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Sample records for monopyrrolide map complexes

  1. 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

  2. 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.

  3. Mapping dynamical systems onto complex networks

    NASA Astrophysics Data System (ADS)

    Borges, E. P.; Cajueiro, D. O.; Andrade, R. F. S.

    2007-08-01

    The objective of this study is to design a procedure to characterize chaotic dynamical systems, in which they are mapped onto a complex network. The nodes represent the regions of space visited by the system, while the edges represent the transitions between these regions. Parameters developed to quantify the properties of complex networks, including those related to higher order neighbourhoods, are used in the analysis. The methodology is tested on the logistic map, focusing on the onset of chaos and chaotic regimes. The corresponding networks were found to have distinct features that are associated with the particular type of dynamics that generated them.

  4. 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.

  5. 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

  6. Is Mapping of Complex Fractionated Electrograms Obsolete?

    PubMed

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

    2015-08-01

    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. Limits on fine mapping of complex traits

    SciTech Connect

    1996-05-01

    We recently published a paper in the journal on high-resolution genetic mapping of complex traits. In that paper, we considered the confidence region for the position of a gene localized by genetic mapping. We showed that the size of this confidence region increases rapidly as the trait becomes more complex (that is, as the relative risk or the proportion of alleles shared by affected relatives decreases). We concluded that using affected-relative-pair analysis to localize a gene conferring a modest increased risk to a region suitable for positional cloning (e.g., 1 cM) requires a large number of relative pairs (or, more generally, meioses). Since the paper appeared, we have discovered an intuitive way to understand the difficulty of fine mapping of susceptibility genes for complex traits. The insight was motivated by a colleague who inquired why one could not simply confine the search for a susceptibility gene to the region of maximum allele sharing in a sib-pair (or other relative pair) data set. The key question is thus: what is the chance that susceptibility gene will not be in the region of maximum allele sharing? The answer is easily obtained by using the methods described in our previous paper. 3 refs.

  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. Strategies for fine-mapping complex traits

    PubMed Central

    Spain, Sarah L.; Barrett, Jeffrey C.

    2015-01-01

    Genome-wide association studies (GWAS) have identified thousands of robust and replicable genetic associations for complex disease. However, the identification of the causal variants that underlie these associations has been more difficult. This problem of fine-mapping association signals predates GWAS, but the last few years have seen a surge of studies aimed at pinpointing causal variants using both statistical evidence from large association data sets and functional annotations of genetic variants. Combining these two approaches can often determine not only the causal variant but also the target gene. Recent contributions include analyses of custom genotyping arrays, such as the Immunochip, statistical methods to identify credible sets of causal variants and the addition of functional genomic annotations for coding and non-coding variation to help prioritize variants and discern functional consequence and hence the biological basis of disease risk. PMID:26157023

  10. Mapping ecological states in a complex environment

    NASA Astrophysics Data System (ADS)

    Steele, C. M.; Bestelmeyer, B.; Burkett, L. M.; Ayers, E.; Romig, K.; Slaughter, A.

    2013-12-01

    analysis provides a platform for classification that more closely resembles human recognition of objects within a remotely sensed image. The analysis presented here compares multiple thematic maps created for test locations on the USDA-ARS Jornada Experimental Range ranch. Three study sites in different pastures, each 300 ha in size, were selected for comparison on the basis of their ecological site type (';Clayey', ';Sandy' and a combination of both) and the degree of complexity of vegetation cover. Thematic maps were produced for each study site using (i) manual interpretation of digital aerial photography (by five independent interpreters); (ii) object-oriented, decision-tree classification of fine and moderate spatial resolution imagery (Quickbird; Landsat Thematic Mapper) and (iii) ground survey. To identify areas of uncertainty, we compared agreement in location, areal extent and class assignation between 5 independently produced, manually-digitized ecological state maps and with the map created from ground survey. Location, areal extent and class assignation of the map produced by object-oriented classification was also assessed with reference to the ground survey map.

  11. Mapping of HCG-receptor complexes.

    PubMed

    Remy, J J; Couture, L; Pantel, J; Haertlé, T; Rabesona, H; Bozon, V; Pajot-Augy, E; Robert, P; Troalen, F; Salesse, R; Bidart, J M

    1996-12-20

    Molecular forms of the porcine LH/CG receptor (pLHR) and complexes between hCG and either the full-length pLHR or its extracellular domain (ectodomain) have been produced in various recombinant systems. In COS cells and in the baculovirus insect cells system, the co-expression of the ecto- and endo-domains reconstituted a functional receptor where the association of the two domains seems to depend upon the presence of disulfide bridges. According to previous observations [39], synthetic peptides mimicking three regions of the ectodomain (21-38, 100-115, 250-272) were found to inhibit hormone binding and stimulation of cAMP production. Antisera raised against these peptides contained anti-peptide antibodies (Ab) able to interfere with hormone signalling. Moreover, the results of peptide mapping indicated that some peptides stretches may be more involved in signalling rather than in binding. Immunochemical mapping based on monoclonal antibodies (mAbs) was used to probe the hCG-ectodomain complex. It appeared that mAbs directed to epitopes present on the 'beta-tip' of hCG (assembled from the beta subunit loops 3 and 1, and previously designated site IIIb) and on the 'alpha-tip' (alpha subunit loops 1 and 3, site IIIa) bound to hCG-receptor complexes, whereas a conformational epitope (defined by the alpha-beta interface between beta seat belt C-terminus and alpha loop 2, site II) was masked. Interestingly, we and others previously reported that, in the hCG-full length receptor complex, site IIIa was shielded to mAb binding. A peptide mimicking the second extracellular loop (EL2) of the receptor endodomain was found to prevent the binding of a mAb directed to site IIIa, suggesting that this region of the endodomain may be interacting with the 'alpha-tip'. In the full-length, membrane anchored pLHR, the EL2 peptide inhibited hCG-induced cAMP production, but not binding. The possibility of inhibiting stimulation without inhibition of binding gives support to the 'negative

  12. A Game Map Complexity Measure Based on Hamming Distance

    NASA Astrophysics Data System (ADS)

    Li, Yan; Su, Pan; Li, Wenliang

    With the booming of PC game market, Game AI has attracted more and more researches. The interesting and difficulty of a game are relative with the map used in game scenarios. Besides, the path-finding efficiency in a game is also impacted by the complexity of the used map. In this paper, a novel complexity measure based on Hamming distance, called the Hamming complexity, is introduced. This measure is able to estimate the complexity of binary tileworld. We experimentally demonstrated that Hamming complexity is highly relative with the efficiency of A* algorithm, and therefore it is a useful reference to the designer when developing a game map.

  13. 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…

  14. Functional mapping - how to map and study the genetic architecture of dynamic complex traits.

    PubMed

    Wu, Rongling; Lin, Min

    2006-03-01

    The development of any organism is a complex dynamic process that is controlled by a network of genes as well as by environmental factors. Traditional mapping approaches for analysing phenotypic data measured at a single time point are too simple to reveal the genetic control of developmental processes. A general statistical mapping framework, called functional mapping, has been proposed to characterize, in a single step, the quantitative trait loci (QTLs) or nucleotides (QTNs) that underlie a complex dynamic trait. Functional mapping estimates mathematical parameters that describe the developmental mechanisms of trait formation and expression for each QTL or QTN. The approach provides a useful quantitative and testable framework for assessing the interplay between gene actions or interactions and developmental changes. PMID:16485021

  15. 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.

  16. 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

  17. 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

  18. 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

    2016-01-01

    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

  19. Degree Complexity of Birational Maps Related to Matrix Inversion

    NASA Astrophysics Data System (ADS)

    Bedford, Eric; Truong, Tuyen Trung

    2010-09-01

    For a q × q matrix x = ( x i, j ) we let {J(x)=(x_{i,j}^{-1})} be the Hadamard inverse, which takes the reciprocal of the elements of x. We let {I(x)=(x_{i,j})^{-1}} denote the matrix inverse, and we define {K=Icirc J} to be the birational map obtained from the composition of these two involutions. We consider the iterates {K^n=Kcirc\\cdotscirc K} and determine the degree complexity of K, which is the exponential rate of degree growth {δ(K)=lim_{ntoinfty}left( deg(K^n) right)^{1/n}} of the degrees of the iterates. Earlier studies of this map were restricted to cyclic matrices, in which case K may be represented by a simpler map. Here we show that for general matrices the value of δ( K) is equal to the value conjectured by Anglès d’Auriac, Maillard and Viallet.

  20. 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

  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. 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.

  4. Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing

    PubMed Central

    Guo, Jianjun; Fan, Jue; Hauser, Bernard A.; Rhee, Seung Y.

    2015-01-01

    Complex traits such as crop performance and human diseases are controlled by multiple genetic loci, many of which have small effects and often go undetected by traditional quantitative trait locus (QTL) mapping. Recently, bulked segregant analysis with large F2 pools and genome-level markers (named extreme-QTL or X-QTL mapping) has been used to identify many QTL. To estimate parameters impacting QTL detection for X-QTL mapping, we simulated the effects of population size, marker density, and sequencing depth of markers on QTL detectability for traits with differing heritabilities. These simulations indicate that a high (>90%) chance of detecting QTL with at least 5% effect requires 5000× sequencing depth for a trait with heritability of 0.4−0.7. For most eukaryotic organisms, whole-genome sequencing at this depth is not economically feasible. Therefore, we tested and confirmed the feasibility of applying deep sequencing of target-enriched markers for X-QTL mapping. We used two traits in Arabidopsis thaliana with different heritabilities: seed size (H2 = 0.61) and seedling greening in response to salt (H2 = 0.94). We used a modified G test to identify QTL regions and developed a model-based statistical framework to resolve individual peaks by incorporating recombination rates. Multiple QTL were identified for both traits, including previously undiscovered QTL. We call our method target-enriched X-QTL (TEX-QTL) mapping; this mapping approach is not limited by the genome size or the availability of recombinant inbred populations and should be applicable to many organisms and traits. PMID:26530422

  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. 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.

  7. Mapping energy transfer channels in fucoxanthin-chlorophyll protein complex.

    PubMed

    Gelzinis, Andrius; Butkus, Vytautas; Songaila, Egidijus; Augulis, Ramūnas; Gall, Andrew; Büchel, Claudia; Robert, Bruno; Abramavicius, Darius; Zigmantas, Donatas; Valkunas, Leonas

    2015-02-01

    Fucoxanthin-chlorophyll protein (FCP) is the key molecular complex performing the light-harvesting function in diatoms, which, being a major group of algae, are responsible for up to one quarter of the total primary production on Earth. These photosynthetic organisms contain an unusually large amount of the carotenoid fucoxanthin, which absorbs the light in the blue-green spectral region and transfers the captured excitation energy to the FCP-bound chlorophylls. Due to the large number of fucoxanthins, the excitation energy transfer cascades in these complexes are particularly tangled. In this work we present the two-color two-dimensional electronic spectroscopy experiments on FCP. Analysis of the data using the modified decay associated spectra permits a detailed mapping of the excitation frequency dependent energy transfer flow with a femtosecond time resolution. PMID:25445318

  8. 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.

  9. Radiofrequency Mapping of Compact HII Regions: The RCW95 Complex

    NASA Astrophysics Data System (ADS)

    Barres de Almeida, U.; Abraham, Z.; Roman-Lopes, A.

    2006-06-01

    We present a 2'-resolution, 43 GHz continuum map of the free-free radio emission of the complex RCW95 made with the 14-meter antennae of the Itapetinga radio observatory in Brazil. RCW95 is a small cloud (10'×10') with coordinates α = 15^{h}44^{m}43^{s} and δ = - 54°05'54'', associated with the radio source G326.7+0.6 and identified as an optical HII region by Rodgers et al. (1960). The region encloses three strong IRAS point sources (IRAS 15408-5356, 15411-5352 and 15412-5359) with colours of compact HII regions. This work was motivated by recent studies of the stellar population of the IRAS source 15408 (Roman-Lopes & Abraham 2004) that revealed that the source is a site of ongoing massive star formation. Previous mapping of the region were conducted by Goss & Shaver (1970) in 5 GHz with low resolution and detected strong continuum emission in this direction, but could not resolve the individual sources. In this mapping we were able to separate the emission of each HII region, identifying the radio counterparts to the IRAS sources and deriving fluxes of 7.3+/-0.3 and 3.4+/-0.5 Jy for IRAS 15408 and 15411, respectively, and an upper limit of 2.0 Jy for the flux of IRAS15412. We could also identify the radio continuum counterpart of the methanol maser detected by Ellingsen et al. (1996), firstly associated by its discoverers with IRAS15408. Finally, we report the results of an unpublished 22.2 GHz water maser survey that resulted on the identification of 7 different emission lines associated with all three IRAS sources in the region, closing the long debate on the nature of IRAS15411-5352 and supporting evidence for IRAS15412 being another star-formation site in the region.

  10. Introduction: Mapping and control of complex cardiac arrhythmias.

    PubMed

    Christini, David J.; Glass, Leon

    2002-09-01

    This paper serves as an introduction to the Focus Issue on mapping and control of complex cardiac arrhythmias. We first introduce basic concepts of cardiac electrophysiology and describe the main clinical methods being used to treat arrhythmia. We then provide a brief summary of the main themes contained in the articles in this Focus Issue. In recent years there have been important advances in the ability to map the spread of excitation in intact hearts and in laboratory settings. This work has been combined with simulations that use increasingly realistic geometry and physiology. Waves of excitation and contraction in the heart do not always propagate with constant velocity but are often subject to instabilities that may lead to fluctuations in velocity and cycle time. Such instabilities are often treated best in the context of simple one- or two-dimensional geometries. An understanding of the mechanisms of propagation and wave stability is leading to the implementation of different stimulation protocols in an effort to modify or eliminate abnormal rhythms. (c) 2002 American Institute of Physics. PMID:12779601

  11. 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.

  12. 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

  13. Mapping Nucleotide Sequences that Encode Complex Binary Disease Traits with HapMap

    PubMed Central

    Cui, Yuehua; Fu, Wenjiang; Sun, Kelian; Romero, Roberto; Wu, Rongling

    2007-01-01

    Detecting the patterns of DNA sequence variants across the human genome is a crucial step for unraveling the genetic basis of complex human diseases. The human HapMap constructed by single nucleotide polymorphisms (SNPs) provides efficient sequence variation information that can speed up the discovery of genes related to common diseases. In this article, we present a generalized linear model for identifying specific nucleotide variants that encode complex human diseases. A novel approach is derived to group haplotypes to form composite diplotypes, which largely reduces the model degrees of freedom for an association test and hence increases the power when multiple SNP markers are involved. An efficient two-stage estimation procedure based on the expectation-maximization (EM) algorithm is derived to estimate parameters. Non-genetic environmental or clinical risk factors can also be fitted into the model. Computer simulations show that our model has reasonable power and type I error rate with appropriate sample size. It is also suggested through simulations that a balanced design with approximately equal number of cases and controls should be preferred to maintain small estimation bias and reasonable testing power. To illustrate the utility, we apply the method to a genetic association study of large for gestational age (LGA) neonates. The model provides a powerful tool for elucidating the genetic basis of complex binary diseases. PMID:19384427

  14. GENOME-WIDE COMPLEX TRAIT DISSECTION THROUGH NESTED ASSOCIATION MAPPING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes), which simultaneously exploits the advantages of both linkage analysis and association mapping. We de...

  15. 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.

  16. 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

  17. 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

  18. 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

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

    PubMed

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

    2016-07-01

    The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. PMID:26801360

  20. Map helps unravel complexities of the southwestern Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Collot, Julien; Vendé-Leclerc, Myriam; Rouillard, Pierrick; Lafoy, Yves; Géli, Louis

    2012-01-01

    The southwestern Pacific Ocean region hosts submerged continental margins, ridges, sedimentary basins, and volcanic arcs located around Papua New Guinea, New Zealand, Australia, and Fiji. The geological history of this vast region has remained controversial, and to improve understanding of the processes that controlled its geodynamical evolution, it is essential to place each piece of available data in a regional spatiotemporal framework. To this end, a new map, entitled “Structural Provinces of the Southwest Pacific,” was released by the Geological Survey of New Caledonia in May 2011. The publication consists of two parts: (1) a 40-page booklet of geological notes, which documents the nature and age of each structure and contains an associated list of references; and (2) a 3- x 4-foot poster of a structural map revealing the nature of the basement, location, and type of the main structural features (see simplified version in Figure 1) and the age of formation using the international standards for geological color codes established by the Commission for the Geological Map of the World (CGMW) (see http://ccgm.free.fr/index.html).

  1. Joined up Thinking? Evaluating the Use of Concept-Mapping to Develop Complex System Learning

    ERIC Educational Resources Information Center

    Stewart, Martyn

    2012-01-01

    In the physical and natural sciences, the complexity of natural systems and their interactions is becoming better understood. With increased emphasis on learning about complex systems, students will be encountering concepts that are dynamic, ill-structured and interconnected. Concept-mapping is a method considered particularly valuable for…

  2. Learning flexible sensori-motor mappings in a complex network.

    PubMed

    Vasilaki, Eleni; Fusi, Stefano; Wang, Xiao-Jing; Senn, Walter

    2009-02-01

    Given the complex structure of the brain, how can synaptic plasticity explain the learning and forgetting of associations when these are continuously changing? We address this question by studying different reinforcement learning rules in a multilayer network in order to reproduce monkey behavior in a visuomotor association task. Our model can only reproduce the learning performance of the monkey if the synaptic modifications depend on the pre- and postsynaptic activity, and if the intrinsic level of stochasticity is low. This favored learning rule is based on reward modulated Hebbian synaptic plasticity and shows the interesting feature that the learning performance does not substantially degrade when adding layers to the network, even for a complex problem. PMID:19153762

  3. 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

  4. Mapping genes of complex psychiatric diseases in Daghestan genetic isolates.

    PubMed

    Bulayeva, Kazima B; Leal, Suzanne M; Pavlova, Tatiana A; Kurbanov, Ruslan M; Glatt, Stephen J; Bulayev, Oleg A; Tsuang, Ming T

    2005-01-01

    Genetic isolates, which provide outstanding opportunities for identification of susceptibility genes for complex diseases, can be classified as primary (having an ancient demographic history in a stable environment) or secondary (having a younger demographic history) Neel [1992: Minority populations: Genetics, demography, and health, pp. 1-13]. Daghestan contains 26 out of 50 indigenous Caucasus ethnicities that have been in existence for hundreds of generations in the same highland region. The ethnic groups are subdivided into numerous primary isolates. The founder effect and gene drift in these primary isolates may have caused aggregation of specific haplotypes with limited numbers of pathogenic alleles and loci in some isolates relative to others. These are expressed as inter-population differences in lifetime prevalence and features of certain complex clinical phenotypes and in patterns of genetic linkage and linkage disequilibrium (LD). Stable highland and ethnic-cultural environments have led to increased penetrance and a reduced number of phenocopies, which typically hamper the identification of any susceptibility genes for complex diseases. Owing to these characteristics of the primary isolates, a comparative linkage study in the primary isolates allows us to define the number of susceptibility genes for any complex disease and to identify the source of variability and non-replication of linkage analysis results. As part of an ongoing study, seven extended schizophrenia and one nonspecific mental retardation kindreds have been ascertained from Daghestan isolates. Lifetime morbid risk for schizophrenia in the isolates varied from 0 to 5%. A genome scan with markers spaced 10 cM apart was carried out on these pedigrees and linkage analysis was performed using descent graph methods, as implemented in Simwalk2. To identify regions containing susceptibility genes within these kindreds, we followed up those regions with non-parametric and parametric linkage

  5. 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

  6. 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. PMID:23708188

  7. Bayesian Multiple Quantitative Trait Loci Mapping for Complex Traits Using Markers of the Entire Genome

    PubMed Central

    Huang, Hanwen; Eversley, Chevonne D.; Threadgill, David W.; Zou, Fei

    2007-01-01

    A Bayesian methodology has been developed for multiple quantitative trait loci (QTL) mapping of complex binary traits that follow liability threshold models. Unlike most QTL mapping methods where only one or a few markers are used at a time, the proposed method utilizes all markers across the genome simultaneously. The outperformance of our Bayesian method over the traditional single-marker analysis and interval mapping has been illustrated via simulations and real data analysis to identify candidate loci associated with colorectal cancer. PMID:17483433

  8. Contemporary Mapping Techniques of Complex Cardiac Arrhythmias - Identifying and Modifying the Arrhythmogenic Substrate.

    PubMed

    Koutalas, Emmanuel; Rolf, Sascha; Dinov, Borislav; Richter, Sergio; Arya, Arash; Bollmann, Andreas; Hindricks, Gerhard; Sommer, Philipp

    2015-05-01

    Cardiac electrophysiology has moved a long way forward during recent decades in the comprehension and treatment of complex cardiac arrhythmias. Contemporary electroanatomical mapping systems, along with state-of-the-art technology in the manufacture of electrophysiology catheters and cardiac imaging modalities, have significantly enriched our armamentarium, enabling the implementation of various mapping strategies and techniques in electrophysiology procedures. Beyond conventional mapping strategies, ablation of complex fractionated electrograms and rotor ablation in atrial fibrillation ablation procedures, the identification and modification of the underlying arrhythmogenic substrate has emerged as a strategy that leads to improved outcomes. Arrhythmogenic substrate modification also has a major role in ventricular tachycardia ablation procedures. Optimisation of contact between tissue and catheter and image integration are a further step forward to augment our precision and effectiveness. Hybridisation of existing technologies with a reasonable cost should be our goal over the next few years. PMID:26835095

  9. Contemporary Mapping Techniques of Complex Cardiac Arrhythmias – Identifying and Modifying the Arrhythmogenic Substrate

    PubMed Central

    Koutalas, Emmanuel; Rolf, Sascha; Dinov, Borislav; Richter, Sergio; Arya, Arash; Bollmann, Andreas; Hindricks, Gerhard

    2015-01-01

    Cardiac electrophysiology has moved a long way forward during recent decades in the comprehension and treatment of complex cardiac arrhythmias. Contemporary electroanatomical mapping systems, along with state-of-the-art technology in the manufacture of electrophysiology catheters and cardiac imaging modalities, have significantly enriched our armamentarium, enabling the implementation of various mapping strategies and techniques in electrophysiology procedures. Beyond conventional mapping strategies, ablation of complex fractionated electrograms and rotor ablation in atrial fibrillation ablation procedures, the identification and modification of the underlying arrhythmogenic substrate has emerged as a strategy that leads to improved outcomes. Arrhythmogenic substrate modification also has a major role in ventricular tachycardia ablation procedures. Optimisation of contact between tissue and catheter and image integration are a further step forward to augment our precision and effectiveness. Hybridisation of existing technologies with a reasonable cost should be our goal over the next few years. PMID:26835095

  10. TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The association mapping of complex traits is becoming the method of choice in plant and animal genetics. In most samples, researchers have to deal with both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed line...

  11. 1.0 Mm Maps and Radial Density Distributions of Southern Hii/molecular Cloud Complexes

    NASA Technical Reports Server (NTRS)

    Cheung, L. H.; Frogel, J. A.; Gezar, D. Y.; Hauser, M. G.

    1980-01-01

    Several 1.0 continuum mapping observations were made of seven southern hemisphere h12/molecular cloud complexes with 65 arcsec resolution. The radial density distribution of the clouds with central luminosity sources was determined observationally. Strong similarities in morphology and general physical conditions were found to exist among all of the southern clouds in the sample.

  12. "Sounds of Intent": Mapping Musical Behaviour and Development in Children and Young People with Complex Needs

    ERIC Educational Resources Information Center

    Welch, Graham; Ockelford, Adam; Carter, Fern-Chantele; Zimmermann, Sally-Anne; Himonides, Evangelos

    2009-01-01

    This article reports on the first year of an Esmee Fairbairn Foundation-funded research project into the design and evaluation of an original "framework" for mapping the behaviour and development in, and through, music for children with complex needs, specifically those with profound and multiple learning difficulties (PMLD). An initial four-month…

  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. Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

    SciTech Connect

    Markillie, Lye Meng; Lin, Chiann Tso; Adkins, Joshua N.; Auberry, Deanna L.; Hill, Eric A.; Hooker, Brian S.; Moore, Priscilla A.; Moore, Ronald J.; Shi, Liang; Wiley, H. S.; Kery, Vladimir

    2005-04-11

    Most of the current methods for purification and identification of protein complexes use endogenous expression of affinity tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, gel separation, in-gel digestion and mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pulldown assay with denaturing elution, trypsin digestion in organic solvent and LC ESI MS/MS protein identification using SEQUEST analysis. Our method is simple, easy to scale up and automate thus suitable for high throughput mapping of protein interaction networks and functional proteomics.

  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

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

    2007-09-01

    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. 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

  19. High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

    PubMed Central

    Cubillos, Francisco A.; Parts, Leopold; Salinas, Francisco; Bergström, Anders; Scovacricchi, Eugenio; Zia, Amin; Illingworth, Christopher J. R.; Mustonen, Ville; Ibstedt, Sebastian; Warringer, Jonas; Louis, Edward J.; Durbin, Richard; Liti, Gianni

    2013-01-01

    A large fraction of human complex trait heritability is due to a high number of variants with small marginal effects and their interactions with genotype and environment. Such alleles are more easily studied in model organisms, where environment, genetic makeup, and allele frequencies can be controlled. Here, we examine the effect of natural genetic variation on heritable traits in a very large pool of baker’s yeast from a multiparent 12th generation intercross. We selected four representative founder strains to produce the Saccharomyces Genome Resequencing Project (SGRP)-4X mapping population and sequenced 192 segregants to generate an accurate genetic map. Using these individuals, we mapped 25 loci linked to growth traits under heat stress, arsenite, and paraquat, the majority of which were best explained by a diverging phenotype caused by a single allele in one condition. By sequencing pooled DNA from millions of segregants grown under heat stress, we further identified 34 and 39 regions selected in haploid and diploid pools, respectively, with most of the selection against a single allele. While the most parsimonious model for the majority of loci mapped using either approach was the effect of an allele private to one founder, we could validate examples of pleiotropic effects and complex allelic series at a locus. SGRP-4X is a deeply characterized resource that provides a framework for powerful and high-resolution genetic analysis of yeast phenotypes and serves as a test bed for testing avenues to attack human complex traits. PMID:24037264

  20. 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.

  1. 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

  2. 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.

  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. Complex 2D matrix model and geometrical map on the complex-Nc plane

    NASA Astrophysics Data System (ADS)

    Nawa, Kanabu; Ozaki, Sho; Nagahiro, Hideko; Jido, Daisuke; Hosaka, Atsushi

    2013-08-01

    We study the parameter dependence of the internal structure of resonance states by formulating a complex two-dimensional (2D) matrix model, where the two dimensions represent two levels of resonances. We calculate a critical value of the parameter at which a "nature transition" with character exchange occurs between two resonance states, from the viewpoint of geometry on complex-parameter space. Such a critical value is useful for identifying the internal structure of resonance states with variation of the parameter in the system. We apply the model to analyze the internal structure of hadrons with variation of the color number N_c from infty to a realistic value 3. By regarding 1/N_c as the variable parameter in our model, we calculate a critical color number of the nature transition between hadronic states in terms of a quark-antiquark pair and a mesonic molecule as exotics from the geometry on the complex-N_c plane. For large-N_c effective theory, we employ the chiral Lagrangian induced by holographic QCD with a D4/D8/overline {D8} multi-D brane system in type IIA superstring theory.

  5. Structure–function mapping of a heptameric module in the nuclear pore complex

    PubMed Central

    Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; Diaz-Avalos, Ruben; Velazquez-Muriel, Javier; Franke, Josef D.; Williams, Rosemary; Stokes, David L.; Chait, Brian T.

    2012-01-01

    The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ∼600-kD heptameric Nup84 complex, to a precision of ∼1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain–mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC’s interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution. PMID:22331846

  6. Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach.

    PubMed Central

    George, A W; Visscher, P M; Haley, C S

    2000-01-01

    There is a growing need for the development of statistical techniques capable of mapping quantitative trait loci (QTL) in general outbred animal populations. Presently used variance component methods, which correctly account for the complex relationships that may exist between individuals, are challenged by the difficulties incurred through unknown marker genotypes, inbred individuals, partially or unknown marker phases, and multigenerational data. In this article, a two-step variance component approach that enables practitioners to routinely map QTL in populations with the aforementioned difficulties is explored. The performance of the QTL mapping methodology is assessed via its application to simulated data. The capacity of the technique to accurately estimate parameters is examined for a range of scenarios. PMID:11102397

  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. 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

  9. Mars radar mapping: Strong depolarized echoes from the Elysium/Amazonis outflow channel complex

    NASA Technical Reports Server (NTRS)

    Harmon, J. K.; Sulzer, M. P.; Perillat, P.

    1991-01-01

    A new technique was used to make radar maps of Mars with the Arecibo radiotelescope. The observations were made during the 1990 opposition (close approach) of Mars. Among the most interesting of the preliminary results is the discovery of strong depolarized echoes from the enormous Elysium/Amazonis outflow channel complex. These strong echoes may represent rough-surface scattering off the youngest lava flows on Mars.

  10. 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

  11. 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).

  12. 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

  13. 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)

  14. 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.

  15. Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane

    PubMed Central

    2014-01-01

    Background The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the genome. We have used the genetic map of a sugarcane cultivar to generate a consensus genetic map to increase genome coverage for comparison to the sorghum genome. We have utilized the recently developed sugarcane DArT array to increase the marker density within the genetic map. The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane. Results Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others. On a macrosyntenic level a good collinearity was observed between sugarcane and sorghum for 4 of the 8 homology groups (HGs). These 4 HGs were syntenic to four sorghum chromosomes with from 98% to 100% of these chromosomes covered by these linked markers. Four major chromosome rearrangements were identified between the other four sugarcane HGs and sorghum, two of which were condensations of chromosomes reducing the basic chromosome number of sugarcane from x = 10 to x = 8. This macro level of synteny was transferred to other members within the Poaceae family such as maize to uncover the important evolutionary relationships that exist between sugarcane and these species. Conclusions Comparative mapping of sugarcane to the sorghum genome has revealed new information on the genome structure of sugarcane which will help guide identification of important genes for use in sugarcane breeding. Furthermore of the four major chromosome rearrangements identified in this study, three were common to maize providing some evidence that chromosome reduction from a common paleo-ancestor of both maize and sugarcane was driven by the same translocation

  16. 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.

  17. 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.

  18. Clustering of complex shaped data sets via Kohonen maps and mathematical morphology

    NASA Astrophysics Data System (ADS)

    Ferreira Costa, Jose A.; de Andrade Netto, Marcio L.

    2001-03-01

    Clustering is the process of discovering groups within the data, based on similarities, with a minimal, if any, knowledge of their structure. The self-organizing (or Kohonen) map (SOM) is one of the best known neural network algorithms. It has been widely studied as a software tool for visualization of high-dimensional data. Important features include information compression while preserving topological and metric relationship of the primary data items. Although Kohonen maps had been applied for clustering data, usually the researcher sets the number of neurons equal to the expected number of clusters, or manually segments a two-dimensional map using some a-priori knowledge of the data. This paper proposes techniques for automatic partitioning and labeling SOM networks in clusters of neurons that may be used to represent the data clusters. Mathematical morphology operations, such as watershed, are performed on the U-matrix, which is a neuron-distance image. The direct application of watershed leads to an oversegmented image. It is used markers to identify significant clusters and homotopy modification to suppress the others. Markers are automatically found by performing a multilevel scan of connected regions of the U-matrix. Each cluster of neurons is a sub-graph that defines, in the input space, complex and non-parametric geometries which approximately describes the shape of the clusters. The process of map partitioning is extended recursively. Each cluster of neurons gives rise to a new map, which are trained with the subset of data that were classified to it. The algorithm produces dynamically a hierarchical tree of maps, which explains the cluster's structure in levels of granularity. The distributed and multiple prototypes cluster representation enables the discoveries of clusters even in the case when we have two or more non-separable pattern classes.

  19. 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

  20. 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.

  1. COnto-Diff: generation of complex evolution mappings for life science ontologies.

    PubMed

    Hartung, Michael; Groß, Anika; Rahm, Erhard

    2013-02-01

    Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management. We propose a novel approach COnto-Diff to determine an expressive and invertible diff evolution mapping between given versions of an ontology. Our approach first matches the ontology versions and determines an initial evolution mapping consisting of basic change operations (insert/update/delete). To semantically enrich the evolution mapping we adopt a rule-based approach to transform the basic change operations into a smaller set of more complex change operations, such as merge, split, or changes of entire subgraphs. The proposed algorithm is customizable in different ways to meet the requirements of diverse ontologies and application scenarios. We evaluate the proposed approach for large life science ontologies including the Gene Ontology and the NCI Thesaurus and compare it with PromptDiff. We further show how the Diff results can be used for version management and annotation migration in collaborative curation. PMID:22580476

  2. Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentus complex) from the Eastern Ukraine

    PubMed Central

    2013-01-01

    Background Hybridogenesis (hemiclonal inheritance) is a kind of clonal reproduction in which hybrids between parental species are reproduced by crossing with one of the parental species. European water frogs (Pelophylax esculentus complex) represent an appropriate model for studying interspecies hybridization, processes of hemiclonal inheritance and polyploidization. P. esculentus complex consists of two parental species, P. ridibundus (the lake frog) and P. lessonae (the pool frog), and their hybridogenetic hybrid – P. esculentus (the edible frog). Parental and hybrid frogs can reproduce syntopically and form hemiclonal population systems. For studying mechanisms underlying the maintenance of water frog population systems it is required to characterize the karyotypes transmitted in gametes of parental and different hybrid animals of both sexes. Results In order to obtain an instrument for characterization of oocyte karyotypes in hybrid female frogs, we constructed cytological maps of lampbrush chromosomes from oocytes of both parental species originating in Eastern Ukraine. We further identified certain molecular components of chromosomal marker structures and mapped coilin-rich spheres and granules, chromosome associated nucleoli and special loops accumulating splicing factors. We recorded the dissimilarities between P. ridibundus and P. lessonae lampbrush chromosomes in the length of orthologous chromosomes, number and location of marker structures and interstitial (TTAGGG)n-repeat sites as well as activity of nucleolus organizer. Satellite repeat RrS1 was mapped in centromere regions of lampbrush chromosomes of the both species. Additionally, we discovered transcripts of RrS1 repeat in oocytes of P. ridibundus and P. lessonae. Moreover, G-rich transcripts of telomere repeat were revealed in association with terminal regions of P. ridibundus and P. lessonae lampbrush chromosomes. Conclusions The constructed cytological maps of lampbrush chromosomes of P

  3. 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.

  4. Application of 13C NMR spectroscopy to paratope mapping for larger antigen-Fab complexes.

    PubMed

    Kim, H; Kato, K; Yamato, S; Igarashi, T; Matsunaga, C; Ohtsuka, H; Higuchi, A; Nomura, N; Noguchi, H; Arata, Y

    1994-06-13

    For the purpose of engineering the antibody combining site, mapping residues that are involved in antigen binding provide us with valuable information. By use of 13C NMR spectroscopy with selectively 13C-labeled Fv fragments, we have established a general strategy to identify the residues that are perturbed upon binding of small antigen (hapten) molecules [(1990) Biochemistry 30, 6604-6610]. In the present paper, we demonstrate that this strategy can be extended to molecular structural analyses of the complexes of an Fab fragment and a larger antigen molecule such as Pseudomonas aeruginosa exotoxin A with a molecular mass of 67 kDa. PMID:8013642

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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.

  7. 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. PMID:11540053

  8. Wide-Area Mapping of 155 Micron Continuum Emission from the Orion Molecular Cloud Complex

    NASA Astrophysics Data System (ADS)

    Arimura, Seikoh; Shibai, Hiroshi; Teshima, Takafumi; Nakagawa, Takao; Narita, Masanao; Makiuti, Shin'itirou; Doi, Yasuo; Verma, Ram Prakash; Ghosh, Swarna Kanti; Rengarajan, Thinnian Naganathan; Tanaka, Makoto; Okuda, Haruyuki

    2004-02-01

    We present the results of a wide-area mapping of the far-infrared continuum emission toward the Orion complex by using a Japanese balloon-borne telescope. The 155-μm continuum emission was detected over a region of 1.5 deg2 around the KL nebula with 3‧ resolution similar to that of the IRAS 100-μm map. Assuming a single-temperature model of the thermal equilibrium dust, maps of the temperature and the optical thickness were derived from the 155-μm intensity and the IRAS 100-μm intensity. The derived dust temperature is 5-15K lower and the derived dust optical depth is 5-300 times larger than those derived from the IRAS 60 and 100-μm intensities due to the significant contribution of the statistically heated very small grains to the IRAS 60-μm intensity. The optical-thickness distribution shows a filamentary dust ridge that has a 1°.5 extent in the north-south direction and well resembles the Integral-Shaped Filament (ISF) molecular gas distribution. The gas-to-dust ratio derived from the CO molecular gas distribution along the ISF is in the range 30-200, which may be interpreted as being an effect of CO depletion due to the photodissociation and/or the freezing on dust grains.

  9. 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

  10. 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.

  11. Recent Mapping and Sampling on Chukchi Borderland and the Alpha/Mendeleev Ridge Complex

    NASA Astrophysics Data System (ADS)

    Mayer, L. A.; Brumley, K.; Andronikov, A.; Chayes, D. N.; Armstrong, A. A.; Calder, B.; Hall, J. K.; Clyde, W. C.; Bothner, W. A.; Gardner, J. V.

    2008-12-01

    Since 2003, four cruises on the icebreaker USCG HEALY have collected high-resolution multibeam sonar mapping data in the Amerasia Basin in support of a potential submission by the U.S. for an extended continental shelf as defined under the United Nations Convention on Law of the Sea Article 76. The latest of these cruises (HEALY0805), completed in early Sept.of 2008, extended this mapping to the southern portions of the Alpha/Mendeleev Ridge complex, and supplemented the mapping with seven dredge stations, providing rare, direct sampling of both regions. While sparse in comparison to complete-coverage multibeam sonar surveys (due to the difficulties associated with operating in ice-covered waters), the new multibeam sonar data still provide an unprecedented new view of the tectonic, sedimentary, glacial and fluid- flow related processes in the Arctic Ocean. The Chukchi Borderland is characterized by shallow plateaus that often show evidence of interaction with icebergs and glaciers (scours and grooves) at depths as great as 900 m, as well as the presence of numerous gas/fluid expulsion features (pockmarks and acoustic wipe-out zones). The topographic highs associated with the Borderland are often bounded by very steep scarps including the eastern edge of Northwind Ridge (the Northwind Escarpment) which is a 600 km long NNE trending feature with an average slope of 10-15 degrees. Similar steep-sided ridges, separated by deep linear valleys also appear in mapped areas of the Alpha/Mendeleev Ridge complex. Some of these features have slopes as great at 60 degrees and thus are excellent targets for dredging. Our dredging of these slopes has returned a wide array of volcanic and sedimentary rock types, many of which appear to be representative of outcrops (rather than ice rafted material). A preliminary shipboard examination of these samples (they were just collected this morning - 3 September 2008 - a few days before the abstract is due) shows them to include mudstone

  12. 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

  13. 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

  14. Extending to the complex line Dulac’s corner maps of non-degenerate planar singularities

    NASA Astrophysics Data System (ADS)

    Teyssier, Loïc

    2015-10-01

    We study the complex Dulac map for a holomorphic foliation of the complex plane, near a non-degenerate singularity (both eigenvalues of the linearization are nonzero) with two separatrices. Following the well-known results of Il’yashenko we provide a geometric approach allowing to study the whole maximal domain of (geometric) definition of the Dulac map. In particular its topology and the regularity of its boundary are completely described. We also study the order of magnitude of the first non-trivial term of its asymptotic expansion and show how to compute it using path integrals supported in the leaves of the linearized foliation. Explicit bounds on the remainder are given. We perform similarly the study of the Dulac time spent around the singularity. All results are formulated in a unified framework taking no heed to the usual dynamical discrimination (i.e. no matter whether the singularity is formally orbitally linearizable or not and regardless of the arithmetic of the eigenvalues ratio).

  15. SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps

    PubMed Central

    Dogrusoz, Ugur; Sumer, Selcuk Onur; Aksoy, Bülent Arman; Babur, Özgün; Demir, Emek

    2015-01-01

    Background Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases. Results Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis. Conclusion SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms. PMID:26030594

  16. Tctex2: a sperm tail surface protein mapping to the t-complex.

    PubMed

    Huw, L Y; Goldsborough, A S; Willison, K; Artzt, K

    1995-07-01

    Transmission ratio distortion (TRD) in mouse t-haplotypes remains the most significant example of meiotic drive in vertebrates. While the underlying mechanism that fuels it is still mysterious, TRD is clearly a complex multigene phenomenon. The characterization of Tctex2 (t-complex testis expressed 2) shows it to be one of several candidates for involvement in TRD. Tctex2 maps to the t-complex and encodes a membrane-associated protein found exclusively on the sperm tail. The t-haplotype form of Tctex2 is aberrant in both the level of its expression and its primary amino acid sequence, but is nonetheless translated and transported to its normal location. The multiple amino acid changes in the t-form make it extremely unlikely that it can function normally and, since it is found on sperm tails, suggest that it may actively interfere with the development of normal gamete function in males. The possible role of Tctex2 in t-complex transmission ratio distortion and sterility is discussed. PMID:7601308

  17. Time Series Analysis OF SAR Image Fractal Maps: The Somma-Vesuvio Volcanic Complex Case Study

    NASA Astrophysics Data System (ADS)

    Pepe, Antonio; De Luca, Claudio; Di Martino, Gerardo; Iodice, Antonio; Manzo, Mariarosaria; Pepe, Susi; Riccio, Daniele; Ruello, Giuseppe; Sansosti, Eugenio; Zinno, Ivana

    2016-04-01

    The fractal dimension is a significant geophysical parameter describing natural surfaces representing the distribution of the roughness over different spatial scale; in case of volcanic structures, it has been related to the specific nature of materials and to the effects of active geodynamic processes. In this work, we present the analysis of the temporal behavior of the fractal dimension estimates generated from multi-pass SAR images relevant to the Somma-Vesuvio volcanic complex (South Italy). To this aim, we consider a Cosmo-SkyMed data-set of 42 stripmap images acquired from ascending orbits between October 2009 and December 2012. Starting from these images, we generate a three-dimensional stack composed by the corresponding fractal maps (ordered according to the acquisition dates), after a proper co-registration. The time-series of the pixel-by-pixel estimated fractal dimension values show that, over invariant natural areas, the fractal dimension values do not reveal significant changes; on the contrary, over urban areas, it correctly assumes values outside the natural surfaces fractality range and show strong fluctuations. As a final result of our analysis, we generate a fractal map that includes only the areas where the fractal dimension is considered reliable and stable (i.e., whose standard deviation computed over the time series is reasonably small). The so-obtained fractal dimension map is then used to identify areas that are homogeneous from a fractal viewpoint. Indeed, the analysis of this map reveals the presence of two distinctive landscape units corresponding to the Mt. Vesuvio and Gran Cono. The comparison with the (simplified) geological map clearly shows the presence in these two areas of volcanic products of different age. The presented fractal dimension map analysis demonstrates the ability to get a figure about the evolution degree of the monitored volcanic edifice and can be profitably extended in the future to other volcanic systems with

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26106896

  19. 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. PMID:26106896

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

    NASA Astrophysics Data System (ADS)

    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 R 2 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.

  1. 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. PMID:23686111

  2. Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.).

    PubMed

    Longhi, Sara; Moretto, Marco; Viola, Roberto; Velasco, Riccardo; Costa, Fabrizio

    2012-02-01

    Fruit ripening is a complex physiological process in plants whereby cell wall programmed changes occur mainly to promote seed dispersal. Cell wall modification also directly regulates the textural properties, a fundamental aspect of fruit quality. In this study, two full-sib populations of apple, with 'Fuji' as the common maternal parent, crossed with 'Delearly' and 'Pink Lady', were used to understand the control of fruit texture by QTL mapping and in silico gene mining. Texture was dissected with a novel high resolution phenomics strategy, simultaneously profiling both mechanical and acoustic fruit texture components. In 'Fuji × Delearly' nine linkage groups were associated with QTLs accounting from 15.6% to 49% of the total variance, and a highly significant QTL cluster for both textural components was mapped on chromosome 10 and co-located with Md-PG1, a polygalacturonase gene that, in apple, is known to be involved in cell wall metabolism processes. In addition, other candidate genes related to Md-NOR and Md-RIN transcription factors, Md-Pel (pectate lyase), and Md-ACS1 were mapped within statistical intervals. In 'Fuji × Pink Lady', a smaller set of linkage groups associated with the QTLs identified for fruit texture (15.9-34.6% variance) was observed. The analysis of the phenotypic variance over a two-dimensional PCA plot highlighted a transgressive segregation for this progeny, revealing two QTL sets distinctively related to both mechanical and acoustic texture components. The mining of the apple genome allowed the discovery of the gene inventory underlying each QTL, and functional profile assessment unravelled specific gene expression patterns of these candidate genes. PMID:22121200

  3. 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

  4. A Model System for Mapping Vascular Responses to Complex Hemodynamics at Arterial Bifurcations In Vivo

    PubMed Central

    Meng, Hui; Swartz, Daniel D.; Wang, Zhijie; Hoi, Yiemeng; Kolega, John; Metaxa, Eleni M.; Szymanski, Michael P.; Yamamoto, Junichi; Sauvageau, Eric; Levy, Elad I.

    2009-01-01

    Objective Cerebral aneurysms are preferentially located at arterial bifurcation apices with complex hemodynamics. To understand disease mechanisms associated with aneurysm initiation, we attempted to establish a causal relationship between local hemodynamics and vascular responses. Methods Arterial bifurcations were surgically created from native common carotid arteries in two dogs, angiographically imaged 2 weeks and 2 months later, and then excised. We characterized local morphological changes in response to specifically manipulated hemodynamics. Computational fluid dynamics simulations were performed on the in vivo images and results mapped onto histological images. Results Local flow conditions, such as high wall shear stress and high wall shear stress gradient, were found to be associated with vascular changes, including an intimal pad in the flow impingement region and a “groove” bearing the characteristics of an early aneurysm. Conclusion This novel method of histohemodynamic micromapping reveals a direct correlation between an altered hemodynamic microenvironment and vascular responses consistent with aneurysm development. PMID:17143243

  5. 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.

  6. 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.

  7. 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.

  8. Generating high peak capacity 2-D maps of complex proteomes using PMMA microchip electrophoresis.

    PubMed

    Osiri, John K; Shadpour, Hamed; Park, Sunjung; Snowden, Brandy C; Chen, Zhi-Yuan; Soper, Steven A

    2008-12-01

    A high peak capacity 2-D protein separation system combining SDS micro-CGE (SDS micro-CGE) with microchip MEKC (micro-MEKC) using a PMMA microfluidic is reported. The utility of the 2-D microchip was demonstrated by generating a 2-D map from a complex biological sample containing a large number of constituent proteins using fetal calf serum (FCS) as the model system. The proteins were labeled with a thiol-reactive AlexaFluor 633 fluorophore (excitation/emission: 633/652 nm) to allow for ultra-sensitive on-chip detection using LIF following the 2-D separation. The high-resolution separation of the proteins was accomplished based on their size in the SDS micro-CGE dimension and their interaction with micelles in the micro-MEKC dimension. A comprehensive 2-D SDS micro-CGE x micro-MEKC separation of the FCS proteins was completed in less than <30 min using this 2-D microchip format, which consisted of 60 mm and 50 mm effective separation lengths for the first and second separation dimensions, respectively. Results obtained from the microchip separation were compared with protein maps acquired using conventional 2-D IEF and SDS-PAGE of a similar FCS sample. The microchip 2-D separation was found to be approximately 60x faster and yielded an average peak capacity of 2600 (+/- 149), nearly three times larger than that obtained using conventional IEF/SDS-PAGE. PMID:19130578

  9. 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

  10. Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM

    PubMed Central

    Jensen, Mikkel R. B.; Łopacińska, Joanna; Schmidt, Michael S.; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mølhave, Kristian

    2013-01-01

    Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells’ interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412

  11. 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

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

    SciTech Connect

    Yashim, Y.; So, A.K.

    1994-09-01

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

  13. 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

  14. 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

  15. 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

  16. A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions.

    PubMed Central

    Fishman, L; Kelly, A J; Morgan, E; Willis, J H

    2001-01-01

    As part of a study of the genetics of floral adaptation and speciation in the Mimulus guttatus species complex, we constructed a genetic linkage map of an interspecific cross between M. guttatus and M. nasutus. We genotyped an F(2) mapping population (N = 526) at 255 AFLP, microsatellite, and gene-based markers and derived a framework map through repeated rounds of ordering and marker elimination. The final framework map consists of 174 marker loci on 14 linkage groups with a total map length of 1780 cM Kosambi. Genome length estimates (2011-2096 cM) indicate that this map provides thorough coverage of the hybrid genome, an important consideration for QTL mapping. Nearly half of the markers in the full data set (49%) and on the framework map (48%) exhibited significant transmission ratio distortion (alpha = 0.05). We localized a minimum of 11 transmission ratio distorting loci (TRDLs) throughout the genome, 9 of which generate an excess of M. guttatus alleles and a deficit of M. nasutus alleles. This pattern indicates that the transmission ratio distortion results from particular interactions between the heterospecific genomes and suggests that substantial genetic divergence has occurred between these Mimulus species. We discuss possible causes of the unequal representation of parental genomes in the F(2) generation. PMID:11779808

  17. 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.

  18. 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

  19. Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes.

    PubMed

    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

    2014-08-01

    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

  20. 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.

  1. 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

  2. Forest structural complexity in a temperate hardwood forest: A geomatics approach to modelling and mapping indicators of habitat and biodiversity

    NASA Astrophysics Data System (ADS)

    Pasher, Jonathan

    Remote sensing has been widely used for modelling and mapping individual structural attributes within forests, however, knowledge of the multivariate nature of structural complexity, which is of specific interest as an indicator of forest habitat and biodiversity, is lacking. This research presents methods and results describing the development of geomatics-based indicators of forest structure, which are spatially continuous, extensive and repeatable. Two distinct, but related, structurally-based indicators derived from high resolution airborne imagery and topographic information were developed: (1) modelling and mapping forest structural complexity, and (2) the detection and mapping of the spatial distribution of dead wood. A Redundancy Analysis (RDA) was used to develop an image-based Structural Complexity Index (SCI) representing structural complexity as measured on the ground. An extensive set of image spectral, spatial, and object-based variables, along with topographic variables, were tested as predictors of structural complexity. The SCI, as a general gradient of structural complexity, accounted for 35% of the original variance in the field data. The model was applied spatially to map the SCI across the entire study area within Gatineau Park, Quebec. Field validation of the extreme conditions (high and low complexity areas) showed the map to be ˜ 80% accurate. Tests using simulated 60 cm and 1 m imagery showed potential for scaling up the RDA modelling procedure to be used with coarser resolution imagery, however map validation at these resolutions was somewhat inconclusive and further investigation using lower resolution airborne imagery and possibly high resolution satellite imagery is required. Additionally, a semi-automated method for detecting and mapping dead wood was investigated, with field validation of detected objects having an accuracy of 94%, and control sites, or areas with no detectable dead wood, showing an accuracy of 90%. The methods

  3. 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

  4. 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…

  5. 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 ...

  6. 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

  7. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping.

    PubMed

    Luders, Eileen; Kurth, Florian; Toga, Arthur W; Narr, Katherine L; Gaser, Christian

    2013-01-01

    Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators-perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

  8. 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.

  9. Groundwater vulnerability and risk mapping in a geologically complex area by using stable isotopes, remote sensing and GIS techniques

    NASA Astrophysics Data System (ADS)

    Dimitriou, Elias; Zacharias, Ierotheos

    2006-11-01

    Groundwater vulnerability and risk mapping is a relatively new scientific approach for facilitating planning and decision making processes in order to protect this valuable resource. Pan European methodology for aquifers vulnerability has recently been developed by assessing all the existing relevant techniques and emphasizing on karstic environments. In the particular study, state-of-the-art methods and tools have been implemented such as remote sensing, isotopic investigations and GIS to map the groundwater vulnerability and pollution risk in a geologically complex area of W. Greece. The updated land use map has been developed from a Landsat 7+TM image elaborated with image analysis software, while the detailed hydrogeologic properties of the area have been recorded with an intensive isotopic study. The local groundwater vulnerability map has been produced following the aforementioned Pan European method, in a GIS environment while the risk map, which was the final product of the study, has been developed after combining the vulnerability and the land use maps. The results indicated that the areas comprised of highly tectonized calcareous formations represented high vulnerability and risk zones while forested areas away from the karstic aquifer illustrated moderate to low vulnerability. Moreover, human activities increase the pollution risk in lowland areas consisting of sedimentary deposits that have been classified as moderate vulnerability. The particular methodology operated efficiently in this study and due to its accuracy and relatively easy implementation can be used as a decision support tool for local authorities.

  10. Advances in Complex-Resistivity Mapping and Characterization of Permafrost (Invited)

    NASA Astrophysics Data System (ADS)

    Grimm, R. E.; Stillman, D. E.

    2013-12-01

    the pathway. Temperature also strongly affects the inferred ice content but the frequency of the dielectric relaxation gives an independent temperature estimate. Complex resistivity is therefore a promising approach to permafrost monitoring and mapping of lateral and vertical variations in ice content.

  11. Interactome and interface protocol (2IP): a novel strategy for high sensitivity topology mapping of protein complexes.

    PubMed

    Weerasekera, Rasanjala; She, Yi-Min; Markham, Kelly A; Bai, Yu; Opalka, Natacha; Orlicky, Stephen; Sicheri, Frank; Kislinger, Thomas; Schmitt-Ulms, Gerold

    2007-11-01

    A few well-characterized protein assemblies aside, little is known about the topology and interfaces of multiconstituent protein complexes. Here we report on a novel indirect strategy for low-resolution topology mapping of protein complexes. Following crosslinking, purified protein complexes are subjected to chemical cleavage with cyanogen bromide (CNBr) and the resulting fragments are resolved by 2-D electrophoresis. The side-by-side comparison of a thus generated and a 2-D CNBr fragment map obtained from uncrosslinked material reveals candidate gel spots harboring crosslinked CNBr fragments. In-gel trypsinization and MALDI MS analysis of these informative spots identify the underlying crosslinked CNBr fragments based on unmodified tryptic peptides. Matching the cumulative theoretical molecular mass and predicted pI of these crosslinked CNBr fragments with original gel spot coordinates is required for confident crosslink assignment. The above strategy was successfully validated with the Escherichia coli RNA polymerase (RNAP) core complex and subsequently applied to query the quaternary structure of components of the yeast Skp1-Cdc53/Cullin-F box (SCF) ubiquitin ligase complex. This protocol requires low picomole sample quantities, can be applied to multisubunit protein complexes, and does not rely on specialized data mining software. PMID:17960736

  12. 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…

  13. DMMFast: a complexity reduction scheme for three-dimensional high-efficiency video coding intraframe depth map coding

    NASA Astrophysics Data System (ADS)

    Sanchez, Gustavo; Saldanha, Mário; Balota, Gabriel; Zatt, Bruno; Porto, Marcelo; Agostini, Luciano

    2015-03-01

    We present a complexity reduction scheme for the depth map intraprediction of three-dimensional high-efficiency video coding (3-D-HEVC). The 3-D-HEVC introduces a new set of specific tools for depth map coding, inserting additional complexity to intraprediction, which results in new challenges in terms of complexity reduction. Therefore, we present the DMMFast (depth modeling modes fast prediction), a scheme composed of two new algorithms: the simplified edge detector (SED) and the gradient-based mode one filter (GMOF). The SED anticipates the blocks that are likely to be better predicted by the traditional intramodes, avoiding the evaluation of DMMs. The GMOF applies a gradient-based filter in the borders of the block and predicts the best positions to evaluate the DMM 1. Software evaluations showed that DMMFast is capable of achieving a time saving of 11.9% on depth map intraprediction, considering the random access mode, without affecting the quality of the synthesized views. Considering the all intraconfigurations, the proposed scheme is capable of achieving, on average, a time saving of 35% considering the whole encoder. Subjective quality assessment was also performed, showing that the proposed technique inserts minimal quality losses in the final encoded video.

  14. Proteome map of the neural complex of the tunicate Ciona intestinalis, the closest living relative to vertebrates.

    PubMed

    Saxena, Sandeep; Dupont, Sam; Meghah, Vuppalapaty; Lakshmi, Mula G Meena; Singh, Sachin K; Swamy, Cherukuvada V Brahmendra; Idris, Mohammed M

    2013-03-01

    Ciona intestinalis (the common sea squirt) is the closest living chordate relative to vertebrates with cosmopolitan presence worldwide. It has a relatively simple nervous system and development, making it a widely studied alternative model system in neuroscience and developmental biology. The use of Ciona as a model organism has increased significantly after the draft genome was published. In this study, we describe the first proteome map of the neural complex of C. intestinalis. A total of 544 proteins were identified based on 1DE and 2DE FTMS/ITMSMS analyses. Proteins were annotated against the Ciona database and analyzed to predict their molecular functions, roles in biological processes, and position in constructed network pathways. The identified Ciona neural complex proteome was found to map onto vertebrate nervous system pathways, including cytoskeleton remodeling neurofilaments, cell adhesion through the histamine receptor signaling pathway, γ-aminobutyric acid-A receptor life cycle neurophysiological process, glycolysis, and amino acid metabolism. The proteome map of the Ciona neural complex is the first step toward a better understanding of several important processes, including the evolution and regeneration capacity of the Ciona nervous system. PMID:23300126

  15. 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

  16. 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

  17. Mapping water quality and substrate cover in optically complex coastal and reef waters: an integrated approach.

    PubMed

    Phinn, S R; Dekker, A G; Brando, V E; Roelfsema, C M

    2005-01-01

    Sustainable management of coastal and coral reef environments requires regular collection of accurate information on recognized ecosystem health indicators. Satellite image data and derived maps of water column and substrate biophysical properties provide an opportunity to develop baseline mapping and monitoring programs for coastal and coral reef ecosystem health indicators. A significant challenge for satellite image data in coastal and coral reef water bodies is the mixture of both clear and turbid waters. A new approach is presented in this paper to enable production of water quality and substrate cover type maps, linked to a field based coastal ecosystem health indicator monitoring program, for use in turbid to clear coastal and coral reef waters. An optimized optical domain method was applied to map selected water quality (Secchi depth, Kd PAR, tripton, CDOM) and substrate cover type (seagrass, algae, sand) parameters. The approach is demonstrated using commercially available Landsat 7 Enhanced Thematic Mapper image data over a coastal embayment exhibiting the range of substrate cover types and water quality conditions commonly found in sub-tropical and tropical coastal environments. Spatially extensive and quantitative maps of selected water quality and substrate cover parameters were produced for the study site. These map products were refined by interactions with management agencies to suit the information requirements of their monitoring and management programs. PMID:15757744

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

    PubMed Central

    2012-01-01

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

  19. Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits

    PubMed Central

    Ljungberg, Kajsa; Mishchenko, Kateryna; Holmgren, Sverker

    2010-01-01

    We present a two-phase strategy for optimizing a multidimensional, nonconvex function arising during genetic mapping of quantitative traits. Such traits are believed to be affected by multiple so called quantitative trait loci (QTL), and searching for d QTL results in a d-dimensional optimization problem with a large number of local optima. We combine the global algorithm DIRECT with a number of local optimization methods that accelerate the final convergence, and adapt the algorithms to problem-specific features. We also improve the evaluation of the QTL mapping objective function to enable exploitation of the smoothness properties of the optimization landscape. Our best two-phase method is demonstrated to be accurate in at least six dimensions and up to ten times faster than currently used QTL mapping algorithms. PMID:21918629

  20. 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.

  1. 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.

  2. 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.

  3. 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.

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

    PubMed Central

    Hoppins, Suzanne; Collins, Sean R.; Cassidy-Stone, Ann; Hummel, Eric; DeVay, Rachel M.; Lackner, Laura L.; Westermann, Benedikt; Schuldiner, Maya

    2011-01-01

    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. PMID:21987634

  5. 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.

  6. An Argument for the Use of Chaos Theory To Map the Complexity of Human Communication.

    ERIC Educational Resources Information Center

    Keaten, James A.; And Others

    Noting that the chance to utilize a new paradigm is an opportunity that rarely presents itself, this paper suggests that chaos theory and communication can be combined to help understand human communication. The paper begins by examining the complexity of human communication--that is, the internal and external factors that affect the complexity of…

  7. Quantitative Mapping of Reversible Mitochondrial Complex I Cysteine Oxidation in a Parkinson Disease Mouse Model*

    PubMed Central

    Danielson, Steven R.; Held, Jason M.; Oo, May; Riley, Rebeccah; Gibson, Bradford W.; Andersen, Julie K.

    2011-01-01

    Differential cysteine oxidation within mitochondrial Complex I has been quantified in an in vivo oxidative stress model of Parkinson disease. We developed a strategy that incorporates rapid and efficient immunoaffinity purification of Complex I followed by differential alkylation and quantitative detection using sensitive mass spectrometry techniques. This method allowed us to quantify the reversible cysteine oxidation status of 34 distinct cysteine residues out of a total 130 present in murine Complex I. Six Complex I cysteine residues were found to display an increase in oxidation relative to controls in brains from mice undergoing in vivo glutathione depletion. Three of these residues were found to reside within iron-sulfur clusters of Complex I, suggesting that their redox state may affect electron transport function. PMID:21196577

  8. “But there are no snakes in the wood”: risk mapping as an outcome measure in evaluating complex interventions

    PubMed Central

    Power, Robert; Langhaug, Lisa; Cowan, Frances

    2007-01-01

    Objectives To complement biological and social behavioural markers in evaluating the complex intervention of sexual and reproductive health among adolescents in rural Zimbabwe, community‐derived markers of effectiveness were sought. Through a participatory workshop with adolescent boys and girls, an innovative “risk map research workshop” was developed to be conducted throughout the study sites. Methods 78 gender‐specific standardised workshops were conducted among secondary school students. Participants drew risk maps of their community. Focus group discussions explored each risk area identified on the map. Grounded Theory was used to create “categories” and “subcategories.” Workshops continued to be held until “saturation”, whereby no new categories emerged. “Axial coding” identified the inter‐relationship between categories and subcategories according to their relevance to sexual and reproductive health risk. Results Six “risk area” Grounded Theory categories emerged from the data: bush/rural terrain, commercial centres, homes, school environs, religious and spiritual venues, and roadsides. 17 subcategories emerged, grouped under each of the risk area categories, such as riverbeds, growth points, homesteads, classrooms, all‐night prayer meetings and truck stops. Risks and the consequences of risks included sexually transmitted infections (including HIV), violence, sexual abuse, expulsion from school and illegal abortion. Conclusions Risk maps provide unique data that can be used to measure more subtle changes that occur as a result of social behavioural interventions aimed at addressing reproductive and sexual health. Another round of risk map research workshops will be held towards the end of the study to explore changes in milieu, behaviour and experiences, and will complement and triangulate the biological and other social behavioural outcome measures. PMID:17344248

  9. 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...

  10. 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.

  11. Mass mapping of a protein complex with the scanning transmission electron microscope.

    PubMed Central

    Engel, A; Baumeister, W; Saxton, W O

    1982-01-01

    A mass map of the hexagonally packed intermediate layer (HPI-layer), a regular protein monolayer from the cell envelope of Micrococcus radiodurans, has been obtained by scanning transmission electron microscopy. Samples were freeze-dried within the microscope, and low-dose images were recorded in the dark-field mode directly in digital form and processed by correlation averaging. The averaged projection of the unstained structure--i.e., the mass map--thus calculated shows a resolution to 3-nm period and reveals morphological features consistent with those obtained by negative staining. The mass of individual morphological domains was extracted by using variously the mass map itself or an average from a negatively stained HPI layer to define the domain boundaries. Protrusions as small as 1,300 daltons could be measured reproducibly within the unit cell of 655,000 daltons. The method developed opens an avenue to identify molecular species in situ and to correlate topographic information with biochemical data. Images PMID:6955791

  12. 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

  13. 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

  14. 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

  15. 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

  16. Disulfide Engineering to Map Subunit Interactions in the Proteasome and Other Macromolecular Complexes

    PubMed Central

    Hochstrasser, Mark; Funakoshi, Minoru

    2013-01-01

    Summary In studies of protein complexes for which high-resolution structural data are unavailable, it is often still possible to determine both nearest-neighbor relationships between subunits and atomic-resolution details of these interactions. The eukaryotic 26S proteasome, a ~2.5 MDa protein complex with at least 33 different subunits, is a prime example. Important information about quaternary organization and assembly of proteasomes has been gained using a combination of sequence alignments with related proteins of known tertiary structure, molecular modeling, and disulfide engineering to allow oxidative crosslinking between predicted polypeptide neighbors. Here we provide detailed protocols for engineered cysteine crosslinking of yeast proteasome subunits in whole cell extracts, in active 26S proteasome complexes first isolated by native polyacrylamide gel electrophoresis, and in subcomplexes that function as potential assembly intermediates. PMID:22350897

  17. 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.

  18. Genetic Mapping of MAPK-Mediated Complex Traits Across S. cerevisiae

    PubMed Central

    Treusch, Sebastian; Albert, Frank W.; Bloom, Joshua S.; Kotenko, Iulia E.; Kruglyak, Leonid

    2015-01-01

    Signaling pathways enable cells to sense and respond to their environment. Many cellular signaling strategies are conserved from fungi to humans, yet their activity and phenotypic consequences can vary extensively among individuals within a species. A systematic assessment of the impact of naturally occurring genetic variation on signaling pathways remains to be conducted. In S. cerevisiae, both response and resistance to stressors that activate signaling pathways differ between diverse isolates. Here, we present a quantitative trait locus (QTL) mapping approach that enables us to identify genetic variants underlying such phenotypic differences across the genetic and phenotypic diversity of S. cerevisiae. Using a Round-robin cross between twelve diverse strains, we identified QTL that influence phenotypes critically dependent on MAPK signaling cascades. Genetic variants under these QTL fall within MAPK signaling networks themselves as well as other interconnected signaling pathways. Finally, we demonstrate how the mapping results from multiple strain background can be leveraged to narrow the search space of causal genetic variants. PMID:25569670

  19. 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

  20. Chromatin marks identify critical cell types for fine mapping complex trait variants.

    PubMed

    Trynka, Gosia; Sandor, Cynthia; Han, Buhm; Xu, Han; Stranger, Barbara E; Liu, X Shirley; Raychaudhuri, Soumya

    2013-02-01

    If trait-associated variants alter regulatory regions, then they should fall within chromatin marks in relevant cell types. However, it is unclear which of the many marks are most useful in defining cell types associated with disease and fine mapping variants. We hypothesized that informative marks are phenotypically cell type specific; that is, SNPs associated with the same trait likely overlap marks in the same cell type. We examined 15 chromatin marks and found that those highlighting active gene regulation were phenotypically cell type specific. Trimethylation of histone H3 at lysine 4 (H3K4me3) was the most phenotypically cell type specific (P < 1 × 10(-6)), driven by colocalization of variants and marks rather than gene proximity (P < 0.001). H3K4me3 peaks overlapped with 37 SNPs for plasma low-density lipoprotein concentration in the liver (P < 7 × 10(-5)), 31 SNPs for rheumatoid arthritis within CD4(+) regulatory T cells (P = 1 × 10(-4)), 67 SNPs for type 2 diabetes in pancreatic islet cells (P = 0.003) and the liver (P = 0.003), and 14 SNPs for neuropsychiatric disease in neuronal tissues (P = 0.007). We show how cell type-specific H3K4me3 peaks can inform the fine mapping of associated SNPs to identify causal variation. PMID:23263488

  1. Human Interactive Analysis Using Video: Mapping the Dynamics of Complex Work Environments.

    ERIC Educational Resources Information Center

    Terrell, William R.; And Others

    1992-01-01

    Explains human interactive analysis as an architecture for using computer interactive technologies in the analysis of complex work environments. A project at the Naval Training Systems Center that used video-audio data to develop a multimedia database is described; the analysis and management of data are discussed; and decision processes are…

  2. 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. PMID:25298978

  3. 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

  4. Mapping of a complex lava flow field using regular surveys with a portable thermal camera

    NASA Astrophysics Data System (ADS)

    Calvari, S.; Lodato, L.; Garfi, G.; Spampinato, L.; Andronico, D.

    2003-04-01

    The use of a portable thermal camera has been applied to routine monitoring of the 2002 Etna flank eruption. The eruption started on 27 October with the opening of a field of fissures on the north and south flanks of the volcano. Abundant ash emission from the whole length of the 10 km long fissure covered the lava flow field, making it impossible to approach the active lava even with helicopters. Additionally, the northern lava flows were spreading into a forest, causing fire and impeding routine measures in field and lava flow mapping from the ground. This situation continued for several days. The only way to obtain an approximate mapping of the flow field was to use a thermal camera from helicopter, obtaining inclined images of the lava flow field. This allowed: (1) an estimation of the speed of the spreading lava and (2) of the position of the lava flow fronts, (3) evaluation of effusion rate, (4) daily covered area, and (5) organisation of evacuation plans for people living close to the area affected by flows. All these information were essential for civil protection purposes. Emission of lava flows from the north fissure stopped on 5 November 2002. During the following phase of the eruption, when lava flows spread for over two months only on the southern flank of the volcano, little ash emission from the craters allowed us a better view of the lava flow field. However, since the active flows were spreading on a limited surface, flanking and overlapping each other several times, distinction between active and inactive lava flows was made possible only by using a thermal camera. This device allowed us to distinguish active lava flows, inflating flow fronts, lava tubes and ephemeral vents, giving us a comprehensive view of the evolution of the lava flow field. It also helped us discover new vent opening from the base of the cinder cone, in a way to advice the Civil Protection authorities about the future path of new lava flows.

  5. 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.

  6. 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

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

    PubMed

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

    2016-02-01

    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

  8. 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.

  9. 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

  10. 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

  11. Two dimensional mass mapping as a general method of data representation in comprehensive analysis of complex molecular mixtures.

    PubMed

    Artemenko, Konstantin A; Zubarev, Alexander R; Samgina, Tatiana Yu; Lebedev, Albert T; Savitski, Mikhail M; Zubarev, Roman A

    2009-05-15

    A recent proteomics-grade (95%+ sequence reliability) high-throughput de novo sequencing method utilizes the benefits of high resolution, high mass accuracy, and the use of two complementary fragmentation techniques collision-activated dissociation (CAD) and electron capture dissociation (ECD). With this high-fidelity sequencing approach, hundreds of peptides can be sequenced de novo in a single LC-MS/MS experiment. The high productivity of the new analysis technique has revealed a new bottleneck which occurs in data representation. Here we suggest a new method of data analysis and visualization that presents a comprehensive picture of the peptide content including relative abundances and grouping into families. The 2D mass mapping consists of putting the molecular masses onto a two-dimensional bubble plot, with the relative monoisotopic mass defect and isotopic shift being the axes and with the bubble area proportional to the peptide abundance. Peptides belonging to the same family form a compact group on such a plot, so that the family identity can in many cases be determined from the molecular mass alone. The performance of the method is demonstrated on the high-throughput analysis of skin secretion from three frogs, Rana ridibunda, Rana arvalis, and Rana temporaria. Two dimensional mass maps simplify the task of global comparison between the species and make obvious the similarities and differences in the peptide contents that are obscure in traditional data presentation methods. Even biological activity of the peptide can sometimes be inferred from its position on the plot. Two dimensional mass mapping is a general method applicable to any complex mixture, peptide and nonpeptide alike. PMID:19382811

  12. The ternary complex factor Net contains two distinct elements that mediate different responses to MAP kinase signalling cascades.

    PubMed

    Ducret, C; Maira, S M; Lutz, Y; Wasylyk, B

    2000-10-19

    The ternary complex factors (TCFs), Elk-1, Sap-1a and Net, are key integrators of the transcriptional response to different signalling pathways. Classically, three MAP kinase pathways, involving ERK, JNK, and p38, transduce various extracellular stimuli to the nucleus. Net is a repressor that is converted into an activator by Ras/ERK signalling. Net is also exported from the nucleus in response to stress stimuli transduced through the JNK pathway, leading to relief from repression. Here we show that ERK and p38 bind to the D box and that binding is required for phosphorylation of the adjacent C-terminally located C-domain. The D box as well as the phosphorylation sites in the C-domain (the DC element) are required for transcription activation by Ras. On the other hand, JNK binds to the J box in the middle of the protein, and binding is required for phosphorylation of the adjacent EXport motif. Both the binding and phosphorylation sites (the JEX element) are important for Net export. In conclusion, specific targeting of Net by MAP kinase pathways involves two different docking sites and phosphorylation of two different domains. These two elements, DC and JEX, mediate two distinct functional responses. PMID:11042694

  13. Functional aspects of the EGF-induced MAP kinase cascade: a complex self-organizing system approach.

    PubMed

    Kosmidis, Efstratios K; Moschou, Vasiliki; Ziogas, Georgios; Boukovinas, Ioannis; Albani, Maria; Laskaris, Nikolaos A

    2014-01-01

    The EGF-induced MAP kinase cascade is one of the most important and best characterized networks in intracellular signalling. It has a vital role in the development and maturation of living organisms. However, when deregulated, it is involved in the onset of a number of diseases. Based on a computational model describing a "surface" and an "internalized" parallel route, we use systems biology techniques to characterize aspects of the network's functional organization. We examine the re-organization of protein groups from low to high external stimulation, define functional groups of proteins within the network, determine the parameter best encoding for input intensity and predict the effect of protein removal to the system's output response. Extensive functional re-organization of proteins is observed in the lower end of stimulus concentrations. As we move to higher concentrations the variability is less pronounced. 6 functional groups have emerged from a consensus clustering approach, reflecting different dynamical aspects of the network. Mutual information investigation revealed that the maximum activation rate of the two output proteins best encodes for stimulus intensity. Removal of each protein of the network resulted in a range of graded effects, from complete silencing to intense activation. Our results provide a new "vista" of the EGF-induced MAP kinase cascade, from the perspective of complex self-organizing systems. Functional grouping of the proteins reveals an organizational scheme contrasting the current understanding of modular topology. The six identified groups may provide the means to experimentally follow the dynamics of this complex network. Also, the vulnerability analysis approach may be used for the development of novel therapeutic targets in the context of personalized medicine. PMID:25372488

  14. Functional Aspects of the EGF-Induced MAP Kinase Cascade: A Complex Self-Organizing System Approach

    PubMed Central

    Kosmidis, Efstratios K.; Moschou, Vasiliki; Ziogas, Georgios; Boukovinas, Ioannis; Albani, Maria; Laskaris, Nikolaos A.

    2014-01-01

    The EGF-induced MAP kinase cascade is one of the most important and best characterized networks in intracellular signalling. It has a vital role in the development and maturation of living organisms. However, when deregulated, it is involved in the onset of a number of diseases. Based on a computational model describing a “surface” and an “internalized” parallel route, we use systems biology techniques to characterize aspects of the network’s functional organization. We examine the re-organization of protein groups from low to high external stimulation, define functional groups of proteins within the network, determine the parameter best encoding for input intensity and predict the effect of protein removal to the system’s output response. Extensive functional re-organization of proteins is observed in the lower end of stimulus concentrations. As we move to higher concentrations the variability is less pronounced. 6 functional groups have emerged from a consensus clustering approach, reflecting different dynamical aspects of the network. Mutual information investigation revealed that the maximum activation rate of the two output proteins best encodes for stimulus intensity. Removal of each protein of the network resulted in a range of graded effects, from complete silencing to intense activation. Our results provide a new “vista” of the EGF-induced MAP kinase cascade, from the perspective of complex self-organizing systems. Functional grouping of the proteins reveals an organizational scheme contrasting the current understanding of modular topology. The six identified groups may provide the means to experimentally follow the dynamics of this complex network. Also, the vulnerability analysis approach may be used for the development of novel therapeutic targets in the context of personalized medicine. PMID:25372488

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Geomorphological mapping and mass-wasting analysis in complex landslides using Terrestrial and Airborne LiDAR

    NASA Astrophysics Data System (ADS)

    Corsini, Alessandro; Bertacchini, Eleonora; Borgatti, Lisa; Capra, Alessandro; Cervi, Federico; Dahne, Alexander; Ronchetti, Francesco

    2010-05-01

    High-Resolution Digital Elevation Models (HR DEMs) obtained with Light Detection and Ranging technology, (LiDAR) have proved to be useful in the analysis of landslide processes in mountainous terrains, for different purposes and at different spatial scales, including improvement of landslide inventories, susceptibility assessment and appraisal of landslide geomorphic features. The application of laser scanning techniques results in data sets with enormous data size, extremely high accuracy (up to cm-scale) and very high spatial resolution. The exploitation of HR DEMs in landslide analysis can be manifold, comprising automated spatial data processing as well as expert knowledge - supervised procedures. First goal of this paper is to stress the advantages given by the usage of Shaded Relief datasets obtained from HR DEMs in geomorphological mapping of complex landslides. Through the use of such datasets, surveyors gain an enhanced capacity to identify slope-scale geomorpho-dynamic units, the possibility to increase the precision of scarps and detachment areas zonation, the capacity to identify and map compressive and extensional features all across the landslide body, and the possibility to retrieve other relevant geomorphological indicators of movement. These advantages are exemplified by presenting maps of large-scale earth slide - earth flows and deep seated rock slides located in the Alps and in the Apennines, that have been obtained by making use of shaded relief maps calculated from regional and local datasets using different scene illumination parameters. Second goal of this paper is to exemplify the usage of Differential HR DEMs is mass-wasting analysis applied to active earth slides - earth flows located in the northern Apennines. This simple DEM subtraction procedure can be carried out using multi-temporal airborne or terrestrial surveys, or by fusing airborne and terrestrial data. Examples are presented of landslides for which mass wasting at the slope

  20. 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.

  1. Mapping drug interactions at the covalent topoisomerase II-DNA complex by bisantrene/amsacrine congeners.

    PubMed

    Capranico, G; Guano, F; Moro, S; Zagotto, G; Sissi, C; Gatto, B; Zunino, F; Menta, E; Palumbo, M

    1998-05-22

    To identify structural determinants for the sequence-specific recognition of covalent topoisomerase II-DNA complexes by anti-cancer drugs, we investigated a number of bisantrene congeners, including a 10-azabioisoster, bearing one or two 4, 5-dihydro-1H-imidazol-2-yl hydrazone side chains at positions 1, 4, or 9 of the anthracene ring system. The studied bisantrene/amsacrine (m-AMSA) hybrid and bisantrene isomers were able to poison DNA topoisomerase II with an intermediate activity between those of bisantrene and m-AMSA. Moving the side chain from the central to a lateral ring (from C-9 to C-1/C-4) only slightly modified the drug DNA affinity, whereas it dramatically affected local base preferences of poison-stimulated DNA cleavage. In contrast, switching the planar aromatic systems of bisantrene and m-AMSA did not substantially alter the sequence specificity of drug action. A computer-assisted steric and electrostatic alignment analysis of the test compounds was in agreement with the experimental data, since a common pharmacophore was shared by bisantrene, m-AMSA, and 9-substituted analogs, whereas the 1-substituted isomer showed a radically changed pharmacophoric structure. Thus, the relative space occupancy and electron distribution of putative DNA binding (aromatic rings) and enzyme binding (side chains) moieties are fundamental in directing the specific action of topoisomerase II poisons and in determining the poison pharmacophore. PMID:9582297

  2. 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

  3. 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. PMID:26147592

  4. Mapping the Protein Interaction Network for TFIIB-Related Factor Brf1 in the RNA Polymerase III Preinitiation Complex

    PubMed Central

    Khoo, Seok-Kooi; Wu, Chih-Chien; Lin, Yu-Chun; Lee, Jin-Cheng

    2014-01-01

    TFIIB-related factor Brf1 is essential for RNA polymerase (Pol) III recruitment and open-promoter formation in transcription initiation. We site specifically incorporated a nonnatural amino acid cross-linker into Brf1 to map its protein interaction targets in the preinitiation complex (PIC). Our cross-linking analysis in the N-terminal domain of Brf1 indicated a pattern of multiple protein interactions reminiscent of TFIIB in the Pol active-site cleft. In addition to the TFIIB-like protein interactions, the Brf1 cyclin repeat subdomain is in contact with the Pol III-specific C34 subunit. With site-directed hydroxyl radical probing, we further revealed the binding between Brf1 cyclin repeats and the highly conserved region connecting C34 winged-helix domains 2 and 3. In contrast to the N-terminal domain of Brf1, the C-terminal domain contains extensive binding sites for TBP and Bdp1 to hold together the TFIIIB complex on the promoter. Overall, the domain architecture of the PIC derived from our cross-linking data explains how individual structural subdomains of Brf1 integrate the protein network from the Pol III active center to the promoter for transcription initiation. PMID:24277937

  5. Mapping the protein interaction network for TFIIB-related factor Brf1 in the RNA polymerase III preinitiation complex.

    PubMed

    Khoo, Seok-Kooi; Wu, Chih-Chien; Lin, Yu-Chun; Lee, Jin-Cheng; Chen, Hung-Ta

    2014-02-01

    TFIIB-related factor Brf1 is essential for RNA polymerase (Pol) III recruitment and open-promoter formation in transcription initiation. We site specifically incorporated a nonnatural amino acid cross-linker into Brf1 to map its protein interaction targets in the preinitiation complex (PIC). Our cross-linking analysis in the N-terminal domain of Brf1 indicated a pattern of multiple protein interactions reminiscent of TFIIB in the Pol active-site cleft. In addition to the TFIIB-like protein interactions, the Brf1 cyclin repeat subdomain is in contact with the Pol III-specific C34 subunit. With site-directed hydroxyl radical probing, we further revealed the binding between Brf1 cyclin repeats and the highly conserved region connecting C34 winged-helix domains 2 and 3. In contrast to the N-terminal domain of Brf1, the C-terminal domain contains extensive binding sites for TBP and Bdp1 to hold together the TFIIIB complex on the promoter. Overall, the domain architecture of the PIC derived from our cross-linking data explains how individual structural subdomains of Brf1 integrate the protein network from the Pol III active center to the promoter for transcription initiation. PMID:24277937

  6. 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.

  7. 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

  8. 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

  9. Satellite-based solar radiation mapping over complex terrain: Validation in the Alps and possible improvements

    NASA Astrophysics Data System (ADS)

    Castelli, Mariapina; Stoeckli, Reto; Tetzlaff, Anke; Ernst Wagner, Jochen; Zardi, Dino; Petitta, Marcello

    2013-04-01

    . Consequently it is recommended to include in the clear-sky model more accurate input than the currently used monthly climatologies of aerosol and the operational 1 day forecast of column water vapor amount from the ECMWF model ouptut. References [1] K. V. Khlopenkov And A. P. Trishchenko, "SPARC: New Cloud, Snow, and Cloud Shadow Detection Scheme for Historical 1-km AVHHR Data over Canada", Journal of Atmospheric and Oceanic Technology, 24, pp. 322-343, 2007. [2] R.W. Müller, C. Matsoukas, A. Gratzki, H.D. Behr, R. Hollmann. "The CM-SAF operational scheme for the satellite based retrieval of solar surface irradiance - A LUT based eigenvector hybrid approach", Remote Sensing of Environment, 113, pp.1012-1024, 2009. [3] R. Stöckli (in prep.). "Supplementing Heliosat for physically-based surface radiation retrieval in complex terrain."

  10. Fine-Mapping and Phenotypic Analysis of the Ity3 Salmonella Susceptibility Locus Identify a Complex Genetic Structure

    PubMed Central

    Khan, Rabia T.; Yuki, Kyoko E.; Malo, Danielle

    2014-01-01

    Experimental animal models of Salmonella infections have been widely used to identify genes important in the host immune response to infection. Using an F2 cross between the classical inbred strain C57BL/6J and the wild derived strain MOLF/Ei, we have previously identified Ity3 (Immunity to Typhimurium locus 3) as a locus contributing to the early susceptibility of MOLF/Ei mice to infection with Salmonella Typhimurium. We have also established a congenic strain (B6.MOLF-Ity/Ity3) with the MOLF/Ei Ity3 donor segment on a C57BL/6J background. The current study was designed to fine map and characterize functionally the Ity3 locus. We generated 12 recombinant sub-congenic strains that were characterized for susceptibility to infection, bacterial load in target organs, cytokine profile and anti-microbial mechanisms. These analyses showed that the impact of the Ity3 locus on survival and bacterial burden was stronger in male mice compared to female mice. Fine mapping of Ity3 indicated that two subloci contribute collectively to the susceptibility of B6.MOLF-Ity/Ity3 congenic mice to Salmonella infection. The Ity3.1 sublocus controls NADPH oxidase activity and is characterized by decreased ROS production, reduced inflammatory cytokine response and increased bacterial burden, thereby supporting a role for Ncf2 (neutrophil cytosolic factor 2 a subunit of NADPH oxidase) as the gene underlying this sublocus. The Ity3.2 sub-locus is characterized by a hyperresponsive inflammatory cytokine phenotype after exposure to Salmonella. Overall, this research provides support to the combined action of hormonal influences and complex genetic factors within the Ity3 locus in the innate immune response to Salmonella infection in wild-derived MOLF/Ei mice. PMID:24505352

  11. 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.

  12. High resolution magnetic field mapping of complex magmatic rock suites and associated tectonic structures in the Southern Andes

    NASA Astrophysics Data System (ADS)

    Díaz-Michelena, Marina; Kilian, Rolf

    2013-04-01

    Magmatic and metamorphic rocks of the southernmost Andes (50 to 55°S) document a complex magmatic and tectonic history of an active continental margin during the past >140 Ma [1]. However, the regional distribution of the multiple magmatic intrusive rock suites and younger systems of basaltic dykes as well as the tectonic control of associated hydrothermal systems are widely unexplored. Since the rocks are often bare exposed they represent an ideal test site for a magnetic field investigation with significant implication for future aeromagnetic mapping. Thus we performed a high resolution near-surface grid of measurements with a scalar and vector magnetometer at selected sites which include different intrusive rocks, tectonic lineaments and hydrothermal alteration with an associated mineralization. The magnetic signature corresponding to the Natural Remanent Magnetisation (NRM) was measured on Mesozoic and Cenozoic gabbroid to granitic plutons with large range chemical and mineralogical variations [1], on distinct basaltic dykes, as well as on mylonites, gneisses and hornfels rocks. The whole-rock chemistry of the selected rock types was determined by Atomic Absorption Spectroscopy and X-ray Fluorescence. The analysed and mapped rocks include the SiO2 range from 45 to 76 wt.%, FeO (tot) contents from 2 to 18 wt.% and Ti2O contents from 0.2 to 2.5 wt.%. The mineral assemblages were analysed by polarization microscopy, with an electron microprobe and X-ray diffraction. In the plutonic rocks the whole rock chemistry often is related to the amount of magnetite and NRM intensities [2]. However, measured magnetic intensities let us estimate the degree of chloritization and associated demagnetisation by magnetite alteration and transformation to maghemite and/or iron-hydroxides. For Miocene basaltic dyke systems of decimetre to several meters extension within granitic plutons, a high resolution magnetic mapping has been also performed. We expected a relationship of

  13. 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

  14. Processing and Correcting Master Images to Analyze and map Metamorphic Core Complexes in the Southern Basin and Range Province

    NASA Astrophysics Data System (ADS)

    Sanchez, S. O.

    2004-12-01

    Metamorphic core complexes (MCCs) have been of great interest to geologists and geophysicists and our goal is to facilitate integrated studies of these intriguing features. Our specific targets are the exposed Whipple Mountains in Southeastern California and the spectrally similar Mohave Mountains in Western Arizona. These two ranges were selected for study using the MODIS/ASTER airborne sensor also known as MASTER, and NASA/JPL acquired the data for us. These two ranges were chosen because of their close proximity to each other in the imagery. This sensor was chosen because it has a good resolution (15m) and 50 different bands ranging from the visible to thermal infrared. However, because it is flown on a light aircraft its flight line patterns and photogrammetric distortions make it hard to georeference and mosaic with other images from adjacent flight lines. The distortions become misalignments of images during mosaicing. This project involved two efforts: 1) developing a method for correcting and processing MASTER multispectral images; and 2) using those images to analyze and map MCCs in the southern Basin and Range Province. Standard image processing techniques available within the ENVI software package were applied to this imagery to geometrically correct, mosaic, and spectrally process it in order to locate defining characteristics of MCCs that are mappable with the imagery. These techniques include the use of warping, histogram matching, mosaicing, classification, Principal Component Analysis, decorrelation stretching, Minimum Noise Fraction Transformation, Pixel Purity Index, and end member analysis.

  15. 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.

  16. 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

  17. Geologic Mapping in Nogal Peak Quadrangle: Geochemistry, Intrusive Relations and Mineralization in the Sierra Blanca Igneous Complex, New Mexico

    NASA Astrophysics Data System (ADS)

    Goff, F.; Kelley, S. A.; Lawrence, J. R.; Cikowski, C. T.; Krier, D. J.; Goff, C. J.; McLemore, V. T.

    2011-12-01

    Nogal Peak quadrangle is located in the northern Sierra Blanca Igneous Complex (SBIC) and contains most of the White Mountain Wilderness (geologic map is available at http://geoinfo.nmt.edu/publications/maps/geologic/ofgm/details.cfml?Volume=134). The geology of the quad consists of a late Eocene to Oligocene volcanic pile (Sierra Blanca Volcanics, mostly alkali basalt to trachyte) intruded by a multitude of dikes, plugs and three stocks: Rialto, 31.4 Ma (mostly syenite), Three Rivers, ca. 29 to 27 Ma (quartz syenite intruded by subordinate alkali granite), and Bonito Lake, 26.6 Ma (mostly monzonite). Three Rivers stock is partially surrounded by alkali rhyolites that geochemically resemble the alkali granites. The circular shape of the stock and surrounding rhyolites suggests they form the root of a probable caldera. SBIC rocks have compositions typical of those found within the Rocky Mountain alkaline belt and those associated with continental rift zone magmatism. Because the volcanic host rocks are deeply eroded, intrusive relations with the stocks are well exposed. Most contacts at stock margins are near vertical. Roof pendants are common near some contacts and stoped blocks up to 700 m long are found within the Three Rivers stock. Contacts, pendants and stoped blocks generally display some combination of hornfelsing, brecciation, fracturing, faulting and mineralization. Sierra Blanca Volcanics display hydrothermal alteration increasing from argillic in the NW sector of the quad to high-temperature porpylitic near stock margins. Retrograde phyllic alteration occurs within breccia pipes and portions of the stocks. Mineral deposits consist of four types: Placer Au, fissure veins (mostly Ag-Pb-Zn±Au), breccia pipes (Au-Mo-Cu), and porphyry Mo-Cu. A singular pipe on the SW margin of Bonito Lake stock contains sapphire-lazulite-alunite. Although Au has been intermittently mined in the quad since 1865, best production of Au originated around the turn of the last

  18. 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

  19. 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

  20. 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

    2015-07-01

    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

  1. Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.

    PubMed

    Hamilton-Williams, Emma E; Rainbow, Daniel B; Cheung, Jocelyn; Christensen, Mikkel; Lyons, Paul A; Peterson, Laurence B; Steward, Charles A; Sherman, Linda A; Wicker, Linda S

    2013-10-01

    Nonobese diabetic (NOD) mice congenic for C57BL/10 (B10)-derived genes in the Idd9 region of chromosome 4 are highly protected from type 1 diabetes (T1D). Idd9 has been divided into three protective subregions (Idd9.1, 9.2, and 9.3), each of which partially prevents disease. In this study we have fine-mapped the Idd9.1 and Idd9.2 regions, revealing further genetic complexity with at least two additional subregions contributing to protection from T1D. Using the NOD sequence from bacterial artificial chromosome clones of the Idd9.1 and Idd9.2 regions as well as whole-genome sequence data recently made available, sequence polymorphisms within the regions highlight a high degree of polymorphism between the NOD and B10 strains in the Idd9 regions. Among numerous candidate genes are several with immunological importance. The Idd9.1 region has been separated into Idd9.1 and Idd9.4, with Lck remaining a candidate gene within Idd9.1. One of the Idd9.2 regions contains the candidate genes Masp2 (encoding mannan-binding lectin serine peptidase 2) and Mtor (encoding mammalian target of rapamycin). From mRNA expression analyses, we have also identified several other differentially expressed candidate genes within the Idd9.1 and Idd9.2 regions. These findings highlight that multiple, relatively small genetic effects combine and interact to produce significant changes in immune tolerance and diabetes onset. PMID:23934554

  2. 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.

  3. 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

  4. 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. PMID:26031785

  5. Ferredoxin/ferredoxin-thioredoxin reductase complex: Complete NMR mapping of the interaction site on ferredoxin by gallium substitution.

    PubMed

    Xu, Xingfu; Kim, Sung-Kun; Schürmann, Peter; Hirasawa, Masakazu; Tripathy, Jatindra N; Smith, Jody; Knaff, David B; Ubbink, Marcellus

    2006-12-11

    The reduction of ferredoxin-thioredoxin reductase (FTR) by plant-type ferredoxin plays an important role in redox regulation in plants and cyanobacteria. Nuclear magnetic resonance (NMR) was used to map the binding sites on Synechocystis ferredoxin for FTR. A gallium-substituted structural analog of this [2Fe-2S] ferredoxin was obtained by reconstituting the apoprotein in a refolding buffer containing gallium. For the first time, the complete interaction interface of a [2Fe-2S] ferredoxin with a target enzyme has been mapped by NMR chemical shift perturbation with this diamagnetic structural analog. PMID:17134703

  6. 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.

  7. 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

  8. A High-Resolution Linkage-Disequilibrium Map of the Human Major Histocompatibility Complex and First Generation of Tag Single-Nucleotide Polymorphisms

    PubMed Central

    Miretti, Marcos M.; Walsh, Emily C.; Ke, Xiayi; Delgado, Marcos; Griffiths, Mark; Hunt, Sarah; Morrison, Jonathan; Whittaker, Pamela; Lander, Eric S.; Cardon, Lon R.; Bentley, David R.; Rioux, John D.; Beck, Stephan; Deloukas, Panos

    2005-01-01

    Autoimmune, inflammatory, and infectious diseases present a major burden to human health and are frequently associated with loci in the human major histocompatibility complex (MHC). Here, we report a high-resolution (1.9 kb) linkage-disequilibrium (LD) map of a 4.46-Mb fragment containing the MHC in U.S. pedigrees with northern and western European ancestry collected by the Centre d'Etude du Polymorphisme Humain (CEPH) and the first generation of haplotype tag single-nucleotide polymorphisms (tagSNPs) that provide up to a fivefold increase in genotyping efficiency for all future MHC-linked disease-association studies. The data confirm previously identified recombination hotspots in the class II region and allow the prediction of numerous novel hotspots in the class I and class III regions. The region of longest LD maps outside the classic MHC to the extended class I region spanning the MHC-linked olfactory-receptor gene cluster. The extended haplotype homozygosity analysis for recent positive selection shows that all 14 outlying haplotype variants map to a single extended haplotype, which most commonly bears HLA-DRB1*1501. The SNP data, haplotype blocks, and tagSNPs analysis reported here have been entered into a multidimensional Web-based database (GLOVAR), where they can be accessed and viewed in the context of relevant genome annotation. This LD map allowed us to give coordinates for the extremely variable LD structure underlying the MHC. PMID:15747258

  9. 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

  10. 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

  11. 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

  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. PMID:27178327

  13. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure.

    PubMed

    Greenberg, Charles H; Kollman, Justin; Zelter, Alex; Johnson, Richard; MacCoss, Michael J; Davis, Trisha N; Agard, David A; Sali, Andrej

    2016-06-01

    Modeling protein complex structures based on distantly related homologues can be challenging due to poor sequence and structure conservation. Therefore, utilizing even low-resolution experimental data can significantly increase model precision and accuracy. Here, we present models of the two key functional states of the yeast γ-tubulin small complex (γTuSC): one for the low-activity "open" state and another for the higher-activity "closed" state. Both models were computed based on remotely related template structures and cryo-EM density maps at 6.9Å and 8.0Å resolution, respectively. For each state, extensive sampling of alignments and conformations was guided by the fit to the corresponding cryo-EM density map. The resulting good-scoring models formed a tightly clustered ensemble of conformations in most regions. We found significant structural differences between the two states, primarily in the γ-tubulin subunit regions where the microtubule binds. We also report a set of chemical cross-links that were found to be consistent with equilibrium between the open and closed states. The protocols developed here have been incorporated into our open-source Integrative Modeling Platform (IMP) software package (http://integrativemodeling.org), and can therefore be applied to many other systems. PMID:26968363

  14. 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

  15. 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

  16. 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…

  17. A Map of Dielectric Heterogeneity in a Membrane Protein: the Hetero-Oligomeric Cytochrome b6f Complex

    PubMed Central

    2015-01-01

    The cytochrome b6f complex, a member of the cytochrome bc family that mediates energy transduction in photosynthetic and respiratory membranes, is a hetero-oligomeric complex that utilizes two pairs of b-hemes in a symmetric dimer to accomplish trans-membrane electron transfer, quinone oxidation–reduction, and generation of a proton electrochemical potential. Analysis of electron storage in this pathway, utilizing simultaneous measurement of heme reduction, and of circular dichroism (CD) spectra, to assay heme–heme interactions, implies a heterogeneous distribution of the dielectric constants that mediate electrostatic interactions between the four hemes in the complex. Crystallographic information was used to determine the identity of the interacting hemes. The Soret band CD signal is dominated by excitonic interaction between the intramonomer b-hemes, bn and bp, on the electrochemically negative and positive sides of the complex. Kinetic data imply that the most probable pathway for transfer of the two electrons needed for quinone oxidation–reduction utilizes this intramonomer heme pair, contradicting the expectation based on heme redox potentials and thermodynamics, that the two higher potential hemes bn on different monomers would be preferentially reduced. Energetically preferred intramonomer electron storage of electrons on the intramonomer b-hemes is found to require heterogeneity of interheme dielectric constants. Relative to the medium separating the two higher potential hemes bn, a relatively large dielectric constant must exist between the intramonomer b-hemes, allowing a smaller electrostatic repulsion between the reduced hemes. Heterogeneity of dielectric constants is an additional structure–function parameter of membrane protein complexes. PMID:24867491

  18. 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

  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. 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

  1. Seismic Refraction Mapping of the K-T Boundary Complex Near the Brazos River, Falls County, Texas

    NASA Astrophysics Data System (ADS)

    Gowan, J. S.; Everett, M. E.

    2007-12-01

    The relationship between the Chicxulub impact and the paleontologically defined boundary between the Cretaceous and Tertiary periods is a hotly debated subject. The K-T complex, with its distinctive yellow spherule- rich clay layer, is capped by sandstone beds in streambed exposures along the Brazos River in Falls County, TX. Studies of the microfossils in the Falls Co. location show that the paleontological K-T boundary is stratigraphically removed from the yellow clay layer associated with Chicxulub. This study is an attempt to construct a 3-D image of the top of "event complex" by the use of geophysical methods. A near surface seismic refraction survey was completed in an area near the exposed K-T sections. Our seismic images may shed some light on competing theories as to the depositional environment at the time the sandstone bed was formed. Important seismically-resolved topographic features such as undulations and discontinuities could play a large role in shaping a better understanding of the K-T boundary complex origins.

  2. 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.

  3. Pulsed Field Gradient NMR with Sigmoid Shape Gradient Sampling To Produce More Detailed Diffusion Ordered Spectroscopy Maps of Real Complex Mixtures: Examples with Medicine Analysis.

    PubMed

    Pagès, Guilhem; Bonny, Alice; Gilard, Véronique; Malet-Martino, Myriam

    2016-03-15

    NMR diffusion measurements are based on signal attenuation. In the case of complex mixtures for which some molecules are diffusing quickly while others are significantly slower, it is challenging to obtain a diffusion ordered spectroscopy (DOSY)-type 2D map giving reliable information on all molecules. In this paper, we propose a new gradient sampling approach based on a sigmoid shape allowing the acquisition of a significant number of points for both the fast and slow diffusing molecules. We applied this new gradient sampling strategy to deformulate two medicines whose composition was known (Esomeprazole) or unknown (Mebendazole). PFG NMR associated with a sigmoid gradient ramp is an exciting strategy to study drugs as a whole, i.e., the active ingredient(s) and excipients. PMID:26905176

  4. Physical Map of Human 6p21.2–6p21.3: Region Flanking the Centromeric End of the Major Histocompatibility Complex

    PubMed Central

    Tripodis, Nicos; Mason, Ruth; Humphray, Sean J.; Davies, Angela F.; Herberg, Jethro A.; Trowsdale, John; Nizetic, Dean; Senger, Gabriele; Ragoussis, Jiannis

    1998-01-01

    We have physically mapped and cloned a 2.5-Mb chromosomal segment flanking the centromeric end of the major histocompatibility complex (MHC). We characterized in detail 27 YACs, 144 cosmids, 51 PACs, and 5 BACs, which will facilitate the complete genomic sequencing of this region of chromosome 6. The contig contains the genes encoding CSBP, p21, HSU09564 serine kinase, ZNF76, TCP-11, RPS10, HMGI(Y), BAK, and the human homolog of Tctex-7 (HSET). The GLO1 gene was mapped further centromeric in the 6p21.2–6p21.1 region toward TCTE-1. The gene order of the GLO1–HMGI(Y) segment in respect to the centromere is similar to the gene order in the mouse t-chromosome distal inversion, indicating that there is conservation in gene content but not gene order between humans and mice in this region. The close linkage of the BAK and CSBP genes to the MHC is of interest because of their possible involvement in autoimmune disease. PMID:9647638

  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 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

  7. Multivariate eQTL mapping uncovers functional variation on the X-chromosome associated with complex disease traits.

    PubMed

    Brumpton, Ben M; Ferreira, Manuel A R

    2016-07-01

    Very few studies have investigated the associations between genetic polymorphisms and gene expression on the X-chromosome. This is a major bottleneck when conducting functional follow-up studies of trait-associated variants, as those identified in genome-wide association studies (GWAS). We used a multivariate approach to test the association between individual single nucleotide polymorphisms (SNPs) and exon expression levels measured in 356 Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) from the Geuvadis RNA sequencing project to identify SNPs associated with variation in gene expression on the X-chromosome, which we refer to as eSNPs. At an FDR of 5 %, we discovered 548 independent [linkage disequilibrium (LD) r (2) < 0.1] eSNPs on the X-chromosome. Of these, 35 were in LD (r (2) > 0.8) with previously published disease- or trait-associated variants identified through GWAS. One of the strongest eSNPs identified was rs35975601, which was associated with F8A1 expression (p value = 3 × 10(-20)) and was in LD with a type 1 diabetes risk variant. Additionally, we identified a number of genes for which eSNPs were in LD with multiple diseases or traits, including DNASE1L1 which was mapped to bilirubin levels, type 1 diabetes and schizophrenia. Our results also indicate that multivariate exon-level analysis provides a more powerful approach than univariate gene-level analysis, particularly when SNPs influence the expression of different exons with different magnitude and/or direction of effect. The associations identified in our study may provide new insights into the molecular process by which gene expression may contribute to trait variation or disease risk in humans. PMID:27155841

  8. Polarized Neutron Diffraction as a Tool for Mapping Molecular Magnetic Anisotropy: Local Susceptibility Tensors in Co(II) Complexes.

    PubMed

    Ridier, Karl; Gillon, Béatrice; Gukasov, Arsen; Chaboussant, Grégory; Cousson, Alain; Luneau, Dominique; Borta, Ana; Jacquot, Jean-François; Checa, Ruben; Chiba, Yukako; Sakiyama, Hiroshi; Mikuriya, Masahiro

    2016-01-11

    Polarized neutron diffraction (PND) experiments were carried out at low temperature to characterize with high precision the local magnetic anisotropy in two paramagnetic high-spin cobalt(II) complexes, namely [Co(II) (dmf)6 ](BPh4 )2 (1) and [Co(II) 2 (sym-hmp)2 ](BPh4 )2 (2), in which dmf=N,N-dimethylformamide; sym-hmp=2,6-bis[(2-hydroxyethyl)methylaminomethyl]-4-methylphenolate, and BPh4 (-) =tetraphenylborate. This allowed a unique and direct determination of the local magnetic susceptibility tensor on each individual Co(II) site. In compound 1, this approach reveals the correlation between the single-ion easy magnetization direction and a trigonal elongation axis of the Co(II) coordination octahedron. In exchange-coupled dimer 2, the determination of the individual Co(II) magnetic susceptibility tensors provides a clear outlook of how the local magnetic properties on both Co(II) sites deviate from the single-ion behavior because of antiferromagnetic exchange coupling. PMID:26728231

  9. ErbB2, EphrinB1, Src Kinase and PTPN13 Signaling Complex Regulates MAP Kinase Signaling in Human Cancers

    PubMed Central

    Vermeer, Paola D.; Bell, Megan; Lee, Kimberly; Vermeer, Daniel W.; Wieking, Byrant G.; Bilal, Erhan; Bhanot, Gyan; Drapkin, Ronny I.; Ganesan, Shridar; Klingelhutz, Aloysius J.; Hendriks, Wiljan J.; Lee, John H.

    2012-01-01

    In non-cancerous cells, phosphorylated proteins exist transiently, becoming de-phosphorylated by specific phosphatases that terminate propagation of signaling pathways. In cancers, compromised phosphatase activity and/or expression occur and contribute to tumor phenotype. The non-receptor phosphatase, PTPN13, has recently been dubbed a putative tumor suppressor. It decreased expression in breast cancer correlates with decreased overall survival. Here we show that PTPN13 regulates a new signaling complex in breast cancer consisting of ErbB2, Src, and EphrinB1. To our knowledge, this signaling complex has not been previously described. Co-immunoprecipitation and localization studies demonstrate that EphrinB1, a PTPN13 substrate, interacts with ErbB2. In addition, the oncogenic V660E ErbB2 mutation enhances this interaction, while Src kinase mediates EphrinB1 phosphorylation and subsequent MAP Kinase signaling. Decreased PTPN13 function further enhances signaling. The association of oncogene kinases (ErbB2, Src), a signaling transmembrane ligand (EphrinB1) and a phosphatase tumor suppressor (PTPN13) suggest that EphrinB1 may be a relevant therapeutic target in breast cancers harboring ErbB2-activating mutations and decreased PTPN13 expression. PMID:22279592

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: use of a photoactivatable reagent.

    PubMed

    Cai, K; Itoh, Y; Khorana, H G

    2001-04-24

    Interaction of light-activated rhodopsin with transducin (T) is the first event in visual signal transduction. We use covalent crosslinking approaches to map the contact sites in interaction between the two proteins. Here we use a photoactivatable reagent, N-[(2-pyridyldithio)-ethyl], 4-azido salicylamide. The reagent is attached to the SH group of cytoplasmic monocysteine rhodopsin mutants by a disulfide-exchange reaction with the pyridylthio group, and the derivatized rhodopsin then is complexed with T by illumination at lambda >495 nm. Subsequent irradiation of the complex at lambda310 nm generates covalent crosslinks between the two proteins. Crosslinking was demonstrated between T and a number of single cysteine rhodopsin mutants. However, sites of crosslinks were investigated in detail only between T and the rhodopsin mutant S240C (cytoplasmic loop V-VI). Crosslinking occurred predominantly with T(alpha). For identification of the sites of crosslinks in T(alpha), the strategy used involved: (i) derivatization of all of the free cysteines in the crosslinked proteins with N-ethylmaleimide; (ii) reduction of the disulfide bond linking the two proteins and isolation of all of the T(alpha) species carrying the crosslinked moiety with a free SH group; (iii) adduct formation of the latter with the N-maleimide moiety of the reagent, maleimido-butyryl-biocytin, containing a biotinyl group; (iv) trypsin degradation of the resulting T(alpha) derivatives and isolation of T(alpha) peptides carrying maleimido-butyryl-biocytin by avidin-agarose chromatography; and (v) identification of the isolated peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We found that crosslinking occurred mainly to two C-terminal peptides in T(alpha) containing the amino acid sequences 310-313 and 342-345. PMID:11320237

  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 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

  17. Remote sensing aids geologic mapping

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

    Remote sensing techniques were 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 used for interpretation of the complex Cenozoic tectonic and geomorphic histories of the area.

  18. 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

  19. 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

  20. 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.

  1. 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...

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Remote and field level quantification of vegetation covariates for malaria mapping in three rice agro-village complexes in Central Kenya

    PubMed Central

    Jacob, Benjamin G; Muturi, Ephantus J; Mwangangi, Joseph M; Funes, Jose; Caamano, Erick X; Muriu, Simon; Shililu, Josephat; Githure, John; Novak, Robert J

    2007-01-01

    Background We examined algorithms for malaria mapping using the impact of reflectance calibration uncertainties on the accuracies of three vegetation indices (VI)'s derived from QuickBird data in three rice agro-village complexes Mwea, Kenya. We also generated inferential statistics from field sampled vegetation covariates for identifying riceland Anopheles arabiensis during the crop season. All aquatic habitats in the study sites were stratified based on levels of rice stages; flooded, land preparation, post-transplanting, tillering, flowering/maturation and post-harvest/fallow. A set of uncertainty propagation equations were designed to model the propagation of calibration uncertainties using the red channel (band 3: 0.63 to 0.69 μm) and the near infra-red (NIR) channel (band 4: 0.76 to 0.90 μm) to generate the Normalized Difference Vegetation Index (NDVI) and the Soil Adjusted Vegetation Index (SAVI). The Atmospheric Resistant Vegetation Index (ARVI) was also evaluated incorporating the QuickBird blue band (Band 1: 0.45 to 0.52 μm) to normalize atmospheric effects. In order to determine local clustering of riceland habitats Gi*(d) statistics were generated from the ground-based and remotely-sensed ecological databases. Additionally, all riceland habitats were visually examined using the spectral reflectance of vegetation land cover for identification of highly productive riceland Anopheles oviposition sites. Results The resultant VI uncertainties did not vary from surface reflectance or atmospheric conditions. Logistic regression analyses of all field sampled covariates revealed emergent vegetation was negatively associated with mosquito larvae at the three study sites. In addition, floating vegetation (-ve) was significantly associated with immature mosquitoes in Rurumi and Kiuria (-ve); while, turbidity was also important in Kiuria. All spatial models exhibit positive autocorrelation; similar numbers of log-counts tend to cluster in geographic space. The

  8. 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

  9. 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.

  10. Active Mapping.

    ERIC Educational Resources Information Center

    Day, Dennis

    1994-01-01

    Explains a social studies lesson for third graders that uses KidPix, a computer software graphics program to help students make maps and map keys. Advantages to using the computer versus hand drawing maps are discussed, and an example of map requirements for the lesson is included. (LRW)

  11. Concept Mapping.

    ERIC Educational Resources Information Center

    Callison, Daniel

    2001-01-01

    Explains concept mapping as a heuristic device that is helpful in visualizing the relationships between and among ideas. Highlights include how to begin a map; brainstorming; map applications, including document or information summaries and writing composition; and mind mapping to strengthen note-taking. (LRW)

  12. 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.

  13. 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

  14. Spatial diversity index mapping of classes in grid cell maps.

    USGS Publications Warehouse

    Robinove, C.J.

    1986-01-01

    The landscape diversity index indicates the number of classes of land that are in proximity to each point in a digital grid cell map. The index is D=100(i-1)/(n-1), where i = the number of landscape classes within a selected distance of each grid cell and n = the total number of mapped classes. The use of the index is illustrated by calculating the diversity index at each grid cell for each of five mapped classes and displaying the resulting diversity index map that portrays the complexity of the scene. The method is applicable to land-use planning, site selection, or description of landscape complexity.-Author

  15. Fast phase processing in off-axis holography using multiplexing with complex encoding and live-cell fluctuation map calculation in real-time.

    PubMed

    Girshovitz, Pinhas; Shaked, Natan T

    2015-04-01

    We present efficient algorithms for rapid reconstruction of quantitative phase maps from off-axis digital holograms. The new algorithms are aimed at speeding up the conventional Fourier-based algorithm. By implementing the new algorithms on a standard personal computer, while using only a single-core processing unit, we were able to reconstruct the unwrapped phase maps from one megapixel off-axis holograms at frame rates of up to 45 frames per second (fps). When phase unwrapping is not required, the same algorithms allow frame rates of up to 150 fps for one megapixel off-axis holograms. In addition to obtaining real-time quantitative visualization of the sample, the increased frame rate allows integrating additional calculations as a part of the reconstruction process, providing sample-related information that was not available in real time until now. We use these new capabilities to extract, for the first time to our knowledge, the dynamic fluctuation maps of red blood cells at frame rate of 31 fps for one megapixel holograms. PMID:25968715

  16. 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

  17. 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...

  18. Kentucky map

    NASA Astrophysics Data System (ADS)

    A wall-sized geological map of Kentucky, the product of 18 years of work, has just been released. Produced by the U.S. Geological Survey (USGS) in cooperation with the Kentucky Geological Survey (KGS) at the University of Kentucky, the map is unique, according to state geologist Donald Haney, because it is the first and only state map ever produced in detailed form from geologic quadrangle maps already available from the KGS.At a scale of 1:250,000, the map shows the surface distribution of various types of rock throughout the state, as well as geologic structure, faults, and surface coal beds. Numerous geologic sections, stratigraphic diagrams, correlation charts, and structure sections accompany the map. Compiled by R. C. McDowell and S. L. Moore of the USGS and by G. J . Grabowski of the KGS, the map was made by photoreducing and generalizing the detailed geologic quadrangle maps.

  19. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genomes of wheat and its relatives in the tribe Triticeae are large, containing nearly 90% repetitive DNA, and some are polyploid. These genomes can currently be completely sequenced only by the ordered-clone genome sequencing approach, which reduces the complexity of sequence assembly from th...

  1. 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....

  2. 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

  3. 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., Jr.; 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.

  4. Genetic Mapping in Human Disease

    PubMed Central

    Altshuler, David; Daly, Mark J.; Lander, Eric S.

    2009-01-01

    Genetic mapping provides a powerful approach to identify genes and biological processes underlying any trait influenced by inheritance, including human diseases. We discuss the intellectual foundations of genetic mapping of Mendelian and complex traits in humans, examine lessons emerging from linkage analysis of Mendelian diseases and genome-wide association studies of common diseases, and discuss questions and challenges that lie ahead. PMID:18988837

  5. 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.

  6. 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.

  7. From Complex B1 Mapping to Local SAR Estimation for Human Brain MR Imaging Using Multi-channel Transceiver Coil at 7T

    PubMed Central

    Zhang, Xiaotong; Schmitter, Sebastian; Van de Moortel, Pierre-François; Liu, Jiaen

    2014-01-01

    Elevated Specific Absorption Rate (SAR) associated with increased main magnetic field strength remains as a major safety concern in ultra-high-field (UHF) Magnetic Resonance Imaging (MRI) applications. The calculation of local SAR requires the knowledge of the electric field induced by radiofrequency (RF) excitation, and the local electrical properties of tissues. Since electric field distribution cannot be directly mapped in conventional MR measurements, SAR estimation is usually performed using numerical model-based electromagnetic simulations which, however, are highly time consuming and cannot account for the specific anatomy and tissue properties of the subject undergoing a scan. In the present study, starting from the measurable RF magnetic fields (B1) in MRI, we conducted a series of mathematical deduction to estimate the local, voxel-wise and subject-specific SAR for each single coil element using a multi-channel transceiver array coil. We first evaluated the feasibility of this approach in numerical simulations including two different human head models. We further conducted experimental study in a physical phantom and in two human subjects at 7T using a multi-channel transceiver head coil. Accuracy of the results is discussed in the context of predicting local SAR in the human brain at UHF MRI using multi-channel RF transmission. PMID:23508259

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. Undersea Mapping.

    ERIC Educational Resources Information Center

    DiSpezio, Michael A.

    1991-01-01

    Presented is a cooperative learning activity in which students assume different roles in an effort to produce a relief map of the ocean floor. Materials, procedures, definitions, student roles, and questions are discussed. A reproducible map for the activity is provided. (CW)

  14. 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…

  15. 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…

  16. 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

  17. Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits.

    PubMed Central

    Schön, Chris C; Utz, H Friedrich; Groh, Susanne; Truberg, Bernd; Openshaw, Steve; Melchinger, Albrecht E

    2004-01-01

    From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F(5) maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the genotypic variance explained by them, and the corresponding bias of estimates for grain yield, grain moisture, and plant height. In addition, we used computer simulations to compare the usefulness of two cross-validation schemes for obtaining unbiased estimates of QTL effects. The maximum, validated genotypic variance explained by QTL in this study was 52.3% for grain moisture despite the large number of detected QTL, thus confirming the infinitesimal model of quantitative genetics. In both simulated and experimental data, the effect of sample size on power of QTL detection as well as on accuracy and precision of QTL estimates was large. The number of detected QTL and the proportion of genotypic variance explained by QTL generally increased more with increasing N than with increasing E. The average bias of QTL estimates and its range were reduced by increasing N and E. Cross-validation performed well with respect to yielding asymptotically unbiased estimates of the genotypic variance explained by QTL. On the basis of our findings, recommendations for planning of QTL mapping experiments and allocation of experimental resources are given. PMID:15166171

  18. Structure of Ce2RhIn8: an example of complementary use of high-resolution neutron powder diffraction and reciprocal-space mapping to study complex materials.

    PubMed

    Moshopoulou, E G; Ibberson, R M; Sarrao, J L; Thompson, J D; Fisk, Z

    2006-04-01

    The room-temperature crystal structure of the heavy fermion antiferromagnet Ce2RhIn8, dicerium rhodium octaindide, has been studied by a combination of high-resolution synchrotron X-ray reciprocal-space mapping of single crystals and high-resolution time-of-flight neutron powder diffraction. The structure is disordered, exhibiting a complex interplay of non-periodic, partially correlated planar defects, coexistence and segregation of polytypic phases (induced by periodic planar ;defects'), mosaicity (i.e. domain misalignment) and non-uniform strain. These effects evolve as a function of temperature in a complicated way, but they remain down to low temperatures. The room-temperature diffraction data are best represented by a complex mixture of two polytypic phases, which are affected by non-periodic, partially correlated planar defects, differ slightly in their tetragonal structures, and exhibit different mosaicities and strain values. Therefore, Ce2RhIn8 approaches the paracrystalline state, rather than the classic crystalline state and thus several of the concepts of conventional single-crystal crystallography are inapplicable. The structural results are discussed in the context of the role of disorder in the heavy-fermion state and in the interplay between superconductivity and magnetism. PMID:16552150

  19. Radiation hybrid mapping in crop plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Map-based cloning and manipulation of genes controlling important traits for crop remains a great challenge due to the complex of crop genomes and lack of a high resolution of genetic and physical maps. In this review article, we compared the various mapping methods available for plant research and ...

  20. 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

  1. 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

  2. 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

  3. Semantic Mapping.

    ERIC Educational Resources Information Center

    Johnson, Dale D.; And Others

    1986-01-01

    Describes semantic mapping, an effective strategy for vocabulary instruction that involves the categorical structuring of information in graphic form and requires students to relate new words to their own experience and prior knowledge. (HOD)

  4. 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)

  5. Map Separates

    USGS Publications Warehouse

    U.S. Geological Survey

    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.

  6. 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.

  7. [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

  8. 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

  9. Parametric mapping

    NASA Astrophysics Data System (ADS)

    Branch, Allan C.

    1998-01-01

    Parametric mapping (PM) lies midway between older and proven artificial landmark based guidance systems and yet to be realized vision based guidance systems. It is a simple yet effective natural landmark recognition system offering freedom from the need for enhancements to the environment. Development of PM systems can be inexpensive and rapid and they are starting to appear in commercial and industrial applications. Together with a description of the structural framework developed to generically describe robot mobility, this paper illustrates clearly the parts of any mobile robot navigation and guidance system and their interrelationships. Among other things, the importance of the richness of the reference map, and not necessarily the sensor map, is introduced, the benefits of dynamic path planners to alleviate the need for separate object avoidance, and the independence of the PM system to the type of sensor input is shown.

  10. 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…

  11. 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.

  12. Disaggregation of soil map units for improved ecological site mapping in rangelands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rangeland soils are often mapped with soil map units consisting of associations, complexes, and undifferentiated groups composed of varied soil components. Because different components may be related to different ecological sites, the unmapped heterogeneity within map units limits the potential uses...

  13. Disaggregation of Soil Map Units for Improved Ecological Site Mapping in Rangelands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rangeland soils are often mapped with soil map units consisting of associations, complexes, and undifferentiated groups composed of varied soil components. Because different components may be related to different ecological sites, the unmapped heterogeneity within map units limits the potential uses...

  14. 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.

  15. 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…

  16. Harvesting geographic features from heterogeneous raster maps

    NASA Astrophysics Data System (ADS)

    Chiang, Yao-Yi

    2010-11-01

    Raster maps offer a great deal of geospatial information and are easily accessible compared to other geospatial data. However, harvesting geographic features locked in heterogeneous raster maps to obtain the geospatial information is challenging. This is because of the varying image quality of raster maps (e.g., scanned maps with poor image quality and computer-generated maps with good image quality), the overlapping geographic features in maps, and the typical lack of metadata (e.g., map geocoordinates, map source, and original vector data). Previous work on map processing is typically limited to a specific type of map and often relies on intensive manual work. In contrast, this thesis investigates a general approach that does not rely on any prior knowledge and requires minimal user effort to process heterogeneous raster maps. This approach includes automatic and supervised techniques to process raster maps for separating individual layers of geographic features from the maps and recognizing geographic features in the separated layers (i.e., detecting road intersections, generating and vectorizing road geometry, and recognizing text labels). The automatic technique eliminates user intervention by exploiting common map properties of how road lines and text labels are drawn in raster maps. For example, the road lines are elongated linear objects and the characters are small connected-objects. The supervised technique utilizes labels of road and text areas to handle complex raster maps, or maps with poor image quality, and can process a variety of raster maps with minimal user input. The results show that the general approach can handle raster maps with varying map complexity, color usage, and image quality. By matching extracted road intersections to another geospatial dataset, we can identify the geocoordinates of a raster map and further align the raster map, separated feature layers from the map, and recognized features from the layers with the geospatial

  17. 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.

  18. 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

  19. Conceptual Mapping: A Tool for Self-Reflection.

    ERIC Educational Resources Information Center

    Holcombe, Melinda; Shonka, Amy

    1993-01-01

    Considers the ways that conceptual mapping as a classroom technique can help students reflect critically on complex conceptual relationships. Shows how teachers can use conceptual mapping in the classroom. (HB)

  20. 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

  1. 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.

  2. Children's Relief Maps of Model Landscapes.

    ERIC Educational Resources Information Center

    Wiegand, Patrick; Stiell, Bernadette

    1997-01-01

    Reports on a study where 111 primary age children were asked to map four model landscapes of increasing complexity. The results show an age-related progression from representing hills in elevation only to early experiments with the use of contours. Includes maps, graphs, and statistical data. (MJP)

  3. 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.

  4. 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.

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

    PubMed

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

    2004-08-01

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

  6. Mapping the Natchez Trace Parkway

    USGS Publications Warehouse

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

    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

  7. 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

  8. A cohomological framework for homotopy moment maps

    NASA Astrophysics Data System (ADS)

    Frégier, Yaël; Laurent-Gengoux, Camille; Zambon, Marco

    2015-11-01

    Given a Lie group acting on a manifold M preserving a closed n + 1-form ω, the notion of homotopy moment map for this action was introduced in Fregier (0000), in terms of L∞-algebra morphisms. In this note we describe homotopy moment maps as coboundaries of a certain complex. This description simplifies greatly computations, and we use it to study various properties of homotopy moment maps: their relation to equivariant cohomology, their obstruction theory, how they induce new ones on mapping spaces, and their equivalences. The results we obtain extend some of the results of Fregier (0000).

  9. 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., III; 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

  10. Geologic mapping of Europa

    NASA Astrophysics Data System (ADS)

    Greeley, Ronald; Collins, Geoffrey C.; Spaun, Nicole A.; Sullivan, Robert J.; Moore, Jeffrey M.; Senske, David A.; Tufts, B. Randall; Johnson, Torrence V.; Belton, Michael J. S.; Tanaka, Kenneth L.

    2000-09-01

    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

  11. 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.

  12. 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…

  13. 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

  14. 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

  15. Maps & minds : mapping through the ages

    USGS Publications Warehouse

    U.S. Geological Survey

    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.

  16. Computer-Based Concept Mapping: Active Studying for Active Learners.

    ERIC Educational Resources Information Center

    Anderson-Inman, Lynne; Zeitz, Leigh

    1993-01-01

    Describes the use of computer-generated concept maps using a new genre of graphics programs that allows students to create, alter and expand maps as they acquire more subject matter knowledge. Four examples of increasingly complex concept maps developed by a high school student studying cellular biology are discussed and illustrated. (Contains 19…

  17. 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)

  18. Mapping Hesperia Planum, Mars

    NASA Technical Reports Server (NTRS)

    Gregg, Tracy K. P.; Crown, David A.

    2008-01-01

    Hesperia Planum, characterized by a high concentration of mare-type wrinkle ridges and ridge rings [1-4], encompasses > 2 million km2 in the southern highlands of Mars (Fig. 1). The most common interpretation is that the plains were emplaced as flood lavas with total thicknesses of <3 km [4-10]. The wrinkle ridges on its surface make Hesperia Planum the type locale for Hesperian-aged ridged plains on Mars [e.g., 9], and recent investigations reveal that wrinkle-ridge formation occurred in more than one episode [4]. Hesperia Planum s stratigraphic position and crater-retention age [e.g., 9, 11-12] define the base of the Hesperian System. However, preliminary results of geologic mapping reveal that the whole of Hesperia Planum is unlikely to be composed of the same materials, emplaced at the same geologic time. To unravel these complexities, we are generating a 1:1.5M-scale geologic map of Hesperia Planum and its surroundings (Fig. 1). To date, we have identified 4 distinct plains units within Hesperia Planum and are attempting to determine the nature and relative ages of these materials (Fig. 2) [13-15].

  19. Human Prostate Cancer Hallmarks Map.

    PubMed

    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

  20. 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

  1. 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…

  2. Fundamentals of Physical Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. 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

  4. 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

  5. National Atlas maps

    USGS Publications Warehouse

    U.S. Geological Survey

    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.

  6. 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

  7. 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

  8. 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.

  9. Global order and local disorder in brain maps.

    PubMed

    Rothschild, Gideon; Mizrahi, Adi

    2015-07-01

    Maps serve as a ubiquitous organizing principle in the mammalian brain. In several sensory systems, such as audition, vision, and somatosensation, topographic maps are evident throughout multiple levels of brain pathways. Topographic maps, like retinotopy and tonotopy, persist from the receptor surface up to the cortex. Other maps, such as those of orientation preference in the visual cortex, are first created in the cortex itself. Despite the prevalence of topographic maps, it is still not clear what function they subserve. Although maps are topographically smooth at the macroscale, they are often locally heterogeneous. Here, we review studies describing the anatomy and physiology of topographic maps across various spatial scales, from the smooth macroscale to the heterogeneous local microarchitecture, with emphasis on maps of the visual and auditory systems. We discuss the potential advantages of local heterogeneity in brain maps, how they reflect complex cortical connectivity, and how they may impact sensory coding and local computations. PMID:25897872

  10. 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…

  11. 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

  12. 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.

  13. A Mathematical Exploration of MAP Kinase Behavior

    NASA Astrophysics Data System (ADS)

    Adams, Rhys; Balazsi, Gabor

    2008-03-01

    Mitogen-Activated Protein (MAP) kinase pathways are highly conserved from yeast to humans and are implicated in cell survival and cell death. Signaling through these pathways starts with the phosphorylation of the most upstream component (MAP kinase kinase kinase, MAPKKK), continues with phosphorylation of a MAP kinase kinase (MAPKK), and ends with phosphorylation of the target MAP kinase (MAPK). Theoretical studies over the past few decades have generated important insights into the dynamical behavior and signal processing capability of these pathways, including bistability, oscillations, signal amplification, etc. Prompted by the possibility of complex behavior in simpler signaling units than a full MAP kinase pathway, we investigate the possibility of In-Band Detection (IBD) within a single step of the cascade. We show that a basal rate of target phosphorylation can lead to IBD in a simpler system than the one described before, and define a precise relationship between the various reaction rates that is necessary to obtain IBD.

  14. A Protein Interaction Map of Drosophila melanogaster

    NASA Astrophysics Data System (ADS)

    Giot, L.; Bader, J. S.; Brouwer, C.; Chaudhuri, A.; Kuang, B.; Li, Y.; Hao, Y. L.; Ooi, C. E.; Godwin, B.; Vitols, E.; Vijayadamodar, G.; Pochart, P.; Machineni, H.; Welsh, M.; Kong, Y.; Zerhusen, B.; Malcolm, R.; Varrone, Z.; Collis, A.; Minto, M.; Burgess, S.; McDaniel, L.; Stimpson, E.; Spriggs, F.; Williams, J.; Neurath, K.; Ioime, N.; Agee, M.; Voss, E.; Furtak, K.; Renzulli, R.; Aanensen, N.; Carrolla, S.; Bickelhaupt, E.; Lazovatsky, Y.; DaSilva, A.; Zhong, J.; Stanyon, C. A.; Finley, R. L.; White, K. P.; Braverman, M.; Jarvie, T.; Gold, S.; Leach, M.; Knight, J.; Shimkets, R. A.; McKenna, M. P.; Chant, J.; Rothberg, J. M.

    2003-12-01

    Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.

  15. Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex

    PubMed Central

    Tripodis, Nicos; Palmer, Sophie; Phillips, Sam; Milne, Sarah; Beck, Stephan; Ragoussis, Jiannis

    2000-01-01

    We have constructed a 2.5-Mb physical and transcription map that spans the human 6p21.2–6p21.3 region and includes the centromeric end of the MHC, using a combination of techniques. In total 88 transcription units including exons, cDNAs, and cDNA contigs were characterized and 60 were confidently positioned on the physical map. These include a number of genes encoding nuclear and splicing factors (Ndr kinase, HSU09564, HSRP20); cell cycle, DNA packaging, and apoptosis related [p21, HMGI(Y), BAK]; immune response (CSBP, SAPK4); transcription activators and zinc finger-containing genes (TEF-5, ZNF76); embryogenesis related (Csa-19); cell signaling (DIPP); structural (HSET), and other genes (TULP1, HSPRARD, DEF-6, EO6811, cyclophilin), as well as a number of RP genes and pseudogenes (RPS10, RPS12-like, RPL12-like, RPL35-like). Furthermore, several novel genes (a Br140-like, a G2S-like, a FBN2-like, a ZNF-like, and B1/KIAA0229) have been identified, as well as cDNAs and cDNA contigs. The detailed map of the gene content of this chromosomal segment provides a number of candidate genes, which may be involved in several biological processes that have been associated with this region, such as spermatogenesis, development, embryogenesis, and neoplasia. The data provide useful tools for synteny studies between mice and humans, for genome structure analysis, gene density comparisons, and studies of nucleotide composition, of different isochores and Giemsa light and Giemsa dark bands. PMID:10779486

  16. 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

  17. Functional mapping of growth and development.

    PubMed

    Li, Yao; Wu, Rongling

    2010-05-01

    Understanding how an organism develops into a fully functioning adult from a mass of undifferentiated cells may reveal different strategies that allow the organism to survive under limiting conditions. Here, we review an analytical model for characterizing quantitative trait loci (QTLs) that underlie variation in growth trajectories and developmental timing. This model, called functional mapping, incorporates fundamental principles behind biological processes or networks that are bridged with mathematical functions into a statistical mapping framework. Functional mapping estimates parameters that determine the shape and function of a particular biological process, thus providing a flexible platform to test biologically meaningful hypotheses regarding the complex relationships between gene action and development. PMID:19930171

  18. 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)

  19. Density Equalizing Map Projections

    SciTech Connect

    Close, E. R.; Merrill, D. W.; Holmes, H. H.

    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 disease can be readily identified, and their statistical significance determined, on a density equalized map.

  20. Density Equalizing Map Projections

    Energy Science and Technology Software Center (ESTSC)

    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

  1. New NSO Solar Surface Activity Maps

    NASA Astrophysics Data System (ADS)

    Henney, C. J.; Harvey, J. W.

    2001-05-01

    Using NSO-Kitt Peak Vacuum Telescope (KPVT) synoptic data, we present several new solar surface activity maps. The motivation is to test conventional wisdom about conditions that are likely to produce solar activity such as flares, coronal mass ejections and high speed solar wind streams. The ultimate goal is to improve real-time, observation-based models for the purpose of predicting solar activity. A large number of maps will eventually be produced based on the wide range of ideas and models of the conditions thought to lead to solar activity events. When data from the new SOLIS instruments becomes available, the range of possible models that can be tested will be greatly expanded. At present, the daily maps include ones that show magnetic field complexity, emerging flux and high speed solar wind sources. As a proxy for local magnetic potential energy, each element of the magnetic complexity map is the distance-weighted rms of the opposing ambient magnetic field. The flux emergence map is the difference between the two most recent absolute magnetic flux images. The solar wind source map is produced from coronal hole area data. The new maps are available on the NSO-Kitt Peak World Wide Web page. This research was supported in part by the Office of Navel Research Grant N00014-91-J-1040. The NSO-Kitt Peak data used here are produced cooperatively by NSF/AURA, NASA/GSFC, and NOAA/SEC.

  2. 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.

  3. 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...

  4. 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 ...

  5. Information-Mapped Chemistry.

    ERIC Educational Resources Information Center

    Olympia, P. L., Jr.

    1979-01-01

    This paper describes the use of information mapping in chemistry and in other related sciences. Information mapping is a way of presenting information without paragraphs and unnecessary transitional phrases. (BB)

  6. 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.

  7. 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)

  8. Using maps in genealogy

    USGS Publications Warehouse

    U.S. Geological Survey

    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

  9. Mapping Surface Accessibility of the C1r/C1s Tetramer by Chemical Modification and Mass Spectrometry Provides New Insights into Assembly of the Human C1 Complex*

    PubMed Central

    Brier, Sébastien; Pflieger, Delphine; Le Mignon, Maxime; Bally, Isabelle; Gaboriaud, Christine; Arlaud, Gérard J.; Daniel, Régis

    2010-01-01

    C1, the complex that triggers the classic pathway of complement, is a 790-kDa assembly resulting from association of a recognition protein C1q with a Ca2+-dependent tetramer comprising two copies of the proteases C1r and C1s. Early structural investigations have shown that the extended C1s-C1r-C1r-C1s tetramer folds into a compact conformation in C1. Recent site-directed mutagenesis studies have identified the C1q-binding sites in C1r and C1s and led to a three-dimensional model of the C1 complex (Bally, I., Rossi, V., Lunardi, T., Thielens, N. M., Gaboriaud, C., and Arlaud, G. J. (2009) J. Biol. Chem. 284, 19340–19348). In this study, we have used a mass spectrometry-based strategy involving a label-free semi-quantitative analysis of protein samples to gain new structural insights into C1 assembly. Using a stable chemical modification, we have compared the accessibility of the lysine residues in the isolated tetramer and in C1. The labeling data account for 51 of the 73 lysine residues of C1r and C1s. They strongly support the hypothesis that both C1s CUB1-EGF-CUB2 interaction domains, which are distant in the free tetramer, associate with each other in the C1 complex. This analysis also provides the first experimental evidence that, in the proenzyme form of C1, the C1s serine protease domain is partly positioned inside the C1q cone and yields precise information about its orientation in the complex. These results provide further structural insights into the architecture of the C1 complex, allowing significant improvement of our current C1 model. PMID:20592021

  10. 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

  11. 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.

  12. 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…

  13. 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…

  14. Mapping Sociological Concepts.

    ERIC Educational Resources Information Center

    Trepagnier, Barbara

    2002-01-01

    Focuses on the use of cognitive mapping within sociology. Describes an assignment where students created a cognitive map that focused on names of theorists and concepts related to them. Discusses sociological imagination in relation to cognitive mapping and the assessment of the assignment. (CMK)

  15. Statistical Mapping by Computer.

    ERIC Educational Resources Information Center

    Utano, Jack J.

    The function of a statistical map is to provide readers with a visual impression of the data so that they may be able to identify any geographic characteristics of the displayed phenomena. The increasingly important role played by the computer in the production of statistical maps is manifested by the varied examples of computer maps in recent…

  16. Using maps in genealogy

    USGS Publications Warehouse

    U.S. Geological Survey

    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.

  17. 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.

  18. Can a Healthcare "Lean Sweep" Deliver on What Matters to Patients? Comment on "Improving Wait Times to Care for Individuals with Multimorbidities and Complex Conditions Using Value Stream Mapping".

    PubMed

    Verma, Jennifer Y; Amar, Claudia

    2015-01-01

    Disconnects and defects in care - such as duplication, poor integration between services or avoidable adverse events - are costly to the health system and potentially harmful to patients and families. For patients living with multiple chronic conditions, such disconnects can be particularly detrimental. Lean is an approach to optimizing value by reducing waste (eg, duplication and defects) and containing costs (eg, improving integration of services) as well as focusing on what matters to patients. Lean works particularly well to optimize existing processes and services. However, as the burden of chronic illness and frailty overtake episodic care needs, health systems require far greater complex, adaptive change. Such change ought to take into account outcomes in population health in addition to care experiences and costs (together, comprising the Triple Aim); and involve patients and families in co-designing new models of care that better address complex, longer-term health needs. PMID:26673343

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Comparing Image-Based Methods for Assessing Visual Clutter in Generalized Maps

    NASA Astrophysics Data System (ADS)

    Touya, G.; Decherf, B.; Lalanne, M.; Dumont, M.

    2015-08-01

    Map generalization abstracts and simplifies geographic information to derive maps at smaller scales. The automation of map generalization requires techniques to evaluate the global quality of a generalized map. The quality and legibility of a generalized map is related to the complexity of the map, or the amount of clutter in the map, i.e. the excessive amount of information and its disorganization. Computer vision research is highly interested in measuring clutter in images, and this paper proposes to compare some of the existing techniques from computer vision, applied to generalized maps evaluation. Four techniques from the literature are described and tested on a large set of maps, generalized at different scales: edge density, subband entropy, quad tree complexity, and segmentation clutter. The results are analyzed against several criteria related to generalized maps, the identification of cluttered areas, the preservation of the global amount of information, the handling of occlusions and overlaps, foreground vs background, and blank space reduction.

  4. 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,…

  5. 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.

  6. Using concept maps in perioperative education.

    PubMed

    Noonan, Pam

    2011-11-01

    Critical thinking and clinical decision making are essential components of the knowledge and skills acquired in the perioperative education process. Although traditional didactic teaching methods remain predominant teaching strategies in perioperative nursing education, programs should include a variety of methods and tools to enhance learning of a considerable amount of complex material. Concept mapping is an active teaching strategy that can be used in nursing education to facilitate the development of critical thinking and decision-making skills. A concept map is a tool consisting of a main idea, subconcepts, and cross-links that organizes knowledge by showing relationships between concepts. Different types of maps can be used to present different types of learning material, depending on the focus of the lesson. Complex knowledge (eg, perioperative technology) can be better learned and retained when the brain works to organize information in a hierarchical framework and the information is built up with interacting concepts. PMID:22035816

  7. 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…

  8. Association Mapping for Enhancing Maize Genetic Improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identification of alleles that can contribute to the enhancement of a target trait. With the developments of high throughput genotyping techniques and advanc...

  9. Efficient Bit-to-Symbol Likelihood Mappings

    NASA Technical Reports Server (NTRS)

    Moision, Bruce E.; Nakashima, Michael A.

    2010-01-01

    This innovation is an efficient algorithm designed to perform bit-to-symbol and symbol-to-bit likelihood mappings that represent a significant portion of the complexity of an error-correction code decoder for high-order constellations. Recent implementation of the algorithm in hardware has yielded an 8- percent reduction in overall area relative to the prior design.

  10. Communication complexity and information complexity

    NASA Astrophysics Data System (ADS)

    Pankratov, Denis

    Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information

  11. 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

  12. 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

  13. Mapping Protein-Protein Interactions of the Resistance-Related Bacterial Zeta Toxin-Epsilon Antitoxin Complex (ε₂ζ₂) with High Affinity Peptide Ligands Using Fluorescence Polarization.

    PubMed

    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

  14. Image inpainting strategy for Kinect depth maps

    NASA Astrophysics Data System (ADS)

    Yao, Huimin; Chen, Yan; Ge, Chenyang

    2013-07-01

    The great advantage of Microsoft Kinect makes the depth acquisition real-time and inexpensive. But the depth maps directly obtained with the Microsoft Kinect device have absent regions and holes caused by optical factors. The noisy depth maps affect lots of complex tasks in computer vision. In order to improve the quality of the depth maps, this paper presents an efficient image inpainting strategy which is based on watershed segmentation and region merging framework of the corresponding color images. The primitive regions produced by watershed transform are merged into lager regions according to color similarity and edge among regions. Finally, mean filter operator to the adjacent pixels is used to fill up missing depth values and deblocking filter is applied for smoothing depth maps.

  15. Evaluation criteria for software classification inventories, accuracies, and maps

    NASA Technical Reports Server (NTRS)

    Jayroe, R. R., Jr.

    1976-01-01

    Statistical criteria are presented for modifying the contingency table used to evaluate tabular classification results obtained from remote sensing and ground truth maps. This classification technique contains information on the spatial complexity of the test site, on the relative location of classification errors, on agreement of the classification maps with ground truth maps, and reduces back to the original information normally found in a contingency table.

  16. Speed-Mapping Quantitative Trait Loci Using Microarrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the genetic architecture of complex traits is important for human health, agriculture, and understanding adaptive evolution, but is challenging because high resolution quantitative trait locus (QTL) mapping requires evaluation of thousands of recombinant individuals for the trait and clo...

  17. Status and Prospects of Association Mapping in Plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analy...

  18. 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

  19. Ripple Effect Mapping: A "Radiant" Way to Capture Program Impacts

    ERIC Educational Resources Information Center

    Kollock, Debra Hansen; Flage, Lynette; Chazdon, Scott; Paine, Nathan; Higgins, Lorie

    2012-01-01

    Learn more about a promising follow-up, participatory group process designed to document the results of Extension educational efforts within complex, real-life settings. The method, known as Ripple Effect Mapping, uses elements of Appreciative Inquiry, mind mapping, and qualitative data analysis to engage program participants and other community…

  20. A technology mapping of boolean functions for CPLDs

    NASA Astrophysics Data System (ADS)

    Kania, Dariusz

    2014-10-01

    The effective technology mapping for PAL-based Complex PLDs is presented. The aim of this approach is to cover a multiple-output function by a minimal number of PAL-based logic blocks. Proposed algorithm, implemented within the PALDec system, has been used for synthesizing the benchmarks. The obtained results are compared with the classical technology mapping.

  1. 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

  2. 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.

  3. Map-likelihood phasing

    PubMed Central

    Terwilliger, Thomas C.

    2001-01-01

    The recently developed technique of maximum-likelihood density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] allows a calculation of phase probabilities based on the likelihood of the electron-density map to be carried out separately from the calculation of any prior phase probabilities. Here, it is shown that phase-probability distributions calculated from the map-likelihood function alone can be highly accurate and that they show minimal bias towards the phases used to initiate the calculation. Map-likelihood phase probabilities depend upon expected characteristics of the electron-density map, such as a defined solvent region and expected electron-density distributions within the solvent region and the region occupied by a macromolecule. In the simplest case, map-likelihood phase-probability distributions are largely based on the flatness of the solvent region. Though map-likelihood phases can be calculated without prior phase information, they are greatly enhanced by high-quality starting phases. This leads to the technique of prime-and-switch phasing for removing model bias. In prime-and-switch phasing, biased phases such as those from a model are used to prime or initiate map-likelihood phasing, then final phases are obtained from map-likelihood phasing alone. Map-likelihood phasing can be applied in cases with solvent content as low as 30%. Potential applications of map-likelihood phasing include unbiased phase calculation from molecular-replacement models, iterative model building, unbiased electron-density maps for cases where 2Fo − Fc or σA-weighted maps would currently be used, structure validation and ab initio phase determination from solvent masks, non-crystallographic symmetry or other knowledge about expected electron density. PMID:11717488

  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. 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,…

  6. Making maps with computers

    USGS Publications Warehouse

    Guptill, S.C.; Starr, L.E.

    1988-01-01

    Soon after their introduction in the 1950s, digital computers were used for various phases of the mapping process, especially for trigonometric calculations of survey data and for orientation of aerial photographs on map manuscripts. In addition, computer-controlled plotters were used to draw simple outline maps. The process of collecting data for the plotters was slow and not as precise as those produced by the best manual cartography. Only during the 1980s has it become technologically feasible and cost-effective to assemble and use the data required to automate the mapping process. -from Authors

  7. DENALI IMAGE MAP.

    USGS Publications Warehouse

    Binnie, Douglas R.; Colvocoresses, Alden P.

    1987-01-01

    The Denali National Park and Preserve 1:250,000-scale image map has been prepared and published as part of the US Geological Survey's (USGS) continuing research to improve image mapping techniques. Nine multispectral scanner (MSS) images were geometrically corrected, digitally mosaicked, and enhanced at the National Mapping Division's (NMD) EROS Data Center (EDC). This process involves ground control and digital resampling to the Universal Tranverse Mercator (UTM) projection. This paper specifically discusses the preparation of the digital mosaic and the production peculiarities associated with the Denali National Park and Preserve image map.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  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. 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

  15. 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.

  16. Outcome mapping for health system integration.

    PubMed

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

    2013-01-01

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

  17. 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.

  18. Chizu Task Mapping Tool

    Energy Science and Technology Software Center (ESTSC)

    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.

  19. The Mapping of Admissionsland.

    ERIC Educational Resources Information Center

    Tyson, Daniel C.

    1982-01-01

    Describes a map designed to help students chart a college application strategy. The map locates each student on a grid by academic coordinates based on G.P.A. and test score index. Colleges are located on the same grid by identifying students admitted and circling dots representing academic locations. (RC)

  20. 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.

  1. Map of Nasca Geoglyphs

    NASA Astrophysics Data System (ADS)

    Hanzalová, K.; Pavelka, K.

    2013-07-01

    The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany) work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

  2. E-Concept Mapping

    ERIC Educational Resources Information Center

    Shmaefsky, Brian R.

    2007-01-01

    Not all demonstrations involve using exciting visual displays of one or a series of scientific principles. Demonstrations can be as simple as showing the interrelationship between scientific concepts or principles using concept maps. Concepts maps are tools that help people conceptualize and remember a conglomeration of facts making up complex…

  3. 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…

  4. 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)

  5. 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.

  6. Association mapping in cacao

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping is becoming important in perennial crops because it is a better alternative to the classical QTL's mapping approaches. The development of large breeding populations (F2, backcrosses and recombinant inbred populations) is a requirement of QTL's discovery; however, this process req...

  7. Mapping of Outdoor Classrooms.

    ERIC Educational Resources Information Center

    Horvath, Victor G.

    Mapping symbols adopted by the Michigan Department of Natural Resources are presented with their explanations. In an effort to provide standardization and familiarity teachers and other school people involved in an outdoor education program are encouraged to utilize the same symbols in constructing maps. (DK)

  8. Mapping the Llano Estacado

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Early maps of North America, prepared in the 18th and early 19th centuries, often depicted the Llano Estacado as a conspicuous blank spot - a terra incognita. A good example is a map of the southwest sketched by Alexander von Humboldt in 1804. In 1830, Stephen F. Austin added little detail to the ...

  9. 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.

  10. 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

  11. 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.

  12. 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…

  13. Geologic map of Mars

    USGS Publications Warehouse

    Tanaka, Kenneth L.; Skinner, James A.; Dohm, James M.; Irwin, Rossman P., III; 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. 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

  15. 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. PMID:25092669

  16. 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

  17. Mapping regulatory factors by immunoprecipitation from native chromatin

    PubMed Central

    Orsi, Guillermo A.; Kasinathan, Sivakanthan; Zentner, Gabriel E.; Henikoff, Steven; Ahmad, Kami

    2015-01-01

    Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin (ORGANIC) is a high-resolution method that can be used to quantitatively map protein-DNA interactions with high specificity and sensitivity. This method uses micrococcal nuclease (MNase) digestion of chromatin and low-salt solubilization to preserve protein-DNA complexes followed by immunoprecipitation and paired-end sequencing for genome-wide mapping of binding sites. In this Unit, we describe methods for isolation of nuclei and MNase digestion of unfixed chromatin, immunoprecipitation of protein-DNA complexes, and high-throughput sequencing to map sites of bound factors. PMID:25827087

  18. 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.

  19. 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.

  20. A Course To Understand Maps.

    ERIC Educational Resources Information Center

    Winter, E. A.

    Secondary students in Tasmania, Australia, can develop their skills in social studies and geography by solving the problems involving map use that this resource book provides. Several different types of maps are covered including: building plans, sketch maps, contours maps, world-grids, atlases, and urban maps. (DB)

  1. 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…

  2. Getting Results with Curriculum Mapping

    ERIC Educational Resources Information Center

    Jacobs, Heidi Hayes

    2004-01-01

    This helpful resource will speed the mapping effort along and apply curriculum mapping to special situations. In this book teachers and administrators offer concrete advice on how to get the most out of curriculum mapping in districts and schools: (1) Steps to implementing mapping procedures and leading the mapping process; (2) Tools and resources…

  3. Visualising interactive flood risk maps in a dynamic Geobrowser

    NASA Astrophysics Data System (ADS)

    Yaw Manful, Desmond; He, Yi; Cloke, Hannah; Pappenberger, Florian; Li, Zhijia; Wetterhall, Fredrik; Huang, Yingchun; Hu, Yuzhong

    2010-05-01

    Communicating flood forecast products effectively to end-users is the final step in the flood event simulation process. A prototype of the Novel Flood Early Warning System (NEWS) based on the TIGGE (THORPEX Interactive Grand Global Ensemble) database explores new avenues to visualise flood forecast products in a dynamic and interactive manner. One of the possibilities NEWS is currently assessing is Google Maps. Google Maps is a basic web mapping service application and technology provided by Google, free (for non-commercial use). It powers many map-based services including maps embedded on third-party websites via the Google Maps API. Creating a customized map interface requires adding the Google JavaScript code to a page, and then using Javascript functions to add points to the map. Flood maps allow end-users to visualise and navigate a world that is too large and complex to be seen directly. The NEWS software will attempt to deal with the following issues: • Uncertainty visualization in hazards maps • Visualizing uncertainty for sector specific risk managers • Uncertainty representation of point and linear data The objective is improve the information content of flood risk maps making them more useful to specific end-users.

  4. 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.

  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. Noise Mapping and Annoyance.

    PubMed

    Knauss, D.

    2002-01-01

    The EC has published a Green Paper on noise policy in the EU and has issued a directive on the assessment and reduction of environmental noise. This directive will make noise mapping mandatory for cities with at least 250.000 inhabitants. Due to the development in computer technology it is possible to calculate noise maps for large urban areas using the available data on buildings, ground profile, road and rail traffic. Examples for noise mapping are Birmingham (GB), Linz (A) and various German cities. Based on noise maps and empirical data on the correlation between annoyance and noise levels annoyance maps for different sources (rail, road, aircraft) can be calculated. Under the assumption that the annoyance for the different sources are only weakly correlated, a combined annoyance map can be calculated. In a second step using the distribution of the population the actual number of annoyed people can be evaluated. This analysis can be used, for example, to identify noise hot spots and to assess the impact of major traffic projects - roads, airports- on the noise situation as well as the impact on the population. Furthermore, the combined annoyance maps can be used to investigate on health effects and to check whether or not empirical correlations between annoyance and noise levels are sufficiently correct. PMID:12678944

  7. 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.

  8. Coastal mapping handbook

    USGS Publications Warehouse

    U.S. Geological Survey; National Oceanic and Atmospheric Administration; Ellis, Melvin Y., (Edited By)

    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.

  9. The geologic mapping of asteroid Vesta

    NASA Astrophysics Data System (ADS)

    Williams, D.; Yingst, A.; Garry, B.

    2014-07-01

    As part of NASA's Dawn mission [1,2] we conducted a geologic mapping campaign to provide a systematic, cartography-based initial characterization of the global and regional geology of asteroid Vesta. The goal of geological maps is to place observations of surface features into their stratigraphic context to develop a geologic history of the evolution of planetary surfaces. Geologic mapping reduces the complexity of heterogeneous planetary surfaces into comprehensible portions, defining and characterizing discrete material units based upon physical attributes related to the geologic processes that produced them, and enabling identification of the relative roles of various processes (impact cratering, tectonism, volcanism, erosion and deposition) in shaping planetary surfaces [3,4]. The Dawn Science Team produced cartographic products of Vesta from the Framing Camera images, including global mosaics as well as 15 regional quadrangles [5], which served as bases for the mapping. We oversaw the geologic mapping campaign during the Nominal Mission, including production of a global geologic map at scale 1:500,000 using images from the High Altitude Mapping Orbit [6] and 15 quadrangle geologic maps at scale 1:250,000 using images from the Low Altitude Mapping Orbit [7]. The goal was to support the Dawn Team by providing geologic and stratigraphic context of surface features and supporting the analysis of data from the Visible and Infrared Spectrometer (VIR) and the Gamma Ray and Neutron Detector (GRaND). Mapping was done using ArcGIS™ software, in which quadrangle mapping built on interpretations derived from the global geologic map but were updated and modified to take advantage of the highest spatial resolution data. Despite challenges (e.g., Vesta's highly sloped surface [8] deforms impact craters and produces mass movements that buries contacts), we were successfully able to map the whole surface of Vesta and identify a geologic history as represented in our maps and

  10. MAP decoding of variable length codes over noisy channels

    NASA Astrophysics Data System (ADS)

    Yao, Lei; Cao, Lei; Chen, Chang Wen

    2005-10-01

    In this paper, we discuss the maximum a-posteriori probability (MAP) decoding of variable length codes(VLCs) and propose a novel decoding scheme for the Huffman VLC coded data in the presence of noise. First, we provide some simulation results of VLC MAP decoding and highlight some features that have not been discussed yet in existing work. We will show that the improvement of MAP decoding over the conventional VLC decoding comes mostly from the memory information in the source and give some observations regarding the advantage of soft VLC MAP decoding over hard VLC MAP decoding when AWGN channel is considered. Second, with the recognition that the difficulty in VLC MAP decoding is the lack of synchronization between the symbol sequence and the coded bit sequence, which makes the parsing from the latter to the former extremely complex, we propose a new MAP decoding algorithm by integrating the information of self-synchronization strings (SSSs), one important feature of the codeword structure, into the conventional MAP decoding. A consistent performance improvement and decoding complexity reduction over the conventional VLC MAP decoding can be achieved with the new scheme.

  11. The design of a map database

    NASA Astrophysics Data System (ADS)

    Xiao, Jihua; Liu, Haiyan; Luan, Xiaoyan; Zhou, Zhao

    2007-06-01

    In the practice of cartography, people always face two kinds of geographic world's models. One is digital landscape model (DLM), and another is digital cartographic model (DCM). In DLM, geographic feature are expressed by coordinate, attribute and relationship among them, it is independent from symbols. Reversely, DCM is closely related with symbols and paper maps which will be published. In this paper I will discuss the design of map database for DCM. First, this paper introduces characteristics of GIS database and Map database to us, and then elaborates their relationships and differences. Second, it represents the contents of map database, which consists of five parts such as spatial location, attributes, spatial relationship, time, symbol and cartographic expert's knowledge for symbolization control. So we can draw a conclusion that the map database is an organic combination of GIS database and cartographic expert's knowledge. Third, this dissertation depicts the implement of map database by an example which is applied in the paper topography mapmaking and infrastructural geographic information's yield. We design data tables according to geographic feature's geometry type such as point, line, polygon, complex and annotation. By foreign keys related to dictionary tables we can divide features into different geography layers (such as vegetation, river, road etc.) and publish layers (such as red point, black line, green polygon, black annotation etc.). Aiming at different geographic feature possessing of different items of attributes, we also design a universal method to store feature's attribute data. Fourth, this dissertation introduces a method using cartographic expert knowledge and experience to control the process of dynamic map symbolization. The authors think it should formalize the fuzzy and ambiguous expert knowledge and build expert knowledge repository. By an example it illustrates how to establish cartographic expert knowledge repository and how the

  12. Mapping luna incognita

    NASA Astrophysics Data System (ADS)

    Westfall, John E.

    1990-11-01

    The portion of the moon near the south and southwestern limbs was poorly photographed by the 1960s lunar missions, and is accordingly designated 'luna incognita'. The Association of Lunar and Planetary Observers accordingly undertook a study of this region from 1972 to 1990 which ultimately encompassed 1509 photographs by terrestrial observers, photographs from the Lunar Orbiters IV and V and from Zond 8, radar maps and images, and charts of the moon's limb profile. On these bases, a shaded-relief topographic map was compiled and executed by a computerized 'shading' program at 1:2.5 million scale. This map is presently reproduced in 1:3.5 million scale.

  13. Automatic cloud cover mapping.

    NASA Technical Reports Server (NTRS)

    Strong, J. P., III; Rosenfeld, A.

    1971-01-01

    A method of converting a picture into a 'cartoon' or 'map' whose regions correspond to differently textured regions is described. Texture edges in the picture are detected, and solid regions surrounded by these (usually broken) edges are 'colored in' using a propagation process. The resulting map is cleaned by comparing the region colors with the textures of the corresponding regions in the picture, and also by merging some regions with others according to criteria based on topology and size. The method has been applied to the construction of cloud cover maps from cloud cover pictures obtained by satellites.

  14. Generalized qudit Choi maps

    SciTech Connect

    Jafarizadeh, M. A.; Rezaee, M.; Ahadpour, S.

    2006-10-15

    Following the linear programming prescription of Jafarizadeh et al. [Phys. Rev. A 72, 062106 (2005)], the d(multiply-in-circle sign)d Bell diagonal entanglement witnesses are provided. By using Jamiolkowski isomorphism, it is shown that the corresponding positive maps are the generalized qudit Choi maps. Also by manipulating particular d(multiply-in-circle sign)d Bell diagonal separable states and constructing corresponding bound entangled states, it is shown that the obtained d(multiply-in-circle sign)d Bell states diagonal entanglement witnesses (consequently qudit Choi maps) are nondecomposable in a certain range of their parameters.

  15. 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.

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

    PubMed Central

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

    2008-01-01

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

  17. 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 ...

  18. Submap joining smoothing and mapping for camera-based indoor localization and mapping

    NASA Astrophysics Data System (ADS)

    Bjärkefur, J.; Karlsson, A.; Grönwall, C.; Rydell, J.

    2011-06-01

    Personnel positioning is important for safety in e.g. emergency response operations. In GPS-denied environments, possible positioning solutions include systems based on radio frequency communication, inertial sensors, and cameras. Many camera-based systems create a map and localize themselves relative to that. The computational complexity of most such solutions grows rapidly with the size of the map. One way to reduce the complexity is to divide the visited region into submaps. This paper presents a novel method for merging conditionally independent submaps (generated using e.g. EKF-SLAM) by the use of smoothing. Using this approach it is possible to build large maps in close to linear time. The method is demonstrated in two indoor scenarios, where data was collected with a trolley-mounted stereo vision camera.

  19. Genome-wide Association Mapping of Fusarium Head Blight Resistance in Contemporary Barley Breeding Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Utilization of quantitative trait loci (QTL) identified in bi-parental mapping populations has had limited success for complex quantitative traits. The use of association mapping in contemporary breeding germplasm may lead to more effective marker strategies for crop improvement. To map Fusarium he...

  20. 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 ...

  1. 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,…

  2. 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.

  3. 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.

  4. 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.

  5. Field Reconnaissance Geologic Mapping of the Columbia Hills, Gusev Crater from MER Spirit Rover and HiRISE Observations

    NASA Astrophysics Data System (ADS)

    Crumpler, L.; Arvidson, R.; Blaney, D.; Cabrol, N.; Desouza, P.; Farrand, W.; Farmer, J.; Greeley, R.; Hurowitz, J.; Lewis, K.; McCoy, T. J.; McEwen, A. S.; McSween, H.; Ming, D. W.; Morris, R. V.; Rice, J. W.; Rice, M.; Ruff, S. W.; Schmidt, M.; Schröder, C.; Squyres, S. W.; Yen, A.; Yingst, A.

    2009-03-01

    This study presents the results of the first field reconnaissance geologic mapping on another planetary surface. We show that geologic units on Mars are complex like their terrestrial counterparts, but can mapped at human and rover scales of observation.

  6. Interest rates mapping

    NASA Astrophysics Data System (ADS)

    Kanevski, M.; Maignan, M.; Pozdnoukhov, A.; Timonin, V.

    2008-06-01

    The present study deals with the analysis and mapping of Swiss franc interest rates. Interest rates depend on time and maturity, defining term structure of the interest rate curves (IRC). In the present study IRC are considered in a two-dimensional feature space-time and maturity. Exploratory data analysis includes a variety of tools widely used in econophysics and geostatistics. Geostatistical models and machine learning algorithms (multilayer perceptron and Support Vector Machines) were applied to produce interest rate maps. IR maps can be used for the visualisation and pattern perception purposes, to develop and to explore economical hypotheses, to produce dynamic asset-liability simulations and for financial risk assessments. The feasibility of an application of interest rates mapping approach for the IRC forecasting is considered as well.

  7. Mars planimetric mapping

    NASA Astrophysics Data System (ADS)

    Batson, R. M.; Bridges, P. M.; Lee, E. M.

    1985-04-01

    The 1:5,000,000 scale shaded relief maps of Mars originally compiled from Mariner 9 pictures are being upgraded by adding details visible on Viking Orbiter images. This work is done by modifying the original airbrush drawings; no attempt is made to reposition features according to the latest control nets. Thirteen of these maps have been published to date, two are in compilation, and two are in press. A hard cover atlas containing reduced scale versions of all Mars cartographic products will be published upon completion of the revisions of the 1:5,000,000 scale maps, the 1:2,000,000 scale photomosaics, and Mars color albedo mapping tasks. This atlas will supersede the existing Atlas of Mars prepared by Batson and others.

  8. 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)

  9. Reading Angles in Maps

    PubMed Central

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

    2013-01-01

    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 2D to 3D 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 2D and 3D displays and that serves to interpret novel spatial symbols. PMID:23647223

  10. 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 ...

  11. 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.

  12. Dating the Vinland Map

    ScienceCinema

    None

    2013-07-17

    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.

  13. Dating the Vinland Map

    SciTech Connect

    2013-01-04

    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.

  14. 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...

  15. 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)

  16. 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)

  17. 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

  18. Map of physics

    NASA Astrophysics Data System (ADS)

    2008-10-01

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

  19. 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). PMID:26072438

  20. A model of electronic map interpretation

    NASA Technical Reports Server (NTRS)

    Aretz, Anthony J.

    1988-01-01

    This paper describes an experiment that provides data for the development of a cognitive model of pilot flight navigation. The model views navigation as a process involving the alignment of mental images with the perceptual view out of the cockpit. The data support a three stage model: (1) the perceptual encoding of the map display, (2) mental rotation of the mental image, and (3) comparison of the image to the environment. The variables that significantly influence the processes embodied in the model in decreasing importance are: speed of processing, display sequencing, map complexity, and rotation angle of the map. The model can be used as a preliminary computational tool in predicting the navigational component of pilot situational awareness.

  1. 100 Weekly Sky Maps

    NASA Technical Reports Server (NTRS)

    2002-01-01

    100 Aum Weekly Sky Maps for mission weeks 4 to 44, and the 100 Aum Annual Average Map. Shows sky coverage each week of the DIRBE mission over the period during which the COBE cryogen supply lasted. As the Earth, with COBE in orbit, revolved around the Sun, DIRBE viewed the sky from an ever-changing vantage point in the solar system, enabling light reflected and emitted by the interplanetary dust cloud to be modeled.

  2. 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.

  3. 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.

  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. Probabilistic drug connectivity mapping

    PubMed Central

    2014-01-01

    Background The aim of connectivity mapping is to match drugs using drug-treatment gene expression profiles from multiple cell lines. This can be viewed as an information retrieval task, with the goal of finding the most relevant profiles for a given query drug. We infer the relevance for retrieval by data-driven probabilistic modeling of the drug responses, resulting in probabilistic connectivity mapping, and further consider the available cell lines as different data sources. We use a special type of probabilistic model to separate what is shared and specific between the sources, in contrast to earlier connectivity mapping methods that have intentionally aggregated all available data, neglecting information about the differences between the cell lines. Results We show that the probabilistic multi-source connectivity mapping method is superior to alternatives in finding functionally and chemically similar drugs from the Connectivity Map data set. We also demonstrate that an extension of the method is capable of retrieving combinations of drugs that match different relevant parts of the query drug response profile. Conclusions The probabilistic modeling-based connectivity mapping method provides a promising alternative to earlier methods. Principled integration of data from different cell lines helps to identify relevant responses for specific drug repositioning applications. PMID:24742351

  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. 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.

  8. 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.

  9. 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.

  10. Parcellating connectivity in spatial maps

    PubMed Central

    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. PMID:25737822

  11. 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.

  12. 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

  13. Geologic mapping of Vesta

    NASA Astrophysics Data System (ADS)

    Yingst, R. A.; Mest, S. C.; Berman, D. C.; Garry, W. B.; Williams, D. A.; Buczkowski, D.; Jaumann, R.; Pieters, C. M.; De Sanctis, M. C.; Frigeri, A.; Le Corre, L.; Preusker, F.; Raymond, C. A.; Reddy, V.; Russell, C. T.; Roatsch, T.; Schenk, P. M.

    2014-11-01

    We report on a preliminary global geologic map of Vesta, based on data from the Dawn spacecraft's High-Altitude Mapping Orbit (HAMO) and informed by Low-Altitude Mapping Orbit (LAMO) data. This map is part of an iterative mapping effort; the geologic map has been refined with each improvement in resolution. Vesta has a heavily-cratered surface, with large craters evident in numerous locations. The south pole is dominated by an impact structure identified before Dawn's arrival. Two large impact structures have been resolved: the younger, larger Rheasilvia structure, and the older, more degraded Veneneia structure. The surface is also characterized by a system of deep, globe-girdling equatorial troughs and ridges, as well as an older system of troughs and ridges to the north. Troughs and ridges are also evident cutting across, and spiraling arcuately from, the Rheasilvia central mound. However, no volcanic features have been unequivocally identified. Vesta can be divided very broadly into three terrains: heavily-cratered terrain; ridge-and-trough terrain (equatorial and northern); and terrain associated with the Rheasilvia crater. Localized features include bright and dark material and ejecta (some defined specifically by color); lobate deposits; and mass-wasting materials. No obvious volcanic features are evident. Stratigraphy of Vesta's geologic units suggests a history in which formation of a primary crust was followed by the formation of impact craters, including Veneneia and the associated Saturnalia Fossae unit. Formation of Rheasilvia followed, along with associated structural deformation that shaped the Divalia Fossae ridge-and-trough unit at the equator. Subsequent impacts and mass wasting events subdued impact craters, rims and portions of ridge-and-trough sets, and formed slumps and landslides, especially within crater floors and along crater rims and scarps. Subsequent to the formation of Rheasilvia, discontinuous low-albedo deposits formed or were

  14. 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.

  15. 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.

  16. 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.

  17. Plasmon and compositional mapping of plasmonic nanostructures

    NASA Astrophysics Data System (ADS)

    Ringe, Emilie; Collins, Sean M.; DeSantis, Christopher J.; Skrabalak, Sara E.; Midgley, Paul A.

    2014-11-01

    Recently, co-reduction of Au and Pd has allowed the synthesis of complex Au core/AuPd shell nanoparticles with elongated tips and cubic-like symmetry. Optical studies have shown strong plasmonic behavior and high refractive index sensitivities. In this paper, we describe the composition and the near-field plasmonic behavior of those complex structures. Monochromated STEM-EELS, Cathodoluminescence, and EDS mapping reveals the different resonant modes in these particles, and shows that Pd, a poor plasmonic metal, does not prevent strong resonances and could actually be extremely helpful for plasmon-enhanced catalysis.

  18. 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.

  19. Monocular SLAM with conditionally independent split mapping.

    PubMed

    Holmes, Steven A; Murray, David W

    2013-06-01

    The recovery of structure from motion in real time over extended areas demands methods that mitigate the effects of computational complexity and arithmetical inconsistency. In this paper, we develop SCISM, an algorithm based on relative frame bundle adjustment, which splits the recovered map of 3D landmarks and keyframes poses so that the camera can continue to grow and explore a local map in real time while, at the same time, a bulk map is optimized in the background. By temporarily excluding certain measurements, it ensures that both maps are consistent, and by using the relative frame representation, new results from the bulk process can update the local process without disturbance. The paper first shows how to apply this representation to the parallel tracking and mapping (PTAM) method, a real-time bundle adjuster, and compares results obtained using global and relative frames. It then explains the relative representation's use in SCISM and describes an implementation using PTAM. The paper provides evidence of the algorithm's real-time operation in outdoor scenes, and includes comparison with a more conventional submapping approach. PMID:23599058

  20. 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.

  1. A quantitative analysis of IRAS maps of molecular clouds

    NASA Astrophysics Data System (ADS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-11-01

    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.

  2. 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

  3. 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…

  4. Complex Clouds

    Atmospheric Science Data Center

    2013-04-16

    ...     View Larger Image The complex structure and beauty of polar clouds are highlighted by these images acquired ... Multi-angle Imaging SpectroRadiometer observes the daylit Earth continuously from pole to pole, and every 9 days views the entire globe ...

  5. 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.

  6. 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.

  7. 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.

  8. Genetic and physical map correlation

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Mapping the University Learning Environment.

    ERIC Educational Resources Information Center

    Mitchell, Alice A.; And Others

    The perceptual mapping technique was used to solicit University of Maryland college freshmen's perceptions of the campus environment. In perceptual mapping respondents are provided with a map of an indoor or outdoor location and their feelings or perceptions about areas on the map are solicited. During this study students participating in regular…

  10. 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

  11. 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 ...

  12. 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…

  13. Complex Generalized Synchronization and Parameter Identification of Nonidentical Nonlinear Complex Systems.

    PubMed

    Wang, Shibing; Wang, Xingyuan; Han, Bo

    2016-01-01

    In this paper, generalized synchronization (GS) is extended from real space to complex space, resulting in a new synchronization scheme, complex generalized synchronization (CGS). Based on Lyapunov stability theory, an adaptive controller and parameter update laws are designed to realize CGS and parameter identification of two nonidentical chaotic (hyperchaotic) complex systems with respect to a given complex map vector. This scheme is applied to synchronize a memristor-based hyperchaotic complex Lü system and a memristor-based chaotic complex Lorenz system, a chaotic complex Chen system and a memristor-based chaotic complex Lorenz system, as well as a memristor-based hyperchaotic complex Lü system and a chaotic complex Lü system with fully unknown parameters. The corresponding numerical simulations illustrate the feasibility and effectiveness of the proposed scheme. PMID:27014879

  14. Complex Generalized Synchronization and Parameter Identification of Nonidentical Nonlinear Complex Systems

    PubMed Central

    Wang, Shibing; Wang, Xingyuan; Han, Bo

    2016-01-01

    In this paper, generalized synchronization (GS) is extended from real space to complex space, resulting in a new synchronization scheme, complex generalized synchronization (CGS). Based on Lyapunov stability theory, an adaptive controller and parameter update laws are designed to realize CGS and parameter identification of two nonidentical chaotic (hyperchaotic) complex systems with respect to a given complex map vector. This scheme is applied to synchronize a memristor-based hyperchaotic complex Lü system and a memristor-based chaotic complex Lorenz system, a chaotic complex Chen system and a memristor-based chaotic complex Lorenz system, as well as a memristor-based hyperchaotic complex Lü system and a chaotic complex Lü system with fully unknown parameters. The corresponding numerical simulations illustrate the feasibility and effectiveness of the proposed scheme. PMID:27014879

  15. 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.

  16. Map display design

    NASA Technical Reports Server (NTRS)

    Aretz, Anthony J.

    1990-01-01

    This paper presents a cognitive model of a pilot's navigation task and describes an experiment comparing a visual momentum map display to the traditional track-up and north-up approaches. The data show the advantage to a track-up map is its congruence with the ego-centered forward view; however, the development of survey knowledge is hindered by the inconsistency of the rotating display. The stable alignment of a north-up map aids the acquisition of survey knowledge, but there is a cost associated with the mental rotation of the display to a track-up alignment for ego-centered tasks. The results also show that visual momentum can be used to reduce the mental rotation costs of a north-up display.

  17. 21-cm Intensity Mapping

    NASA Astrophysics Data System (ADS)

    Chang, Tzu-Ching; GBT-HIM Team

    2016-01-01

    The redshifted 21-cm emission from neutral hydrogen has emerged as a powerful probe for large-scale structure; a significant fraction of the observable universe can be mapped in the Intensity Mapping regime out to high redshifts. At redshifts around unity, the 21-cm emission traces the matter distribution and can be used to measure the Baryon Acoustic Oscillation (BAO) signature and constrain dark energy properties. I will describe our HI Intensity Mapping program at the Green Bank Telescope (GBT), aiming at measuring the 21cm power spectrum at z=0.8. A 800-MHz multi-beam focal-plane array for the GBT is currently under construction in order to facilitate a large-scale survey for BAO and the redshift-space distortion measurements for cosmological constraints.

  18. A genetic linkage map for the saltwater crocodile (Crocodylus porosus)

    PubMed Central

    2009-01-01

    Background Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1). Conclusion We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers

  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. Advances in Bayesian Multiple QTL Mapping in Experimental Crosses

    PubMed Central

    Yi, Nengjun; Shriner, Daniel

    2016-01-01

    Many complex human diseases and traits of biological and/or economic importance are determined by interacting networks of multiple quantitative trait loci (QTL) and environmental factors. Mapping QTL is critical for understanding the genetic basis of complex traits, and for ultimate identification of responsible genes. A variety of sophisticated statistical methods for QTL mapping have been developed. Among these developments, the evolution of Bayesian approaches for multiple QTL mapping over the past decade has been remarkable. Bayesian methods can jointly infer the number of QTL, their genomic positions, and their genetic effects. Here, we review recently developed and still developing Bayesian methods and associated computer software for mapping multiple QTL in experimental crosses. We compare and contrast these methods to clearly describe the relationships among different Bayesian methods. We conclude this review by highlighting some areas of future research. PMID:17987056