyrus, the right fusiform and cerebellum. Using clinical symptoms, cognitive profiles and lesion mapping we showed that beyond visual perception, CFC performance is supported by three functional networks: one for high-level motor control, a visuo-motor transformation component, and multistep object use network. PMID:27182489

  20. Comparative chromosome mapping of the rRNA genes and telomeric repeats in three Italian pine voles of the Microtus savii s.l. complex (Rodentia, Cricetidae).

    PubMed

    Gornung, Ekaterina; Bezerra, Alexandra M R; Castiglia, Riccardo

    2011-01-01

    The Microtus (Terricola) savii s. l. complex is a group of five species/subspecies of the Italian pine voles, which diverged at different times either with or without chromosomal differentiation. The evidence of chromosomal diversification has so far concerned the shape of the sex chromosomes, especially the X chromosome. Three taxa of the group, Microtus savii savii, Microtus savii nebrodensis, and Microtus savii tolfetanus have identical karyotypes with metacentric X chromosomes. The X chromosomes of Microtus brachycercus and Microtus brachycercus niethammericus are, respectively, subtelocentric and acrocentric in shape. The Microtus savii complex has been long an object of conventional karyological studies, but comparative molecular cytogenetic data were completely missing. Therefore, we conducted a comparative chromosomal mapping of rRNA genes (rDNA) and telomeric repeats in three of the five taxa of the group: Microtus savii savii, Microtus savii nebrodensis, and Microtus brachycercus niethammericus, each of which belongs to a distinct mitochondrial clade.The survey revealed that differentiation of the clades was accompanied by remarkable changes with regard to the number and locations of the rDNA sites. Thus, Microtus savii savii and Microtus savii nebrodensis have especially high numbers of rDNA sites, which are located in the centromeric regions of, correspondingly, 18 and 13 chromosome pairs, whereas Microtus brachycercus niethammericus shows variable (8-10) and heteromorphic rDNA sites on both centromeric and telomeric regions. Interstitial telomeric sites (ITS), which are believed to indicate possible breakpoints of recurring chromosomal rearrangements, are present on the largest biarmed chromosomes and on the metacentric X chromosomes in Microtus savii savii and Microtus savii nebrodensis. These preliminary results are discussed in the context of recent advances in phylogeny of the group, as well as the rDNA genomic organization and X chromosome

  1. Mapping gas-phase organic reactivity and concomitant secondary organic aerosol formation: chemometric dimension reduction techniques for the deconvolution of complex atmospheric datasets

    NASA Astrophysics Data System (ADS)

    Wyche, K. P.; Monks, P. S.; Smallbone, K. L.; Hamilton, J. F.; Alfarra, M. R.; Rickard, A. R.; McFiggans, G. B.; Jenkin, M. E.; Bloss, W. J.; Ryan, A. C.; Hewitt, C. N.; MacKenzie, A. R.

    2015-01-01

    Highly non-linear dynamical systems, such as those found in atmospheric chemistry, necessitate hierarchical approaches to both experiment and modeling in order, ultimately, to identify and achieve fundamental process-understanding in the full open system. Atmospheric simulation chambers comprise an intermediate in complexity, between a classical laboratory experiment and the full, ambient system. As such, they can generate large volumes of difficult-to-interpret data. Here we describe and implement a chemometric dimension reduction methodology for the deconvolution and interpretation of complex gas- and particle-phase composition spectra. The methodology comprises principal component analysis (PCA), hierarchical cluster analysis (HCA) and positive least squares-discriminant analysis (PLS-DA). These methods are, for the first time, applied to simultaneous gas- and particle-phase composition data obtained from a comprehensive series of environmental simulation chamber experiments focused on biogenic volatile organic compound (BVOC) photooxidation and associated secondary organic aerosol (SOA) formation. We primarily investigated the biogenic SOA precursors isoprene, α-pinene, limonene, myrcene, linalool and β-caryophyllene. The chemometric analysis is used to classify the oxidation systems and resultant SOA according to the controlling chemistry and the products formed. Furthermore, a holistic view of results across both the gas- and particle-phases shows the different SOA formation chemistry, initiating in the gas-phase, proceeding to govern the differences between the various BVOC SOA compositions. The results obtained are used to describe the particle composition in the context of the oxidized gas-phase matrix. An extension of the technique, which incorporates into the statistical models data from anthropogenic (i.e. toluene) oxidation and "more realistic" plant mesocosm systems, demonstrates that such an ensemble of chemometric mapping has the potential to be

  2. SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

    PubMed

    Mora, Freddy; Quitral, Yerko A; Matus, Ivan; Russell, Joanne; Waugh, Robbie; Del Pozo, Alejandro

    2016-01-01

    This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5-22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5-35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint. PMID:27446139

  3. SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

    PubMed

    Mora, Freddy; Quitral, Yerko A; Matus, Ivan; Russell, Joanne; Waugh, Robbie; Del Pozo, Alejandro

    2016-01-01

    This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5-22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5-35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

  4. SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach

    PubMed Central

    Mora, Freddy; Quitral, Yerko A.; Matus, Ivan; Russell, Joanne; Waugh, Robbie; del Pozo, Alejandro

    2016-01-01

    This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint. PMID:27446139

  5. Genetic mapping of Cmv1 in the region of mouse chromosome 6 encoding the NK gene complex-associated loci Ly49 and musNKR-P1

    SciTech Connect

    Scalzo, A.A.; Lyons, P.A.; Fitzgerald, N.A.

    1995-06-10

    The Cmv1 resistance gene controls splenic replication of murine cytomegalovirus (MCMV) and confers natural killer (NK) cell-mediated resistance to otherwise lethal infection. The Cmv1 phenotypes of 13 inbred mouse strains have been assessed, and it was found that the Cmv1{sup r} resistance phenotype was restricted to the C57BL/6J and Ma/MyJ strains. We have further analyzed the linkage of Cmv1 to the NK gene complex (NKC) mapping to distal mouse chromosome 6 in 99 (BALB/c x C57BL/6J)F{sub 1} x BALB/c backcross mice using cloned gene probes and microsatellite markers from this region. No recombinants were observed between Cmv1 and the NKC-associated Ly49 and musNKR-P1 multigene families, nor the Kap locus, nor with 7 microsatellite markers, indicating that Cmv1 is closely linked (<1 cM) to all of these markers. Analysis of the genotype of the MCMV-susceptible BXD8 RI strain around the NKC region revealed that it had C57BL/6J alleles at microsatellite markers immediately proximal and distal to Cmv1. This suggests that the Cmv1{sup s} phenotype of this strain is due to a germ-line mutation. Thus, the close linkage of Cmv1 to the Ly49 and musNK-R-P1 multigene families suggests that it may represent an NK cell recognition structure encoded in the NKC region. 37 refs., 3 figs., 1 tab.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. GIS-mapping of environmental assessment of the territories in the region of intense activity for the oil and gas complex for achievement the goals of the Sustainable Development (on the example of Russia)

    NASA Astrophysics Data System (ADS)

    Yermolaev, Oleg

    2014-05-01

    The uniform system of complex scientific-reference ecological-geographical should act as a base for the maintenance of the Sustainable Development (SD) concept in the territories of the Russian Federation subjects or certain regions. In this case, the assessment of the ecological situation in the regions can be solved by the conjugation of the two interrelated system - the mapping and the geoinformational. The report discusses the methodological aspects of the Atlas-mapping for the purposes of SD in the regions of Russia. The Republic of Tatarstan viewed as a model territory where a large-scale oil-gas complex "Tatneft" PLC works. The company functions for more than 60 years. Oil fields occupy an area of more than 38 000 km2; placed in its territory about 40 000 oil wells, more than 55 000 km of pipelines; more than 3 billion tons of oil was extracted. Methods for to the structure and requirements for the Atlas's content were outlined. The approaches to mapping of "an ecological dominant" of SD conceptually substantiated following the pattern of a large region of Russia. Several trends of thematically mapping were suggested to be distinguished in the Atlas's structure: • The background history of oil-fields mine working; • The nature preservation technologies while oil extracting; • The assessment of natural conditions of a humans vital activity; • Unfavorable and dangerous natural processes and phenomena; • The anthropogenic effect and environmental surroundings change; • The social-economical processes and phenomena. • The medical-ecological and geochemical processes and phenomena; Within these groups the other numerous groups can distinguished. The maps of unfavorable and dangerous processes and phenomena subdivided in accordance with the types of processes - of endogenous and exogenous origin. Among the maps of the anthropogenic effects on the natural surroundings one can differentiate the maps of the influence on different nature's spheres

  8. Probabilistic Hazard for Seismically-Induced Tsunamis in Complex Tectonic Contexts: Event Tree Approach to Seismic Source Variability and Practical Feasibility of Inundation Maps

    NASA Astrophysics Data System (ADS)

    Lorito, Stefano; Selva, Jacopo; Basili, Roberto; Romano, Fabrizio; Tiberti, Mara Monica; Piatanesi, Alessio

    2014-05-01

    Probabilistic Tsunami Hazard Analysis (PTHA) rests on computationally demanding numerical simulations of the tsunami generation and propagation up to the inundated coastline. We here focus on tsunamis generated by the co-seismic sea floor displacement, which constitute the vast majority of the observed tsunami events, i.e. on Seismic PTHA (SPTHA). For incorporating the full expected seismic source variability, aiming at a complete SPTHA, a very large number of numerical tsunami scenarios is typically needed, especially for complex tectonic contexts, where SPTHA is not dominated by large subduction earthquakes only. Here, we propose a viable approach for reducing the number of simulations for a given set of input earthquakes representing the modelled aleatory uncertainties of the seismic rupture parameters. Our approach is based on a preliminary analysis of the SPTHA of maximum offshore wave height (HMax) at a given target location, and assuming computationally cheap linear propagation. We start with defining an operational SPTHA framework in which we then introduce a simplified Event Tree approach, combined with a Green's functions approach, for obtaining a first controlled sampling and reduction of the effective source parameter space size. We then apply a two-stage filtering procedure to the 'linear' SPTHA results. The first filter identifies and discards all the sources producing a negligible contribution at the target location, for example the smallest earthquakes or those directing most of tsunami energy elsewhere. The second filter performs a cluster analysis aimed at selecting groups of source parameters producing comparable HMax profiles for each earthquake magnitude at the given test site. We thus select a limited set of sources that is subsequently used for calculating 'nonlinear' probabilistic inundation maps at the target location. We find that the optimal subset of simulations needed for inundation calculations can be obtained basing on just the

  9. Planetary maps

    USGS Publications Warehouse

    ,

    1992-01-01

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

  10. Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member.

    PubMed

    Gariou-Papalexiou, Angeliki; Giardini, María Cecilia; Augustinos, Antonios A; Drosopoulou, Elena; Lanzavecchia, Silvia B; Cladera, Jorge L; Caceres, Carlos; Bourtzis, Kostas; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone

    2016-01-01

    Genetic and cytogenetic studies constitute a significant basis for understanding the biology of insect pests and the design and the construction of genetic tools for biological control strategies. Anastrepha fraterculus is an important pest of the Tephritidae family. It is distributed from southern Texas through eastern Mexico, Central America and South America causing significant crop damage and economic losses. Currently it is considered as a species complex; until now seven members have been described based on multidisciplinary approaches. Here we report the cytogenetic analysis of an Argentinian population characterized as Af. sp.1 member of the Anastrepha fraterculus species complex. The mitotic karyotype and the first detailed photographic maps of the salivary gland polytene chromosomes are presented. The mitotic metaphase complement consists of six (6) pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes that correspond to the five autosomes of the mitotic karyotype and a heterochromatic network corresponding to the sex chromosomes. Comparison of the polytene chromosome maps between this species and Anastrepha ludens shows significant similarity. The polytene maps presented here are suitable for cytogenetic studies that could shed light on the species limits within this species complex and support the development of genetic tools for sterile insect technique (SIT) applications. PMID:27362546

  11. Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member.

    PubMed

    Gariou-Papalexiou, Angeliki; Giardini, María Cecilia; Augustinos, Antonios A; Drosopoulou, Elena; Lanzavecchia, Silvia B; Cladera, Jorge L; Caceres, Carlos; Bourtzis, Kostas; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone

    2016-01-01

    Genetic and cytogenetic studies constitute a significant basis for understanding the biology of insect pests and the design and the construction of genetic tools for biological control strategies. Anastrepha fraterculus is an important pest of the Tephritidae family. It is distributed from southern Texas through eastern Mexico, Central America and South America causing significant crop damage and economic losses. Currently it is considered as a species complex; until now seven members have been described based on multidisciplinary approaches. Here we report the cytogenetic analysis of an Argentinian population characterized as Af. sp.1 member of the Anastrepha fraterculus species complex. The mitotic karyotype and the first detailed photographic maps of the salivary gland polytene chromosomes are presented. The mitotic metaphase complement consists of six (6) pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes that correspond to the five autosomes of the mitotic karyotype and a heterochromatic network corresponding to the sex chromosomes. Comparison of the polytene chromosome maps between this species and Anastrepha ludens shows significant similarity. The polytene maps presented here are suitable for cytogenetic studies that could shed light on the species limits within this species complex and support the development of genetic tools for sterile insect technique (SIT) applications.

  12. Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member

    PubMed Central

    Augustinos, Antonios A.; Drosopoulou, Elena; Lanzavecchia, Silvia B.; Cladera, Jorge L.; Caceres, Carlos; Bourtzis, Kostas; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone

    2016-01-01

    Genetic and cytogenetic studies constitute a significant basis for understanding the biology of insect pests and the design and the construction of genetic tools for biological control strategies. Anastrepha fraterculus is an important pest of the Tephritidae family. It is distributed from southern Texas through eastern Mexico, Central America and South America causing significant crop damage and economic losses. Currently it is considered as a species complex; until now seven members have been described based on multidisciplinary approaches. Here we report the cytogenetic analysis of an Argentinian population characterized as Af. sp.1 member of the Anastrepha fraterculus species complex. The mitotic karyotype and the first detailed photographic maps of the salivary gland polytene chromosomes are presented. The mitotic metaphase complement consists of six (6) pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes that correspond to the five autosomes of the mitotic karyotype and a heterochromatic network corresponding to the sex chromosomes. Comparison of the polytene chromosome maps between this species and Anastrepha ludens shows significant similarity. The polytene maps presented here are suitable for cytogenetic studies that could shed light on the species limits within this species complex and support the development of genetic tools for sterile insect technique (SIT) applications. PMID:27362546

  13. Constructing a Theory- and Evidence-Based Treatment Rationale for Complex eHealth Interventions: Development of an Online Alcohol Intervention Using an Intervention Mapping Approach

    PubMed Central

    Johansen, Ayna; Nesvåg, Sverre; Kok, Gerjo; Duckert, Fanny

    2013-01-01

    Background Due to limited reporting of intervention rationale, little is known about what distinguishes a good intervention from a poor one. To support improved design, there is a need for comprehensive reports on novel and complex theory-based interventions. Specifically, the emerging trend of just-in-time tailoring of content in response to change in target behavior or emotional state is promising. Objective The objective of this study was to give a systematic and comprehensive description of the treatment rationale of an online alcohol intervention called Balance. Methods We used the intervention mapping protocol to describe the treatment rationale of Balance. The intervention targets at-risk drinking, and it is delivered by email, mobile phone text messaging, and tailored interactive webpages combining text, pictures, and prerecorded audio. Results The rationale of the current treatment was derived from a self-regulation perspective, and the overarching idea was to support continued self-regulation throughout the behavior change process. Maintaining the change efforts over time and coping adaptively during critical moments (eg, immediately before and after a lapse) are key factors to successful behavior change. Important elements of the treatment rationale to achieving these elements were: (1) emotion regulation as an inoculation strategy against self-regulation failure, (2) avoiding lapses by adaptive coping, and (3) avoiding relapse by resuming the change efforts after a lapse. Two distinct and complementary delivery strategies were used, including a day-to-day tunnel approach in combination with just-in-time therapy. The tunnel strategy was in accordance with the need for continuous self-regulation and it functions as a platform from which just-in-time therapy was launched. Just-in-time therapy was used to support coping during critical moments, and started when the client reports either low self-efficacy or that they were drinking above target levels

  14. Map accuracy

    USGS Publications Warehouse

    ,

    1981-01-01

    An inaccurate map is not a reliable map. "X" may mark the spot where the treasure is buried, but unless the seeker can locate "X" in relation to known landmarks or positions, the map is not very useful.

  15. Principles of electroanatomic mapping.

    PubMed

    Bhakta, Deepak; Miller, John M

    2008-01-01

    Electrophysiologic testing and radiofrequency ablation have evolved as curative measures for a variety of rhythm disturbances. As experience in this field has grown, ablation is progressively being used to address more complex rhythm disturbances. Paralleling this trend are technological advancements to facilitate these efforts, including electroanatomic mapping (EAM). At present, several different EAM systems utilizing various technologies are available to facilitate mapping and ablation. Use of these systems has been shown to reduce fluoroscopic exposure and radiation dose, with less significant effects on procedural duration and success rates. Among the data provided by EAM are chamber reconstruction, tagging of important anatomic landmarks and ablation lesions, display of diagnostic and mapping catheters without using fluoroscopy, activation mapping, and voltage (or scar) mapping. Several EAM systems have specialized features, such as enhanced ability to map non-sustained or hemodynamically unstable arrhythmias, ability to display diagnostic as well as mapping catheter positions, and wide compatibility with a variety of catheters. Each EAM system has its strengths and weaknesses, and the system chosen must depend upon what data is required for procedural success (activation mapping, substrate mapping, cardiac geometry), the anticipated arrhythmia, the compatibility of the system with adjunctive tools (i.e. diagnostic and ablation catheters), and the operator's familiarity with the selected system. While EAM can offer significant assistance during an EP procedure, their incorrect or inappropriate application can substantially hamper mapping efforts and procedural success, and should not replace careful interpretation of data and strict adherence to electrophysiologic principles.

  16. Bovine leukemia virus matrix-associated protein MA(p15): further processing and formation of a specific complex with the dimer of the 5'-terminal genomic RNA fragment.

    PubMed Central

    Katoh, I; Kyushiki, H; Sakamoto, Y; Ikawa, Y; Yoshinaka, Y

    1991-01-01

    The retrovirus precursor protein has an arrangement of several characteristic domains with which it achieves selective and efficient packaging of the genome RNA during particle assembly. In this study, we analyzed the composition of the bovine leukemia virus (BLV) gag proteins and examined their RNA-binding properties in gel mobility shift assays, using various genomic RNA probes synthesized in vitro. Results obtained in amino acid sequence and composition analyses indicate that the matrix-associated protein MA(p15) is further processed by the BLV protease (PR) to generate MA(p10), a short peptide of seven amino acid residues, and p4. The gag precursor is now mapped as NH2-MA(p10)-p4-CA(p24)-NC(p12)-COOH. MA(p15) formed a specific complex with the dimer RNA of the U5-5' gag region presumed to contain the BLV packaging signal but not with other RNAs. The NH2-terminal cleavage product, MA(p10), bound all RNA fragments tested, while the COOH-terminal peptides with a sequence common to mammalian type C retroviruses had little affinity for RNA. The nucleocapsid protein NC(p12) bound to RNAs nonspecifically and randomly in the presence or absence of zinc ions. These results suggest a possible interaction of the NH2 terminus of the gag precursor with the 5' terminus of the genomic RNA in an early phase of particle assembly, when the conserved structure between the MA and CA domains might be involved. Images PMID:1658378

  17. Chromite deposits in central part Stillwater Complex, Sweet Grass County, Montana: a digital database for the geologic map of the east slope of Iron Mountain

    USGS Publications Warehouse

    Howland, A.L.; Moyer, Lorre A.

    2001-01-01

    In 1940, A.L. Howland and J. W. Peoples, assisted by W.R. Jones and M.G. Bennett, mapped the geology of the east slope of Iron Mountain, Montana. The map was revised and extended by Howland in 1942 and published in 1955 as plate 10 of the U.S. Geological Survey Bulletin 1015-D (Howland, 1955). In 2000, the USGS contracted Optronics Specialty Co., Inc. of Northridge, CA to prepare a scanned digital version of plate 10. Geospatial editing and attributing of the scanned map of the east slope of Iron Mountain was performed by the USGS in order to produce an interim digital product. This digital geospatial database is one of many being created by the U.S. Geological Survey as an ongoing effort to provide geologic information in a geographic information system (GIS) for use in spatial analysis.

  18. Exploring maps

    USGS Publications Warehouse

    ,

    1993-01-01

    Exploring Maps is an interdisciplinary set of materials on mapping for grades 7-12. Students will learn basic mapmaking and map reading skills and will see how maps can answer fundamental geographic questions: "Where am I?" "What else is here?" "Where am I going?"

  19. Contour Mapping

    NASA Technical Reports Server (NTRS)

    1995-01-01

    In the early 1990s, the Ohio State University Center for Mapping, a NASA Center for the Commercial Development of Space (CCDS), developed a system for mobile mapping called the GPSVan. While driving, the users can map an area from the sophisticated mapping van equipped with satellite signal receivers, video cameras and computer systems for collecting and storing mapping data. George J. Igel and Company and the Ohio State University Center for Mapping advanced the technology for use in determining the contours of a construction site. The new system reduces the time required for mapping and staking, and can monitor the amount of soil moved.

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

    PubMed Central

    Luo, Ming-Cheng; Gu, Yong Q.; You, Frank M.; Deal, Karin R.; Ma, Yaqin; Hu, Yuqin; Huo, Naxin; Wang, Yi; Wang, Jirui; Chen, Shiyong; Jorgensen, Chad M.; Zhang, Yong; McGuire, Patrick E.; Pasternak, Shiran; Stein, Joshua C.; Ware, Doreen; Kramer, Melissa; McCombie, W. Richard; Kianian, Shahryar F.; Martis, Mihaela M.; Mayer, Klaus F. X.; Sehgal, Sunish K.; Li, Wanlong; Gill, Bikram S.; Bevan, Michael W.; Šimková, Hana; Doležel, Jaroslav; Weining, Song; Lazo, Gerard R.; Anderson, Olin D.; Dvorak, Jan

    2013-01-01

    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 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions. PMID:23610408

  1. Complexities of chromosome landing in a highly duplicated genome: toward map-based cloning of a gene controlling blackleg resistance in Brassica napus.

    PubMed

    Mayerhofer, Reinhold; Wilde, Kris; Mayerhofer, Marion; Lydiate, Derek; Bansal, Vipan K; Good, Allen G; Parkin, Isobel A P

    2005-12-01

    The LmR1 locus, which controls seedling resistance to the blackleg fungus Leptosphaeria maculans in the Brassica napus cultivar Shiralee, was positioned on linkage group N7. Fine genetic mapping in a population of 2500 backcross lines identified three molecular markers that cosegregated with LmR1. Additional linkage mapping in a second population colocalized a seedling resistance gene, ClmR1, from the cultivar Cresor to the same genetic interval on N7 as LmR1. Both genes were located in a region that showed extensive inter- and intragenomic duplications as well as intrachromosomal tandem duplications. The tandem duplications seem to have occurred in the Brassica lineage before the divergence of B. rapa and B. oleracea but after the separation of Brassica and Arabidopsis from a common ancestor. Microsynteny was found between the region on N7 carrying the resistance gene and the end of Arabidopsis chromosome 1, interrupted by a single inversion close to the resistance locus. The collinear region in Arabidopsis was assayed for the presence of possible candidate genes for blackleg resistance. These data provided novel insights into the genomic structure and evolution of plant resistance loci and an evaluation of the candidate gene approach using comparative mapping with a model organism.

  2. Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites.

    PubMed

    Abney, Mark; Ober, Carole; McPeek, Mary Sara

    2002-04-01

    We present methods for linkage and association mapping of quantitative traits for a founder population with a large, known genealogy. We detect linkage to quantitative-trait loci (QTLs) through a multipoint homozygosity-mapping method. We propose two association methods, one of which is single point and uses a general two-allele model and the other of which is multipoint and uses homozygosity by descent for a particular allele. In all three methods, we make extensive use of the pedigree and genotype information, while keeping the computations simple and efficient. To assess significance, we have developed a permutation-based test that takes into account the covariance structure due to relatedness of individuals and can be used to determine empirical genomewide and locus-specific P values. In the case of multivariate-normally distributed trait data, the permutation-based test is asymptotically exact. The test is broadly applicable to a variety of mapping methods that fall within the class of linear statistical models (e.g., variance-component methods), under the assumption of random ascertainment with respect to the phenotype. For obtaining genomewide P values, our proposed method is appropriate when positions of markers are independent of the observed linkage signal, under the null hypothesis. We apply our methods to a genome screen for fasting insulin level in the Hutterites. We detect significant genomewide linkage on chromosome 19 and suggestive evidence of QTLs on chromosomes 1 and 16.

  3. RICH MAPS

    EPA Science Inventory

    Michael Goodchild recently gave eight reasons why traditional maps are limited as communication devices, and how interactive internet mapping can overcome these limitations. In the past, many authorities in cartography, from Jenks to Bertin, have emphasized the importance of sim...

  4. Map adventures

    USGS Publications Warehouse

    1994-01-01

    Map Adventures, with seven accompanying lessons, is appropriate for grades K-3. Students will learn basic concepts for visualizing objects from different perspectives and how to understand /and use maps.

  5. Monoaryloxide Pyrrolide (MAP) Imido Alkylidene Complexes of Molybdenum and Tungsten That Contain 2,6-Bis(2,5-R2-pyrrolyl)phenoxide (R = i-Pr, Ph) Ligands and an Unsubstituted Metallacyclobutane on Its Way to Losing Ethylene

    PubMed Central

    2013-01-01

    We report the synthesis of Mo and W MAP complexes that contain O-2,6-(2,5-R2-pyrrolyl)2C6H3 (2,6-dipyrrolylphenoxide or ODPPR) ligands in which R = i-Pr, Ph. W(NAr)(CH-t-Bu)(Pyr)(ODPPPh) (4a; Ar = 2,6-disopropylphenyl, Pyr = pyrrolide) reacts readily with ethylene to yield a metallacyclobutane complex, W(NAr)(C3H6)(Pyr)(ODPPPh) (5). The structure of 5 in the solid state shows that it is approximately a square pyramid with the WC4 ring spanning apical and basal positions. This SP′ structure, which has never been observed as an actual intermediate, must now be regarded as an integral feature of the metathesis reaction. PMID:23794779

  6. Historical Mapping

    USGS Publications Warehouse

    ,

    1999-01-01

    Maps become out of date over time. Maps that are out of date, however, can be useful to historians, attorneys, environmentalists, genealogists, and others interested in researching the background of a particular area. Local historians can compare a series of maps of the same area compiled over a long period of time to learn how the area developed. A succession of such maps can provide a vivid picture of how a place changed over time.

  7. Topographic mapping

    USGS Publications Warehouse

    ,

    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.

  8. Particle complexation of mitochondrial iron produces superoxide generation and activates MAP kinases, NF-kappa B, nrf-2 in human respiratory epithelial cell

    EPA Science Inventory

    The biological effect of particles is associated with a disruption in cell iron homeostasis. We tested the postulate that complexation of cell iron by silica (Si02) results in both an oxidative stress and biological effect. BEAS-2B cells were exposed to either media or 100 ug/ml....

  9. Pitfalls in homozygosity mapping.

    PubMed

    Miano, M G; Jacobson, S G; Carothers, A; Hanson, I; Teague, P; Lovell, J; Cideciyan, A V; Haider, N; Stone, E M; Sheffield, V C; Wright, A F

    2000-11-01

    There is much interest in use of identity-by-descent (IBD) methods to map genes, both in Mendelian and in complex disorders. Homozygosity mapping provides a rapid means of mapping autosomal recessive genes in consanguineous families by identifying chromosomal regions that show homozygous IBD segments in pooled samples. In this report, we point out some potential pitfalls that arose during the course of homozygosity mapping of the enhanced S-cone syndrome gene, resulting from (1) unexpected allelic heterogeneity, so that the region containing the disease locus was missed as a result of pooling; (2) identification of a homozygous IBD region unrelated to the disease locus; and (3) the potential for inflation of LOD scores as a result of underestimation of the extent of inbreeding, which Broman and Weber suggest may be quite common.

  10. How to Map Noise.

    PubMed

    Hinton, John

    2002-01-01

    Noise mapping is a method of presenting complex noise information in a clear and simple way either on a physical map or in a database. This mapping information can be either calculated or measured using a variety of techniques and methods. Furthermore, the results of such exercises can be presented in many different ways and used for a number of different purposes. This paper attempts to examine these issues in the light of the "mapping requirements" outlined in the recently proposed Directive of the European Parliament and of the Council, relating to the Assessment and Management of Environmental Noise (Comm (2000) 468 final). This proposed Directive was laid before the Parliament and Council in the autumn of 2000. The First Reading of the proposal was successfully negotiated just before Christmas 2000. The Second Reading is likely to commence shortly.

  11. New geologic mapping combined with geochemical, paleomagnetic, and high-precision 40Ar/39Ar analyses reveal multiple overlapping calderas formed 16.4-15.7 Ma at High Rock caldera complex, northwestern Nevada

    NASA Astrophysics Data System (ADS)

    Coble, M. A.; Mahood, G. A.

    2012-12-01

    We present new evidence from 1:100,000- and 1:24,000-scale geologic mapping for the presence of at least four overlapping calderas, 24 to 40 km in diameter, that formed in an interval of only 0.7 m.y. during the mid-Miocene at High Rock caldera complex in northwest Nevada and southern Oregon. In total, an estimated minimum volume of ~725 km3 of rhyolitic magma erupted from the complex between 16.5 and 15.5 Ma, covering an area of ~9,000 km2. Rapid eruption of numerous units at volumetric rates as high as 3,000-4,000 km3/m.y., strong welding of lithic-poor ignimbrites, extensive vapor-phase alteration of lavas and ignimbrites alike, a limited range of phenocryst content and assemblage, silicification along faults, and a lack of well-exposed stratigraphic sections has hindered previous reconnaissance-scale mapping and identification of caldera centers. Calderas are located based on truncation of precaldera rhyolitic lavas by caldera topographic walls, by arcuate patterns of rhyolite lavas that erupted along buried caldera ring faults, and by the presence of pumiceous caldera lake sediments. We attribute formation of the Virgin Valley, Badger Mountain, Hanging Rock, and Cottonwood Creek Calderas to collapse on eruption, respectively, of the ca. 16.37 Ma Idaho Canyon Tuff, the 16.34 Ma Summit Lake Tuff, the 16.0 Ma Soldier Meadows Tuff, and the 15.7 Ma Tuff of Yellow Rock Canyon. Additional smaller-volume pyroclastic units erupted during emplacement of geochemically similar rhyolitic lavas. More than 60 new 40Ar/39Ar ages were obtained on ignimbrites, fall deposits, and rhyolitic, trachytic and basaltic lavas. Many of the eruptive units in the HRCC differ in age by less than 100 k.y., which, at ca. 16 Ma, requires precision at the 1-2‰ (2σ standard error) level to distinguish units using 40Ar/39Ar geochronology. The high-precision of the analyses of sanidine in the rhyolites, coupled with geochemical and paleomagnetic measurements, allowed us to correlate far

  12. Bedrock geologic map of Vermont

    USGS Publications Warehouse

    Ratcliffe, Nicholas M.; Stanley, Rolfe S.; Gale, Marjorie H.; Thompson, Peter J.; Walsh, Gregory J.; With contributions by Hatch, Norman L.; Rankin, Douglas W.; Doolan, Barry L.; Kim, Jonathan; Mehrtens, Charlotte J.; Aleinikoff, John N.; McHone, J. Gregory; Cartography by Masonic, Linda M.

    2011-01-01

    The Bedrock Geologic Map of Vermont is the result of a cooperative agreement between the U.S. Geological Survey (USGS) and the State of Vermont. The State's complex geology spans 1.4 billion years of Earth's history. The new map comes 50 years after the most recent map of the State by Charles G. Doll and others in 1961 and a full 150 years since the publication of the first geologic map of Vermont by Edward Hitchcock and others in 1861. At a scale of 1:100,000, the map shows an uncommon level of detail for State geologic maps. Mapped rock units are primarily based on lithology, or rock type, to facilitate derivative studies in multiple disciplines. The 1961 map was compiled from 1:62,500-scale or smaller maps. The current map was created to integrate more detailed (1:12,000- to 1:24,000-scale) modern and older (1:62,500-scale) mapping with the theory of plate tectonics to provide a framework for geologic, tectonic, economic, hydrogeologic, and environmental characterization of the bedrock of Vermont. The printed map consists of three oversize sheets (52 x 76 inches). Sheets 1 and 2 show the southern and northern halves of Vermont, respectively, and can be trimmed and joined so that the entire State can be displayed as a single entity. These sheets also include 10 cross sections and a geologic structure map. Sheet 3 on the front consists of descriptions of 486 map units, a correlation of map units, and references cited. Sheet 3 on the back features a list of the 195 sources of geologic map data keyed to an index map of 7.5-minute quadrangles in Vermont, as well as a table identifying ages of rocks dated by uranium-lead zircon geochronology.

  13. Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex*

    PubMed Central

    Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M.; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B.; Sauder, J. Michael; Burley, Stephen K.; Chait, Brian T.; Almo, Steven C.; Rout, Michael P.; Sali, Andrej

    2014-01-01

    The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup13355–502) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332–1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes. PMID:25139911

  14. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

    PubMed

    Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B; Sauder, J Michael; Burley, Stephen K; Chait, Brian T; Almo, Steven C; Rout, Michael P; Sali, Andrej

    2014-11-01

    The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133(55-502)) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup133(2-1157). Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes. PMID:25139911

  15. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

    PubMed

    Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B; Sauder, J Michael; Burley, Stephen K; Chait, Brian T; Almo, Steven C; Rout, Michael P; Sali, Andrej

    2014-11-01

    The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133(55-502)) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup133(2-1157). Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.

  16. Mapping Van

    NASA Technical Reports Server (NTRS)

    1994-01-01

    A NASA Center for the Commercial Development of Space (CCDS) - developed system for satellite mapping has been commercialized for the first time. Global Visions, Inc. maps an area while driving along a road in a sophisticated mapping van equipped with satellite signal receivers, video cameras and computer systems for collecting and storing mapping data. Data is fed into a computerized geographic information system (GIS). The resulting amps can be used for tax assessment purposes, emergency dispatch vehicles and fleet delivery companies as well as other applications.

  17. Remote sensing aids geologic mapping.

    NASA Technical Reports Server (NTRS)

    Knepper, D. H., Jr.; Marrs, R. W.

    1973-01-01

    Remote sensing techniques have been applied to general geologic mapping along the Rio Grande rift zone in central Colorado. A geologic map of about 1,100 square miles was prepared utilizing (1) prior published and unpublished maps, (2) detailed and reconnaissance field maps made for this study, and (3) remote sensor data interpretations. The map is to be used for interpretation of the complex Cenozoic tectonic and geomorphic histories of the area. Regional and local geologic mapping can be aided by the proper application of remote sensing techniques. Conventional color and color infrared photos contain a large amount of easily-extractable general geologic information and are easily used by geologists untrained in the field of remote sensing. Other kinds of sensor data used in this study, with the exception of SLAR imagery, were generally found to be impractical or unappropriate for broad-scale general geologic mapping.

  18. Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology.

    PubMed

    Wang, Shi-Bo; Wen, Yang-Jun; Ren, Wen-Long; Ni, Yuan-Li; Zhang, Jin; Feng, Jian-Ying; Zhang, Yuan-Ming

    2016-01-01

    Composite interval mapping (CIM) is the most widely-used method in linkage analysis. Its main feature is the ability to control genomic background effects via inclusion of co-factors in its genetic model. However, the result often depends on how the co-factors are selected, especially for small-effect and linked quantitative trait loci (QTL). To address this issue, here we proposed a new method under the framework of genome-wide association studies (GWAS). First, a single-locus random-SNP-effect mixed linear model method for GWAS was used to scan each putative QTL on the genome in backcross or doubled haploid populations. Here, controlling background via selecting markers in the CIM was replaced by estimating polygenic variance. Then, all the peaks in the negative logarithm P-value curve were selected as the positions of multiple putative QTL to be included in a multi-locus genetic model, and true QTL were automatically identified by empirical Bayes. This called genome-wide CIM (GCIM). A series of simulated and real datasets was used to validate the new method. As a result, the new method had higher power in QTL detection, greater accuracy in QTL effect estimation, and stronger robustness under various backgrounds as compared with the CIM and empirical Bayes methods.

  19. Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology

    PubMed Central

    Wang, Shi-Bo; Wen, Yang-Jun; Ren, Wen-Long; Ni, Yuan-Li; Zhang, Jin; Feng, Jian-Ying; Zhang, Yuan-Ming

    2016-01-01

    Composite interval mapping (CIM) is the most widely-used method in linkage analysis. Its main feature is the ability to control genomic background effects via inclusion of co-factors in its genetic model. However, the result often depends on how the co-factors are selected, especially for small-effect and linked quantitative trait loci (QTL). To address this issue, here we proposed a new method under the framework of genome-wide association studies (GWAS). First, a single-locus random-SNP-effect mixed linear model method for GWAS was used to scan each putative QTL on the genome in backcross or doubled haploid populations. Here, controlling background via selecting markers in the CIM was replaced by estimating polygenic variance. Then, all the peaks in the negative logarithm P-value curve were selected as the positions of multiple putative QTL to be included in a multi-locus genetic model, and true QTL were automatically identified by empirical Bayes. This called genome-wide CIM (GCIM). A series of simulated and real datasets was used to validate the new method. As a result, the new method had higher power in QTL detection, greater accuracy in QTL effect estimation, and stronger robustness under various backgrounds as compared with the CIM and empirical Bayes methods. PMID:27435756

  20. Mapping the binding surface of interleukin-8 complexed with an N-terminal fragment of the type 1 human interleukin-8 receptor.

    PubMed

    Clubb, R T; Omichinski, J G; Clore, G M; Gronenborn, A M

    1994-01-24

    Interleukin-8 and its receptors are key mediators of immune and inflammatory responses. Heteronuclear NMR spectroscopy has been utilized to map the binding surface on interleukin-8 (IL-8) for an N-terminal fragment of the human Type-1 IL-8 receptor. A peptide corresponding to residues 1-40 of the IL-8 type 1 receptor (IL8-r1) was titrated into a sample of uniformly 15N-labeled IL-8. IL8-r1 binds to IL-8 with a dissociation constant of 170 +/- 50 microM assuming the peptide binds with a stoichiometry of one peptide per IL-8 monomer, exchanges rapidly (> 900 s-1) between free and bound states, and selectively perturbs the chemical environment of several IL-8 residues. The binding surface on IL-8 suggested by our results is comprised of residues in strand beta 3 of the beta-sheet (Glu48 to Cys50), the turn preceding beta 3 (Ser44), the C-terminal alpha-helix (Val61) and the irregular N-terminal loop region (Thr12, Lys15, Phe17, His18, Lys20 and Phe21). The IL-8 dimer appears to present two symmetrical binding surfaces for the IL8-r1 peptide, suggesting two receptor peptides may bind per dimer. PMID:8307164

  1. Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology.

    PubMed

    Wang, Shi-Bo; Wen, Yang-Jun; Ren, Wen-Long; Ni, Yuan-Li; Zhang, Jin; Feng, Jian-Ying; Zhang, Yuan-Ming

    2016-01-01

    Composite interval mapping (CIM) is the most widely-used method in linkage analysis. Its main feature is the ability to control genomic background effects via inclusion of co-factors in its genetic model. However, the result often depends on how the co-factors are selected, especially for small-effect and linked quantitative trait loci (QTL). To address this issue, here we proposed a new method under the framework of genome-wide association studies (GWAS). First, a single-locus random-SNP-effect mixed linear model method for GWAS was used to scan each putative QTL on the genome in backcross or doubled haploid populations. Here, controlling background via selecting markers in the CIM was replaced by estimating polygenic variance. Then, all the peaks in the negative logarithm P-value curve were selected as the positions of multiple putative QTL to be included in a multi-locus genetic model, and true QTL were automatically identified by empirical Bayes. This called genome-wide CIM (GCIM). A series of simulated and real datasets was used to validate the new method. As a result, the new method had higher power in QTL detection, greater accuracy in QTL effect estimation, and stronger robustness under various backgrounds as compared with the CIM and empirical Bayes methods. PMID:27435756

  2. Pygmy squids and giant brains: mapping the complex cephalopod CNS by phalloidin staining of vibratome sections and whole-mount preparations.

    PubMed

    Wollesen, T; Loesel, R; Wanninger, A

    2009-04-30

    Among bilaterian invertebrates, cephalopod molluscs (e.g., squids, cuttlefish and octopuses) have a central nervous system (CNS) that rivals in complexity that of the phylogenetically distant vertebrates (e.g., mouse and human). However, this prime example of convergent evolution has rarely been the subject of recent developmental and evolutionary studies, which may partly be due to the lack of suitable neural markers and the large size of cephalopod brains. Here, we demonstrate the usefulness of fluorescence-coupled phalloidin to characterize the CNS of cephalopods using histochemistry combined with confocal laser scanning microscopy. Whole-mount preparations of developmental stages as well as vibratome sections of embryonic and adult brains were analyzed and the benefits of this technique are illustrated. Compared to classical neuroanatomical and antibody-based studies, phalloidin labeling experiments are less time-consuming and allow a high throughput of samples. Besides other advantages summarized here, phalloidin reliably labels the entire neuropil of the CNS of all squids, cuttlefish and octopuses investigated. This facilitates high-resolution in toto reconstructions of the CNS and contributes to a better understanding of the organization of neural networks. Amenable for multi-labeling experiments employing antibodies against neurotransmitters, proteins and enzymes, phalloidin constitutes an excellent neuropil marker for the complex cephalopod CNS.

  3. Genome-wide Mapping of the Coactivator Ada2p Yields Insight into the Functional Roles of SAGA/ADA Complex in Candida albicans

    PubMed Central

    Sellam, Adnane; Askew, Christopher; Epp, Elias; Lavoie, Hugo; Whiteway, Malcolm

    2009-01-01

    The SAGA/ADA coactivator complex, which regulates numerous cellular processes by coordinating histone acetylation, is widely conserved throughout eukaryotes, and analysis of the Candida albicans genome identifies the components of this complex in the fungal pathogen. We investigated the multiple functions of SAGA/ADA in C. albicans by determining the genome-wide occupancy of Ada2p using chromatin immunoprecipitation (ChIP). Ada2p is recruited to 200 promoters upstream of genes involved in different stress-response functions and metabolic processes. Phenotypic and transcriptomic analysis of ada2 mutant showed that Ada2p is required for the responses to oxidative stress, as well as to treatments with tunicamycin and fluconazole. Ada2p recruitment to the promoters of oxidative resistance genes is mediated by the transcription factor Cap1p, and coactivator function were also established for Gal4p, which recruits Ada2p to the promoters of glycolysis and pyruvate metabolism genes. Cooccupancy of Ada2p and the drug resistance regulator Mrr1p on the promoters of core resistance genes characterizing drug resistance in clinical strains was also demonstrated. Ada2p recruitment to the promoters of these genes were shown to be completely dependent on Mrr1p. Furthermore, ADA2 deletion causes a decrease in H3K9 acetylation levels of target genes, thus illustrating its importance for histone acetyl transferase activity. PMID:19279142

  4. COL5A1: Fine genetic mapping, intron/exon organization, and exclusion as candidate gene in families with tuberous sclerosis complex 1, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos syndrome type II

    SciTech Connect

    Greenspan, D.S.; Papenberg, K.A.; Marchuk, D.A.

    1994-09-01

    Type V collagen is the only fibrillar collagen which has yet to be implicated in the pathogenesis of genetic diseases in humans or mice. To begin examining the possible role of type V collagen in genetic disease, we have previously mapped COL5A1, the gene for the {alpha}1 chain of type V collagen, to 9q23.2{r_arrow}q34.3 and described two restriction site polymorphisms which allowed us to exclude COL5A1 as candidate gene for nail-patella syndrome. We have now used these polymorphisms to exclude COL5A1 as candidate gene for tuberous sclerosis complex 1 and Ehlers-Danlos syndrome type II. In addition, we describe a CA repeat, with observed heterozygosity of about 0.5, in a COL5A1 intron, which has allowed us to exclude COL5A1 as a candidate gene in hereditary hemorrhagic telangiectasia and to place COL5A1 on the CEPH family genetic map between markers D9S66 and D9S67. We have also determined the entire intron/exon organization of COL5A1, which will facilitate characterization of mutations in genetic diseases with which COL5A1 may be linked in future studies.

  5. A scheme for the uniform mapping and monitoring of earth resources and environmental complexes: An assessment of natural vegetation, environmental, and crop analogs. [Sierra-Lahontan and Colorado Plateaus, Northern Great Valley (CA), and Louisiana Coastal Plain

    NASA Technical Reports Server (NTRS)

    Poulton, C. E.; Welch, R. I. (Principal Investigator)

    1975-01-01

    The author has identified the following significant results. A study was performed to develop and test a procedure for the uniform mapping and monitoring of natural ecosystems in the semi-arid and wood regions of the Sierra-Lahontan and Colorado Plateau areas, and for the estimating of rice crop production in the Northern Great Valley (Ca.) and the Louisiana Coastal Plain. ERTS-1 and high flight and low flight aerial photos were used in a visual photointerpretation scheme to identify vegetation complexes, map acreages, and evaluate crop vigor and stress. Results indicated that the vegetation analog concept is valid; that depending on the kind of vegetation and its density, analogs are interpretable at different levels in the hierarchical classification from second to the fourth level. The second level uses physiognomic growth form-structural criteria, and the fourth level uses floristic or taxonomic criteria, usually at generic level. It is recommended that analog comparisons should be made in relatively small test areas where large homogeneous examples can be found of each analog.

  6. Question Mapping

    ERIC Educational Resources Information Center

    Martin, Josh

    2012-01-01

    After accepting the principal position at Farmersville (TX) Junior High, the author decided to increase instructional rigor through question mapping because of the success he saw using this instructional practice at his prior campus. Teachers are the number one influence on student achievement (Marzano, 2003), so question mapping provides a…

  7. Concept Mapping

    ERIC Educational Resources Information Center

    Technology & Learning, 2005

    2005-01-01

    Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

  8. Map Adventures.

    ERIC Educational Resources Information Center

    Geological Survey (Dept. of Interior), Reston, VA.

    This curriculum packet about maps, with seven accompanying lessons, is appropriate for students in grades K-3. Students learn basic concepts for visualizing objects from different perspectives and how to understand and use maps. Lessons in the packet center on a story about a little girl, Nikki, who rides in a hot-air balloon that gives her, and…

  9. Mapping cellular processes in the mesenchyme during palatal development in the absence of Tbx1 reveals complex proliferation changes and perturbed cell packing and polarity.

    PubMed

    Brock, Lara J; Economou, Andrew D; Cobourne, Martyn T; Green, Jeremy B A

    2016-03-01

    The 22q11 deletion syndromes represent a spectrum of overlapping conditions including cardiac defects and craniofacial malformations. Amongst the craniofacial anomalies that are seen, cleft of the secondary palate is a common feature. Haploinsufficiency of TBX1 is believed to be a major contributor toward many of the developmental structural anomalies that occur in these syndromes, and targeted deletion of Tbx1 in the mouse reproduces many of these malformations, including cleft palate. However, the cellular basis of this defect is only poorly understood. Here, palatal development in the absence of Tbx1 has been analysed, focusing on cellular properties within the whole mesenchymal volume of the palatal shelves. Novel image analyses and data presentation tools were applied to quantify cell proliferation rates, including regions of elevated as well as reduced proliferation, and cell packing in the mesenchyme. Also, cell orientations (nucleus-Golgi axis) were mapped as a potential marker of directional cell movement. Proliferation differed only subtly between wild-type and mutant until embryonic day (E)15.5 when proliferation in the mutant was significantly lower. Tbx1(-/-) palatal shelves had slightly different cell packing than wild-type, somewhat lower before elevation and higher at E15.5 when the wild-type palate has elevated and fused. Cell orientation is biased towards the shelf distal edge in the mid-palate of wild-type embryos but is essentially random in the Tbx1(-/-) mutant shelves, suggesting that polarised processes such as directed cell rearrangement might be causal for the cleft phenotype. The implications of these findings in the context of further understanding Tbx1 function during palatogenesis and of these methods for the more general analysis of genotype-phenotype functional relationships are discussed.

  10. Mapping cellular processes in the mesenchyme during palatal development in the absence of Tbx1 reveals complex proliferation changes and perturbed cell packing and polarity.

    PubMed

    Brock, Lara J; Economou, Andrew D; Cobourne, Martyn T; Green, Jeremy B A

    2016-03-01

    The 22q11 deletion syndromes represent a spectrum of overlapping conditions including cardiac defects and craniofacial malformations. Amongst the craniofacial anomalies that are seen, cleft of the secondary palate is a common feature. Haploinsufficiency of TBX1 is believed to be a major contributor toward many of the developmental structural anomalies that occur in these syndromes, and targeted deletion of Tbx1 in the mouse reproduces many of these malformations, including cleft palate. However, the cellular basis of this defect is only poorly understood. Here, palatal development in the absence of Tbx1 has been analysed, focusing on cellular properties within the whole mesenchymal volume of the palatal shelves. Novel image analyses and data presentation tools were applied to quantify cell proliferation rates, including regions of elevated as well as reduced proliferation, and cell packing in the mesenchyme. Also, cell orientations (nucleus-Golgi axis) were mapped as a potential marker of directional cell movement. Proliferation differed only subtly between wild-type and mutant until embryonic day (E)15.5 when proliferation in the mutant was significantly lower. Tbx1(-/-) palatal shelves had slightly different cell packing than wild-type, somewhat lower before elevation and higher at E15.5 when the wild-type palate has elevated and fused. Cell orientation is biased towards the shelf distal edge in the mid-palate of wild-type embryos but is essentially random in the Tbx1(-/-) mutant shelves, suggesting that polarised processes such as directed cell rearrangement might be causal for the cleft phenotype. The implications of these findings in the context of further understanding Tbx1 function during palatogenesis and of these methods for the more general analysis of genotype-phenotype functional relationships are discussed. PMID:26689739

  11. ETD Allows for Native Surface Mapping of a 150 kDa Noncovalent Complex on a Commercial Q-TWIMS-TOF Instrument

    NASA Astrophysics Data System (ADS)

    Lermyte, Frederik; Konijnenberg, Albert; Williams, Jonathan P.; Brown, Jeffery M.; Valkenborg, Dirk; Sobott, Frank

    2014-03-01

    Top-down approaches for the characterization of intact proteins and macromolecular complexes are becoming increasingly popular, since they potentially simplify and speed up the assignment process. Here we demonstrate how, on a commercially available Q-TWIMS-TOF instrument, we performed top-down ETD of the native form of tetrameric alcohol dehydrogenase. We achieved good sequence coverage throughout the first 81 N-terminal amino acids of ADH, with the exception of a loop located on the inside of the protein. This is in agreement with the exposed parts of the natively folded protein according to the crystal structure. Choosing the right precursor charge state and applying supplemental activation were found to be key to obtaining a high ETD fragmentation efficiency. Finally, we briefly discuss opportunities to further increase the performance of ETD based on our results.

  12. LA-ICP-MS mapping of olivine from the Brahin and Brenham meteorites: Complex elemental distributions in the pallasite olivine precursor

    NASA Astrophysics Data System (ADS)

    McKibbin, Seann J.; O'Neill, Hugh St. C.; Mallmann, Guilherme; Halfpenny, Angela

    2013-10-01

    To investigate the early history of olivine from the Main-Group pallasites Brahin and Brenham, we have spatially mapped their trace-element distributions using laser-ablation inductively-coupled-plasma mass spectrometry (LA-ICP-MS). Brahin olivine interiors contain ∼100-200 μm patches enriched in Cr, Al, Ti, V, Sc and Ga, separated by linear enrichments of P; these structures bear no relation to current crystal morphologies. Rather, cross-cutting relationships suggest they predate olivine-metal mixing. Brenham olivine also has internal variations for these elements. By contrast, Ni and Co concentrations in olivine from both meteorites decrease near crystal margins, as expected for freezing-in of profiles formed during diffusive re-equilibration with metal during cooling. Brenham olivine also has decreasing Al, Cr and Ti near the margin. Correlations between concentrations of Cr and Al exist for individual Brahin olivine grains, but do not hold over multiple grains, indicating a heterogeneous precursor. Al and Ti are correlated over multiple grains in Brahin, interpreted as Ti cations decorating pre-existing Al-defects. In Brenham olivine, similar geochemical trends exist, but the Cr-Al relationship probably represents both grain margin effects and pre-existing internal heterogeneity. The preservation of structure for elements which are normally fast diffusers in olivine hinges on coupled substitutions involving Al, which along with P diffuses much more slowly than most other elements under some conditions. Al concentrations in olivine are low and variable (3-33 ppm) which is inconsistent with crystallisation from a normal silicate melt; Al-in-olivine thermometers indicate that pallasite olivine was formed in a low-temperature environment. Following its delivery to the magma ocean/core-mantle boundary, Al-P systematics were not substantially modified. Assuming diffusivities for Al and P that are similar to Si (since they reside in the same crystallographic site

  13. Mapping racism.

    PubMed

    Moss, Donald B

    2006-01-01

    The author uses the metaphor of mapping to illuminate a structural feature of racist thought, locating the degraded object along vertical and horizontal axes. These axes establish coordinates of hierarchy and of distance. With the coordinates in place, racist thought begins to seem grounded in natural processes. The other's identity becomes consolidated, and parochialism results. The use of this kind of mapping is illustrated via two patient vignettes. The author presents Freud's (1905, 1927) views in relation to such a "mapping" process, as well as Adorno's (1951) and Baldwin's (1965). Finally, the author conceptualizes the crucial status of primitivity in the workings of racist thought.

  14. Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug

    DOE PAGES

    Aggarwal, Mayank; Kovalevsky, Andrey Y.; Velazquez, Hector; Fisher, S. Zoë; Smith, Jeremy C.; McKenna, Robert

    2016-07-22

    Carbonic anhydrases (CAs; EC 4.2.1.1) catalyze the interconversion of CO 2 and HCO 3 − , and their inhibitors have long been used as diuretics and as a therapeutic treatment for many disorders such as glaucoma and epilepsy. Acetazolamide (AZM) and methazolamide (MZM, a methyl derivative of AZM) are two of the classical CA inhibitory drugs that have been used clinically for decades. The jointly refined X-ray/neutron structure of MZM in complex with human CA isoform II (hCA II) has been determined to a resolution of 2.2 Å with an R cryst of ∼16.0%. Presented in this article, along withmore » only the second neutron structure of a clinical drug-bound hCA, is an in-depth structural comparison and analyses of differences in hydrogen-bonding network, water-molecule orientation and solvent displacement that take place upon the binding of AZM and MZM in the active site of hCA II. Even though MZM is slightly more hydrophobic and displaces more waters than AZM, the overall binding affinity ( K i ) for both of the drugs against hCA II is similar (∼10 n M ). The plausible reasons behind this finding have also been discussed using molecular dynamics and X-ray crystal structures of hCA II–MZM determined at cryotemperature and room temperature. This study not only allows a direct comparison of the hydrogen bonding, protonation states and solvent orientation/displacement of AZM and MZM, but also shows the significant effect that the methyl derivative has on the solvent organization in the hCA II active site.« less

  15. Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques

    PubMed Central

    Han, Liangrong; Jing, Xin; Liu, Hailiang; Yang, Chuanchun; Zhang, Fengting; Hu, Yue; Yue, Hongni; Ning, Ying

    2016-01-01

    Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques. PMID:27218255

  16. Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques.

    PubMed

    Pan, Qiong; Hu, Hao; Han, Liangrong; Jing, Xin; Liu, Hailiang; Yang, Chuanchun; Zhang, Fengting; Hu, Yue; Yue, Hongni; Ning, Ying

    2016-01-01

    Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques. PMID:27218255

  17. Mapping Biodiversity.

    ERIC Educational Resources Information Center

    World Wildlife Fund, Washington, DC.

    This document features a lesson plan that examines how maps help scientists protect biodiversity and how plants and animals are adapted to specific ecoregions by comparing biome, ecoregion, and habitat. Samples of instruction and assessment are included. (KHR)

  18. MAPS of Cancer

    NASA Technical Reports Server (NTRS)

    Gray, Lincoln

    1998-01-01

    Our goal was to produce an interactive visualization from a mathematical model that successfully predicts metastases from head and neck cancer. We met this goal early in the project. The visualization is available for the public to view. Our work appears to fill a need for more information about this deadly disease. The idea of this project was to make an easily interpretable visualization based on what we call "functional maps" of disease. A functional map is a graphic summary of medical data, where distances between parts of the body are determined by the probability of disease, not by anatomical distances. Functional maps often beat little resemblance to anatomical maps, but they can be used to predict the spread of disease. The idea of modeling the spread of disease in an abstract multidimensional space is difficult for many people. Our goal was to make the important predictions easy to see. NASA must face this problem frequently: how to help laypersons and professionals see important trends in abstract, complex data. We took advantage of concepts perfected in NASA's graphics libraries. As an analogy, consider a functional map of early America. Suppose we choose travel times, rather than miles, as our measures of inter-city distances. For Abraham Lincoln, travel times would have been the more meaningful measure of separation between cities. In such a map New Orleans would be close to Memphis because of the Mississippi River. St. Louis would be close to Portland because of the Oregon Trail. Oklahoma City would be far from Little Rock because of the Cheyenne. Such a map would look puzzling to those of us who have always seen physical maps, but the functional map would be more useful in predicting the probabilities of inter-site transit. Continuing the analogy, we could predict the spread of social diseases such as gambling along the rivers and cattle rustling along the trails. We could simply print the functional map of America, but it would be more interesting

  19. Planetary Mapping

    NASA Astrophysics Data System (ADS)

    Greeley, Ronald; Batson, Raymond M.

    2007-02-01

    Preface; List of contributors; 1. Introduction R. Greeley and R. M. Batson; 2. History of planetary cartography R. M. Batson, E. A. Whitaker and D. E. Wilhelms; 3. Cartography R. M. Batson; 4. Planetary nomenclature M. E. Strobell and H. Masursky; 5. Geodetic control M. E. Davies; 6. Topographic mapping S. S. C. Wu and F. J. Doyle; 7. Geologic mapping D. E. Wilhelms; Appendices R. M. Batson and J. L. Inge; Index.

  20. Map Separates

    USGS Publications Warehouse

    ,

    2001-01-01

    U.S. Geological Survey (USGS) topographic maps are printed using up to six colors (black, blue, green, red, brown, and purple). To prepare your own maps or artwork based on maps, you can order separate black-and-white film positives or negatives for any color printed on a USGS topographic map, or for one or more of the groups of related features printed in the same color on the map (such as drainage and drainage names from the blue plate.) In this document, examples are shown with appropriate ink color to illustrate the various separates. When purchased, separates are black-and-white film negatives or positives. After you receive a film separate or composite from the USGS, you can crop, enlarge or reduce, and edit to add or remove details to suit your special needs. For example, you can adapt the separates for making regional and local planning maps or for doing many kinds of studies or promotions by using the features you select and then printing them in colors of your choice.

  1. Venus mapping

    NASA Technical Reports Server (NTRS)

    Batson, R. M.; Morgan, H. F.; Sucharski, Robert

    1991-01-01

    Semicontrolled image mosaics of Venus, based on Magellan data, are being compiled at 1:50,000,000, 1:10,000,000, 1:5,000,000, and 1:1,000,000 scales to support the Magellan Radar Investigator (RADIG) team. The mosaics are semicontrolled in the sense that data gaps were not filled and significant cosmetic inconsistencies exist. Contours are based on preliminary radar altimetry data that is subjected to revision and improvement. Final maps to support geologic mapping and other scientific investigations, to be compiled as the dataset becomes complete, will be sponsored by the Planetary Geology and Geophysics Program and/or the Venus Data Analysis Program. All maps, both semicontrolled and final, will be published as I-maps by the United States Geological Survey. All of the mapping is based on existing knowledge of the spacecraft orbit; photogrammetric triangulation, a traditional basis for geodetic control on planets where framing cameras were used, is not feasible with the radar images of Venus, although an eventual shift of coordinate system to a revised spin-axis location is anticipated. This is expected to be small enough that it will affect only large-scale maps.

  2. [Carney complex].

    PubMed

    Kacerovská, D; Michal, M; Síma, R; Grossmann, P; Kazakov, D V

    2011-10-01

    Carney complex is a clinically and genetically heterogeneous disease, with at least two genetic loci including the PRKAR1A gene located on chromosome 17 and the CNC2 locus mapped to chromosome 2. Clinically this syndrome is characterized by multiple myxomas occurring in different anatomic sites, mucocutaneous pigmentary lesions, and a variety of non-endocrine and endocrine tumors, often causing endocrine abnormalities, involving various organs. Knowledge of morphological findings in CNC patients with their typical locations is necessary to raise suspicion of this syndrome by pathologists. Confirmation of the diagnosis allows regular clinical check-ups and early treatment of these patients. PMID:22145222

  3. The High Rock caldera complex, NW Nevada: Geologic mapping, volcanology, geochemistry, and ultra-high precision 40Ar/39Ar dating of early Yellowstone hotspot magmatism

    NASA Astrophysics Data System (ADS)

    Hausback, B.; Smith, J.; Henry, C. D.; Hilton, R. P.; McIntosh, W. C.; Heizler, M. T.; Noble, D. C.

    2012-12-01

    Our new work reveals a complex evolution of the High Rock caldera, one of the oldest calderas related to initiation of the Yellowstone hotspot. The caldera formed at 16.43±0.01 Ma (n=2, Fish Canyon sanidine = 28.201 Ma; all ages reported here agree with stratigraphy) during eruption of the zoned (metaluminous, high-silica dacite to slightly peralkaline, low-silica rhyolite), abundantly porphyritic Summit Lake Tuff. The only exposed precaldera rocks are a suite of intermediate lavas along the western margin. They are undated but compositionally similar to 30 Ma rocks in the region, so probably unrelated to the caldera. The caldera margin is entirely buried by moat domes and post-collapse lavas and tuff. Sparsely porphyritic rhyolite lavas erupted at 16.30±0.01 Ma (n=1) north of the caldera, possibly along the ring fracture. A large suite of petrographically and compositionally nearly indistinguishable, abundantly porphyritic, peralkaline rhyolite lavas and tuffs, the Soldier Meadow (SM) rock type, erupted from vents around the entire caldera margin in two pulses at 16.14±0.01 and 16.09±0.01 Ma (n=6 and 3). The first pulse includes lavas along the western and eastern margin; the Soldier Meadow Tuff (SMT, a moderately peralkaline, crystal-rich welded ignimbrite that is thinly-layered with coarse lag breccias in the proximal area and massive in distal locations), which erupted along the eastern caldera margin; and accidental blocks (up to 3m) of SMT brought up in the interior of the caldera by later eruptions. The second pulse includes several more lavas and associated small-volume flow, fall, and surge(?) tuffs along the northeastern and southwestern margin. Distribution of the SM rock type suggests that its magma chamber underlay the entire caldera. Rocks of the second pulse are distinguished only by higher incompatible element concentrations (Rb, Zr, Nb, Th), which suggests the magma body continued to differentiate between pulses. The tuffs of Alkali Flat and

  4. Automated geologic mapping using rock reflectances.

    NASA Technical Reports Server (NTRS)

    Watson, R. D.; Rowan, L. C.

    1971-01-01

    Investigation of the feasibility of preparing geologic maps automatically through computer processing of calibrated narrow-band visible and near IR reflectivity data collected with a 12-channel scanner. Five procedures were followed in the computer analysis of the radiances recorded as voltages on analog magnetic tape. Three recognition maps have been generated iteratively using a progressively more complex classification scheme. The overall accuracy of the first recognition map was 80%, but the discrimination of the limestone and dolomite was only 50-60%. All three maps are very accurate outcrop maps. The results demonstrate the feasibility of automated geologic mapping in this relatively simple setting.

  5. Mole Mapping.

    ERIC Educational Resources Information Center

    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)

  6. Memphis Maps.

    ERIC Educational Resources Information Center

    Hyland, Stanley; Cox, David; Martin, Cindy

    1998-01-01

    The Memphis Maps program, a collaborative effort of Memphis (Tennessee) educational institutions, public agencies, a bank, and community programs, trains local students in Geographic Information Systems technology and provides the community with valuable demographic and assessment information. The program is described, and factors contributing to…

  7. Automated mapping of hammond's landforms

    USGS Publications Warehouse

    Gallant, A.L.; Brown, D.D.; Hoffer, R.M.

    2005-01-01

    We automated a method for mapping Hammond's landforms over large landscapes using digital elevation data. We compared our results against Hammond's published landform maps, derived using manual interpretation procedures. We found general agreement in landform patterns mapped by the manual and the automated approaches, and very close agreement in characterization of local topographic relief. The two approaches produced different interpretations of intermediate landforms, which relied upon quantification of the proportion of landscape having gently sloping terrain. This type of computation is more efficiently and consistently applied by computer than human. Today's ready access to digital data and computerized geospatial technology provides a good foundation for mapping terrain features, but the mapping criteria guiding manual techniques in the past may not be appropriate for automated approaches. We suggest that future efforts center on the advantages offered by digital advancements in refining an approach to better characterize complex landforms. ?? 2005 IEEE.

  8. The Circumpolar Arctic vegetation map

    USGS Publications Warehouse

    Walker, Donald A.; Raynolds, Martha K.; Daniels, F.J.A.; Einarsson, E.; Elvebakk, A.; Gould, W.A.; Katenin, A.E.; Kholod, S.S.; Markon, C.J.; Melnikov, E.S.; Moskalenko, N.G.; Talbot, S. S.; Yurtsev, B.A.; Bliss, L.C.; Edlund, S.A.; Zoltai, S.C.; Wilhelm, M.; Bay, C.; Gudjonsson, G.; Ananjeva, G.V.; Drozdov, D.S.; Konchenko, L.A.; Korostelev, Y.V.; Ponomareva, O.E.; Matveyeva, N.V.; Safranova, I.N.; Shelkunova, R.; Polezhaev, A.N.; Johansen, B.E.; Maier, H.A.; Murray, D.F.; Fleming, Michael D.; Trahan, N.G.; Charron, T.M.; Lauritzen, S.M.; Vairin, B.A.

    2005-01-01

    Question: What are the major vegetation units in the Arctic, what is their composition, and how are they distributed among major bioclimate subzones and countries? Location: The Arctic tundra region, north of the tree line. Methods: A photo-interpretive approach was used to delineate the vegetation onto an Advanced Very High Resolution Radiometer (AVHRR) base image. Mapping experts within nine Arctic regions prepared draft maps using geographic information technology (ArcInfo) of their portion of the Arctic, and these were later synthesized to make the final map. Area analysis of the map was done according to bioclimate subzones, and country. The integrated mapping procedures resulted in other maps of vegetation, topography, soils, landscapes, lake cover, substrate pH, and above-ground biomass. Results: The final map was published at 1:7 500 000 scale map. Within the Arctic (total area = 7.11 x 106 km 2), about 5.05 ?? 106 km2 is vegetated. The remainder is ice covered. The map legend generally portrays the zonal vegetation within each map polygon. About 26% of the vegetated area is erect shrublands, 18% peaty graminoid tundras, 13% mountain complexes, 12% barrens, 11% mineral graminoid tundras, 11% prostrate-shrub tundras, and 7% wetlands. Canada has by far the most terrain in the High Arctic mostly associated with abundant barren types and prostrate dwarf-shrub tundra, whereas Russia has the largest area in the Low Arctic, predominantly low-shrub tundra. Conclusions: The CAVM is the first vegetation map of an entire global biome at a comparable resolution. The consistent treatment of the vegetation across the circumpolar Arctic, abundant ancillary material, and digital database should promote the application to numerous land-use, and climate-change applications and will make updating the map relatively easy. ?? IAVS; Opulus Press.

  9. Mining Concept Maps to Understand University Students' Learning

    ERIC Educational Resources Information Center

    Yoo, Jin Soung; Cho, Moon-Heum

    2012-01-01

    Concept maps, visual representations of knowledge, are used in an educational context as a way to represent students' knowledge, and identify mental models of students; however there is a limitation of using concept mapping due to its difficulty to evaluate the concept maps. A concept map has a complex structure which is composed of concepts and…

  10. Map projections

    USGS Publications Warehouse

    ,

    1993-01-01

    A map projection is used to portray all or part of the round Earth on a flat surface. This cannot be done without some distortion. Every projection has its own set of advantages and disadvantages. There is no "best" projection. The mapmaker must select the one best suited to the needs, reducing distortion of the most important features. Mapmakers and mathematicians have devised almost limitless ways to project the image of the globe onto paper. Scientists at the U. S. Geological Survey have designed projections for their specific needs—such as the Space Oblique Mercator, which allows mapping from satellites with little or no distortion. This document gives the key properties, characteristics, and preferred uses of many historically important projections and of those frequently used by mapmakers today.

  11. A physical map of the human genome

    SciTech Connect

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

    2001-01-01

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

  12. Advanced Electrophysiologic Mapping Systems

    PubMed Central

    2006-01-01

    Executive Summary Objective To assess the effectiveness, cost-effectiveness, and demand in Ontario for catheter ablation of complex arrhythmias guided by advanced nonfluoroscopy mapping systems. Particular attention was paid to ablation for atrial fibrillation (AF). Clinical Need Tachycardia Tachycardia refers to a diverse group of arrhythmias characterized by heart rates that are greater than 100 beats per minute. It results from abnormal firing of electrical impulses from heart tissues or abnormal electrical pathways in the heart because of scars. Tachycardia may be asymptomatic, or it may adversely affect quality of life owing to symptoms such as palpitations, headaches, shortness of breath, weakness, dizziness, and syncope. Atrial fibrillation, the most common sustained arrhythmia, affects about 99,000 people in Ontario. It is associated with higher morbidity and mortality because of increased risk of stroke, embolism, and congestive heart failure. In atrial fibrillation, most of the abnormal arrhythmogenic foci are located inside the pulmonary veins, although the atrium may also be responsible for triggering or perpetuating atrial fibrillation. Ventricular tachycardia, often found in patients with ischemic heart disease and a history of myocardial infarction, is often life-threatening; it accounts for about 50% of sudden deaths. Treatment of Tachycardia The first line of treatment for tachycardia is antiarrhythmic drugs; for atrial fibrillation, anticoagulation drugs are also used to prevent stroke. For patients refractory to or unable to tolerate antiarrhythmic drugs, ablation of the arrhythmogenic heart tissues is the only option. Surgical ablation such as the Cox-Maze procedure is more invasive. Catheter ablation, involving the delivery of energy (most commonly radiofrequency) via a percutaneous catheter system guided by X-ray fluoroscopy, has been used in place of surgical ablation for many patients. However, this conventional approach in catheter ablation

  13. Spatial mapping takes time.

    PubMed

    Whishaw, I Q

    1998-01-01

    The experiment tested the prediction that spatial mapping takes time and asked whether time use is reflected in the overt behavior of a performing animal. The study examines this question by exploiting the expected behavioral differences of control rats and rats with hippocampal formation damage induced with fimbria-fornix (FF) lesions on a spatial navigation task. Previous studies have shown that control rats use a mapping strategy, in which they use the relative positions of environmental cues to reach places in space, whereas FF rats use a cue-based strategy, in which they are guided by a single cue or their own body orientation. Therefore, control and FF rats were overtrained on a complex foraging task in which they left a burrow to retrieve eight food pellets hidden around the perimeter of a circular table. The control rats retrieved the food pellets in order of their distance from the burrow, took direct routes to the food, and made few errors, all of which suggested they used a spatial strategy. The FF rats were less likely to retrieve food as a function of its distance, took a circular path around the perimeter of the table, and made many errors, suggesting they used a cue-based strategy. Despite taking shorter routes than the FF rats, the control rats had proportionally slower response speeds. Their slow response speeds support the hypothesis that spatial mapping takes time and that mapping time is reflected in behavior. The results are discussed in relation to their relevance to spatial mapping theory, hippocampal function, and the evolution of foraging strategies.

  14. Cat-Map: putting cataract on the map

    PubMed Central

    Bennett, Thomas M.; Hejtmancik, J. Fielding

    2010-01-01

    Lens opacities, or cataract(s), may be inherited as a classic Mendelian disorder usually with early-onset or, more commonly, acquired with age as a multi-factorial or complex trait. Many genetic forms of cataract have been described in mice and other animal models. Considerable progress has been made in mapping and identifying the genes and mutations responsible for inherited forms of cataract, and genetic determinants of age-related cataract are beginning to be discovered. To provide a convenient and accurate summary of current information focused on the increasing genetic complexity of Mendelian and age-related cataract we have created an online chromosome map and reference database for cataract in humans and mice (Cat-Map). PMID:21042563

  15. A map of the universe

    SciTech Connect

    Gott III, J. Richard; Juric, Mario; Schlegel, David; Hoyle, Fiona; Vogeley, Michael; Tegmark, Max; Bahcall, Neta; Brinkmann, Jon

    2003-10-20

    We have produced a new conformal map of the universe illustrating recent discoveries, ranging from Kuiper belt objects in the Solar system, to the galaxies and quasars from the Sloan Digital Sky Survey. This map projection, based on the logarithm map of the complex plane, preserves shapes locally, and yet is able to display the entire range of astronomical scales from the Earth s neighborhood to the cosmic microwave background. The conformal nature of the projection, preserving shapes locally, may be of particular use for analyzing large scale structure. Prominent in the map is a Sloan Great Wall of galaxies 1.37 billion light years long, 80 percent longer than the Great Wall discovered by Geller and Huchra and therefore the largest observed structure in the universe.

  16. The MAP Propulsion Subsystem

    NASA Technical Reports Server (NTRS)

    Davis, Gary T.; Bauer, Frank H. (Technical Monitor)

    2002-01-01

    This paper describes the requirements, design, integration, test, performance, and lessons learned of NASA's Microwave Anisotropy Probe (MAP) propulsion subsystem. MAP was launched on a Delta-II launch vehicle from NASA's Kennedy Space Center on June 30, 2001. Due to instrument thermal stability requirements, the Earth-Sun L2 Lagrange point was selected for the mission orbit. The L2 trajectory incorporated phasing loops and a lunar gravity assist. The propulsion subsystem's requirements are to manage momentum, perform maneuvers during the phasing loops to set up the lunar swingby, and perform stationkeeping at L2 for 2 years. MAP's propulsion subsystem uses 8 thrusters which are located and oriented to provide attitude control and momentum management about all axes, and delta-V in any direction without exposing the instrument to the sun. The propellant tank holds 72 kg of hydrazine, which is expelled by unregulated blowdown pressurization. Thermal management is complex because no heater cycling is allowed at L2. Several technical challenges presented themselves during I and T, such as in-situ weld repairs and in-situ bending of thruster tubes to accommodate late changes in the observatory CG. On-orbit performance has been nominal, and all phasing loop, mid-course correction, and stationkeeping maneuvers have been successfully performed to date.

  17. Autonomous exploration and mapping of unknown environments

    NASA Astrophysics Data System (ADS)

    Owens, Jason; Osteen, Phil; Fields, MaryAnne

    2012-06-01

    Autonomous exploration and mapping is a vital capability for future robotic systems expected to function in arbitrary complex environments. In this paper, we describe an end-to-end robotic solution for remotely mapping buildings. For a typical mapping system, an unmanned system is directed to enter an unknown building at a distance, sense the internal structure, and, barring additional tasks, while in situ, create a 2-D map of the building. This map provides a useful and intuitive representation of the environment for the remote operator. We have integrated a robust mapping and exploration system utilizing laser range scanners and RGB-D cameras, and we demonstrate an exploration and metacognition algorithm on a robotic platform. The algorithm allows the robot to safely navigate the building, explore the interior, report significant features to the operator, and generate a consistent map - all while maintaining localization.

  18. Mapping the Natchez Trace Parkway

    USGS Publications Warehouse

    Rangoonwala, Amina; Bannister, Terri; Ramsey, Elijah W.

    2011-01-01

    Based on a National Park Service (NPS) landcover classification, a landcover map of the 715-km (444-mile) NPS Natchez Trace Parkway (hereafter referred to as the "Parkway") was created. The NPS landcover classification followed National Vegetation Classification (NVC) protocols. The landcover map, which extended the initial landcover classification to the entire Parkway, was based on color-infrared photography converted to 1-m raster-based digital orthophoto quarter quadrangles, according to U.S. Geological Survey mapping standards. Our goal was to include as many alliance classes as possible in the Parkway landcover map. To reach this goal while maintaining a consistent and quantifiable map product throughout the Parkway extent, a mapping strategy was implemented based on the migration of class-based spectral textural signatures and the congruent progressive refinement of those class signatures along the Parkway. Progressive refinement provided consistent mapping by evaluating the spectral textural distinctiveness of the alliance-association classes, and where necessary, introducing new map classes along the Parkway. By following this mapping strategy, the use of raster-based image processing and geographic information system analyses for the map production provided a quantitative and reproducible product. Although field-site classification data were severely limited, the combination of spectral migration of class membership along the Parkway and the progressive classification strategy produced an organization of alliances that was internally highly consistent. The organization resulted from the natural patterns or alignments of spectral variance and the determination of those spectral patterns that were compositionally similar in the dominant species as NVC alliances. Overall, the mapped landcovers represented the existent spectral textural patterns that defined and encompassed the complex variety of compositional alliances and associations of the Parkway. Based

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

    PubMed Central

    Ariyadasa, Ruvini; Stein, Nils

    2012-01-01

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

  20. Geologic mapping of Europa

    USGS Publications Warehouse

    Greeley, R.; Figueredo, P.H.; Williams, D.A.; Chuang, F.C.; Klemaszewski, J.E.; Kadel, S.D.; Prockter, L.M.; Pappalardo, R.T.; Head, J. W.; Collins, G.C.; Spaun, N.A.; Sullivan, R.J.; Moore, Johnnie N.; Senske, D.A.; Tufts, B.R.; Johnson, T.V.; Belton, M.J.S.; Tanaka, K.L.

    2000-01-01

    Galileo data enable the major geological units, structures, and surface features to be identified on Europa. These include five primary units (plains, chaos, band, ridge, and crater materials) and their subunits, along with various tectonic structures such as faults. Plains units are the most widespread. Ridged plains material spans a wide range of geological ages, including the oldest recognizable features on Europa, and appears to represent a style of tectonic resurfacing, rather than cryovolcanism. Smooth plains material typically embays other terrains and units, possibly as a type of fluid emplacement, and is among the youngest material units observed. At global scales, plains are typically mapped as undifferentiated plains material, although in some areas differences can be discerned in the near infrared which might be related to differences in ice grain size. Chaos material is composed of plains and other preexisting materials that have been severely disrupted by inferred internal activity; chaos is characterized by blocks of icy material set in a hummocky matrix. Band material is arrayed in linear, curvilinear, wedge-shaped, or cuspate zones with contrasting albedo and surface textures with respect to the surrounding terrain. Bilateral symmetry observed in some bands and the relationships with the surrounding units suggest that band material forms by the lithosphere fracturing, spreading apart, and infilling with material derived from the subsurface. Ridge material is mapped as a unit on local and some regional maps but shown with symbols at global scales. Ridge material includes single ridges, doublet ridges, and ridge complexes. Ridge materials are considered to represent tectonic processes, possibly accompanied by the extrusion or intrusion of subsurface materials, such as diapirs. The tectonic processes might be related to tidal flexing of the icy lithosphere on diurnal or longer timescales. Crater materials include various interior (smooth central

  1. The National Map: from geography to mapping and back again

    USGS Publications Warehouse

    Kelmelis, John A.; DeMulder, Mark L.; Ogrosky, Charles E.; Van Driel, J. Nicholas; Ryan, Barbara J.

    2003-01-01

    When the means of production for national base mapping were capital intensive, required large production facilities, and had ill-defined markets, Federal Government mapping agencies were the primary providers of the spatial data needed for economic development, environmental management, and national defense. With desktop geographic information systems now ubiquitous, source data available as a commodity from private industry, and the realization that many complex problems faced by society need far more and different kinds of spatial data for their solutions, national mapping organizations must realign their business strategies to meet growing demand and anticipate the needs of a rapidly changing geographic information environment. The National Map of the United States builds on a sound historic foundation of describing and monitoring the land surface and adds a focused effort to produce improved understanding, modeling, and prediction of land-surface change. These added dimensions bring to bear a broader spectrum of geographic science to address extant and emerging issues. Within the overarching construct of The National Map, the U.S. Geological Survey (USGS) is making a transition from data collector to guarantor of national data completeness; from producing paper maps to supporting an online, seamless, integrated database; and from simply describing the Nation’s landscape to linking these descriptions with increased scientific understanding. Implementing the full spectrum of geographic science addresses a myriad of public policy issues, including land and natural resource management, recreation, urban growth, human health, and emergency planning, response, and recovery. Neither these issues nor the science and technologies needed to deal with them are static. A robust research agenda is needed to understand these changes and realize The National Map vision. Initial successes have been achieved. These accomplishments demonstrate the utility of

  2. Human Mind Maps

    ERIC Educational Resources Information Center

    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…

  3. Geologic Mapping of Athabasca Valles

    NASA Technical Reports Server (NTRS)

    Keszthelyi, L. P.; Jaeger, W. L.; Tanaka, K.; Hare, T.

    2008-01-01

    Two factors drive us to map the Athabasca Valles area in unusual detail: (1) the extremely well-preserved and exposed surface morphologies and (2) the extensive high resolution imaging. In particular, the near-complete CTX coverage of Athabasca Valles proper and the extensive coverage of its surroundings have been invaluable. The mapping has been done exclusively in ArcGIS, using individual CTX, THEMIS VIS, and MOC frames overlying the THEMIS IR daytime basemap. MOLA shot points and gridded DTMs are also included. It was found that CTX images processed through ISIS are almost always within 300 m of the MOLA derived locations, and usually within tens of meters, with no adjustments to camera pointing. THEMIS VIS images appear to be systematically shifted to the southwest of their correct positions and MOC images are often kilometers off. The good SNR and minimal artifacts make the CTX images vastly more useful than the THEMIS VIS or MOC images. The bulk of the mapping was done at 1:50,000 scale on CTX images. In more complex areas, mapping at 1:24,000 proved necessary. The CTX images were usually simultaneously viewed on a second monitor using the ISIS3 qview program to display the full dynamic range of the CTX data. Where CTX data was not available, mapping was often done at 1:100,000 and most contacts are mapped as approximate.

  4. Beebook: light field mapping app

    NASA Astrophysics Data System (ADS)

    De Donatis, Mauro; Di Pietro, Gianfranco; Rinnone, Fabio

    2014-05-01

    In the last decade the mobile systems for field digital mapping were developed (see Wikipedia for "Digital geologic mapping"), also against many skeptic traditional geologists. Until now, hardware was often heavy (tablet PC) and software sometime difficult also for expert GIS users. At present, the advent of light tablet and applications makes things easier, but we are far to find a whole solution for a complex survey like the geological one where you have to manage complexities such information, hypothesis, data, interpretation. Beebook is a new app for Android devices, has been developed for fast ad easy mapping work in the field trying to try to solve this problem. The main features are: • off-line raster management, GeoTIFF ed other raster format using; • on-line map visualisation (Google Maps, OSM, WMS, WFS); • SR management and conversion using PROJ.4; • vector file mash-up (KML and SQLite format); • editing of vector data on the map (lines, points, polygons); • augmented reality using "Mixare" platform; • export of vector data in KML, CSV, SQLite (Spatialite) format; • note: GPS or manual point inserting linked to other application files (pictures, spreadsheet, etc.); • form: creation, edition and filling of customized form; • GPS: status control, tracker and positioning on map; • sharing: synchronization and sharing of data, forms, positioning and other information can be done among users. The input methods are different from digital keyboard to fingers touch, from voice recording to stylus. In particular the most efficient way of inserting information is the stylus (or pen): field geologists are familiar with annotation and sketches. Therefore we suggest the use of devices with stylus. The main point is that Beebook is the first "transparent" mobile GIS for tablet and smartphone deriving from previous experience as traditional mapping and different previous digital mapping software ideation and development (MapIT, BeeGIS, Geopaparazzi

  5. Concept Mapping

    PubMed Central

    Brennan, Laura K.; Brownson, Ross C.; Kelly, Cheryl; Ivey, Melissa K.; Leviton, Laura C.

    2016-01-01

    Background From 2003 to 2008, 25 cross-sector, multidisciplinary community partnerships funded through the Active Living by Design (ALbD) national program designed, planned, and implemented policy and environmental changes, with complementary programs and promotions. This paper describes the use of concept-mapping methods to gain insights into promising active living intervention strategies based on the collective experience of community representatives implementing ALbD initiatives. Methods Using Concept Systems software, community representatives (n=43) anonymously generated actions and changes in their communities to support active living (183 original statements, 79 condensed statements). Next, respondents (n=26, from 23 partnerships) sorted the 79 statements into self-created categories, or active living intervention approaches. Respondents then rated statements based on their perceptions of the most important strategies for creating community changes (n=25, from 22 partnerships) and increasing community rates of physical activity (n=23, from 20 partnerships). Cluster analysis and multidimensional scaling were used to describe data patterns. Results ALbD community partnerships identified three active living intervention approaches with the greatest perceived importance to create community change and increase population levels of physical activity: changes to the built and natural environment, partnership and collaboration efforts, and land-use and transportation policies. The relative importance of intervention approaches varied according to subgroups of partnerships working with different populations. Conclusions Decision makers, practitioners, and community residents can incorporate what has been learned from the 25 community partnerships to prioritize active living policy, physical project, promotional, and programmatic strategies for work in different populations and settings. PMID:23079266

  6. Maps & minds : mapping through the ages

    USGS Publications Warehouse

    ,

    1984-01-01

    Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

  7. Mapping: A Course.

    ERIC Educational Resources Information Center

    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)

  8. Mapping with the Masses: Google Map Maker

    NASA Astrophysics Data System (ADS)

    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!

  9. Resultant as the determinant of a Koszul complex

    NASA Astrophysics Data System (ADS)

    Anokhina, A. S.; Morozov, A. Yu.; Shakirov, Sh. R.

    2009-09-01

    The determinant is a very important characteristic of a linear map between vector spaces. Two generalizations of linear maps are intensively used in modern theory: linear complexes (nilpotent chains of linear maps) and nonlinear maps. The determinant of a complex and the resultant are then the corresponding generalizations of the determinant of a linear map. It turns out that these two quantities are related: the resultant of a nonlinear map is the determinant of the corresponding Koszul complex. We give an elementary introduction into these notions and relations, which will definitely play a role in the future development of theoretical physics.

  10. Human Prostate Cancer Hallmarks Map.

    PubMed

    Datta, Dipamoy; Aftabuddin, Md; Gupta, Dinesh Kumar; Raha, Sanghamitra; Sen, Prosenjit

    2016-08-01

    Human prostate cancer is a complex heterogeneous disease that mainly affects elder male population of the western world with a high rate of mortality. Acquisitions of diverse sets of hallmark capabilities along with an aberrant functioning of androgen receptor signaling are the central driving forces behind prostatic tumorigenesis and its transition into metastatic castration resistant disease. These hallmark capabilities arise due to an intense orchestration of several crucial factors, including deregulation of vital cell physiological processes, inactivation of tumor suppressive activity and disruption of prostate gland specific cellular homeostasis. The molecular complexity and redundancy of oncoproteins signaling in prostate cancer demands for concurrent inhibition of multiple hallmark associated pathways. By an extensive manual curation of the published biomedical literature, we have developed Human Prostate Cancer Hallmarks Map (HPCHM), an onco-functional atlas of human prostate cancer associated signaling and events. It explores molecular architecture of prostate cancer signaling at various levels, namely key protein components, molecular connectivity map, oncogenic signaling pathway map, pathway based functional connectivity map etc. Here, we briefly represent the systems level understanding of the molecular mechanisms associated with prostate tumorigenesis by considering each and individual molecular and cell biological events of this disease process.

  11. Human Prostate Cancer Hallmarks Map

    PubMed Central

    Datta, Dipamoy; Aftabuddin, Md.; Gupta, Dinesh Kumar; Raha, Sanghamitra; Sen, Prosenjit

    2016-01-01

    Human prostate cancer is a complex heterogeneous disease that mainly affects elder male population of the western world with a high rate of mortality. Acquisitions of diverse sets of hallmark capabilities along with an aberrant functioning of androgen receptor signaling are the central driving forces behind prostatic tumorigenesis and its transition into metastatic castration resistant disease. These hallmark capabilities arise due to an intense orchestration of several crucial factors, including deregulation of vital cell physiological processes, inactivation of tumor suppressive activity and disruption of prostate gland specific cellular homeostasis. The molecular complexity and redundancy of oncoproteins signaling in prostate cancer demands for concurrent inhibition of multiple hallmark associated pathways. By an extensive manual curation of the published biomedical literature, we have developed Human Prostate Cancer Hallmarks Map (HPCHM), an onco-functional atlas of human prostate cancer associated signaling and events. It explores molecular architecture of prostate cancer signaling at various levels, namely key protein components, molecular connectivity map, oncogenic signaling pathway map, pathway based functional connectivity map etc. Here, we briefly represent the systems level understanding of the molecular mechanisms associated with prostate tumorigenesis by considering each and individual molecular and cell biological events of this disease process. PMID:27476486

  12. Efficient and selective formation of macrocyclic disubstituted Z alkenes by ring-closing metathesis (RCM) reactions catalyzed by Mo- or W-based monoaryloxide pyrrolide (MAP) complexes: applications to total syntheses of epilachnene, yuzu lactone, ambrettolide, epothilone C, and nakadomarin A.

    PubMed

    Wang, Chenbo; Yu, Miao; Kyle, Andrew F; Jakubec, Pavol; Dixon, Darren J; Schrock, Richard R; Hoveyda, Amir H

    2013-02-18

    The first broadly applicable set of protocols for efficient Z-selective formation of macrocyclic disubstituted alkenes through catalytic ring-closing metathesis (RCM) is described. Cyclizations are performed with 1.2-7.5 mol% of a Mo- or W-based monoaryloxide pyrrolide (MAP) complex at 22 °C and proceed to complete conversion typically within two hours. Utility is demonstrated by synthesis of representative macrocyclic alkenes, such as natural products yuzu lactone (13-membered ring: 73% Z) epilachnene (15-membered ring: 91% Z), ambrettolide (17-membered ring: 91% Z), an advanced precursor to epothilones C and A (16-membered ring: up to 97% Z), and nakadomarin A (15-membered ring: up to 97% Z). We show that catalytic Z-selective cyclizations can be performed efficiently on gram-scale with complex molecule starting materials and catalysts that can be handled in air. We elucidate several critical principles of the catalytic protocol: 1) The complementary nature of the Mo catalysts, which deliver high activity but can be more prone towards engendering post-RCM stereoisomerization, versus W variants, which furnish lower activity but are less inclined to cause loss of kinetic Z selectivity. 2) Reaction time is critical to retaining kinetic Z selectivity not only with MAP species but with the widely used Mo bis(hexafluoro-tert-butoxide) complex as well. 3) Polycyclic structures can be accessed without significant isomerization at the existing Z alkenes within the molecule.

  13. Hemispherical map for the human brain cortex

    NASA Astrophysics Data System (ADS)

    Tosun, Duygu; Prince, Jerry L.

    2001-07-01

    Understanding the function of the human brain cortex is a primary goal in human brain mapping. Methods to unfold and flatten the cortical surface for visualization and measurement have been described in previous literature; but comparison across multiple subjects is still difficult because of the lack of a standard mapping technique. We describe a new approach that maps each hemisphere of the cortex to a portion of a sphere in a standard way, making comparison of anatomy and function across different subjects possible. Starting with a three-dimensional magnetic resonance image of the brain, the cortex is segmented and represented as a triangle mesh. Defining a cut around the corpus collosum identifies the left and right hemispheres. Together, the two hemispheres are mapped to the complex plane using a conformal mapping technique. A Mobius transformation, which is conformal, is used to transform the points on the complex plane so that a projective transformation maps each brain hemisphere onto a spherical segment comprising a sphere with a cap removed. We determined the best size of the spherical cap by minimizing the relative area distortion between hemispherical maps and original cortical surfaces. The relative area distortion between the hemispherical maps and the original cortical surfaces for fifteen human brains is analyzed.

  14. Mapping the Heart

    ERIC Educational Resources Information Center

    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…

  15. Data Assimilation with Optimal Maps

    NASA Astrophysics Data System (ADS)

    El Moselhy, T.; Marzouk, Y.

    2012-12-01

    Tarek El Moselhy and Youssef Marzouk Massachusetts Institute of Technology We present a new approach to Bayesian inference that entirely avoids Markov chain simulation and sequential importance resampling, by constructing a map that pushes forward the prior measure to the posterior measure. Existence and uniqueness of a suitable measure-preserving map is established by formulating the problem in the context of optimal transport theory. The map is written as a multivariate polynomial expansion and computed efficiently through the solution of a stochastic optimization problem. While our previous work [1] focused on static Bayesian inference problems, we now extend the map-based approach to sequential data assimilation, i.e., nonlinear filtering and smoothing. One scheme involves pushing forward a fixed reference measure to each filtered state distribution, while an alternative scheme computes maps that push forward the filtering distribution from one stage to the other. We compare the performance of these schemes and extend the former to problems of smoothing, using a map implementation of the forward-backward smoothing formula. Advantages of a map-based representation of the filtering and smoothing distributions include analytical expressions for posterior moments and the ability to generate arbitrary numbers of independent uniformly-weighted posterior samples without additional evaluations of the dynamical model. Perhaps the main advantage, however, is that the map approach inherently avoids issues of sample impoverishment, since it explicitly represents the posterior as the pushforward of a reference measure, rather than with a particular set of samples. The computational complexity of our algorithm is comparable to state-of-the-art particle filters. Moreover, the accuracy of the approach is controlled via the convergence criterion of the underlying optimization problem. We demonstrate the efficiency and accuracy of the map approach via data assimilation in

  16. National Atlas maps

    USGS Publications Warehouse

    ,

    1991-01-01

    The National Atlas of the United States of America was published by the U.S. Geological Survey in 1970. Its 765 maps and charts are on 335 14- by 19-inch pages. Many of the maps span facing pages. It's worth a quick trip to the library just to leaf through all 335 pages of this book. Rapid scanning of its thematic maps yields rich insights to the geography of issues of continuing national interest. On most maps, the geographic patterns are still valid, though the data are not current. The atlas is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. The maps dated after 1970 are either revisions of original atlas maps, or new maps published in atlas format. The titles of the separate maps are listed here.

  17. Mapping the distribution of the main host for plague in a complex landscape in Kazakhstan: An object-based approach using SPOT-5 XS, Landsat 7 ETM+, SRTM and multiple Random Forests.

    PubMed

    Wilschut, L I; Addink, E A; Heesterbeek, J A P; Dubyanskiy, V M; Davis, S A; Laudisoit, A; M Begon; Burdelov, L A; Atshabar, B B; de Jong, S M

    2013-08-01

    Plague is a zoonotic infectious disease present in great gerbil populations in Kazakhstan. Infectious disease dynamics are influenced by the spatial distribution of the carriers (hosts) of the disease. The great gerbil, the main host in our study area, lives in burrows, which can be recognized on high resolution satellite imagery. In this study, using earth observation data at various spatial scales, we map the spatial distribution of burrows in a semi-desert landscape. The study area consists of various landscape types. To evaluate whether identification of burrows by classification is possible in these landscape types, the study area was subdivided into eight landscape units, on the basis of Landsat 7 ETM+ derived Tasselled Cap Greenness and Brightness, and SRTM derived standard deviation in elevation. In the field, 904 burrows were mapped. Using two segmented 2.5 m resolution SPOT-5 XS satellite scenes, reference object sets were created. Random Forests were built for both SPOT scenes and used to classify the images. Additionally, a stratified classification was carried out, by building separate Random Forests per landscape unit. Burrows were successfully classified in all landscape units. In the 'steppe on floodplain' areas, classification worked best: producer's and user's accuracy in those areas reached 88% and 100%, respectively. In the 'floodplain' areas with a more heterogeneous vegetation cover, classification worked least well; there, accuracies were 86 and 58% respectively. Stratified classification improved the results in all landscape units where comparison was possible (four), increasing kappa coefficients by 13, 10, 9 and 1%, respectively. In this study, an innovative stratification method using high- and medium resolution imagery was applied in order to map host distribution on a large spatial scale. The burrow maps we developed will help to detect changes in the distribution of great gerbil populations and, moreover, serve as a unique empirical

  18. Mapping the distribution of the main host for plague in a complex landscape in Kazakhstan: An object-based approach using SPOT-5 XS, Landsat 7 ETM+, SRTM and multiple Random Forests.

    PubMed

    Wilschut, L I; Addink, E A; Heesterbeek, J A P; Dubyanskiy, V M; Davis, S A; Laudisoit, A; M Begon; Burdelov, L A; Atshabar, B B; de Jong, S M

    2013-08-01

    Plague is a zoonotic infectious disease present in great gerbil populations in Kazakhstan. Infectious disease dynamics are influenced by the spatial distribution of the carriers (hosts) of the disease. The great gerbil, the main host in our study area, lives in burrows, which can be recognized on high resolution satellite imagery. In this study, using earth observation data at various spatial scales, we map the spatial distribution of burrows in a semi-desert landscape. The study area consists of various landscape types. To evaluate whether identification of burrows by classification is possible in these landscape types, the study area was subdivided into eight landscape units, on the basis of Landsat 7 ETM+ derived Tasselled Cap Greenness and Brightness, and SRTM derived standard deviation in elevation. In the field, 904 burrows were mapped. Using two segmented 2.5 m resolution SPOT-5 XS satellite scenes, reference object sets were created. Random Forests were built for both SPOT scenes and used to classify the images. Additionally, a stratified classification was carried out, by building separate Random Forests per landscape unit. Burrows were successfully classified in all landscape units. In the 'steppe on floodplain' areas, classification worked best: producer's and user's accuracy in those areas reached 88% and 100%, respectively. In the 'floodplain' areas with a more heterogeneous vegetation cover, classification worked least well; there, accuracies were 86 and 58% respectively. Stratified classification improved the results in all landscape units where comparison was possible (four), increasing kappa coefficients by 13, 10, 9 and 1%, respectively. In this study, an innovative stratification method using high- and medium resolution imagery was applied in order to map host distribution on a large spatial scale. The burrow maps we developed will help to detect changes in the distribution of great gerbil populations and, moreover, serve as a unique empirical

  19. Mapping the distribution of the main host for plague in a complex landscape in Kazakhstan: An object-based approach using SPOT-5 XS, Landsat 7 ETM+, SRTM and multiple Random Forests

    NASA Astrophysics Data System (ADS)

    Wilschut, L. I.; Addink, E. A.; Heesterbeek, J. A. P.; Dubyanskiy, V. M.; Davis, S. A.; Laudisoit, A.; Begon, M.; Burdelov, L. A.; Atshabar, B. B.; de Jong, S. M.

    2013-08-01

    Plague is a zoonotic infectious disease present in great gerbil populations in Kazakhstan. Infectious disease dynamics are influenced by the spatial distribution of the carriers (hosts) of the disease. The great gerbil, the main host in our study area, lives in burrows, which can be recognized on high resolution satellite imagery. In this study, using earth observation data at various spatial scales, we map the spatial distribution of burrows in a semi-desert landscape. The study area consists of various landscape types. To evaluate whether identification of burrows by classification is possible in these landscape types, the study area was subdivided into eight landscape units, on the basis of Landsat 7 ETM+ derived Tasselled Cap Greenness and Brightness, and SRTM derived standard deviation in elevation. In the field, 904 burrows were mapped. Using two segmented 2.5 m resolution SPOT-5 XS satellite scenes, reference object sets were created. Random Forests were built for both SPOT scenes and used to classify the images. Additionally, a stratified classification was carried out, by building separate Random Forests per landscape unit. Burrows were successfully classified in all landscape units. In the ‘steppe on floodplain’ areas, classification worked best: producer's and user's accuracy in those areas reached 88% and 100%, respectively. In the ‘floodplain’ areas with a more heterogeneous vegetation cover, classification worked least well; there, accuracies were 86 and 58% respectively. Stratified classification improved the results in all landscape units where comparison was possible (four), increasing kappa coefficients by 13, 10, 9 and 1%, respectively. In this study, an innovative stratification method using high- and medium resolution imagery was applied in order to map host distribution on a large spatial scale. The burrow maps we developed will help to detect changes in the distribution of great gerbil populations and, moreover, serve as a unique

  20. GIS Surface Effects Map Archive, Nevada Test Site, Nevada

    SciTech Connect

    Grasso, Dennis N.

    2003-08-28

    The GIS Surface Effects Map Archive contains a comprehensive collection of maps showing the surface effects produced by underground nuclear testing at the Nevada Test Site. From 1951 to 1992, scientists with the U.S. Geological Survey and agencies of the U.S. Department of Energy used field and aerial-photo mapping techniques to painstakingly map such surface effects as collapse sinks, craters, cracks, fractures, faults, and pressure ridges. Shortly after each test, a complex surface effects map was produced. Of the more than 920 underground detonations conducted at the Nevada Test Site, 688 were mapped for surface effects. This archive preserves these original maps in digital format. A Geographic Information System (GIS) was used to digitally reproduce each original, hand-drawn surface effects map and to assemble these maps into the digital data sets of this archive. The archive was designed to allow easy access to the maps, while preserving the original maps for perpetuity. Users can query the detonation sites database; prepare, view, and print individual or composite maps; and perform various types of scientific analysis and management tasks. Spatial analyses and queries can be performed on detonation sites and related surface effects in conjunction with other chronological, geographical, geological, or hydrological information via links to external maps and databases. This browser interface provides information about the archive, the history of surface effects mapping at the Nevada Test Site, the methods used to produce the digital surface effects maps, and links to published reports, data tables, and maps. Location maps show testing areas, operational areas, and detonation sites. Demonstration maps illustrate the methods used to produce the digital surface effects maps and exhibit some of the characteristics and uses for these data. Use the links below to view and print individual surface effects maps, retrieve information about the detonations and types of

  1. Google Maps: You Are Here

    ERIC Educational Resources Information Center

    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…

  2. Online Exhibits & Concept Maps

    NASA Astrophysics Data System (ADS)

    Douma, M.

    2009-12-01

    Presenting the complexity of geosciences to the public via the Internet poses a number of challenges. For example, utilizing various - and sometimes redundant - Web 2.0 tools can quickly devour limited time. Do you tweet? Do you write press releases? Do you create an exhibit or concept map? The presentation will provide participants with a context for utilizing Web 2.0 tools by briefly highlighting methods of online scientific communication across several dimensions. It will address issues of: * breadth and depth (e.g. from narrow topics to well-rounded views), * presentation methods (e.g. from text to multimedia, from momentary to enduring), * sources and audiences (e.g. for experts or for the public, content developed by producers to that developed by users), * content display (e.g. from linear to non-linear, from instructive to entertaining), * barriers to entry (e.g. from an incumbent advantage to neophyte accessible, from amateur to professional), * cost and reach (e.g. from cheap to expensive), and * impact (e.g. the amount learned, from anonymity to brand awareness). Against this backdrop, the presentation will provide an overview of two methods of online information dissemination, exhibits and concept maps, using the WebExhibits online museum (www.webexhibits.org) and SpicyNodes information visualization tool (www.spicynodes.org) as examples, with tips on how geoscientists can use either to communicate their science. Richly interactive online exhibits can serve to engage a large audience, appeal to visitors with multiple learning styles, prompt exploration and discovery, and present a topic’s breadth and depth. WebExhibits, which was among the first online museums, delivers interactive information, virtual experiments, and hands-on activities to the public. While large, multidisciplinary exhibits on topics like “Color Vision and Art” or “Calendars Through the Ages” require teams of scholars, user interface experts, professional writers and editors

  3. The APPL "Learning Map"

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Root Learning, a learning consulting organization with a background in strategic planning, recognizes the knowledge gap that frequently exists between a leadership team and the rest of an organization. Team members supposedly working toward the same goal don't always have the same vision as to where the organization is headed, and they may not understand how the piece they are accountable for fits into the big picture. To address these complex problems, Root Learning utilizes the age-old tools of sarcasm, metaphor and graphics (much in the same way that ASK uses a traditional storytelling format.) The company is best known for creating "Learning Maps" like this one: humorous drawings based on the inner workings of an organization. Their purpose is to put complex topics on the table, to stimulate discussion, and to ultimately give team members a common vision of where the organization is going and what role they personally play in getting there. APPL knows how effective it is to incorporate new and engaging techniques into its knowledge sharing programs. By collaborating with Root Learning, we were able to expand the knowledge of the organization and add one more of these techniques to our repertoire.

  4. Map reading tools for map libraries.

    USGS Publications Warehouse

    Greenberg, G.L.

    1982-01-01

    Engineers, navigators and military strategists employ a broad array of mechanical devices to facilitate map use. A larger number of map users such as educators, students, tourists, journalists, historians, politicians, economists and librarians are unaware of the available variety of tools which can be used with maps to increase the speed and efficiency of their application and interpretation. This paper identifies map reading tools such as coordinate readers, protractors, dividers, planimeters, and symbol-templets according to a functional classification. Particularly, arrays of tools are suggested for use in determining position, direction, distance, area and form (perimeter-shape-pattern-relief). -from Author

  5. A mathematical structure for analyzing maps

    NASA Astrophysics Data System (ADS)

    Berry, Joseph K.

    1987-07-01

    The growing use of computers in environmental management is profoundly changing data collection procedures, analytic processes, and even the decision-making environment itself. The emerging technology of geographic information systems (GIS) is expanding this revolution to integrate spatial information fully into research, planning, and management of land. In one sense, this technology is similar to conventional map processing involving traditional maps and drafting aids, such as pens, rub-on shading, rulers, planimeters, dot grids, and acetate sheets for light-table overlays. In another sense, these systems provide advanced analytic capabilities, enabling managers to address complex issues in entirely new ways. This report discusses a fundamental approach to computer-assisted map analysis that treats entire maps as variables. The set of analytic procedures for processing mapped data forms a mathematical structure analogous to traditional statistics and algebra. All of the procedures discussed are available for personal computer environments.

  6. Mapping the distribution of the main host for plague in a complex landscape in Kazakhstan: An object-based approach using SPOT-5 XS, Landsat 7 ETM+, SRTM and multiple Random Forests

    PubMed Central

    Wilschut, L.I.; Addink, E.A.; Heesterbeek, J.A.P.; Dubyanskiy, V.M.; Davis, S.A.; Laudisoit, A.; M.Begon; Burdelov, L.A.; Atshabar, B.B.; de Jong, S.M.

    2013-01-01

    Plague is a zoonotic infectious disease present in great gerbil populations in Kazakhstan. Infectious disease dynamics are influenced by the spatial distribution of the carriers (hosts) of the disease. The great gerbil, the main host in our study area, lives in burrows, which can be recognized on high resolution satellite imagery. In this study, using earth observation data at various spatial scales, we map the spatial distribution of burrows in a semi-desert landscape. The study area consists of various landscape types. To evaluate whether identification of burrows by classification is possible in these landscape types, the study area was subdivided into eight landscape units, on the basis of Landsat 7 ETM+ derived Tasselled Cap Greenness and Brightness, and SRTM derived standard deviation in elevation. In the field, 904 burrows were mapped. Using two segmented 2.5 m resolution SPOT-5 XS satellite scenes, reference object sets were created. Random Forests were built for both SPOT scenes and used to classify the images. Additionally, a stratified classification was carried out, by building separate Random Forests per landscape unit. Burrows were successfully classified in all landscape units. In the ‘steppe on floodplain’ areas, classification worked best: producer's and user's accuracy in those areas reached 88% and 100%, respectively. In the ‘floodplain’ areas with a more heterogeneous vegetation cover, classification worked least well; there, accuracies were 86 and 58% respectively. Stratified classification improved the results in all landscape units where comparison was possible (four), increasing kappa coefficients by 13, 10, 9 and 1%, respectively. In this study, an innovative stratification method using high- and medium resolution imagery was applied in order to map host distribution on a large spatial scale. The burrow maps we developed will help to detect changes in the distribution of great gerbil populations and, moreover, serve as a unique

  7. Mapping the Future of Map Librarianship.

    ERIC Educational Resources Information Center

    Lang, Laura

    1992-01-01

    Discussion of electronic versions of maps focuses on TIGER files (i.e., electronic maps distributed by the U.S. Bureau of the Census) and their manipulation using geographic information system (GIS) technology. Topics addressed include applications of GIS software, projects to improve access to TIGER files, and the role of GIS in libraries. (MES)

  8. A global map of dominant malaria vectors

    PubMed Central

    2012-01-01

    Background Global maps, in particular those based on vector distributions, have long been used to help visualise the global extent of malaria. Few, however, have been created with the support of a comprehensive and extensive evidence-based approach. Methods Here we describe the generation of a global map of the dominant vector species (DVS) of malaria that makes use of predicted distribution maps for individual species or species complexes. Results Our global map highlights the spatial variability in the complexity of the vector situation. In Africa, An. gambiae, An. arabiensis and An. funestus are co-dominant across much of the continent, whereas in the Asian-Pacific region there is a highly complex situation with multi-species coexistence and variable species dominance. Conclusions The competence of the mapping methodology to accurately portray DVS distributions is discussed. The comprehensive and contemporary database of species-specific spatial occurrence (currently available on request) will be made directly available via the Malaria Atlas Project (MAP) website from early 2012. PMID:22475528

  9. Mapping Human Epigenomes

    PubMed Central

    Rivera, Chloe M.; Ren, Bing

    2013-01-01

    As the second dimension to the genome, the epigenome contains key information specific to every type of cells. Thousands of human epigenome maps have been produced in recent years thanks to rapid development of high throughput epigenome mapping technologies. In this review, we discuss the current epigenome mapping toolkit and utilities of epigenome maps. We focus particularly on mapping of DNA methylation, chromatin modification state and chromatin structures, and emphasize the use of epigenome maps to delineate human gene regulatory sequences and developmental programs. We also provide a perspective on the progress of the epigenomics field and challenges ahead. PMID:24074860

  10. Density Equalizing Map Projections

    1995-07-01

    A geographic map is mathematically transformed so that the subareas of the map are proportional to a given quantity such as population. In other words, population density is equalized over the entire map. The transformed map can be used as a display tool, or it can be statistically analyzed. For example, cases of disease plotted on the transformed map should be uniformly distributed at random, if disease rates are everywhere equal. Geographic clusters of diseasemore » can be readily identified, and their statistical significance determined, on a density equalized map.« less

  11. Mapping subunit contacts in the regulatory complex of the 26 S proteasome. S2 and S5b form a tetramer with ATPase subunits S4 and S7.

    PubMed

    Gorbea, C; Taillandier, D; Rechsteiner, M

    2000-01-14

    The 19 S regulatory complex (RC) of the 26 S proteasome is composed of at least 18 different subunits, including six ATPases that form specific pairs S4-S7, S6-S8, and S6'-S10b in vitro. One of the largest regulatory complex subunits, S2, was translated in reticulocyte lysate containing [(35)S]methionine and used to probe membranes containing SDS-polyacrylamide gel electrophoresis separated RC subunits. S2 bound to two ATPases, S4 and S7. Association of S2 with regulatory complex subunits was also assayed by co-translation and sedimentation. S2 formed an immunoprecipitable heterotrimer upon co-translation with S4 and S7. The non-ATPase S5b also formed a ternary complex with S4 and S7 and the three proteins assembled into a tetramer with S2. Neither S2 nor S5b formed complexes with S6'-S10b dimers or with S6-S8 oligomers. The use of chimeric ATPases demonstrated that S2 binds the NH(2)-terminal region of S4 and the COOH-terminal two-thirds of S7. Conversely, S5b binds the COOH-terminal two-thirds of S4 and to S7's NH(2)-terminal region. The demonstrated association of S2 with ATPases in the mammalian 19 S regulatory complex is consistent with and extends the recent finding that the yeast RC is composed of two subcomplexes, the lid and the base (Glickman, M. H., Rubin, D. M., Coux, O., Wefes, I., Pfeifer, G., Cejka, Z., Baumeister, W., Fried, V. A., and Finley, D. (1998) Cell 94, 615-623).

  12. Some additional considerations in modelling the dynamic traits and genome-wide association studies. Comments on "Mapping complex traits as a dynamic system" by L. Sun and R. Wu

    NASA Astrophysics Data System (ADS)

    Das, Kiranmoy

    2015-06-01

    The revolution in the genetic research in our time is mainly due to (i) the successful completion of human genome project (2003) and its derivative hapmap project (2005), (ii) advanced statistical methodologies for analyzing ultrahigh dimensional data and (iii) the availability of statistical softwares (R, SAS etc.) to analyze large datasets. When complex traits are to be modeled as dynamic systems, the statistical issues regarding the complexity in the model, predictive power of the model, computational cost etc. are to be addressed adequately for powerful inferences. I will mention two additional considerations (statistical) which make dynamic models more meaningful and the results from GWAS more reliable.

  13. New map data catalog

    NASA Astrophysics Data System (ADS)

    Map byproducts, including aerial photographs, color separations, map data in computer form, and other materials used in or produced during mapmaking, are described in a new catalog published by the U.S. Geological Survey.The 48-page hardcover catalog is the first listing of the unpublished USGS civilian cartographic holdings. It covers such items as mapping photographs, computer-enhanced LANDSAT pictures of Earth, cartographic data in computer form, microfilm and microfiche records, and a variety of features, including color separations, made in compiling and printing maps. The catalog also describes out-of-print maps available from USGS, along with land-use and land-cover maps, and other unusual items, such as slope maps and orthophotoquads. The catalog explains how to order advance copies of maps before they are published.

  14. Riparian Wetlands: Mapping

    EPA Science Inventory

    Riparian wetlands are critical systems that perform functions and provide services disproportionate to their extent in the landscape. Mapping wetlands allows for better planning, management, and modeling, but riparian wetlands present several challenges to effective mapping due t...

  15. Active Fire Mapping Program

    MedlinePlus

    ... Incidents (Home) New Large Incidents Fire Detection Maps MODIS Satellite Imagery VIIRS Satellite Imagery Fire Detection GIS ... Data Web Services Latest Detected Fire Activity Other MODIS Products Frequently Asked Questions About Active Fire Maps ...

  16. Creative Concept Mapping.

    ERIC Educational Resources Information Center

    Brown, David S.

    2002-01-01

    Recommends the use of concept mapping in science teaching and proposes that it be presented as a creative activity. Includes a sample lesson plan of a potato stamp concept mapping activity for astronomy. (DDR)

  17. Using maps in genealogy

    USGS Publications Warehouse

    ,

    1994-01-01

    In genealogy, maps are most often used as clues to where public or other records about an ancestor are likely to be found. Searching for maps seldom begins until a newcomer to genealogy has mastered basic genealogical routines

  18. Linkage map integration

    SciTech Connect

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

    1996-08-15

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

  19. The Seismotectonic Map of Africa

    NASA Astrophysics Data System (ADS)

    Meghraoui, Mustapha

    2015-04-01

    We present the Seismotectonic Map of Africa based on a geological, geophysical and geodetic database including the instrumental seismicity and re-appraisal of large historical events with harmonization and homogenization of earthquake parameters in catalogues. Although the seismotectonic framework and mapping of the African continent is a difficult task, several previous and ongoing projects provide a wealth of data and outstanding results. The database of large and moderate earthquakes in different geological domains includes the coseismic and Quaternary faulting that reveals the complex nature of the active tectonics in Africa. The map also benefits from previous works on local and regional seismotectonic maps that needed to be integrated with the lithospheric and upper mantle structures from tomographic anisotropy and gravity anomaly into a continental framework. The synthesis of earthquake and volcanic studies with the analysis of long-term (late Quaternary) and short-term (last decades and centuries) active deformation observed with geodetic and other approaches presented along with the seismotectonic map serves as a basis for hazard calculations and the reduction of seismic risks. The map may also be very useful in the assessment of seismic hazard and mitigation of earthquake risk for significant infrastructures and their implications in the socio-economic impact in Africa. In addition, the constant population increase and infrastructure growth in the continent that exacerbate the earthquake risk justify the necessity for a continuous updating of the seismotectonic map. The database and related map are prepared in the framework of the IGC Project-601 "Seismotectonics and Seismic Hazards in Africa" of UNESCO-IUGS, funded by the Swedish International Development Agency and UNESCO-Nairobi for a period of 4 years (2011 - 2014), extended to 2016. * Mustapha Meghraoui (Coordinator) EOST - IPG Strasbourg CNRS-UMR 7516 m.meghraoui@unistra.fr corresponding author

  20. What Do Maps Show?

    ERIC Educational Resources Information Center

    Geological Survey (Dept. of Interior), Reston, VA.

    This curriculum packet, appropriate for grades 4-8, features a teaching poster which shows different types of maps (different views of Salt Lake City, Utah), as well as three reproducible maps and reproducible activity sheets which complement the maps. The poster provides teacher background, including step-by-step lesson plans for four geography…

  1. Quantitative DNA fiber mapping

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  2. Oil Exploration Mapping

    NASA Technical Reports Server (NTRS)

    1994-01-01

    After concluding an oil exploration agreement with the Republic of Yemen, Chevron International needed detailed geologic and topographic maps of the area. Chevron's remote sensing team used imagery from Landsat and SPOT, combining images into composite views. The project was successfully concluded and resulted in greatly improved base maps and unique topographic maps.

  3. Applications of Concept Mapping

    ERIC Educational Resources Information Center

    De Simone, Christina

    2007-01-01

    This article reviews three major uses of the concept-mapping strategies for postsecondary learning: the external representation of concept maps as an external scratch pad to represent major ideas and their organization, the mental construction of concept maps when students are seeking a time-efficient tool, and the electronic construction and…

  4. Reading Angles in Maps

    ERIC Educational Resources Information Center

    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…

  5. Mapping with Young Children.

    ERIC Educational Resources Information Center

    Sunal, Cynthia Szymanski; Warash, Bobbi Gibson

    Techniques for encouraging young children to discover the purpose and use of maps are discussed. Motor activity and topological studies form a base from which the teacher and children can build a mapping program of progressive sophistication. Concepts important to mapping include boundaries, regions, exteriors, interiors, holes, order, point of…

  6. Using maps in genealogy

    USGS Publications Warehouse

    ,

    1999-01-01

    Maps are one of many sources you may need to complete a family tree. In genealogical research, maps can provide clues to where our ancestors may have lived and where to look for written records about them. Beginners should master basic genealogical research techniques before starting to use topographic maps.

  7. Mapping of wildlife habitat in Farmington Bay, Utah

    NASA Technical Reports Server (NTRS)

    Jaynes, R. A.; Willie, R. D. (Principal Investigator)

    1982-01-01

    Mapping was accomplished through the interpretation of high-altitude color infrared photography. The feasibility of utilizing LANDSAT digital data to augment the analysis was explored; complex patterns of wildlife habitat and confusion of spectral classes resulted in the decision to make limited use of LANDSAT data in the analysis. The final product is a map which delineates wildlife habitat at a scale of 1:24,000. The map is registered to and printed on a screened U.S.G.S. quadrangle base map. Screened delineations of shoreline contours, mapped from a previous study, are also shown on the map. Intensive field checking of the map was accomplished for the Farmington Bay Waterfowl Management Area in August 1981; other areas on the map received only spot field checking.

  8. Putting chromium on the map for N2 reduction: production of hydrazine and ammonia. A study of cis-M(N2)2 (M = Cr, Mo, W) bis(diphosphine) complexes.

    PubMed

    Egbert, Jonathan D; O'Hagan, Molly; Wiedner, Eric S; Bullock, R Morris; Piro, Nicholas A; Kassel, W Scott; Mock, Michael T

    2016-07-19

    The first complete structurally and spectroscopically characterized series of isostructural Group 6 N2 complexes is reported. Protonolysis experiments on cis-[M(N2)2(P(Et)N(R)P(Et))2] (M = Cr, Mo, W; R = 2,6-difluorobenzyl) reveal that only Cr affords N2H5(+) and NH4(+) from the reduction of the N2 ligands. PMID:27331373

  9. Map projections for larger-scale mapping

    NASA Technical Reports Server (NTRS)

    Snyder, J. P.

    1982-01-01

    For the U.S. Geological Survey maps at 1:1,000,000-scale and larger, the most common projections are conformal, such as the Transverse Mercator and Lambert Conformal Conic. Projections for these scales should treat the Earth as an ellipsoid. In addition, the USGS has conceived and designed some new projections, including the Space Oblique Mercator, the first map projection designed to permit low-distortion mapping of the Earth from satellite imagery, continuously following the groundtrack. The USGS has programmed nearly all pertinent projection equations for inverse and forward calculations. These are used to plot maps or to transform coordinates from one projection to another. The projections in current use are described.

  10. Subunit structure of the dihydrolipoyl transacylase component of branched-chain. cap alpha. -keto acid dehydrogenase complex from bovine liver: mapping of the lipoyl-bearing domain by limited proteolysis

    SciTech Connect

    Not Available

    1986-01-05

    To characterize the lipoyl-bearing domain of the dihydrolipoyl transacylase (E/sub 2/) component, purified branched-chain ..cap alpha..-keto acid dehydrogenase complex from bovine liver was reductively acylated with (U-/sup 14/C)..cap alpha..-ketoisovalerate in the presence of thiamin pyrophosphate and N-ethylmaleimide. Digestion of the modified complex with increasing concentrations of trypsin sequentially cleaved the E/sub 2/ polypeptide chain (M/sub r/ = 52,000) into five radiolabeled lipoyl-containing fragments, L/sub 1/-L/sub 5/. In addition, a lipoate-free inner E/sub 2/ core consisting of fragment A and fragment B was produced. Fragment A contains the active site for transacylation reaction and fragment B is the subunit-binding domain. Fragment L/sub 5/ and fragment B were stable and resistant to further tryptic digestion. Mouse antiserium against E/sub 2/ reacted only with fragments L/sub 1/, L/sub 2/, and L/sub 3/, and did not bind fragments L/sub 4/, L/sub 5/, A, and B as judged by immunoblotting analysis. The anti-E/sub 2/ serum-strongly inhibited the overall reaction catalyzed by the complex, but was without effect on the transacylation activity of E/sub 2/. Measurement of incorporation of (1-/sup 14/C)isobutyryl groups into the E/sub 2/ subunit indicated the presence of 1 lipoyl residue/E/sub 2/ chain.

  11. Cartographic mapping study

    NASA Technical Reports Server (NTRS)

    Wilson, C.; Dye, R.; Reed, L.

    1982-01-01

    The errors associated with planimetric mapping of the United States using satellite remote sensing techniques are analyzed. Assumptions concerning the state of the art achievable for satellite mapping systems and platforms in the 1995 time frame are made. An analysis of these performance parameters is made using an interactive cartographic satellite computer model, after first validating the model using LANDSAT 1 through 3 performance parameters. An investigation of current large scale (1:24,000) US National mapping techniques is made. Using the results of this investigation, and current national mapping accuracy standards, the 1995 satellite mapping system is evaluated for its ability to meet US mapping standards for planimetric and topographic mapping at scales of 1:24,000 and smaller.

  12. On genetic map functions

    SciTech Connect

    Zhao, Hongyu; Speed, T.P.

    1996-04-01

    Various genetic map functions have been proposed to infer the unobservable genetic distance between two loci from the observable recombination fraction between them. Some map functions were found to fit data better than others. When there are more than three markers, multilocus recombination probabilities cannot be uniquely determined by the defining property of map functions, and different methods have been proposed to permit the use of map functions to analyze multilocus data. If for a given map function, there is a probability model for recombination that can give rise to it, then joint recombination probabilities can be deduced from this model. This provides another way to use map functions in multilocus analysis. In this paper we show that stationary renewal processes give rise to most of the map functions in the literature. Furthermore, we show that the interevent distributions of these renewal processes can all be approximated quite well by gamma distributions. 43 refs., 4 figs.

  13. A fast image encryption algorithm based on chaotic map

    NASA Astrophysics Data System (ADS)

    Liu, Wenhao; Sun, Kehui; Zhu, Congxu

    2016-09-01

    Derived from Sine map and iterative chaotic map with infinite collapse (ICMIC), a new two-dimensional Sine ICMIC modulation map (2D-SIMM) is proposed based on a close-loop modulation coupling (CMC) model, and its chaotic performance is analyzed by means of phase diagram, Lyapunov exponent spectrum and complexity. It shows that this map has good ergodicity, hyperchaotic behavior, large maximum Lyapunov exponent and high complexity. Based on this map, a fast image encryption algorithm is proposed. In this algorithm, the confusion and diffusion processes are combined for one stage. Chaotic shift transform (CST) is proposed to efficiently change the image pixel positions, and the row and column substitutions are applied to scramble the pixel values simultaneously. The simulation and analysis results show that this algorithm has high security, low time complexity, and the abilities of resisting statistical analysis, differential, brute-force, known-plaintext and chosen-plaintext attacks.

  14. Complexity Survey.

    ERIC Educational Resources Information Center

    Gordon, Sandra L.; Anderson, Beth C.

    To determine whether consensus existed among teachers about the complexity of common classroom materials, a survey was administered to 66 pre-service and in-service kindergarten and prekindergarten teachers. Participants were asked to rate 14 common classroom materials as simple, complex, or super-complex. Simple materials have one obvious part,…

  15. TRENDS IN ENGINEERING GEOLOGIC AND RELATED MAPPING.

    USGS Publications Warehouse

    Varnes, David J.; Keaton, Jeffrey R.

    1983-01-01

    Progress is reviewed that has been made during the period 1972-1982 in producing medium- and small-scale engineering geologic maps with a variety of content. Improved methods to obtain and present information are evolving. Standards concerning text and map content, soil and rock classification, and map symbols have been proposed. Application of geomorphological techniques in terrain evaluation has increased, as has the use of aerial photography and other remote sensing. Computers are being used to store, analyze, retrieve, and print both text and map information. Development of offshore resources, especially petroleum, has led to marked improvement and growth in marine engineering geology and geotechnology. Coordinated planning for societal needs has required broader scope and increased complexity of both engineering geologic and environmental geologic studies. Refs.

  16. Assessing the Structure of a Concept Map

    ERIC Educational Resources Information Center

    Giouvanakis, Thanasis; Samaras, Haido; Kehris, Evangelos; Mpakavos, Asterios

    2013-01-01

    This paper presents a framework for the evaluation of concept maps. We focus on supporting the student in dealing with ill-structured and complex problems. We argue that these problems require the application of "the modularity approach." In view of this, the paper describes ways of providing student support for the implementation of…

  17. Facile removal of high mannose structures prior to extracting complex type N-glycans from de-N-glycosylated peptides retained by C18 solid phase to allow more efficient glycomic mapping

    PubMed Central

    Lin, Chi-Hung; Kuo, Chu-Wei; Jarvis, Donald L; Khoo, Kay-Hooi

    2014-01-01

    The relative amount of high mannose structures within an N-glycomic pool differs from one source to another but quite often it predominates over the larger size complex type structures carrying biologically important glyco-epitopes. An efficient method to separate these two classes of N-glycans would significantly aid in detecting the lower abundant components by mass spectrometry. Capitalizing on an initial observation that only high mannose type structures were recovered in the flow through fraction when PNGase F digested peptides were passed through a C18 cartridge in 0.1% formic acid, we demonstrated here that native complex type N-glycans can be retained by C18 cartridge and to be efficiently separated from both the smaller high mannose type structures, as well as de-N-glycosylated peptides by stepwise elution with increasing acetonitrile concentration. The weak retention of the largely hydrophilic N-glycans on C18 resin is dependent not only on size but also increased by the presence of α6-fucosylation. This was shown by comparing the resulting N-glycomic profiles of the washed and low acetonitrile eluted fractions derived from both a human cancer cell line and an insect cell line. PMID:24174266

  18. Epitope mapping of monoclonal antibodies to the Escherichia coli F1 ATPase alpha subunit in relation to activity effects and location in the enzyme complex based on cryoelectron microscopy.

    PubMed

    Aggeler, R; Capaldi, R A; Dunn, S; Gogol, E P

    1992-08-01

    The interaction of Escherichia coli F1 ATPase (ECF1) with several different monoclonal antibodies (mAbs) specific for the alpha subunit has been examined. The epitopes for each of the mAbs have been localized by using molecular biological approaches to generate fragments of the alpha subunit. The binding of several of the mAbs has also been examined by cryoelectron microscopy of ECF1 Fab complexes. One of the mAbs, alpha II, bound in the region Asn 109-Val 153 without affecting ATPase activity. Most of the mAbs bound in the C-terminal third of the alpha subunit. MAb alpha 1 bound between residues Gln 443 and Trp 513. This mAb activated ATPase activity and was visualized in cryoelectron microscopy, superimposed on the alpha subunit, indicating that the epitope was on the top or bottom of ECF1 in the hexagonal projection. Other mAbs to the C-terminus, including alpha D which also activated the enzyme, reacted between Gly 371 and Trp 513 but failed to bind to small overlapping fragments within this sequence. The epitopes for these mAbs are probably formed by the folded polypeptide which occurs only in Western analysis when long stretches of the alpha subunit are present, suggesting that the C-terminus of alpha is a self-folding domain. In cryoelectron microscopy, Fab fragments for alpha D were seen extending from the sides of the ECF1 complex in hexagonal projection. PMID:1378717

  19. Mapping Protein–Protein Interactions of the Resistance-Related Bacterial Zeta Toxin–Epsilon Antitoxin Complex (ε2ζ2) with High Affinity Peptide Ligands Using Fluorescence Polarization

    PubMed Central

    Fernández-Bachiller, María Isabel; Brzozowska, Iwona; Odolczyk, Norbert; Zielenkiewicz, Urszula; Zielenkiewicz, Piotr; Rademann, Jörg

    2016-01-01

    Toxin–antitoxin systems constitute a native survival strategy of pathogenic bacteria and thus are potential targets of antibiotic drugs. Here, we target the Zeta–Epsilon toxin–antitoxin system, which is responsible for the stable maintenance of certain multiresistance plasmids in Gram-positive bacteria. Peptide ligands were designed on the basis of the ε2ζ2 complex. Three α helices of Zeta forming the protein–protein interaction (PPI) site were selected and peptides were designed conserving the residues interacting with Epsilon antitoxin while substituting residues binding intramolecularly to other parts of Zeta. Designed peptides were synthesized with an N-terminal fluoresceinyl-carboxy-residue for binding assays and provided active ligands, which were used to define the hot spots of the ε2ζ2 complex. Further shortening and modification of the binding peptides provided ligands with affinities <100 nM, allowing us to determine the most relevant PPIs and implement a robust competition binding assay. PMID:27438853

  20. A male linkage map constructed for QTL mapping in Spanish Churra sheep.

    PubMed

    Gutiérrez-Gil, B; Arranz, J J; El-Zarei, M F; Alvarez, L; Pedrosa, S; San Primitivo, F; Bayón, Y

    2008-06-01

    A male ovine linkage map has been constructed on the basis of 11 half-sib families of a commercial population of Spanish Churra sheep as part of a genome scan for quantitative trait loci mapping. A total of 1421 daughters and their sires were genotyped for 182 microsatellite markers evenly distributed along the ovine autosomes. A total of 259,192 genotypes were obtained, generating an average of 669 informative meioses per marker. An autosomal genome length of 3262 cM was estimated for the Churra population with a mean marker interval of 17.86 cM. Our map represents an approximate 90% coverage of the autosomal ovine genome and constitutes a useful tool for the genetic dissection of complex traits in this breed. General agreement was found between the Churra map and other published maps for sheep, despite certain length discrepancies.

  1. StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

    PubMed

    Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

    2016-04-26

    Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. PMID:27119636

  2. Predicting Behavior from Cognitive Cause Maps of a Work Setting.

    ERIC Educational Resources Information Center

    Komocar, John

    Cognitive cause maps permit a topological investigation of the complexity of organizational events and behaviors. Because cognitive cause maps are believed to be ordered according to a givens-means-ends schema, they contain information about an individual's motivation structure. In a work setting an individual engages in several different acts.…

  3. Heat Capacity Mapping Mission

    NASA Technical Reports Server (NTRS)

    Nilsson, C. S.; Andrews, J. C.; Scully-Power, P.; Ball, S.; Speechley, G.; Latham, A. R. (Principal Investigator)

    1980-01-01

    The Tasman Front was delineated by airborne expendable bathythermograph survey; and an Heat Capacity Mapping Mission (HCMM) IR image on the same day shows the same principal features as determined from ground-truth. It is clear that digital enhancement of HCMM images is necessary to map ocean surface temperatures and when done, the Tasman Front and other oceanographic features can be mapped by this method, even through considerable scattered cloud cover.

  4. Regularity of mappings inverse to Sobolev mappings

    SciTech Connect

    Vodop'yanov, Sergei K

    2012-10-31

    For homeomorphisms {phi}:{Omega}{yields}{Omega}' on Euclidean domains in R{sup n}, n{>=}2, necessary and sufficient conditions ensuring that the inverse mapping belongs to a Sobolev class are investigated. The result obtained is used to describe a new two-index scale of homeomorphisms in some Sobolev class such that their inverses also form a two-index scale of mappings, in another Sobolev class. This scale involves quasiconformal mappings and also homeomorphisms in the Sobolev class W{sup 1}{sub n-1} such that rankD{phi}(x){<=}n-2 almost everywhere on the zero set of the Jacobian det D{phi}(x). Bibliography: 65 titles.

  5. In Silico Identification and Evaluation of Leads for the Simultaneous Inhibition of Protease and Helicase Activities of HCV NS3/4A Protease Using Complex Based Pharmacophore Mapping and Virtual Screening

    PubMed Central

    Wadood, Abdul; Riaz, Muhammad; Uddin, Reaz; ul-Haq, Zaheer

    2014-01-01

    Hepatitis C virus (HCV) infection is an alarming and growing threat to public health. The present treatment gives limited efficacy and is poorly tolerated, recommending the urgent medical demand for novel therapeutics. NS3/4A protease is a significant emerging target for the treatment of HCV infection. This work reports the complex-based pharmacophore modeling to find out the important pharmacophoric features essential for the inhibition of both protease and helicase activity of NS3/4A protein of HCV. A seven featured pharmacophore model of HCV NS3/4A protease was developed from the crystal structure of NS3/4A protease in complex with a macrocyclic inhibitor interacting with both protease and helicase sites residues via MOE pharmacophore constructing tool. It consists of four hydrogen bond acceptors (Acc), one hydrophobic (Hyd), one for lone pair or active hydrogen (Atom L) and a heavy atom feature (Atom Q). The generated pharmacophore model was validated by a test database of seventy known inhibitors containing 55 active and 15 inactive/least active compounds. The validated pharmacophore model was used to virtually screen the ChemBridge database. As a result of screening 1009 hits were retrieved and were subjected to filtering by Lipinski’s rule of five on the basis of which 786 hits were selected for further assessment using molecular docking studies. Finally, 15 hits of different scaffolds having interactions with important active site residues were predicted as lead candidates. These candidates having unique scaffolds have a strong likelihood to act as further starting points in the development of novel and potent NS3/4A protease inhibitors. PMID:24551230

  6. Chaotic Polynomial Maps

    NASA Astrophysics Data System (ADS)

    Zhang, Xu

    This paper introduces a class of polynomial maps in Euclidean spaces, investigates the conditions under which there exist Smale horseshoes and uniformly hyperbolic invariant sets, studies the chaotic dynamical behavior and strange attractors, and shows that some maps are chaotic in the sense of Li-Yorke or Devaney. This type of maps includes both the Logistic map and the Hénon map. For some diffeomorphisms with the expansion dimension equal to one or two in three-dimensional spaces, the conditions under which there exist Smale horseshoes and uniformly hyperbolic invariant sets on which the systems are topologically conjugate to the two-sided fullshift on finite alphabet are obtained; for some expanding maps, the chaotic region is analyzed by using the coupled-expansion theory and the Brouwer degree theory. For three types of higher-dimensional polynomial maps with degree two, the conditions under which there are Smale horseshoes and uniformly hyperbolic invariant sets are given, and the topological conjugacy between the maps on the invariant sets and the two-sided fullshift on finite alphabet is obtained. Some interesting maps with chaotic attractors and positive Lyapunov exponents in three-dimensional spaces are found by using computer simulations. In the end, two examples are provided to illustrate the theoretical results.

  7. BOREAS Hardcopy Maps

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Nelson, Elizabeth; Newcomer, Jeffrey A.

    2000-01-01

    Boreal Ecosystem-Atmospheric Study (BOREAS) hardcopy maps are a collection of approximately 1,000 hardcopy maps representing the physical, climatological, and historical attributes of areas covering primarily the Manitoba and Saskatchewan provinces of Canada. These maps were collected by BOREAS Information System (BORIS) and Canada for Remote Sensing (CCRS) staff to provide basic information about site positions, manmade features, topography, geology, hydrology, land cover types, fire history, climate, and soils of the BOREAS study region. These maps are not available for distribution through the BOREAS project but may be used as an on-site resource. Information is provided within this document for individuals who want to order copies of these maps from the original map source. Note that the maps are not contained on the BOREAS CD-ROM set. An inventory listing file is supplied on the CD-ROM to inform users of the maps that are available. This inventory listing is available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). For hardcopies of the individual maps, contact the sources provided.

  8. Exploring Students' Mapping Behaviors and Interactive Discourses in a Case Diagnosis Problem: Sequential Analysis of Collaborative Causal Map Drawing Processes

    ERIC Educational Resources Information Center

    Lee, Woon Jee

    2012-01-01

    The purpose of this study was to explore the nature of students' mapping and discourse behaviors while constructing causal maps to articulate their understanding of a complex, ill-structured problem. In this study, six graduate-level students were assigned to one of three pair groups, and each pair used the causal mapping software program,…

  9. Correlated optical measurements and plasmon mapping of silver nanorods

    SciTech Connect

    Guiton, Beth S; Iberi, Vighter; Li, Shuzhou; Leonard, Donovan N; Parish, Chad M; Kotula, Paul G; Varela del Arco, Maria; Schatz, George C.; Pennycook, Stephen J; Camden, Jon P

    2011-01-01

    Plasmonics is a rapidly growing field, yet imaging of the plasmonic modes in complex nanoscale architectures is extremely challenging. Here we obtain spatial maps of the localized surface plasmon modes of high-aspect-ratio silver nanorods using electron energy loss spectroscopy (EELS) and correlate to optical data and classical electrodynamics calculations from the exact same particles. EELS mapping is thus demonstrated to be an invaluable technique for elucidating complex and overlapping plasmon modes.

  10. Correlated optical measurements and plasmon mapping of silver nanorods.

    PubMed

    Guiton, Beth S; Iberi, Vighter; Li, Shuzhou; Leonard, Donovan N; Parish, Chad M; Kotula, Paul G; Varela, Maria; Schatz, George C; Pennycook, Stephen J; Camden, Jon P

    2011-08-10

    Plasmonics is a rapidly growing field, yet imaging of the plasmonic modes in complex nanoscale architectures is extremely challenging. Here we obtain spatial maps of the localized surface plasmon modes of high-aspect-ratio silver nanorods using electron energy loss spectroscopy (EELS) and correlate to optical data and classical electrodynamics calculations from the exact same particles. EELS mapping is thus demonstrated to be an invaluable technique for elucidating complex and overlapping plasmon modes.

  11. On the Mandelbrot set for pairs of linear maps

    NASA Astrophysics Data System (ADS)

    Bandt, Christoph

    2002-07-01

    A Mandelbrot set M for pairs of complex linear maps was introduced by Barnsley and Harrington in 1985. Bousch proved that M is locally connected, and Odlyzko and Poonen studied the related set of all complex roots of polynomials with coefficients 0 and 1. We give an algorithm to construct this set and study its geometric structure. In contrast to the Mandelbrot set for quadratic maps, it is shown that M is not simply connected.

  12. Tectonic map of Uruguay

    NASA Astrophysics Data System (ADS)

    Sanchez Bettucci, L.; Oyhantcabal, P.

    2008-05-01

    A compilation of available data about the geology of Uruguay allowed the definition of its main events and tectonic units. Based on a critical revision of different tectonic hypothesis found in the literature, a parsimonious tectonic evolution schema is presented, in the context of Western Gondwana. The tectonic map illustrates the general features of the structure and main tectonic units of Uruguay. The Precambrian shield, cropping out in the South and Southeast of the country is an Archean to Paleoprtoerozoic basement divided in three main tectonostratigraphic terrranes: the Piedra Alta (PAT) a juvenile Paleoproterozoic unit not reworked by later events; the Nico Pérez (NPT) a complex unit composed of several blocks where Archean to Mesoproterozoic events are recognised. The NPT was strongly reworked by Neoproterozoic (Brasiliano) orogeny. The Dom Feliciano Belt cropping out in eastern Uruguay is related to Western Gondwana amalgamation. Different tectonic settings are considered: pre-Brasiliano Basement inliers; supracrustal successions representing the evolution from a back- arc to a foreland basin; a magmatic arc; and post-collisional basins and related magmatism. In lower Paleozoic the Paraná foreland basin was generated as a consequence of orogenic events. The sedimentary successions in Uruguay include continental to shallow marine deposits where the influence of carboniferous to Permian glacial episode is recorded. The Mesozoic record is characterised by the influence of extension related to the break-up of Gondwana and the formation of the Atlantic Ocean: huge amounts of tholeiitic basalt were erupted (near 30.000 km3 in Uruguay), followed by cretaceous sediments in the northern area of the country while in the south-east, bimodal magmatism and sediments of the same age are associated to rift basins. The Cenozoic is characterised by tectonic quiescence. Subsidence is only observed in the western region (Chaco-Paraná Basin) and in the east (Laguna Mer

  13. Maps and Map Learning in Social Studies

    ERIC Educational Resources Information Center

    Bednarz, Sarah Witham; Acheson, Gillian; Bednarz, Robert S.

    2006-01-01

    The importance of maps and other graphic representations has become more important to geography and geographers. This is due to the development and widespread diffusion of geographic (spatial) technologies. As computers and silicon chips have become more capable and less expensive, geographic information systems (GIS), global positioning satellite…

  14. Lyman Alpha Mapping Project (LAMP) Brightness Maps

    NASA Astrophysics Data System (ADS)

    Retherford, Kurt D.; Gladstone, G.; Stern, S.; Egan, A. F.; Miles, P. F.; Parker, J. W.; Greathouse, T. K.; Davis, M. W.; Slater, D. C.; Kaufmann, D. E.; Versteeg, M. H.; Feldman, P. D.; Hurley, D. M.; Pryor, W. R.; Hendrix, A. R.

    2010-10-01

    The Lyman Alpha Mapping Project (LAMP) is an ultraviolet (UV) spectrograph on the Lunar Reconnaissance Orbiter (LRO) that is designed to map the lunar albedo at far-UV wavelengths. LAMP primarily measures interplanetary Hydrogen Lyman-alpha sky-glow and far-UV starlight reflected from the night-side lunar surface, including permanently shadowed regions (PSRs) near the poles. Dayside observations are also obtained. Brightness maps sorted by wavelength (including the Lyman-alpha wavelength of 121.6 nm) are reported for the polar regions, with a few regions of interest reported in more detail. LAMP's spectral range of 58 nm to 196 nm includes a water ice spectral feature near 160 nm, which provides a diagnostic tool for detecting water on the lunar surface that is complementary to recent discoveries using infrared and radio frequency techniques. Progress towards producing far-UV albedo maps and searching for water ice signatures will be reported. We'll discuss how LAMP data may address questions regarding how water is formed on the moon, transported through the lunar atmosphere, and deposited in the PSRs.

  15. Gardony Map Drawing Analyzer: Software for quantitative analysis of sketch maps.

    PubMed

    Gardony, Aaron L; Taylor, Holly A; Brunyé, Tad T

    2016-03-01

    Sketch maps are effective tools for assessing spatial memory. However, despite their widespread use in cognitive science research, sketch map analysis techniques remain unstandardized and carry limitations. In the present article, we present the Gardony Map Drawing Analyzer (GMDA), an open-source software package for sketch map analysis. GMDA combines novel and established analysis techniques into a graphical user interface that permits rapid computational sketch map analysis. GMDA calculates GMDA-unique measures based on pairwise comparisons between landmarks, as well as bidimensional regression parameters (Friedman & Kohler, 2003), which together reflect sketch map quality at two levels: configural and individual landmark. The configural measures assess the overall landmark configuration and provide a whole-map analysis. Individual landmark measures, introduced in GMDA, assess individual landmark placement and indicate how individual landmarks contribute to the configural scores. Together, these measures provide a more complete psychometric picture of sketch map analysis, allowing for comparisons between sketch maps and between landmarks. The calculated measures reflect specific and cognitively relevant aspects of interlandmark spatial relationships, including distance and angular representation. GMDA supports complex environments (up to 48 landmarks) and two software modes that capture aspects of maps not addressed by existing techniques, such as landmark size and shape variation and interlandmark containment relationships. We describe the software and its operation and present a formal specification of calculation procedures for its unique measures. We then validate the software by demonstrating the capabilities and reliability of its measures using simulation and experimental data. The most recent version of GMDA is available at www.aarongardony.com/tools/map-drawing-analyzer.

  16. Gardony Map Drawing Analyzer: Software for quantitative analysis of sketch maps.

    PubMed

    Gardony, Aaron L; Taylor, Holly A; Brunyé, Tad T

    2016-03-01

    Sketch maps are effective tools for assessing spatial memory. However, despite their widespread use in cognitive science research, sketch map analysis techniques remain unstandardized and carry limitations. In the present article, we present the Gardony Map Drawing Analyzer (GMDA), an open-source software package for sketch map analysis. GMDA combines novel and established analysis techniques into a graphical user interface that permits rapid computational sketch map analysis. GMDA calculates GMDA-unique measures based on pairwise comparisons between landmarks, as well as bidimensional regression parameters (Friedman & Kohler, 2003), which together reflect sketch map quality at two levels: configural and individual landmark. The configural measures assess the overall landmark configuration and provide a whole-map analysis. Individual landmark measures, introduced in GMDA, assess individual landmark placement and indicate how individual landmarks contribute to the configural scores. Together, these measures provide a more complete psychometric picture of sketch map analysis, allowing for comparisons between sketch maps and between landmarks. The calculated measures reflect specific and cognitively relevant aspects of interlandmark spatial relationships, including distance and angular representation. GMDA supports complex environments (up to 48 landmarks) and two software modes that capture aspects of maps not addressed by existing techniques, such as landmark size and shape variation and interlandmark containment relationships. We describe the software and its operation and present a formal specification of calculation procedures for its unique measures. We then validate the software by demonstrating the capabilities and reliability of its measures using simulation and experimental data. The most recent version of GMDA is available at www.aarongardony.com/tools/map-drawing-analyzer. PMID:25673320

  17. Maps--Map Reading and Aerial Photography. [2 Units].

    ERIC Educational Resources Information Center

    Haakonsen, Harry O., Ed.

    Included in this set of materials are two units: (1) Maps and Map Reading and (2) Aerial Photography. Each unit includes student guide sheets, reference material, and tape script. A set of 35mm slides and audiotapes are usually used with the materials. The unit on Maps and Map Reading is designed to develop map reading skills and the use of these…

  18. Statistical and computational challenges in physical mapping

    SciTech Connect

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

    1994-06-01

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

  19. Risk maps for navigation in liver surgery

    NASA Astrophysics Data System (ADS)

    Hansen, C.; Zidowitz, S.; Schenk, A.; Oldhafer, K.-J.; Lang, H.; Peitgen, H.-O.

    2010-02-01

    The optimal transfer of preoperative planning data and risk evaluations to the operative site is challenging. A common practice is to use preoperative 3D planning models as a printout or as a presentation on a display. One important aspect is that these models were not developed to provide information in complex workspaces like the operating room. Our aim is to reduce the visual complexity of 3D planning models by mapping surgically relevant information onto a risk map. Therefore, we present methods for the identification and classification of critical anatomical structures in the proximity of a preoperatively planned resection surface. Shadow-like distance indicators are introduced to encode the distance from the resection surface to these critical structures on the risk map. In addition, contour lines are used to accentuate shape and spatial depth. The resulting visualization is clear and intuitive, allowing for a fast mental mapping of the current resection surface to the risk map. Preliminary evaluations by liver surgeons indicate that damage to risk structures may be prevented and patient safety may be enhanced using the proposed methods.

  20. Outcome mapping for health system integration

    PubMed Central

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

    2013-01-01

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

  1. Mapping Symbolic Development.

    ERIC Educational Resources Information Center

    Perry, Martha Davis; Wolf, Dennie Palmer

    In an investigation of the development of mapping as distinct from drawing, 39 middle and lower class Cambridge, Massachusetts children in kindergarten and first- and second-grades were shown a small three-dimensional model town, asked to make a smaller, three-dimensional copy of the model, and then asked to make a map showing each item in the…

  2. Mapping Microbial Biodiversity

    SciTech Connect

    Stoner, Daphne Lisabet; Micah C. Geary; White, Luke James; Lee, Randy Dean; Brizzee, Julie Ann; Rodman, A. C.; Rope, Ronald C

    2001-09-01

    We report the development of a prototype database that "maps" microbial diversity in the context of the geochemical and geological environment and geographic location. When it is fully implemented, scientists will be able to conduct database searches, construct maps containing the information of interest, download files, and enter data over the Internet.

  3. Chizu Task Mapping Tool

    SciTech Connect

    2014-07-01

    Chizu is a tool for Mapping MPI processes or tasks to physical processors or nodes for optimizing communication performance. It takes the communication graph of a High Performance Computing (HPC) application and the interconnection topology of a supercomputer as input. It outputs a new MPI rand to processor mapping, which can be used when launching the HPC application.

  4. Map Skills with Meaning.

    ERIC Educational Resources Information Center

    Hamilton, Paula; And Others

    1993-01-01

    Presents hands-on activities to help teach elementary students map skills during Geography Awareness Week. The map skills are made fun by being incorporated into meaningful activities like learning about global resources, tracking the progress of sports teams, and conducting climate experiments in faraway places. (SM)

  5. MAP3K1

    PubMed Central

    Pham, Trang T.; Angus, Steven P.

    2013-01-01

    MAP3K1 is a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family of serine/threonine kinases. MAP3K1 regulates JNK activation and is unique among human kinases in that it also encodes an E3 ligase domain that ubiquitylates c-Jun and ERK1/2. Full length MAP3K1 regulates cell migration and contributes to pro-survival signaling while its caspase 3-mediated cleavage generates a C-terminal kinase domain that promotes apoptosis. The critical function of MAP3K1 in cell fate decisions suggests that it may be a target for deregulation in cancer. Recent large-scale genomic studies have revealed that MAP3K1 copy number loss and somatic missense or nonsense mutations are observed in a significant number of different cancers, being most prominent in luminal breast cancer. The alteration of MAP3K1 in diverse cancer types demonstrates the importance of defining phenotypes for possible therapeutic targeting of tumor cell vulnerabilities created when MAP3K1 function is lost or gained. PMID:24386504

  6. Site and Watershed Mapping.

    ERIC Educational Resources Information Center

    Institute for Environmental Education, Cleveland, OH.

    Presented as part of a larger unit on watershed investigations are a slideshow script and a map and compass unit intended to help high school students better visualize the relationship between a water sampling site, the entire stream, community, and watershed. The script discusses features of a topographical map, shows how to read one, and…

  7. Temporal mapping and analysis

    NASA Technical Reports Server (NTRS)

    O'Hara, Charles G. (Inventor); Shrestha, Bijay (Inventor); Vijayaraj, Veeraraghavan (Inventor); Mali, Preeti (Inventor)

    2011-01-01

    A compositing process for selecting spatial data collected over a period of time, creating temporal data cubes from the spatial data, and processing and/or analyzing the data using temporal mapping algebra functions. In some embodiments, the temporal data cube is creating a masked cube using the data cubes, and computing a composite from the masked cube by using temporal mapping algebra.

  8. Acoustic mapping velocimetry

    NASA Astrophysics Data System (ADS)

    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.

  9. The Map Corner.

    ERIC Educational Resources Information Center

    Cheyney, Arnold B.; Capone, Donald L.

    This teaching resource is aimed at helping students develop the skills necessary to locate places on the earth. Designed as a collection of map skill exercises rather than a sequential program of study, this program expects that students have access to and some knowledge of how to use globes, maps, atlases, and encyclopedias. The volume contains 6…

  10. Handmade Multitextured Maps.

    ERIC Educational Resources Information Center

    Trevelyan, Simon

    1984-01-01

    Tactile maps for visually impaired persons can be made by drawing lines with an aqueous adhesive solution, dusting with thermoengraving powder, and exposing the card to a source of intense heat (such as a heat gun or microwave oven). A raised line map results. (CL)

  11. What do maps show?

    USGS Publications Warehouse

    ,

    1994-01-01

    The purpose of the teaching package is to help students understand and use maps. The U.S. Geological Survey (USGS) has provided the package as a service to educators so that more Americans will learn to understand the world of information on maps. Everything in the package teaches and reinforces geographic skills that are required in your curriculum.

  12. Geologic Map of the Thaumasia Region, Mars

    USGS Publications Warehouse

    Dohm, Janes M.; Tanaka, Kenneth L.; Hare, Trent M.

    2001-01-01

    The geology of the Thaumasia region (fig. 1, sheet 3) includes a wide array of rock materials, depositional and erosional landforms, and tectonic structures. The region is dominated by the Thaumasia plateau, which includes central high lava plains ringed by highly deformed highlands; the plateau may comprise the ancestral center of Tharsis tectonism (Frey, 1979; Plescia and Saunders, 1982). The extensive structural deformation of the map region, which is without parallel on Mars in both complexity and diversity, occurred largely throughout the Noachian and Hesperian periods (Tanaka and Davis, 1988; Scott and Dohm, 1990a). The deformation produced small and large extensional and contractional structures (fig. 2, sheet 3) that resulted from stresses related to the formation of Tharsis (Frey, 1979; Wise and others, 1979; Plescia and Saunders, 1982; Banerdt and others, 1982, 1992; Watters and Maxwell, 1986; Tanaka and Davis, 1988; Francis, 1988; Watters, 1993; Schultz and Tanaka, 1994), from magmatic-driven uplifts, such as at Syria Planum (Tanaka and Davis, 1988; Dohm and others, 1998; Dohm and Tanaka, 1999) and central Valles Marineris (Dohm and others, 1998, Dohm and Tanaka, 1999), and from the Argyre impact (Wilhelms, 1973; Scott and Tanaka, 1986). In addition, volcanic, eolian, and fluvial processes have highly modified older surfaces in the map region. Local volcanic and tectonic activity often accompanied episodes of valley formation. Our mapping depicts and describes the diverse terrains and complex geologic history of this unique ancient tectonic region of Mars. The geologic (sheet 1), paleotectonic (sheet 2), and paleoerosional (sheet 3) maps of the Thaumasia region were compiled on a Viking 1:5,000,000-scale digital photomosaic base. The base is a combination of four quadrangles: the southeast part of Phoenicis Lacus (MC–17), most of the southern half of Coprates (MC–18), a large part of Thaumasia (MC–25), and the northwest margin of Argyre (MC–26

  13. Geologic map of Mars

    USGS Publications Warehouse

    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.

  14. Bodily maps of emotions

    PubMed Central

    Nummenmaa, Lauri; Glerean, Enrico; Hari, Riitta; Hietanen, Jari K.

    2014-01-01

    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. PMID:24379370

  15. Iconicity as structure mapping

    PubMed Central

    Emmorey, Karen

    2014-01-01

    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. PMID:25092669

  16. Iconicity as structure mapping.

    PubMed

    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.

  17. Bodily maps of emotions.

    PubMed

    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.

  18. Complex derivatives

    NASA Astrophysics Data System (ADS)

    Battiston, Stefano; Caldarelli, Guido; Georg, Co-Pierre; May, Robert; Stiglitz, Joseph

    2013-03-01

    The intrinsic complexity of the financial derivatives market has emerged as both an incentive to engage in it, and a key source of its inherent instability. Regulators now faced with the challenge of taming this beast may find inspiration in the budding science of complex systems.

  19. Designing Complexity

    ERIC Educational Resources Information Center

    Glanville, Ranulph

    2007-01-01

    This article considers the nature of complexity and design, as well as relationships between the two, and suggests that design may have much potential as an approach to improving human performance in situations seen as complex. It is developed against two backgrounds. The first is a world view that derives from second order cybernetics and radical…

  20. Maximally Informative Statistics for Localization and Mapping

    NASA Technical Reports Server (NTRS)

    Deans, Matthew C.

    2001-01-01

    This paper presents an algorithm for localization and mapping for a mobile robot using monocular vision and odometry as its means of sensing. The approach uses the Variable State Dimension filtering (VSDF) framework to combine aspects of Extended Kalman filtering and nonlinear batch optimization. This paper describes two primary improvements to the VSDF. The first is to use an interpolation scheme based on Gaussian quadrature to linearize measurements rather than relying on analytic Jacobians. The second is to replace the inverse covariance matrix in the VSDF with its Cholesky factor to improve the computational complexity. Results of applying the filter to the problem of localization and mapping with omnidirectional vision are presented.

  1. Interpreting fMRI data: maps, modules and dimensions

    PubMed Central

    Op de Beeck, Hans P.; Haushofer, Johannes; Kanwisher, Nancy G.

    2009-01-01

    Neuroimaging research over the past decade has revealed a detailed picture of the functional organization of the human brain. Here we focus on two fundamental questions that are raised by the detailed mapping of sensory and cognitive functions and illustrate these questions with findings from the object-vision pathway. First, are functionally specific regions that are located close together best understood as distinct cortical modules or as parts of a larger-scale cortical map? Second, what functional properties define each cortical map or module? We propose a model in which overlapping continuous maps of simple features give rise to discrete modules that are selective for complex stimuli. PMID:18200027

  2. Mental Mapping: A Classroom Strategy

    ERIC Educational Resources Information Center

    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…

  3. Evolution of a Laser Hybrid Welding Map

    NASA Astrophysics Data System (ADS)

    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.

  4. Noise maps for acoustically sensitive navigation

    NASA Astrophysics Data System (ADS)

    Martinson, Eric; Arkin, Ronald C.

    2004-12-01

    More and more robotic applications are equipping robots with microphones to improve the sensory information available to them. However, in most applications the auditory task is very low-level, only processing data and providing auditory event information to higher-level navigation routines. If the robot, and therefore the microphone, ends up in a bad acoustic location, then the results from that sensor will remain noisy and potentially useless for accomplishing the required task. To solve this problem, there are at least two possible solutions. The first is to provide bigger and more complex filters, which is the traditional signal processing approach. An alternative solution is to move the robot in concert with providing better audition. In this work, the second approach is followed by introducing noise maps as a tool for acoustically sensitive navigation. A noise map is a guide to noise in the environment, pinpointing locations which would most likely interfere with auditory sensing. A traditional noise map, in an acoustic sense, is a graphical display of the average sound pressure level at any given location. An area with high sound pressure level corresponds to high ambient noise that could interfere with an auditory application. Such maps can be either created by hand, or by allowing the robot to first explore the environment. Converted into a potential field, a noise map then becomes a useful tool for reducing the interference from ambient noise. Preliminary results with a real robot on the creation and use of noise maps are presented.

  5. Analyzing thematic maps and mapping for accuracy

    USGS Publications Warehouse

    Rosenfield, G.H.

    1982-01-01

    Two problems which exist while attempting to test the accuracy of thematic maps and mapping are: (1) evaluating the accuracy of thematic content, and (2) evaluating the effects of the variables on thematic mapping. Statistical analysis techniques are applicable to both these problems and include techniques for sampling the data and determining their accuracy. In addition, techniques for hypothesis testing, or inferential statistics, are used when comparing the effects of variables. A comprehensive and valid accuracy test of a classification project, such as thematic mapping from remotely sensed data, includes the following components of statistical analysis: (1) sample design, including the sample distribution, sample size, size of the sample unit, and sampling procedure; and (2) accuracy estimation, including estimation of the variance and confidence limits. Careful consideration must be given to the minimum sample size necessary to validate the accuracy of a given. classification category. The results of an accuracy test are presented in a contingency table sometimes called a classification error matrix. Usually the rows represent the interpretation, and the columns represent the verification. The diagonal elements represent the correct classifications. The remaining elements of the rows represent errors by commission, and the remaining elements of the columns represent the errors of omission. For tests of hypothesis that compare variables, the general practice has been to use only the diagonal elements from several related classification error matrices. These data are arranged in the form of another contingency table. The columns of the table represent the different variables being compared, such as different scales of mapping. The rows represent the blocking characteristics, such as the various categories of classification. The values in the cells of the tables might be the counts of correct classification or the binomial proportions of these counts divided by

  6. Employing Geodatabases for Planetary Mapping Conduct - Requirements, Concepts and Solutions

    NASA Technical Reports Server (NTRS)

    vanGasselt, Stephan; Nass, A.

    2010-01-01

    Planetary geologic mapping has become complex in terms of merging and co-registering a variety of different datasets for analysis and mapping. But it has also become more convenient when it comes to conducting actual (geoscientific) mapping with the help of desktop Geographic Information Systems (GIS). The complexity and variety of data, however, are major issues that need to be taken care of in order to provide mappers with a consistent and easy-to-use mapping basis. Furthermore, a high degree of functionality and interoperability of various commercial and open-source GIS and remote sensing applications allow mappers to organize map data, map components and attribute data in a more sophisticated and intuitional way when compared to workflows 15 years ago. Integration of mapping results of different groups becomes an awkward task as each mapper follows his/her own style, especially if mapping conduct is not coordinated and organized programmatically. Problems of data homogenization start with various interpretations and implementations of planetary map projections and reference systems which form the core component of any mapping and analysis work. If the data basis is inconsistent, mapping results in terms of objects georeference become hard to integrate. Apart from data organization and referencing issues, which are important on the mapping as well as the data-processing side of every project, the organization of planetary geologic map units and attributes, as well as their representation within a common GIS environment, are key components that need to be taken care of in a consistent and persistent way.

  7. A fruit quality gene map of Prunus

    PubMed Central

    2009-01-01

    Background Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance. Results A genetic linkage map of 211 markers was constructed for an intraspecific peach (Prunus persica) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the Prunus reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG. Conclusion The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the

  8. Three-dimensional mapping of differential amino acids of human, murine, canine and equine TLR4/MD-2 receptor complexes conferring endotoxic activation by lipid A, antagonism by Eritoran and species-dependent activities of Lipid IVA in the mammalian LPS sensor system

    PubMed Central

    Scior, Thomas; Lozano-Aponte, Jorge; Figueroa-Vazquez, Vianihuini; Yunes-Rojas, Julian A.; Zähringer, Ulrich; Alexander, Christian

    2013-01-01

    A literature review concerning the unexpected species differences of the vertebrate innate immune response to lipid IVA was published in CSBJ prior to the present computational study to address the unpaired activity-sequence correlation of prototypic E. coli -type lipid A and its precursor lipid IVA regarding human, murine, equine and canine species. To this end, their sequences and structures of hitherto known Toll-like receptor 4 (TLR4) and myeloid differentiation factor 2 (MD-2) complexes were aligned and their differential side chain patterns studied. If required due to the lack of the corresponding X-ray crystallographic data, three-dimensional models of TLR4/MD-2/ligand complexes were generated using mono and dimeric crystal structures as templates and in silico docking of the prototypic ligands lipid A, lipid IVA and Eritoran. All differential amino acids were mapped to pinpoint species dependency on an atomic scale, i.e. the possible concert of mechanistically relevant side chains. In its most abstract and general form the three-dimensional (3D-) models devise a triangular interface or “wedge” where molecular interactions between TLR4, MD-2 and ligand itself take place. This study identifies two areas in the wedge related to either agonism or antagonism reflecting why ligands like lipid IVA can possess a species dependent dual activity. Lipid IVA represents an imperfect (underacylated and backbone-flipped), low affinity ligand of mammalian TLR4/MD-2 complexes. Its specific but weak antagonistic activity in the human system is in particular due to the loss of phosphate attraction in the wedge-shaped region conferred by nonhomologous residue changes when compared to crystal and modeled structures of the corresponding murine and equine TLR4/MD-2 complexes. The counter-TLR4/MD-2 unit was also taken into account since agonist-mediated dimerization in a defined m-shaped complex composed of two TLR4/MD-2/agonist subunits triggers intracellular signaling during

  9. Three-dimensional mapping of differential amino acids of human, murine, canine and equine TLR4/MD-2 receptor complexes conferring endotoxic activation by lipid A, antagonism by Eritoran and species-dependent activities of Lipid IVA in the mammalian LPS sensor system.

    PubMed

    Scior, Thomas; Lozano-Aponte, Jorge; Figueroa-Vazquez, Vianihuini; Yunes-Rojas, Julian A; Zähringer, Ulrich; Alexander, Christian

    2013-01-01

    A literature review concerning the unexpected species differences of the vertebrate innate immune response to lipid IVA was published in CSBJ prior to the present computational study to address the unpaired activity-sequence correlation of prototypic E. coli -type lipid A and its precursor lipid IVA regarding human, murine, equine and canine species. To this end, their sequences and structures of hitherto known Toll-like receptor 4 (TLR4) and myeloid differentiation factor 2 (MD-2) complexes were aligned and their differential side chain patterns studied. If required due to the lack of the corresponding X-ray crystallographic data, three-dimensional models of TLR4/MD-2/ligand complexes were generated using mono and dimeric crystal structures as templates and in silico docking of the prototypic ligands lipid A, lipid IVA and Eritoran. All differential amino acids were mapped to pinpoint species dependency on an atomic scale, i.e. the possible concert of mechanistically relevant side chains. In its most abstract and general form the three-dimensional (3D-) models devise a triangular interface or "wedge" where molecular interactions between TLR4, MD-2 and ligand itself take place. This study identifies two areas in the wedge related to either agonism or antagonism reflecting why ligands like lipid IVA can possess a species dependent dual activity. Lipid IVA represents an imperfect (underacylated and backbone-flipped), low affinity ligand of mammalian TLR4/MD-2 complexes. Its specific but weak antagonistic activity in the human system is in particular due to the loss of phosphate attraction in the wedge-shaped region conferred by nonhomologous residue changes when compared to crystal and modeled structures of the corresponding murine and equine TLR4/MD-2 complexes. The counter-TLR4/MD-2 unit was also taken into account since agonist-mediated dimerization in a defined m-shaped complex composed of two TLR4/MD-2/agonist subunits triggers intracellular signaling during the

  10. State hydrologic unit maps

    USGS Publications Warehouse

    Seaber, P.R.; Kapinos, F.P.; Knapp, G.L.

    1984-01-01

    A set of maps depicting approved boundaries of, and numerical codes for, river-basin units of the United States has been developed by the U.S. Geological Survey. These ' State Hydrologic Unit Maps ' are four-color maps that present information on drainage, culture, hydrography, and hydrologic boundaries and codes: (1) the 21 major water-resources regions and the 222 subregions designated by the U.S. Water Resources Council; (2) the 352 accounting units of the U.S. Geological Survey 's National Water Data Network; and (3) the 2,149 cataloging units of the U.S. Geological Survey 's Catalog of Information on Water Data. The maps are plotted on the Geological Survey State base-map series at a scale of 1:500,000 and, except for Alaska, depict hydrologic unit boundaries for all drainage basins greater than 700 mi squared (1,813 km squared). A complete list of all the hydrologic units, along with their drainage areas, their names, and the names of the States or outlying areas in which they reside, is contained in the report. These maps and associated codes provide a standardized base for use by water-resources organizations in locating, storing, retrieving, and exchanging hydrologic data. The Hydrologic Unit Codes shown on the maps have been approved as a Federal Information Processing Standard for use by the Federal establishment. (USGS)

  11. Color on emergency mapping

    NASA Astrophysics Data System (ADS)

    Jiang, Lili; Qi, Qingwen; Zhang, An

    2007-06-01

    There are so many emergency issues in our daily life. Such as typhoons, tsunamis, earthquake, fires, floods, epidemics, etc. These emergencies made people lose their lives and their belongings. Every day, every hour, even every minute people probably face the emergency, so how to handle it and how to decrease its hurt are the matters people care most. If we can map it exactly before or after the emergencies; it will be helpful to the emergency researchers and people who live in the emergency place. So , through the emergency map, before emergency is occurring we can predict the situation, such as when and where the emergency will be happen; where people can refuge, etc. After disaster, we can also easily assess the lost, discuss the cause and make the lost less. The primary effect of mapping is offering information to the people who care about the emergency and the researcher who want to study it. Mapping allows the viewers to get a spatial sense of hazard. It can also provide the clues to study the relationship of the phenomenon in emergency. Color, as the basic element of the map, it can simplify and clarify the phenomenon. Color can also affects the general perceptibility of the map, and elicits subjective reactions to the map. It is to say, structure, readability, and the reader's psychological reactions can be affected by the use of color.

  12. Coastal mapping handbook

    USGS Publications Warehouse

    ,; ,; Ellis, Melvin Y.

    1978-01-01

    Passage of the Coastal Zone Management Act of 1972 focused attention on the Nation's coastal land and water areas. As plans for more effective management of the coastal zone evolved, it soon became apparent that improved maps and charts of these areas were needed. This handbook was prepared with the requirements of the entire coastal community in mind, giving greatest attention to the needs of coastal zone managers and planners at the State and local levels. Its principal objective is to provide general information and guidance; it is neither a textbook nor a technical manual, but rather a primer on coastal mapping. This handbook should help planners and managers of coastal programs to determine their mapping requirements, select the best maps and charts for their particular needs, and to deal effectively with personnel who gather data and prepare maps. The sections on "Sources of Assistance and Advice" and "Product and Data Sources" should be especially useful to all involved in mapping the coastal zone. Brief summaries of the mapping efforts of several State coastal zone management programs are included. "Future outlook" discusses anticipated progress and changes in mapping procedures and techniques. Illustrations are inserted, where appropriate, to illustrate the products and equipment discussed. Because of printing restrictions, the colors in map illustrations may vary from those in the original publication. The appendixes include substantial material which also should be of interest. In addition a glossary and an index are included to provide easy and quick access to the terms and concepts used in the text. For those interested in more technical detail than is provided in this handbook, the "Selected references" will be useful. Also, the publications of the professional societies listed in appendix 4 will provide technical information in detail.

  13. Topographic map symbols

    USGS Publications Warehouse

    ,

    2005-01-01

    Interpreting the colored lines, areas, and other symbols is the first step in using topographic maps. Features are shown as points, lines, or areas, depending on their size and extent. For example, individual houses may be shown as small black squares. For larger buildings, the actual shapes are mapped. In densely built-up areas, most individual buildings are omitted and an area tint is shown. On some maps, post offices, churches, city halls, and other landmark buildings are shown within the tinted area.

  14. Mapping the Baby Universe

    NASA Technical Reports Server (NTRS)

    Wanjek, Christopher

    2003-01-01

    In June, NASA plans to launch the Microwave Anisotropy Probe (MAP) to survey the ancient radiation in unprecedented detail. MAP will map slight temperature fluctuations within the microwave background that vary by only 0.00001 C across a chilly radiation that now averages 2.73 C above absolute zero. The temperature differences today point back to density differences in the fiery baby universe, in which there was a little more matter here and a little less matter there. Areas of slightly enhanced density had stronger gravity than low-density areas. The high-density areas pulled back on the background radiation, making it appear slightly cooler in those directions.

  15. Map and Compass Skills for the Elementary School. Instructional Activities Series IA/E-9.

    ERIC Educational Resources Information Center

    Larkin, Robert P.; Grogger, Paul K.

    Twenty activities are described that can be used to develop map and compass skills in elementary grades. The activities range from simple, beginners' projects to more complex tasks as students acquire more skills. Most can be carried out in the classroom, schoolyard, or local neighborhood. Map activities include drawing maps of the classroom,…

  16. Reliable Radiation Hybrid Maps: An Efficient Scalable Clustering-based Approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The process of mapping markers from radiation hybrid mapping (RHM) experiments is equivalent to the traveling salesman problem and, thereby, has combinatorial complexity. As an additional problem, experiments typically result in some unreliable markers that reduce the overall quality of the map. We ...

  17. Ordered and isomorphic mapping of periodic structures in the parametrically forced logistic map

    NASA Astrophysics Data System (ADS)

    Maranhão, Dariel M.

    2016-09-01

    We investigate the periodic domains found in the parametrically forced logistic map, the classical logistic map when its control parameter changes dynamically. Phase diagrams in two-parameter spaces reveal intricate periodic structures composed of patterns of intersecting superstable orbits curves, defining the cell of a periodic window. Cells appear multifoliated and ordered, and they are isomorphically mapped when one changes the map parameters. Also, we identify the characteristics of simplest cell and apply them to other more complex, discussing how the topography on parameter space is affected. By use of the winding number as defined in periodically forced oscillators, we show that the hierarchical organization of the periodic domains is manifested in global and local scales.

  18. Carney Complex

    MedlinePlus

    ... Screening guidelines may change over time as new technologies are developed and more is learned about Carney complex. It is important to talk with your doctor about appropriate screening tests. Learn more about what to expect when having ...

  19. Uniqueness of the momentum map

    NASA Astrophysics Data System (ADS)

    Esposito, Chiara; Nest, Ryszard

    2016-08-01

    We give a detailed discussion of existence and uniqueness of the momentum map associated to Poisson Lie actions, which was defined by Lu. We introduce a weaker notion of momentum map, called infinitesimal momentum map, which is defined on one-forms and we analyze its integrability to the Lu's momentum map. Finally, the uniqueness of the Lu's momentum map is studied by describing, explicitly, the tangent space to the space of momentum maps.

  20. Mean maps for cosmic web structures in cosmological initial conditions

    NASA Astrophysics Data System (ADS)

    Aung, Han; Cohn, J. D.

    2016-02-01

    Haloes, filaments, sheets and voids in the cosmic web can be defined in terms of the eigenvalues of the smoothed shear tensor and a threshold λth. Using analytic methods, we construct mean maps centred on these types of structures for Gaussian random fields corresponding to cosmological initial conditions. Each map also requires a choice of shear at the origin; we consider three possibilities. We find characteristic sizes, shapes and other properties of the central objects in these mean maps and explore how these properties change with varying the threshold and smoothing scale, i.e. varying the separation of the cosmic web into different kinds of components. The mean maps become increasingly complex as the threshold λth decreases to zero. We also describe scatter around these mean maps, subtleties which can arise in their construction, and some comparisons between haloes in the maps and collapsed haloes at final times.

  1. Geological mapping goes 3-D in response to societal needs

    USGS Publications Warehouse

    Thorleifson, H.; Berg, R.C.; Russell, H.A.J.

    2010-01-01

    The transition to 3-D mapping has been made possible by technological advances in digital cartography, GIS, data storage, analysis, and visualization. Despite various challenges, technological advancements facilitated a gradual transition from 2-D maps to 2.5-D draped maps to 3-D geological mapping, supported by digital spatial and relational databases that can be interrogated horizontally or vertically and viewed interactively. Challenges associated with data collection, human resources, and information management are daunting due to their resource and training requirements. The exchange of strategies at the workshops has highlighted the use of basin analysis to develop a process-based predictive knowledge framework that facilitates data integration. Three-dimensional geological information meets a public demand that fills in the blanks left by conventional 2-D mapping. Two-dimensional mapping will, however, remain the standard method for extensive areas of complex geology, particularly where deformed igneous and metamorphic rocks defy attempts at 3-D depiction.

  2. DAM - detection and mapping

    NASA Technical Reports Server (NTRS)

    1977-01-01

    Integrated set of manual procedures, computer programs, and graphic devices processes multispectral scanner data from orbiting Landsat into precisely registered and formatted maps of surface water and other resources at variety of scales, sheet formats, and tick intervals.

  3. Pictometry digital video mapping

    NASA Astrophysics Data System (ADS)

    Ciampa, John A.

    1995-09-01

    Pictometry is a proprietary digital imaging process which computationally maps each pixel of a digital land image to actual geographic coordinates, so that features in a mosaic of land images may be located and or measured.

  4. Interpreting Weather Maps.

    ERIC Educational Resources Information Center

    Smith, P. Sean; Ford, Brent A.

    1994-01-01

    Presents a brief introduction of our atmosphere, a guide to reading and interpreting weather maps, and a set of activities to facilitate teachers in helping to enhance student understanding of the Earth's atmosphere. (ZWH)

  5. Barrier Island Hazard Mapping.

    ERIC Educational Resources Information Center

    Pilkey, Orrin H.; Neal, William J.

    1980-01-01

    Describes efforts to evaluate and map the susceptibility of barrier islands to damage from storms, erosion, rising sea levels and other natural phenomena. Presented are criteria for assessing the safety and hazard potential of island developments. (WB)

  6. Obesity Prevalence Maps

    MedlinePlus

    ... Physical Activity Overweight & Obesity Healthy Weight Breastfeeding Micronutrient Malnutrition State and Local Programs Adult Obesity Prevalence Maps ... Physical Activity Overweight & Obesity Healthy Weight Breastfeeding Micronutrient Malnutrition State and Local Programs File Formats Help: How ...

  7. Mapping Earth Science Concepts.

    ERIC Educational Resources Information Center

    McDuffie, Thomas E., Jr.; Van Dine, William E.

    1978-01-01

    Presents two experiments concerned with mapping skills. Directions are given for calculating the circumference of the earth and for developing a model of the solar system using familiar territory as a frame of reference. (MA)

  8. Dating the Vinland Map

    ScienceCinema

    None

    2016-07-12

    Scientists from Brookhaven National Laboratory, the University of Arizona, and the Smithsonian Institution used carbon-dating technology to determine the age of a controversial parchment that might be the first-ever map of North America.

  9. Irrigation on Topographic Maps.

    ERIC Educational Resources Information Center

    Raitz, Karl B.

    1979-01-01

    Describes how study of irrigation practices on topographic maps can help students in introductory high school and college geography courses understand man and land relationships to geography. (Author/DB)

  10. enceladus_stress_map

    NASA Video Gallery

    This is a map of the changing stress on the surface of Enceladus' icy crust from the wobble and gravitational tides. Blue lines show the direction of forces pulling the crust apart, and red lines s...

  11. MAPPING IN MICRONESIA.

    USGS Publications Warehouse

    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.

  12. Reading angles in maps.

    PubMed

    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 appeared without any relevant length or distance information. Children were able to read these map fragments and compare two-dimensional to three-dimensional angles. However, this ability appeared both variable and fragile among the youngest children of the sample. These findings suggest that 4-year-old children begin to form an abstract concept of angle that applies both to two-dimensional and three-dimensional displays and that serves to interpret novel spatial symbols. PMID:23647223

  13. Irreversible quantum baker map.

    PubMed

    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.

  14. Hydrologic unit maps

    USGS Publications Warehouse

    Seaber, Paul R.; Kapinos, F. Paul; Knapp, George L.

    1987-01-01

    A set of maps depicting approved boundaries of, and numerical codes for, river-basin units of the United States has been developed by the U.S . Geological Survey. These 'Hydrologic Unit Maps' are four-color maps that present information on drainage, culture, hydrography, and hydrologic boundaries and codes of (1) the 21 major water-resources regions and the 222 subregions designated by the U.S . Water Resources Council, (2) the 352 accounting units of the U.S. Geological Survey's National Water Data Network, and (3) the 2,149 cataloging units of the U.S . Geological Survey's 'Catalog of information on Water Data:' The maps are plotted on the Geological Survey State base-map series at a scale of 1 :500,000 and, except for Alaska, depict hydrologic unit boundaries for all drainage basins greater than 700 square miles (1,813 square kilometers). A complete list of all the hydrologic units, along with their drainage areas, their names, and the names of the States or outlying areas in which they reside, is contained in the report. These maps and associated codes provide a standardized base for use by water-resources organizations in locating, storing, retrieving, and exchanging hydrologic data, in indexing and inventorying hydrologic data and information, in cataloging water-data acquisition activities, and in a variety of other applications. Because the maps have undergone extensive review by all principal Federal, regional, and State water-resource agencies, they are widely accepted for use in planning and describing water-use and related land-use activities, and in geographically organizing hydrologic data . Examples of these uses are given in the report . The hydrologic unit codes shown on the maps have been approved as a Federal Information Processing Standard for use by the Federal establishment.

  15. Mapping the human genome

    SciTech Connect

    Annas, G.C.; Elias, S.

    1992-01-01

    This article is a review of the book Mapping the Human Genome: Using Law and Ethics as Guides, edited by George C. Annas and Sherman Elias. The book is a collection of essays on the subject of using ethics and laws as guides to justify human gene mapping. It addresses specific issues such problems related to eugenics, patents, insurance as well as broad issues such as the societal definitions of normality.

  16. Wind Resource Maps (Postcard)

    SciTech Connect

    Not Available

    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.

  17. Non-invasive Mapping of Cardiac Arrhythmias.

    PubMed

    Shah, Ashok; Hocini, Meleze; Haissaguerre, Michel; Jaïs, Pierre

    2015-08-01

    Since more than 100 years, 12-lead electrocardiography (ECG) is the standard-of-care tool, which involves measuring electrical potentials from limited sites on the body surface to diagnose cardiac disorder, its possible mechanism, and the likely site of origin. Several decades of research has led to the development of a 252-lead ECG and computed tomography (CT) scan-based three-dimensional electro-imaging modality to non-invasively map abnormal cardiac rhythms including fibrillation. These maps provide guidance towards ablative therapy and thereby help advance the management of complex heart rhythm disorders. Here, we describe the clinical experience obtained using non-invasive technique in mapping the electrical disorder and guide the catheter ablation of atrial arrhythmias (premature atrial beat, atrial tachycardia, atrial fibrillation), ventricular arrhythmias (premature ventricular beats), and ventricular pre-excitation (Wolff-Parkinson-White syndrome).

  18. Spectral Mapping Reconstruction of Extended Sources

    NASA Astrophysics Data System (ADS)

    Smith, J. D. T.; Armus, L.; Dale, D. A.; Roussel, H.; Sheth, K.; Buckalew, B. A.; Jarrett, T. H.; Helou, G.; Kennicutt, R. C., Jr.

    2007-10-01

    Three-dimensional spectroscopy of extended sources is typically performed with dedicated integral field spectrographs. We describe a method of reconstructing full spectral cubes, with two spatial and one spectral dimension, from rastered spectral mapping observations employing a single slit in a traditional slit spectrograph. When the background and image characteristics are stable, as is often achieved in space, the use of traditional long slits for integral field spectroscopy can substantially reduce instrument complexity over dedicated integral field designs, without loss of mapping efficiency-particularly compelling when a long-slit mode for single unresolved source follow-up is separately required. We detail a custom flux-conserving cube reconstruction algorithm, discuss issues of extended-source flux calibration, and describe CUBISM, a tool that implements these methods for spectral maps obtained with the Spitzer Space Telescope's Infrared Spectrograph.

  19. Geologic Mapping of Mars

    NASA Astrophysics Data System (ADS)

    Price, Katherine H.

    1998-05-01

    Planetary geologic mapping involves integrating a terrestrial-based understanding of surface and subsurface processes and mapping principles to investigate scientific questions. Mars mappers must keep in mind that physical processes, such as wind and flowing water on Mars, are or were different from terrestrial processes because the planetary atmospheres have changed differently over time. Geologic mapping of Mars has traditionally been done by hand using overlays on photomosaics of Viking Orbiter and Mariner images. Photoclinometry and shadow measurements have been used to determine elevations, and the distribution and size of craters have been used to determine the relative ages of surfaces- more densely cratered surfaces are older. Some mappers are now using computer software (ranging from Photoshop to ArcInfo) to facilitate mapping, though their applications must be carefully executed so that registration of the images remains true. Images and some mapping results are now available on the internet, and new data from recent missions to Mars (Pathfinder and Surveyor) will offer clarifying information to mapping efforts. This paper consists chiefly of pictures and diagrams.

  20. Creating Heliophysics Concept Maps

    NASA Astrophysics Data System (ADS)

    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.

  1. Global Water Maps

    NASA Astrophysics Data System (ADS)

    Maidment, D. R.; Salas, F.; Teng, W. L.

    2013-12-01

    A global water map is a coverage of the earth that describes the state of water circulation in a phase of the hydrologic cycle. This information can be published as a map showing the state of the water variable at a particular point in time, or charted as a time series showing the temporal variation of that variable at a point in space. Such maps can be created through the NASA Land Data Assimilation System (LDAS) for precipitation, evaporation, soil moisture, and other parameters describing the vertical exchange of water between the land and atmosphere, through a combination of observations and simulation modeling. Point observations of water variables such as precipitation and streamflow are carried out by local hydrologic measurement agencies associated with a particular area. These point observations are now being published as web services in the WaterML language and federated using the Global Earth Observing System of Systems to enable the publication of water observations maps for these variables. By combining water maps derived from LDAS with those from federated point observations, a deeper understanding of global water conditions and movement can be created. This information should be described in a Hydrologic Data Book that specifies the information content of each of these map layers so that they can be appropriately used and combined.

  2. Interactive Metro Map Editing.

    PubMed

    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

    USGS Publications Warehouse

    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. Jupiter Atmospheric Map

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Huge cyclonic storms, the Great Red Spot and the Little Red Spot, and wispy cloud patterns are seen in fascinating detail in this map of Jupiter's atmosphere obtained January 14-15, 2007, by the New Horizons Long Range Reconnaissance Imager (LORRI).

    The map combines information from 11 different LORRI images that were taken every hour over a 10-hour period -- a full Jovian day -- from 17:42 UTC on January 14 to 03:42 UTC on January 15. The New Horizons spacecraft was approximately 72 million kilometers (45 million miles) from Jupiter at the time.

    The LORRI pixels on the 'globe' of Jupiter were projected onto a rectilinear grid, similar to the way flat maps of Earth are created. The LORRI pixel intensities were corrected so that every point on the map appears as if the sun were directly overhead; some image sharpening was also applied to enhance detail. The polar regions of Jupiter are not shown on the map because the LORRI images do not sample those latitudes very well and artifacts are produced during the map-projection process.

  5. The National Map - Orthoimagery

    USGS Publications Warehouse

    Mauck, James; Brown, Kim; Carswell, William J.

    2009-01-01

    Orthorectified digital aerial photographs and satellite images of 1-meter (m) pixel resolution or finer make up the orthoimagery component of The National Map. The process of orthorectification removes feature displacements and scale variations caused by terrain relief and sensor geometry. The result is a combination of the image characteristics of an aerial photograph or satellite image and the geometric qualities of a map. These attributes allow users to: *Measure distance *Calculate areas *Determine shapes of features *Calculate directions *Determine accurate coordinates *Determine land cover and use *Perform change detection *Update maps The standard digital orthoimage is a 1-m or finer resolution, natural color or color infra-red product. Most are now produced as GeoTIFFs and accompanied by a Federal Geographic Data Committee (FGDC)-compliant metadata file. The primary source for 1-m data is the National Agriculture Imagery Program (NAIP) leaf-on imagery. The U.S. Geological Survey (USGS) utilizes NAIP imagery as the image layer on its 'Digital- Map' - a new generation of USGS topographic maps (http://nationalmap.gov/digital_map). However, many Federal, State, and local governments and organizations require finer resolutions to meet a myriad of needs. Most of these images are leaf-off, natural-color products at resolutions of 1-foot (ft) or finer.

  6. Building Better Volcanic Hazard Maps Through Scientific and Stakeholder Collaboration

    NASA Astrophysics Data System (ADS)

    Thompson, M. A.; Lindsay, J. M.; Calder, E.

    2015-12-01

    All across the world information about natural hazards such as volcanic eruptions, earthquakes and tsunami is shared and communicated using maps that show which locations are potentially exposed to hazards of varying intensities. Unlike earthquakes and tsunami, which typically produce one dominant hazardous phenomenon (ground shaking and inundation, respectively) volcanic eruptions can produce a wide variety of phenomena that range from near-vent (e.g. pyroclastic flows, ground shaking) to distal (e.g. volcanic ash, inundation via tsunami), and that vary in intensity depending on the type and location of the volcano. This complexity poses challenges in depicting volcanic hazard on a map, and to date there has been no consistent approach, with a wide range of hazard maps produced and little evaluation of their relative efficacy. Moreover, in traditional hazard mapping practice, scientists analyse data about a hazard, and then display the results on a map that is then presented to stakeholders. This one-way, top-down approach to hazard communication does not necessarily translate into effective hazard education, or, as tragically demonstrated by Nevado del Ruiz, Columbia in 1985, its use in risk mitigation by civil authorities. Furthermore, messages taken away from a hazard map can be strongly influenced by its visual design. Thus, hazard maps are more likely to be useful, usable and used if relevant stakeholders are engaged during the hazard map process to ensure a) the map is designed in a relevant way and b) the map takes into account how users interpret and read different map features and designs. The IAVCEI Commission on Volcanic Hazards and Risk has recently launched a Hazard Mapping Working Group to collate some of these experiences in graphically depicting volcanic hazard from around the world, including Latin America and the Caribbean, with the aim of preparing some Considerations for Producing Volcanic Hazard Maps that may help map makers in the future.

  7. Comparative gene map of hypertriglyceridaemia.

    PubMed

    Seda, O

    2004-01-01

    Elevated triglyceride levels in the circulation are currently recognized as an independent risk factor for coronary artery disease. Hypertriglyceridaemia represents one of the attributes of metabolic syndrome and is present in the most common genetic dyslipidaemia, the familial combined hyperlipidaemia. The factual concentration of triglycerides is determined by a complex interaction of environmental and genetic components. Deeper understanding of the causative gene variants and the mode of their participation in the pathogenesis of hypertriglyceridaemia is required for devising efficient therapy of hypertriglyceridaemia. This is the first systematic review of linkage and candidate gene studies dealing with the dissection of genetic determinants of (hyper)triglyceridaemia in human and two major mammalian model species, mouse and rat. Based on the merged sets of data, a synthetic view of the genetic component of triglyceridaemia, the "hypertriglyceridaemia gene map", is presented.

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

    USGS Publications Warehouse

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

    2001-01-01

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

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

    USGS Publications Warehouse

    Keane, Robert E.; Burgan, Robert E.; Van Wagtendonk, Jan W.

    2001-01-01

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

  10. MAP Algorithms for Decoding Linear Block Codes Based on Sectionalized Trellis Diagrams

    NASA Technical Reports Server (NTRS)

    Lui, Ye; Lin, Shu; Fossorier, Marc P. C.

    2000-01-01

    The maximum a posteriori probability (MAP) algorithm is a trellis-based MAP decoding algorithm. It is the heart of turbo (or iterative) decoding that achieves an error performance near the Shannon limit. Unfortunately, the implementation of this algorithm requires large computation and storage. Furthermore, its forward and backward recursions result in long decoding delay. For practical applications, this decoding algorithm must be simplified and its decoding complexity and delay must be reduced. In this paper, the MAP algorithm and its variations, such as log-MAP and max-log-MAP algorithms, are first applied to sectionalized trellises for linear block codes and carried out as two-stage decodings. Using the structural properties of properly sectionalized trellises, the decoding complexity and delay of the MAP algorithms can be reduced. Computation-wise optimum sectionalizations of a trellis for MAP algorithms are investigated. Also presented in this paper are bidirectional and parallel MAP decodings.

  11. Complex networks: Patterns of complexity

    NASA Astrophysics Data System (ADS)

    Pastor-Satorras, Romualdo; Vespignani, Alessandro

    2010-07-01

    The Turing mechanism provides a paradigm for the spontaneous generation of patterns in reaction-diffusion systems. A framework that describes Turing-pattern formation in the context of complex networks should provide a new basis for studying the phenomenon.

  12. Complex Networks in Psychological Models

    NASA Astrophysics Data System (ADS)

    Wedemann, R. S.; Carvalho, L. S. A. V. D.; Donangelo, R.

    We develop schematic, self-organizing, neural-network models to describe mechanisms associated with mental processes, by a neurocomputational substrate. These models are examples of real world complex networks with interesting general topological structures. Considering dopaminergic signal-to-noise neuronal modulation in the central nervous system, we propose neural network models to explain development of cortical map structure and dynamics of memory access, and unify different mental processes into a single neurocomputational substrate. Based on our neural network models, neurotic behavior may be understood as an associative memory process in the brain, and the linguistic, symbolic associative process involved in psychoanalytic working-through can be mapped onto a corresponding process of reconfiguration of the neural network. The models are illustrated through computer simulations, where we varied dopaminergic modulation and observed the self-organizing emergent patterns at the resulting semantic map, interpreting them as different manifestations of mental functioning, from psychotic through to normal and neurotic behavior, and creativity.

  13. Development of base maps' role in soil mapping

    NASA Astrophysics Data System (ADS)

    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.

  14. Geologic Mapping of Vesta

    NASA Technical Reports Server (NTRS)

    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

  15. Parcellating connectivity in spatial maps.

    PubMed

    Baldassano, Christopher; Beck, Diane M; Fei-Fei, Li

    2015-01-01

    A common goal in biological sciences is to model a complex web of connections using a small number of interacting units. We present a general approach for dividing up elements in a spatial map based on their connectivity properties, allowing for the discovery of local regions underlying large-scale connectivity matrices. Our method is specifically designed to respect spatial layout and identify locally-connected clusters, corresponding to plausible coherent units such as strings of adjacent DNA base pairs, subregions of the brain, animal communities, or geographic ecosystems. Instead of using approximate greedy clustering, our nonparametric Bayesian model infers a precise parcellation using collapsed Gibbs sampling. We utilize an infinite clustering prior that intrinsically incorporates spatial constraints, allowing the model to search directly in the space of spatially-coherent parcellations. After showing results on synthetic datasets, we apply our method to both functional and structural connectivity data from the human brain. We find that our parcellation is substantially more effective than previous approaches at summarizing the brain's connectivity structure using a small number of clusters, produces better generalization to individual subject data, and reveals functional parcels related to known retinotopic maps in visual cortex. Additionally, we demonstrate the generality of our method by applying the same model to human migration data within the United States. This analysis reveals that migration behavior is generally influenced by state borders, but also identifies regional communities which cut across state lines. Our parcellation approach has a wide range of potential applications in understanding the spatial structure of complex biological networks.

  16. Parallel algorithms for mapping pipelined and parallel computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1988-01-01

    Many computational problems in image processing, signal processing, and scientific computing are naturally structured for either pipelined or parallel computation. When mapping such problems onto a parallel architecture it is often necessary to aggregate an obvious problem decomposition. Even in this context the general mapping problem is known to be computationally intractable, but recent advances have been made in identifying classes of problems and architectures for which optimal solutions can be found in polynomial time. Among these, the mapping of pipelined or parallel computations onto linear array, shared memory, and host-satellite systems figures prominently. This paper extends that work first by showing how to improve existing serial mapping algorithms. These improvements have significantly lower time and space complexities: in one case a published O(nm sup 3) time algorithm for mapping m modules onto n processors is reduced to an O(nm log m) time complexity, and its space requirements reduced from O(nm sup 2) to O(m). Run time complexity is further reduced with parallel mapping algorithms based on these improvements, which run on the architecture for which they create the mappings.

  17. Complex chimerism

    PubMed Central

    Ma, Kimberly K.; Petroff, Margaret G.; Coscia, Lisa A.; Armenti, Vincent T.; Adams Waldorf, Kristina M.

    2013-01-01

    Thousands of women with organ transplantation have undergone successful pregnancies, however little is known about how the profound immunologic changes associated with pregnancy might influence tolerance or rejection of the allograft. Pregnant women with a solid organ transplant are complex chimeras with multiple foreign cell populations from the donor organ, fetus, and mother of the pregnant woman. We consider the impact of complex chimerism and pregnancy-associated immunologic changes on tolerance of the allograft both during pregnancy and the postpartum period. Mechanisms of allograft tolerance are likely dynamic during pregnancy and affected by the influx of fetal microchimeric cells, HLA relationships (between the fetus, pregnant woman and/or donor), peripheral T cell tolerance to fetal cells, and fetal minor histocompatibility antigens. Further research is necessary to understand the complex immunology during pregnancy and the postpartum period of women with a solid organ transplant. PMID:23974274

  18. Geologic Mapping in Southern Margaritifer Terra

    NASA Technical Reports Server (NTRS)

    Irwin, R. P., III; Grant, J. A.

    2010-01-01

    Margaritifer Terra records a complex geologic history [1-5], and the area from Holden crater through Ladon Valles, Ladon basin, and up to Morava Valles is no exception [e.g., 6-13]. The 1:500,000 geologic map of MTM quadrangles -15027, -20027, -25027, and -25032 (Figs. 1 and 2 [14]) identifies a range of units that delineate the history of water-related activity and regional geologic context.

  19. Reachability Maps for In Situ Operations

    NASA Technical Reports Server (NTRS)

    Deen, Robert G.; Leger, Patrick C.; Robinson, Matthew L.; Bonitz, Robert G.

    2013-01-01

    This work covers two programs that accomplish the same goal: creation of a "reachability map" from stereo imagery that tells where operators of a robotic arm can reach or touch the surface, and with which instruments. The programs are "marsreach" (for MER) and "phxreach." These programs make use of the planetary image geometry (PIG) library. However, unlike the other programs, they are not multi-mission. Because of the complexity of arm kinematics, the programs are specific to each mission.

  20. Computer-aided mapping of brain tissue

    SciTech Connect

    Rogers, W.T.; Schwaber, J.S.

    1987-08-15

    A computer-microscope system is described for use in capturing accurate, quantitative schematic (map) information from anatomical tissue sections. The system provides a rapid and convenient environment for acquisition and analysis for complex structures spread over large 3-D regions of the tissue. As a consequence of the complexity and subtlety of tissue analysis, most of the data acquisition functions of the system involve tight coupling between the hardware and the microscopist to preserve access to human judgment and intelligence. The instrument profoundly affects the ease and accuracy of neurobiological data analysis, making it practical to address previously inaccessible problems. Examples of data analyzed using the system are shown.

  1. Electronically-implemented coupled logistic maps

    NASA Astrophysics Data System (ADS)

    L'Her, Alexandre; Amil, Pablo; Rubido, Nicolás; Marti, Arturo C.; Cabeza, Cecilia

    2016-03-01

    The logistic map is a paradigmatic dynamical system originally conceived to model the discrete-time demographic growth of a population, which shockingly, shows that discrete chaos can emerge from trivial low-dimensional non-linear dynamics. In this work, we design and characterize a simple, low-cost, easy-to-handle, electronic implementation of the logistic map. In particular, our implementation allows for straightforward circuit-modifications to behave as different one-dimensional discrete-time systems. Also, we design a coupling block in order to address the behavior of two coupled maps, although, our design is unrestricted to the discrete-time system implementation and it can be generalized to handle coupling between many dynamical systems, as in a complex system. Our findings show that the isolated and coupled maps' behavior has a remarkable agreement between the experiments and the simulations, even when fine-tuning the parameters with a resolution of ~10-3. We support these conclusions by comparing the Lyapunov exponents, periodicity of the orbits, and phase portraits of the numerical and experimental data for a wide range of coupling strengths and map's parameters.

  2. A quantitative analysis of IRAS maps of molecular clouds

    NASA Technical Reports Server (NTRS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  3. Novice to Expert Cognition During Geologic Bedrock Mapping

    NASA Astrophysics Data System (ADS)

    Petcovic, H. L.; Libarkin, J.; Hambrick, D. Z.; Baker, K. M.; Elkins, J. T.; Callahan, C. N.; Turner, S.; Rench, T. A.; LaDue, N.

    2011-12-01

    Bedrock geologic mapping is a complex and cognitively demanding task. Successful mapping requires domain-specific content knowledge, visuospatial ability, navigation through the field area, creating a mental model of the geology that is consistent with field data, and metacognition. Most post-secondary geology students in the United States receive training in geologic mapping, however, not much is known about the cognitive processes that underlie successful bedrock mapping, or about how these processes change with education and experience. To better understand cognition during geologic mapping, we conducted a 2-year research study in which 67 volunteers representing a range from undergraduate sophomore to 20+ years professional experience completed a suite of cognitive measures plus a 1-day bedrock mapping task in the Rocky Mountains, Montana, USA. In addition to participants' geologic maps and field notes, the cognitive suite included tests and questionnaires designed to measure: (1) prior geologic experience, via a self-report survey; (2) geologic content knowledge, via a modified version of the Geoscience Concept Inventory; (3) visuospatial ability, working memory capacity, and perceptual speed, via paper-and-pencil and computerized tests; (4) use of space and time during mapping via GPS tracking; and (5) problem-solving in the field via think-aloud audio logs during mapping and post-mapping semi-structured interviews. Data were examined for correlations between performance on the mapping task and other measures. We found that both geological knowledge and spatial visualization ability correlated positively with accuracy in the field mapping task. More importantly, we found a Visuospatial Ability × Geological Knowledge interaction, such that visuospatial ability positively predicted mapping performance at low, but not high, levels of geological knowledge. In other words, we found evidence to suggest that visuospatial ability mattered for bedrock mapping for the

  4. Mapping strategies: Chromosome 16 workshop

    SciTech Connect

    Not Available

    1989-01-01

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

  5. Elementary maps on nest algebras

    NASA Astrophysics Data System (ADS)

    Li, Pengtong

    2006-08-01

    Let , be algebras and let , be maps. An elementary map of is an ordered pair (M,M*) such that for all , . In this paper, the general form of surjective elementary maps on standard subalgebras of nest algebras is described. In particular, such maps are automatically additive.

  6. Sri Lanka Malaria Maps

    PubMed Central

    Briët, Olivier JT; Gunawardena, Dissanayake M; van der Hoek, Wim; Amerasinghe, Felix P

    2003-01-01

    Background Despite a relatively good national case reporting system in Sri Lanka, detailed maps of malaria distribution have not been publicly available. Methods In this study, monthly records over the period 1995 – 2000 of microscopically confirmed malaria parasite positive blood film readings, at sub-district spatial resolution, were used to produce maps of malaria distribution across the island. Also, annual malaria trends at district resolution were displayed for the period 1995 – 2002. Results The maps show that Plasmodium vivax malaria incidence has a marked variation in distribution over the island. The incidence of Plasmodium falciparum malaria follows a similar spatial pattern but is generally much lower than that of P. vivax. In the north, malaria shows one seasonal peak in the beginning of the year, whereas towards the south a second peak around June is more pronounced. Conclusion This paper provides the first publicly available maps of both P. vivax and P. falciparum malaria incidence distribution on the island of Sri Lanka at sub-district resolution, which may be useful to health professionals, travellers and travel medicine professionals in their assessment of malaria risk in Sri Lanka. As incidence of malaria changes over time, regular updates of these maps are necessary. PMID:12914667

  7. Maps for America

    USGS Publications Warehouse

    Thompson, Morris M.

    1981-01-01

    "Maps for America" was originally published in 1979 as a Centennial Volume commemorating the Geological Survey's hundred years of service (1879-1979) in the earth sciences. It was an eminently fitting Centennial Year publication, for, since its establishment, the Geological Survey has continuously carried on an extensive program of mapping to provide knowledge of the topography, geology, hydrology, and natural resources of our Nation. This volume contains an organized presentation of information about the maps produced by the Geological Survey and other American organizations, public and private. Such maps are important tools for those in government and in private endeavors who are working to assure the wisest choices in managing the Nation's resources. They are particularly supportive of the Department of the Interior's role as the Nation's principal conservation agency. The second edition of "Maps for America" is intended primarily to replenish the dwindling supply of copies of the book, but it also contains a number of changes to correct or update the text and to provide more suitable illustrations in certain instances.

  8. Prioritising Infectious Disease Mapping

    PubMed Central

    Pigott, David M.; Howes, Rosalind E.; Wiebe, Antoinette; Battle, Katherine E.; Golding, Nick; Gething, Peter W.; Dowell, Scott F.; Farag, Tamer H.; Garcia, Andres J.; Kimball, Ann M.; Krause, L. Kendall; Smith, Craig H.; Brooker, Simon J.; Kyu, Hmwe H.; Vos, Theo; Murray, Christopher J. L.; Moyes, Catherine L.; Hay, Simon I.

    2015-01-01

    Background Increasing volumes of data and computational capacity afford unprecedented opportunities to scale up infectious disease (ID) mapping for public health uses. Whilst a large number of IDs show global spatial variation, comprehensive knowledge of these geographic patterns is poor. Here we use an objective method to prioritise mapping efforts to begin to address the large deficit in global disease maps currently available. Methodology/Principal Findings Automation of ID mapping requires bespoke methodological adjustments tailored to the epidemiological characteristics of different types of diseases. Diseases were therefore grouped into 33 clusters based upon taxonomic divisions and shared epidemiological characteristics. Disability-adjusted life years, derived from the Global Burden of Disease 2013 study, were used as a globally consistent metric of disease burden. A review of global health stakeholders, existing literature and national health priorities was undertaken to assess relative interest in the diseases. The clusters were ranked by combining both metrics, which identified 44 diseases of main concern within 15 principle clusters. Whilst malaria, HIV and tuberculosis were the highest priority due to their considerable burden, the high priority clusters were dominated by neglected tropical diseases and vector-borne parasites. Conclusions/Significance A quantitative, easily-updated and flexible framework for prioritising diseases is presented here. The study identifies a possible future strategy for those diseases where significant knowledge gaps remain, as well as recognising those where global mapping programs have already made significant progress. For many conditions, potential shared epidemiological information has yet to be exploited. PMID:26061527

  9. Tokamak divertor maps

    NASA Astrophysics Data System (ADS)

    Punjabi, Alkesh; Verma, Arun; Boozer, Allen

    1994-08-01

    A mapping method is developed to investigate the problem of determination and control of heat-deposition patterns on the plates of a tokamak divertor. The deposition pattern is largely determined by the magnetic field lines, which are mathematically equivalent to the trajectories of a single-degree-of-freedom time-dependent Hamiltonian system. Maps are natural tools to study the generic features of such systems. The general theory of maps is presented, and methods for incorporating various features of the magnetic field and particle motion in divertor tokamaks are given. Features of the magnetic field include the profile of the rotational transform, single- versus double-null divertor, reverse map, the effects of naturally occurring low M and N, and externally imposed high-M, high-N perturbations. Particle motion includes radial diffusion, pitch angle and energy scattering, and the electric sheath at the plate. The method is illustrated by calculating the stochastic broadening in a single- null divertor tokamak. Maps provide an efficient, economic and elegant method to study the problem of motion of plasma particles in the stochastic scrape-off layer.

  10. Researching Complexity.

    ERIC Educational Resources Information Center

    Sumara, Dennis J.

    2000-01-01

    Discusses what Complexity Theory (presented as a rubric that collects theoretical understandings from a number of domains such as ecology, biology, neurology, and education) suggests about mind, selfhood, intelligence, and practices of reading, and the import of these reconceptualizations to reader-response researchers. Concludes that developing…

  11. Complex interactions

    NASA Astrophysics Data System (ADS)

    de Régules, Sergio

    2016-04-01

    Complexity science - which describes phenomena such as collective and emergent behaviour - is the focus of a new centre where researchers are examining everything from the spread of influenza to what a healthy heartbeat looks like. Sergio de Régules reports.

  12. Amorphic complexity

    NASA Astrophysics Data System (ADS)

    Fuhrmann, G.; Gröger, M.; Jäger, T.

    2016-02-01

    We introduce amorphic complexity as a new topological invariant that measures the complexity of dynamical systems in the regime of zero entropy. Its main purpose is to detect the very onset of disorder in the asymptotic behaviour. For instance, it gives positive value to Denjoy examples on the circle and Sturmian subshifts, while being zero for all isometries and Morse-Smale systems. After discussing basic properties and examples, we show that amorphic complexity and the underlying asymptotic separation numbers can be used to distinguish almost automorphic minimal systems from equicontinuous ones. For symbolic systems, amorphic complexity equals the box dimension of the associated Besicovitch space. In this context, we concentrate on regular Toeplitz flows and give a detailed description of the relation to the scaling behaviour of the densities of the p-skeletons. Finally, we take a look at strange non-chaotic attractors appearing in so-called pinched skew product systems. Continuous-time systems, more general group actions and the application to cut and project quasicrystals will be treated in subsequent work.

  13. Mapping the Complexity of Public Pedagogy Scholarship: 1894-2010

    ERIC Educational Resources Information Center

    Sandlin, Jennifer A.; O'Malley, Michael P.; Burdick, Jake

    2011-01-01

    The term "public pedagogy" first appeared in 1894 and has been widely deployed as a theoretical construct in education research to focus on processes and sites of education beyond formal schooling, with a proliferation of its use by feminist and critical theorists occurring since the mid-1990s. This integrative literature review provides the first…

  14. Heat Map Visualization of Complex Environmental and Biomarker Measurements

    EPA Science Inventory

    Over the past decade, the assessment of human systems interactions with the environment has permeated all phases of environmental and public health research. We are invoking lessons learned from the broad discipline of Systems Biology research that focuses primarily on molecular ...

  15. Using KML for Thematic Mapping

    NASA Astrophysics Data System (ADS)

    Sandvik, B.

    2008-12-01

    Thematic mapping has a long history in cartography, but the new geobrowsers tend not to focus on this aspect of geographical information representation. This talk demonstrates how Keyhole Markup Language (KML) and geobrowsers can be used for thematic mapping. Due to their huge public interest and relative accessibility, geobrowsers are potentially capable of bringing thematic maps or visualisations to a wider audience. KML is not targeted towards thematic mapping, but it is possible to use KML elements in ways that were probably not intended. Current possibilities for making proportional symbol maps, chart maps, choropleth maps and animated maps with KML will be presented. An open source Thematic Mapping Engine (TME) has been developed as a proof-of-concept. This application allows the user to make thematic maps through an easy-to-use web interface. TME provides a low-cost solution suitable for non-profits and public- benefit organisations.

  16. Mapping the EEZ

    NASA Astrophysics Data System (ADS)

    Richman, Barbara T.

    A cooperative, multi-year program to map the largely uncharted Exclusive Economic Zone (EEZ), begun last month, has the potential for piggybacking scientific observations and research. On March 10, 1983, President Ronald Reagan proclaimed the mineral-rich zone as the area between the U.S. shoreline and 200 nautical miles outward. The United States has sovereign rights for exploration, exploitation, conservation, and management of all living and nonliving resources within the zone.The National Oceanic and Atmospheric Administration (NOAA) and the U.S. Geological Survey (USGS) will cooperate in the project that will map an area nearly twice the area of U.S. land. USGS responsibilities include definition of seafloor geology and definition of geological processes and resources, including sand and gravel, placers, phosphorites, manganese nodules, cobalt crusts, and sulfides (Eos, March 20, 1984, p. 105). NOAA, meanwhile, will be surveying, mapping, analyzing resources, and managing fisheries.

  17. Plasmid mapping computer program.

    PubMed

    Nolan, G P; Maina, C V; Szalay, A A

    1984-01-11

    Three new computer algorithms are described which rapidly order the restriction fragments of a plasmid DNA which has been cleaved with two restriction endonucleases in single and double digestions. Two of the algorithms are contained within a single computer program (called MPCIRC). The Rule-Oriented algorithm, constructs all logical circular map solutions within sixty seconds (14 double-digestion fragments) when used in conjunction with the Permutation method. The program is written in Apple Pascal and runs on an Apple II Plus Microcomputer with 64K of memory. A third algorithm is described which rapidly maps double digests and uses the above two algorithms as adducts. Modifications of the algorithms for linear mapping are also presented. PMID:6320105

  18. Ergodicity of polygonal slap maps

    NASA Astrophysics Data System (ADS)

    Del Magno, Gianluigi; Lopes Dias, João; Duarte, Pedro; Gaivão, José Pedro

    2014-08-01

    Polygonal slap maps are piecewise affine expanding maps of the interval obtained by projecting the sides of a polygon along their normals onto the perimeter of the polygon. These maps arise in the study of polygonal billiards with non-specular reflection laws. We study the absolutely continuous invariant probabilities (acips) of the slap maps for several polygons, including regular polygons and triangles. We also present a general method for constructing polygons with slap maps with more than one ergodic acip.

  19. Mapping your competitive position.

    PubMed

    D'Aveni, Richard A

    2007-11-01

    A price-benefit positioning map helps you see, through your customers' eyes, how your product compares with all its competitors in a market. You can draw such a map quickly and objectively, without having to resort to costly, time-consuming consumer surveys or subjective estimates of the excellence of your product and the shortcomings of all the others. Creating a positioning map involves three steps: First, define your market to include everything your customers might consider to be your product's competitors or substitutes. Second, track the price your customers actually pay (wholesale or retail? bundled or unbundled?) and identify what your customers see as your offering's primary benefit. This is done through regression analysis, determining which of the product's attributes (as described objectively by rating services, government agencies, R&D departments, and the like) explains most of the variance in its price. Third, draw the map by plotting on a graph the position of every product in the market you've selected according to its price and its level of primary benefit, and draw a line that runs through the middle of the points. What you get is a picture of the competitive landscape of your market, where all the products above the line command a price premium owing to some secondary benefit customers value, and all those below the line are positioned to earn market share through lower prices and reduced secondary benefits. Using examples as varied as Harley-Davidson motorcycles, Motorola cell phones, and the New York restaurant market, Tuck professor D'Aveni demonstrates some of the many ways the maps can be used: to locate unoccupied or less-crowded spaces in highly competitive markets, for instance, or to identify opportunities created through changes in the relationship between the primary benefit and prices. The maps even allow companies to anticipate--and counter-- rivals' strategies. R eprint RO711G PMID:18159791

  20. Mapping your competitive position.

    PubMed

    D'Aveni, Richard A

    2007-11-01

    A price-benefit positioning map helps you see, through your customers' eyes, how your product compares with all its competitors in a market. You can draw such a map quickly and objectively, without having to resort to costly, time-consuming consumer surveys or subjective estimates of the excellence of your product and the shortcomings of all the others. Creating a positioning map involves three steps: First, define your market to include everything your customers might consider to be your product's competitors or substitutes. Second, track the price your customers actually pay (wholesale or retail? bundled or unbundled?) and identify what your customers see as your offering's primary benefit. This is done through regression analysis, determining which of the product's attributes (as described objectively by rating services, government agencies, R&D departments, and the like) explains most of the variance in its price. Third, draw the map by plotting on a graph the position of every product in the market you've selected according to its price and its level of primary benefit, and draw a line that runs through the middle of the points. What you get is a picture of the competitive landscape of your market, where all the products above the line command a price premium owing to some secondary benefit customers value, and all those below the line are positioned to earn market share through lower prices and reduced secondary benefits. Using examples as varied as Harley-Davidson motorcycles, Motorola cell phones, and the New York restaurant market, Tuck professor D'Aveni demonstrates some of the many ways the maps can be used: to locate unoccupied or less-crowded spaces in highly competitive markets, for instance, or to identify opportunities created through changes in the relationship between the primary benefit and prices. The maps even allow companies to anticipate--and counter-- rivals' strategies. R eprint RO711G